Thermp Scientific - Operating Manual Focus GC

Thermo Scientific
FOCUS GC Version For MS

Gas Chromatograph
Instruction Manual
PN 317 094 27, Revision May 2007
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FOCUS™ GC Version for MS - Instruction Manual
May 2007 Edition
Part Number 317 094 27
© 2007 Thermo Fisher Scientific Inc All rights reserved.
Printed in Italy
Published by Thermo Electron S.p.A., Strada Rivoltana, 20090 Rodano - Milan - Italy
Tel: +39 02 95059355 Fax: +39 02 95059388
Printing History: First Edition, released September 2003

Second Edition, released April 2004
Third Edition, released June 2004
Fourth Esdition, released January 2005
Fifth Edition, released October 2005
Sixth Edition, released May 2007
Disclaimer
Technical Information contained in this publication is for reference purposes only and is subject to change without notice. Every effort has
been made to supply complete and accurate information; however, Thermo Fisher Scientific assumes no responsibility and will not be liable
for any errors, omissions, damage, or loss that might result from any use of this manual or the information contained therein (even if this
information is properly followed and problems still arise).
This publication is not part of the Agreement of Sale between Thermo Fisher Scientific and the purchaser of a FOCUS™ GC Version for MS
system. In the event of any conflict between the provisions of this document and those contained in Thermo Fisher Scientific’s Terms and
Conditions, the provisions of the Terms and Conditions shall govern.
Reference to System Configurations and Specifications supercede all previous information and are subject to change without notice.
Trademarks
FOCUS™ GC is a trademark of Thermo Fisher Scientific Inc., and its subsidiaries Other brand and product names may be trademarks
or registered trademarks of their respective companies.
Declaration
Manufacturer: Thermo Electron S.p.A.
Thermo Electron S.p.A. is the manufacturer of the instrument described in this
manual and, as such, is responsible for the instrument safety, reliability and
performance only if:
• installation
• re-calibration
• changes and repairs
have been carried out by authorized personnel and if:

• the local installation complies with local law regulations
• the instrument is used according to the instructions provided and if its
operation is only entrusted to qualified trained personnel
Thermo Electron S.p.A. is not liable for any damages derived from the
non-compliance with the aforementioned recommendations.
Thermo Electron S.p.A.

Strada Rivoltana
20090 RODANO (MI)
ITALY
FOCUS GC MS Version -Instruction Manual iii

iv FOCUS GC MS Version -Instruction Manual
Contents
About This Manual...............................................................................................................................xiii
Overview .................................................................................................................................xiii
Conventions Used in This Manual........................................................................................... xv
Instrument Markings and Symbols .......................................................................................xviii
Using the FOCUS GC Version for MS Document Set ............................................................ xx
Classification of the Instrument ..............................................................................................xxi
Technical Features ..................................................................................................................xxi
Safety Information .................................................................................................................xxii
Use of Gases..............................................................................................................xxii
Using Hydrogen ....................................................................................................................xxiii
Using the Hydrogen Sensor .....................................................................................xxiv
Cleaning and Decontamination .............................................................................................xxiv
Chapter 1
FOCUS GC Description .................................................................................................................... 25
Instrument Overview................................................................................................................ 26
FOCUS GC Components ............................................................................................ 26
Pneumatic Compartment................................................................................ 26
Analytical Unit............................................................................................... 26
Electronic Compartment ................................................................................ 27
Status Panel.................................................................................................... 27
Gas Control ................................................................................................................. 27
Carrier Gas Control........................................................................................ 27
Column Oven .............................................................................................................. 28
Injector ........................................................................................................................ 28
Column........................................................................................................................ 28
MS Detector ................................................................................................................ 29
Instrument Automation ............................................................................................... 29
GC Parts Description................................................................................................................ 30
Front Panel .................................................................................................................. 30
Column Oven ................................................................................................. 31
Status Panel.................................................................................................... 31
Electronic Compartment ................................................................................ 32
Rear Panel ................................................................................................................... 34
Carrier Gas Inlet Port ..................................................................................... 35
Electrical Connections ................................................................................... 35
Oven Exhaust Vent ........................................................................................ 37
Top Panel .................................................................................................................... 37
FOCUS GC Version for MS - Instruction Manual v

Contents
GC Left Hand-side Panel............................................................................................ 38

Virtual Keypad ........................................................................................................... 39
Chapter 2
Gas Control ........................................................................................................................................41
Gas Supplies ............................................................................................................................ 42
Carrier Gas Regulation ............................................................................................................ 44
Carrier Gas Parameters ............................................................................................................ 45
Flow Mode Selection Group Box............................................................................... 46
Constant Flow................................................................................................ 46
Constant Pressure .......................................................................................... 46
On/Off Check Box......................................................................................... 47
Vacuum Compensation ................................................................................. 47
Gas Saver Selection Group Box ................................................................................. 48
Enable Check Box ......................................................................................... 48
Flow (ml/min)................................................................................................ 48
Time (min)..................................................................................................... 48
Chapter 3
Column Oven .....................................................................................................................................49
Column Oven Overview .......................................................................................................... 50
Oven Safety ................................................................................................................ 51
Oven Parameters...................................................................................................................... 52
Graph .......................................................................................................................... 53
Ramps Group Box ...................................................................................................... 53
Arrow Keys ................................................................................................... 53
Initial / Temp Text Box ................................................................................. 54
Initial / Hold Time text box ........................................................................... 54
Ramp / Rate Text Boxes................................................................................ 54
Ramp / Temp Text Boxes.............................................................................. 54
Ramp / Hold Time Text Boxes...................................................................... 54
Oven Group Box......................................................................................................... 54
Max Temp Text Box ..................................................................................... 55
PrepRun Timeout........................................................................................... 55
Equilibration Time (min) text box................................................................. 55
vi FOCUS GC Version for MS - Instruction Manual

Contents
Chapter 4
Split/Splitless Injector (S/SL) ........................................................................................................... 57
S/SL Overview ......................................................................................................................... 58
Septum ........................................................................................................................ 62
Liners .......................................................................................................................... 62
Packed Columns............................................................................................. 64
S/SL Injection Techniques ....................................................................................................... 67
Split Injection Technique ............................................................................................ 67
Splitless Injection Technique ...................................................................................... 69
Refocusing the Sample .................................................................................. 71
Flooding ......................................................................................................... 72
S/SL Inlet Parameters............................................................................................................... 73
Mode List Box ............................................................................................................ 74
Split ................................................................................................................ 74
Splitless .......................................................................................................... 74
Splitless w/surge ............................................................................................ 74
Inlet Group Box .......................................................................................................... 74
Temperature check box and text box ............................................................. 75
Split Flow check box and text box................................................................. 75
Split Ratio text box ........................................................................................ 75
Splitless Time text box................................................................................... 75
Purge Group Box ........................................................................................................ 75
Constant Septum Purge check box ................................................................ 76
Stop Purge Time text box .............................................................................. 76
Surge Group Box ........................................................................................................ 76
Surge Pressure................................................................................................ 76
Surge Duration ............................................................................................... 76
Chapter 5
Column .............................................................................................................................................. 77
Introduction .............................................................................................................................. 78
Using Correct Fittings................................................................................................. 78
Column Ferrules............................................................................................. 78
Retaining Nuts ............................................................................................... 78
Installation................................................................................................................................ 79
Keeping Leaks Under Control ................................................................................................. 82
Column Evaluation ..................................................................................................... 82
Identifying and Removing Leaks................................................................................ 82
FOCUS GC Version for MS - Instruction Manual vii

Contents
Expected K Factor ...................................................................................................... 85

K Factor Tables .......................................................................................................... 85
Helium Carrier Gas Theoretical K Factor ..................................................... 86
Nitrogen Carrier Gas Theoretical K Factor ................................................... 87
Hydrogen Carrier Gas Theoretical K Factor ................................................. 88
Column Conditioning .............................................................................................................. 91
Chapter 6
Getting Started ..................................................................................................................................93
Configuring the FOCUS GC ................................................................................................... 94
Connections Group Box ................................................................................ 95
Option Group Box ......................................................................................... 95
Use Roadmap-Home Page....................................................................................................... 96
GC Status and Actual Values ..................................................................................... 96
Status Page..................................................................................................... 97
Actual Values Page........................................................................................ 98
FOCUS GC Setup.................................................................................................................... 99
Carrier Box .................................................................................................. 100
Handshake Group Box ................................................................................ 100
Valves Group Box ....................................................................................... 101
Buttons......................................................................................................... 101
Focus GC Pull-up Menu ........................................................................................................ 102
Method Editing ...................................................................................................................... 103
Oven....................................................................................................................................... 104
Ramps Group Box .................................................................................................... 105
Oven Group Box....................................................................................................... 106
Inlet SSL ................................................................................................................................ 108
Mode List Box .......................................................................................................... 109
Inlet Group Box ........................................................................................................ 109
Purge Group Box ...................................................................................................... 110
Surge Group Box ...................................................................................................... 110
Carrier .................................................................................................................................... 114
Flow Group Box ....................................................................................................... 115
Gas Saver.................................................................................................................. 115
MS Transfer Line................................................................................................................... 117
MS Transfer Line Group Box................................................................................... 117
Run Table............................................................................................................................... 118
Time, Item, and Settings Group Box........................................................................ 119
viii FOCUS GC Version for MS - Instruction Manual

Contents
Initial Values Group Box .......................................................................................... 119

Buttons ...................................................................................................................... 119
Add/Edit Run-Time Event Screen ............................................................................ 120
Event Time Group Box................................................................................ 120
Valve Event.................................................................................................. 120
External Event Group Box........................................................................... 121
Virtual Keypad ....................................................................................................................... 122
Description ................................................................................................................ 122
Display Panel ............................................................................................... 122
GC Status LEDs........................................................................................... 122
Action Keys ................................................................................................. 123
Data Entry Keys........................................................................................... 123
Keypad Menu............................................................................................................ 123
File Menu ..................................................................................................... 123
Send Method to GC ..................................................................................... 123
Close ............................................................................................................ 123
Valves Manual Activations .................................................................................................... 124
Inlet SSL Valves Group Box .................................................................................... 124
Valve Vents Group Box............................................................................................ 124
Instrument Start-up................................................................................................................. 125
Chapter 7
Maintenance and Troubleshooting ................................................................................................. 127
Maintenance ........................................................................................................................... 128
How To Perform Maintenance.................................................................................. 128
Suggested Maintenance Schedule............................................................................. 128
Septa............................................................................................................. 128
Ferrules and Seals ........................................................................................ 129
Traps ............................................................................................................ 129
Detector Unit................................................................................................ 129
Maintenance Schedule Table .................................................................................... 129
Instrument Cleaning.................................................................................................. 130
Maintaining a SSL Injector .................................................................................................... 131
When Replacing the Septum..................................................................................... 131
When Cleaning or Replacing the Liner..................................................................... 131
If the Glass Liner Breaks Inside the Injector ............................................................ 132
Troubleshooting ..................................................................................................................... 140
Instrument Troubleshooting...................................................................................... 141
FOCUS GC Version for MS - Instruction Manual ix

Contents
Error Messages ...................................................................................................................... 142

Guide to Solve Analytical Problems...................................................................................... 143
Chapter 8
Use of the Virtual Keypad .................................................................................................................147
Overview................................................................................................................................ 148
The Display............................................................................................................... 148
The Display LEDs .................................................................................................... 149
The FOCUS GC Virtual Keypad.............................................................................. 150
Parameters Entry ......................................................................................... 151
Virtual Keypad Main Menu................................................................................................... 152
Oven.......................................................................................................................... 152
Inlet........................................................................................................................... 153
Carrier....................................................................................................................... 153
How to Perform a Leak Check .................................................................... 154
How to perform a Column Evaluation ........................................................ 155
Detector .................................................................................................................... 155
Signal ........................................................................................................................ 155
Autosampler.............................................................................................................. 155
Others........................................................................................................................ 156
Time....................................................................................................................................... 157
Valves .................................................................................................................................... 158
Run Time Events ................................................................................................................... 159
Run-Log................................................................................................................................. 160
Configuration......................................................................................................................... 162
When to Configure ................................................................................................... 162
Configuration Menu ................................................................................................. 162
Oven Configuration Menu........................................................................... 163
Carrier Configuration Menu ........................................................................ 163
Autosampler Configuration Menu............................................................... 164
General Configuration Menu....................................................................... 164
Keyboard & Display Configuration Menu .................................................. 164
Handshake Configuration Menu.................................................................. 165
Time Configuration Menu........................................................................... 166
Valves Configuration Menu ........................................................................ 166
Info/Diagnostics..................................................................................................................... 167
x FOCUS GC Version for MS - Instruction Manual

Contents
Appendix A
Customer Communication................................................................................................................ 169
How To Contact Us................................................................................................................ 169
Europe ....................................................................................................................... 169
Africa, Asia and Oceania .......................................................................................... 171
North, Central and South America............................................................................ 172
Reader Survey ........................................................................................................... 173
Glossary ..............................................................................................................................................175
Index ....................................................................................................................................................181
FOCUS GC Version for MS - Instruction Manual xi

Contents
xii FOCUS GC Version for MS - Instruction Manual

About This Manual
Overview
This Instruction Manual contains descriptions of the features and components of
the FOCUS GC Version for MS gas chromatograph. Inside, you will find all of
the information necessary for routine operation of your GC, including operating
sequences, sample injection techniques, and diagrams and descriptions of the
major components.
Chapter 1, FOCUS GC Version for MS Description, provides a basic overview of

the features and options of the FOCUS GC gas chromatograph in the version for
MS. After each brief description of a FOCUS GC component, you will find
references to chapters in this manual containing more detailed information.
Chapter 2, Gas Control, contains information on controlling and programming the

carrier and detector gas flows to the FOCUS GC.
Chapter 3, Column Oven, describes the features of the FOCUS GC column oven.
Chapter 4, Split/Splitless Injector (S/SL), describes the Split/Splitless (S/SL)

injector and contains operating sequences for the different split/splitless operating
modes.
Chapter 5, Column, describes the analytical columns installed in the FOCUS GC

oven. The column is the heart of the gas chromatograph where the separation
takes place.
Chapter 6, Getting Started, This chapter contains instructions to configure, set

operating parameters and control your FOCUS GC Version for MS through
Xcalibur software. Instructions to start-up the instrument are also included.
Chapter 7, Maintenance and Troubleshooting, contains information and operating

sequences to perform the necessary maintenance of the instrument and also
information concerning troubleshooting in case of malfunctioning.
Chapter 8, Use of the Virtual Keypad, provides basic information about of the
functions and menus of the FOCUS GC Version for MS virtual keypad.
FOCUS GC Version for MS - Instruction Manual xiii

About This Manual Overview
Appendix A, Customer Communication, contains contact information for Thermo

Fisher Scientific offices worldwide. Use the Reader Survey in this section to give
us feedback on this manual and help us improve the quality of our documentation.
The Glossary contains definitions of terms used in this manual. This also includes
abbreviations, acronyms, metric prefixes, and symbols.
The Index contains an alphabetical list of key terms and topics in this guide,
including cross references and the corresponding page numbers.
xiv FOCUS GC Version for MS - Instruction Manual

Conventions Used in This Manual About This Manual
Conventions Used in This Manual

The following symbols and typographical conventions are used throughout this
manual.
Bold Bold text indicates names of windows, dialog boxes, and

fields.
Italic Italic indicates cross references, first references to important
terms defined in the glossary, and special emphasis.
Monospace Monospace, or Courier, indicates filenames and filepaths or
text the user should enter with the keyboard.
Monospace Monospace Bold indicates messages, prompts, or menu titles
Bold displayed on the computer screen or on a digital display.
» This symbol illustrates menu paths to select, such as
File»Open….
KEY NAME Bold, uppercase sans serif font indicates the name of a key on
a keyboard or keypad, such as ENTER.
This symbol alerts you to an action or sequence that, if
CAUTION performed improperly, could damage the instrument.
This symbol alerts you to important information related to the

NOTE text in the previous paragraph.
This symbol alerts you to an action or sequence that, if

WARNING! improperly performed, could result in damage to the
instrument or possible physical harm to the user. This symbol
may be followed by icons indicating special precautions that
should be taken to avoid injury.
This symbol indicates an electric shock hazard.
FOCUS GC Version for MS - Instruction Manual xv

About This Manual Conventions Used in This Manual
This symbol indicates danger from hazardous chemicals.
This symbol indicates danger from high temperature surfaces

or substances.
This symbol indicates a fire hazard.
This symbol indicates an explosion hazard.
This symbol indicates a toxic hazard.
This symbol indicates the presence of flammable materials.
This symbol indicates the presence of radioactive material.
This symbol indicates an operation or sequence that must not

be performed by the user. A Thermo Fisher Scientific
authorized Customer Support Engineer must perform this
sequence.
This symbol indicates all metal objects, such as watches and
jewelry, must be taken off.
This symbol indicates an eye hazard. Eye protection must be

worn.
This symbol indicates the user must wear a protective screen

when performing the sequence.
xvi FOCUS GC Version for MS - Instruction Manual

Conventions Used in This Manual About This Manual
This symbol indicates the user must wear protective shoes

This symbol indicates the user must wear protective clothing

This symbol indicates the user must wear gloves when

performing the sequence.
FOCUS GC Version for MS - Instruction Manual xvii

About This Manual Instrument Markings and Symbols
Instrument Markings and Symbols

The following table explains the symbols used on Thermo Fisher Scientific
instruments. Only a few of them are used on the FOCUS GC gas chromatograph.
Symbol Description
Direct Current
Alternating Current
Both direct and alternating current
Three-phase alternating current

3
Earth (ground) terminal
Protective conductor terminal
Frame or chassis terminal
Equipotentiality
On (Supply)
Off (Supply)
xviii FOCUS GC Version for MS - Instruction Manual

Instrument Markings and Symbols About This Manual
Symbol Description
Equipment protected throughout by DOUBLE
INSULATION or REINFORCED INSULATION
(Equivalent to Class II of IEC 536)
Indicates that the user must refer to the manual for
specific Warning or Caution information to avoid
personal injury or damage to the product.
Caution, risk of electric shock
Caution, hot surface
Caution (refer to accompanying documents)
In-position of a bistable push control
Out-position of a bistable push control
Symbol in compliance to the Directive 2002/96/EC on

Waste Electrical and Electronic Equipments (WEEE)
placed on the european market after August, 13, 2005.
FOCUS GC Version for MS - Instruction Manual xix

About This Manual Using the FOCUS GC Version for MS Document Set
Using the FOCUS GC Version for MS Document

Set
The FOCUS GC Version for MS Document Set (CD-Rom PN 317 095 35)
includes all manuals in electronic format, and serves as your library for
information about the FOCUS hardware and software.
The FOCUS GC Version for MS Document Set (PN 317 094 30) as paper copy is
also available Furthermore, Thermo Fisher Scientific part numbers (PN) for the
paper copy manuals are provided for each book title.
Site Preparation and Installation Manual (PN 317 094 28)

This manual and diskette describes how to set up a workspace for the FOCUS GC
and how to connect the FOCUS GC to the gas supplies and peripheral devices.
Instruction Manual (PN 317 094 27)

This manual provides descriptions of the FOCUS GC hardware and software and
instructions for their use.
Spare Parts Catalog (PN 317 094 29)

This catalog contains a list of spare parts for the FOCUS GC.
xx FOCUS GC Version for MS - Instruction Manual

Classification of the Instrument About This Manual
Classification of the Instrument

Environmental Conditions
• Internal use.
• Altitude up to 2000 meters.
• Temperature from 15 to 35 °C.
• Maximum relative humidity between 30% and 85%.
• Voltage variations not exceeding 10% of the nominal value.
• Transients according to installation categories II.
• Degree of pollution according to IEC 664 (3.7.3) 2.
Technical Features
The following table summarizes the major technical features of the FOCUS GC
Features Description
• External Interface
— RS232 Serial Line
• Power Supply
— 120 Vac; 50/60 Hz; 1600 VA
— 230 Vac; 50/60 Hz; 1600 VA
• Dimensions
— 680 x 640 x 440 mm (h x l x w)
• Mass
—About 30 kg
FOCUS GC Version for MS - Instruction Manual xxi

About This Manual Safety Information
Safety Information
WARNING! The instrument must be used according to the specifications of this guide. Improper
use can adversely affect the instrument protection. The analytical operation requires
the use of chemical substances having different hazard specifications. Before using
chemicals, please read the hazard indications and information reported in the Safety
Sheet supplied by the manufacturer referring to the relevant CAS (Chemical
Abstract Service) number.
Use of Gases
WARNING! Before using gases, carefully read the hazard indications and information reported
in the Safety Sheet supplied by the manufacturer referring to the CAS (Chemical
Abstract Service) number. It is the user’s responsibility to see that all local safety
regulations for the use of gases are obeyed.
xxii FOCUS GC Version for MS - Instruction Manual

Using Hydrogen About This Manual
Using Hydrogen
The use of hydrogen as a carrier gas or as fuel for certain flame detectors requires
the operator’s strict attention and compliance with special precautions due to the
hazards involved.
Hydrogen is a dangerous gas, particularly in an enclosed area when it reaches a
concentration corresponding to its lower explosion level (4% in volume). When
mixed with air it can create an explosive mixture. An explosion hazard could
develop in the GC oven when hydrogen is used as a carrier gas if oven elements
are not perfectly connected to each other, or if the connection materials are worn
out, broken, or otherwise faulty.
Use the following safety precautions when using hydrogen:

• Ensure that all hydrogen cylinders comply with the safety requirements for
proper use and storage. Hydrogen cylinders and delivery systems must
comply with local regulations.
• Make sure the gas supply is turned completely off when connecting hydrogen
lines.
• Perform a bubble test to ensure that the hydrogen lines are leak-tight before
using the instrument. Perform this test after the pressure test described in the
Testing for Leaks paragraph in FOCUS GC Site Preparation and Installa-
tion Guide Manual. Repeat this test to eliminate all leaks.
• Ensure your GC column oven has a Thermo Fisher Scientific hydrogen sen-
sor. A hydrogen sensor continuously monitors the hydrogen level in the GC
column oven.
If your GC oven does not have a hydrogen sensor already installed, contact your
Thermo Fisher Scientific sales representative. To comply with instrument safety
requirements, a Thermo Fisher Scientific CSE or authorized service technician
should install the sensor.
If you plan to use a sensor other than the recommended Thermo Fisher Scientific
sensor, you must verify its ability to perform the functions listed above before
installing it. It must comply with your local safety regulations, or with the IEC
61010 regulations if local regulations do not exist.
FOCUS GC Version for MS - Instruction Manual xxiii

About This Manual Cleaning and Decontamination
Using the Hydrogen Sensor

The lower limit of the hydrogen sensor is 0.5% in volume. You should adjust the
detection threshold to 1% in volume, which is 25% of the hydrogen lower limit of
explosion (4% in volume). In cases where the connections begin to leak or the
column breaks, the sensor alerts the operator. Then it automatically cuts off the
gas supply and heating to the active zones, and sweeps the column oven with
forced air ventilation. If the sensor detects anomalies or leaks during GC
operation due to instrument malfunction, the operator must immediately:
• close the hydrogen supply
• switch off the gas chromatograph
• air out the room
The reliability of the sensor depends on careful maintenance. After the sensor is in
use, you must periodically check its operating performance and calibration as
recommended by the manufacturer. Refer to your hydrogen sensor’s instruction
manual for maintenance guidelines.
WARNING! Never use hydrogen in FOCUS GC unless your GC oven has a hydrogen sensor
installed.
Thermo Fisher Scientific CSEs are not authorized to install or repair any instrument
using hydrogen as a carrier gas unless the instrument is equipped with the appro-
priate sensor.
Cleaning and Decontamination

Normal usage of the FOCUS GC can cause the exterior to get dirty. Clean the
outer surfaces by wiping them with a cloth dampened with water.
In the event that a hazardous material is spilled on or in the instrument, clean the
spill according to the procedures in the Material Safety Data Sheet for that
substance.
xxiv FOCUS GC Version for MS - Instruction Manual

FOCUS GC Version for MS
1
Description
This chapter provides a basic overview of the features and options of the FOCUS
GC Version for MS gas chromatograph. After each brief description of a FOCUS
GC component, you will find references to chapters in this manual containing
more detailed information.
Chapter at a Glance…
Instrument Overview ............................................................................................26
GC Parts Description............................................................................................30
FOCUS GC Version for MS - Instruction Manual 25

Chapter 1
FOCUS GC Version for MS Description Instrument Overview
Instrument Overview
The FOCUS GC Version for MS consists of four major components, as shown in
Figure 1-1.
FOCUS GC Components
1
1
3 3 4
1. Pneumatic Compartment 3. Electronic Compartment

2. Analytical Unit 4. Status Panel
Figure 1-1. FOCUS GC Components
Pneumatic Compartment
The pneumatic compartment contains the carrier gas control circuit. It is
completely electronic (digital pneumatics).
Analytical Unit
The analytical unit consists of two subcompartments:
• the column oven
• the injector compartment
26 FOCUS GC Version for MS - Instruction Manual

Chapter 1
Instrument Overview FOCUS GC Version for MS Description
Electronic Compartment
The electronic compartment consists of two subcompartments:
• the high-voltage compartment
• the low voltage compartment
Status Panel
The status panel make up the FOCUS GC Version for MS user interface.
Gas Control
The GC is equipped with digital pneumatics for carrier gas control.
Carrier Gas Control

Carrier gas is controlled electronically through an electronic pneumatic control
module Digital Pressure Flow Control (DPFC) mounted in the pneumatic
compartment.
DPFC Module
The DPFC module features the following:
• constant pressure or constant flow operating modes
• inlet pressure control (in kPa, psi, or bar) and column flow rate control
(in mL/min)
• split flow control (in mL/min)
• septum purge flow control (in mL/min)
The DPFC module also allows the following operations:

— Column Evaluation
To automatically calculate the column constant.
— Leak Check
To keep the system under control.

Chapter 1
FOCUS GC Version for MS Description Instrument Overview
— Gas Saver Function

To reduce the split flow after an injection to avoid the waste of expensive
gases.
Refer to...
Chapter 2, Gas Control.
Column Oven
The FOCUS GC column oven has a high degree of thermal stability and fast
heating and cooling. The air circulation in the oven ensures the column is kept in a
thermally homogenous and stable zone. This provides more precise analytical
performance and helps prevent chromatogram peak distortion.
Refer To…
Chapter 3. Column Oven.
Injector
FOCUS GC is designed to operate with the Split/Splitless (S/SL) injector.
This injector minimizes heavy component discrimination with optimized sample
transfer to the column. You can use capillary and wide-bore columns with the
Split/Splitless injector. With the appropriate adapter kit, you can also use packed
columns.
Refer to...
Chapter 4, Split/Splitless Injector (S/SL)
Column
The column is where the chromatographic separation of the sample occurs.
Several types of columns are available for different chromatographic applications.
Refer to…
Chapter 5, Column

Chapter 1
Instrument Overview FOCUS GC Version for MS Description
MS Detector
FOCUS GC is designed to be coupled with a DSQ Mass Detector.
Instrument Automation
FOCUS GC Version for MS is fully controlled by the computer through Xcalibur
software that is also used for data handling and interpretation of the acquired
results. Therefore the instrument is not provided with independent keyboard and
display. On the instrument front there is a Status Panel where you can monitor the
instrument status.

Chapter 1
FOCUS GC Version for MS Description GC Parts Description
GC Parts Description
This paragraph gives you a detailed description of the instrument components.
Front Panel
1 2
4 3
1. Column Oven Door 3. Status Panel

2. Column Oven Door Push Button 4. Electronic Compartment
Figure 1-2. Front Panel
Front Panel comprises the following parts:

• Column Oven
• Status Panel
• Electronic Compartment

Chapter 1
GC Parts Description FOCUS GC Version for MS Description
Column Oven
The column oven, shown in Figure 1-3, is accessible opening the column oven
door by pushing the relevant button.
Figure 1-3. Column Oven Internal View
Refer To...Chapter 4, Column Oven
Status Panel
Status panel, shown in Figure 1-4, is the user interface of the GC. It consists of a
series of four Status LEDs showing the instrument’s status.
Figure 1-4. Status Panel
Refer also to Virtual Keypad.
The LEDs (Light Emitting Diodes) on the left side of the display screen indicate
the FOCUS GC’s operating status. The status LEDs indicate the current operating
mode and special settings activated by the operator. Table 1-1 lists and explains
each status LED.

Chapter 1
Table 1-1. Status LED Descriptions

LED Description
Not Ready/Error This LED lights when the GC is not ready to make a run,
usually because the specified oven temperature has not
been reached. It remains lit if any additional equilibration
time has been configured. It blinks when the GC has one
or more error conditions.
Standby/Prep Run This LED lights when the GC is in Standby, waiting to be
advanced to the Ready status.
It blinks links while the GC prepares for a run, for example,
while opening or closing valves as required by the method.
Ready to Inject This LED lights when the prep run has finished,
indicating you can inject a sample or start an autosampler.
Run This LED lights when a run is in progress.
Electronic Compartment
It is located on the bottom part of the GC, and it is accessible only by authorized
Thermo Fisher Scientific technical personnel.
WARNING! Before opening the electrical compartment, cut off power supply to the instrument
and disconnect the power cord.
The electronic compartment, shown in Figure 1-5, comprises:
• Low Voltage Section
• High Voltage Section

Chapter 1
Figure 1-5. Electronic Compartment
Low Voltage Section

It contains the electronic circuits to operate and control the instrument.
WARNING! A Li 3 V; 220 mA/h unrechargeable battery is present on the Main Board. The battery
replacement must be performed only by specialized technical personnel.
High Voltage Section

It contains the power circuits. The configuration of the instrument 120 or 230 Vac
power supply is determined by the position of the voltage selector, factory set,
located on the Main Board. According to the instrument power supply
configuration, the breaker ON/OFF main switch changes as follows:
Power Supply Breaker

120 Vac 15A
230 Vac 7A
The high voltage section is provided with a series of protection fuses as reported
in the following table:

Chapter 1
Fuse Type Protection

F1 F2A; IEC 127/I; (5 x 20 mm) Injector heater element
F2 F1A; IEC 127/I; (5 x 20 mm) 230 Vac Main power (Breaker)
120 Vac Main power (Breaker)
F3 F2A; IEC 127/I; (5 x 20 mm) Auxiliary heater element
F4 F0.63A; IEC 127/I; (5 x 20 mm) Oven fan motor
F5 F0.63A; IEC 127/I; (5 x 20 mm) Oven fan motor
Rear Panel
The Rear Panel is shown in Figure 13.
1. Gas Inlet Port 3. Oven Exhaust Vent Area

2. Electrical connections
Figure 1-6. Rear Panel

Chapter 1
Rear Panel comprises the following parts:

• Carrier Gas inlet port
• Electrical Connections
• Oven Exhaust Vent
Carrier Gas Inlet Port

It is located on the middle upper part of the instrument rear panel. Gas inlet port is
directly connected to the DPFC module.
WARNING! Gas pressure must be controlled on the gauges provided on the gas tank of the
supply gas line. The maximum inlet pressure is 1000 kPa (120 psi) to allow DPFC
module to adjust pressure up to 1000 kPa.
Commonly used gases are helium, hydrogen and nitrogen.
The default pressure unit is the kilopascal (kPa). You specify the pressure units in
the Configuration menu. Refer to Configuring the Carrier Gas in Chapter 2.
The following gives a brief conversion guide for the most commonly used
pressure units in gas chromatography.
To Convert To Multiply by
kPa bar 0.01
psi 0.145
bar kPa 100
psi 14.51
psi kPa 6.89
bar 0.0689
100 kPa = 1 bar = 14.51 psi
Electrical Connections
Electrical connections al located on the rear part of the electronic compartment.
As shown in Figure 1-7.

Chapter 1
5 3
ON
I TIMED EVENTS
AUTOSAMPLER
P
O
W
E GENERIC SAMPLER
R HANDSHAKE SIGNAL SIGNAL COMPUTER
O
OFF
1 2 6 7 8 4
Figure 1-7. Electrical Connections
1. Breaker marked POWER to switch the instrument On/Off
• Position I = instrument ON
• Position O = instrument OFF
2. 120 or 230 Vac 50/60 Hz Main socket marked
3. 9-pin connector marked AUTOSAMPLER

Not Used. Autosampler must be connected directly to PC.
4. 9-pin connector marked COMPUTER to dialog with the computer via

RS232 serial line.
5. 15-pin connector marked TIMED EVENTS to automatically drive up to

external valves.
6. 6-pin connector marked SAMPLER SIGNALS for the autosampler Start/

Stop signals. It can be used also for an optional remote Start button when an
autosampler is not used.
7. 8-pin connection marked GENERIC HANDSHAKE to cooperate with the

Mass Detector during analysis.
8. 4-pin connection marked SIGNAL 0–1V-10V-GND for the detector analog

signal output

Chapter 1
Oven Exhaust Vent

Hot air [350°C (660°F)] exits through this vent during GC operation.
Any material exposed to the oven exhaust must be able to withstand repeated
exposure to temperatures of up to 350°C (660 °F).
WARNING! Oven exhaust vent can cause severe burns. Avoid working behind the instrument
when the oven vents during cooling-down cycles. Do not expose gas tanks or
bottles, chemicals, regulators, electrical cords, or other temperature-sensitive items
to oven exhaust.
Top Panel
Top panel is shown in Figure 1-8.
1. Injector Port Split and Purge Vents

Figure 1-8. Rear Panel
Top Panel comprises the following parts:

• Injector port
• Split and Purge vents
For details refer to Chapter Split/Splitless Injector (S/SL)

Chapter 1
GC Left Hand-side Panel

It is shown in Figure 1-9.
1. Detector Transfer Line Insertion Hole 2. Transfer Line Heater Connection

Figure 1-9. GC Left Hand-side Internal View
It is provided with:
• a hole to allow the insertion of the mass detector transfer line inside the GC
column oven
• a connection for the transfer line heater
The insulating material covering the hole must be removed before inserting the
detector transfer line.

Chapter 1
Virtual Keypad
Figure 1-10 illustrates the virtual keypad for FOCUS GC available only by
Xcalibur software.
Virtual keypad has three components:

• a line-line display
• display LEDs showing the instrument’s status
• a keypad for data entry.
Figure 1-10. User Interface
For detailed information about the Virtual Keypad refer to Chapter 8

Chapter 1

Gas Control
2
This chapter contains information on controlling and programming the carrier gas
flow to the FOCUS GC.
Gas Supplies .........................................................................................................42
Carrier Gas Regulation .........................................................................................44
Carrier Gas Parameters.........................................................................................45
Operating Sequences
Configuring the Carrier Gas .................................................................................43
Configuring the Pressure Unit ..............................................................................43

Chapter 2
Gas Control Gas Supplies
Gas Supplies
Commonly used carrier gas is helium, however FOCUS GC can be configured to
use also nitrogen or hydrogen. You can specify the type of gas and pressure units
the FOCUS GC displays.
• The default carrier gas is Helium (He)
• The default pressure unit is the kilo pascal (kPa).
WARNING! Hydrogen is a dangerous gas that, when mixed with air, may create an explosive
mixture. The use of hydrogen as a carrier gas requires the operator’s extreme
caution. Special precautions must be taken because of the risk of explosion. The
gas chromatograph must be equipped with a hydrogen sensor if you use hydrogen
as a carrier gas. Refer to Using Hydrogen for more information. All Thermo Fisher
Scientific gas chromatographs are designed to use an inert gas as the carrier gas. If
you wish to use hydrogen as a carrier gas, you must install a hydrogen sensor.
Contact a Thermo Fisher Scientific sales representative if you plan to use hydrogen
as the carrier gas in FOCUS GC. If you don’t have the hydrogen sensor, you must
use an inert carrier gas.
You specify the pressure units and the type of carrier gas in Configuration
menu operating as described in the following Operating Sequences

Chapter 2
Gas Supplies Gas Control
OPERATING SEQUENCE
Configuring the Carrier Gas
Carrier gas is already configured to Helium. To change the configuration, proceed
as follows:
In Xcalibur FOCUS GC Setup page set the gas type required as carrier gas.
OPERATING SEQUENCE
Configuring the Pressure Unit
The Pressure Unit is already configured to kPa (kilo pascal). To change the
configuration, use the virtual keypad as described in chapter 8 Use of the Virtual
Keypad.
Once the pressure unit is selected, you must change also the Xcalibur
configuration as follows:
In Xcalibur FOCUS GC Configuration page set the pressure unit required.

Chapter 2
Gas Control Carrier Gas Regulation
Carrier Gas Regulation

This paragraph describes the automatic Digital Pressure and Flow Control
(DPFC) of the FOCUS GC. You control the gas flow by programming parameters
in the Carrier gas page. See Carrier Gas Parameters.
The DPFC module, provides:

• Flow and pressure control for the S/SL injector
• Gas saver mode
The DPFC module pneumatic circuit is represented in Figure 2-1.
1 3
A
2
4 5
B
C
6 7 8 9
1. Flow Sensor 1 2. Proportional Valve 1
3. Pressure Sensor 4. Fixed Flow Regulator 5 mL/min
5. On/Off Valve 1 6. Flow Sensor 2
7. Proportional Valve 2 8 Trap
9. On/Off Valve 2 A: Carrier Gas Inlet
B. Septum Purge Line C: Split Line
Figure 2-1. DPFC Module

Chapter 2
Carrier Gas Parameters Gas Control
Carrier Gas Parameters

The carrier is the gas used as mobile phase in gas chromatography. The carrier gas
carries the analyte mixture through the GC column, where it is separated into its
individual components. The carrier gas flows through the GC column at a specific
rate, measured either as a linear velocity (cm/sec) or as a flow rate (mL/min).
Carrier page is accessible from the Roadmap-Home Page by clicking the

icon. The instrument Setup dialog windows displays all configuration tabs.
Figure 2-2. Carrier Gas Page

Chapter 2
Gas Control Carrier Gas Parameters
This page contains two group boxes:

• Flow Mode Selection Group Box
• Gas Saver Selection Group Box
Flow Mode Selection Group Box

The controls you see on this page are dependent on the flow mode selection.
Please select one of the following modes and jump to that topic for detailed
information.
Two flow modes are available.
Constant Flow
In constant flow mode, the column flow is kept constant throughout the analysis.
The pressure at the column head will change with the column temperature to
maintain a consistent flow.
Constant Pressure
In constant pressure mode, the pressure at the column head is kept constant
throughout the analysis.
According to the carrier gas mode selected, the Flow List Box may visualize:
Flow or Pressure.

Chapter 2
Carrier Gas Parameters Gas Control
• Flow (ml/min)
Enter a column flow for the analytical column.
• Pressure (kPa)
Enter the inlet pressure for the analytical run
On/Off Check Box

Check this box to enable flow (or pressure) to the inlet.
When unchecked, the flow (or pressure) is cut off to the inlet
Vacuum Compensation
Check this box to compensate for a vacuum at the end of the analytical column.
This is usually the case when the detector is a mass spectrometer. If the box is not
checked, calculations are made for a normal GC detector, which is usually at
atmospheric or slightly higher pressure.

Chapter 2
Gas Control Carrier Gas Parameters
Gas Saver Selection Group Box
This group box contains gas saver controls, which reduce carrier gas
consumption, especially when a large split flow is used.
Enable Check Box

Check this box to activate the gas saver (Flow, Time).
Flow (ml/min)
It is the value which the split flow is reduced after the injection for gas saving.
This value is also maintained while the GC is in stand-by condition.
Time (min)
The time after the injection when gas saver flow will be activated.

Column Oven
3
This chapter describes the features of the FOCUS GC column oven.
Column Oven Overview.......................................................................................50
Oven Parameters...................................................................................................52

Chapter 3
Column Oven Column Oven Overview
Column Oven Overview

The FOCUS GC column oven, shown in Figure 3-1, provides a stable heating
environment for the analytical column. The oven heats and cools quickly.
Efficient air circulation ensures a high degree of thermal stability.
Figure 3-1. The Column Oven
Opening the oven door activates a safety microswitch, which automatically

switches off the oven heating and the motor for the air circulation fans. Resistor
elements powered by a circuit located within the GC control unit heats the oven.
The oven temperature is monitored by a PT 100 platinum wire sensor and
controlled by the GC control unit.
The column oven has the following capabilities:

• maximum temperature of 350 °C
• maximum temperature increase rate of 120 °C/min
• seven linear temperature ramps and eight levels
• minimum operating temperature of a few degrees above ambient, which is
obtained by two modulated cooling flaps controlled by the GC, schematically
shown in Figure 3-2.

Chapter 3
Column Oven Overview Column Oven
• temperature control through

— Heater control
— Fine control of hot air exhaust
— Ambient air intake
• Usable space
— Width about 230 mm
— Height about 230 mm
— Depth about 150 mm
1. Oven 2. Fan
3. Air 4. Cooling Flaps
Figure 3-2. Oven Air Circulation
Oven Safety
Opening the oven door cuts off the power to the oven heater and fan. The
setpoints are kept in memory.
To return to normal operation, close the oven door.
WARNING! The oven vents at the rear of the GC discharge hot air during cooling.

Chapter 3
Column Oven Oven Parameters
Hydrogen is a potentially dangerous gas. When hydrogen is used as a carrier gas,

the column oven must have a hydrogen sensor. Refer to Using Hydrogen for
hydrogen safety information.
Oven Parameters
This page is the method editor for setting up parameters in the GC run.
Oven page provides you full control of the GC
Oven page is accessible from the Roadmap-Home Page by clicking the icon.
The instrument Setup dialog windows displays all configuration tabs.
Controls are for running complex temperature programs (with up to seven levels
of ramps) and controlling post run events.
Figure 3-3. Oven Page

Chapter 3
Oven Parameters Column Oven
This page contains three selection boxes

• Graph
• Ramps Group Box
• Oven Group Box
Graph
The graph display a graphical representations of the oven temperature program
including any post run events. The axes are temperature in degrees centigrade and
time in minutes. An isothermal run just gives a flat line
Ramps Group Box

Ramps controls allows to add or delete temperature ramps for the oven
temperature program
Arrow Keys
Use the up-down control to add or subtract the number of ramps to use in the oven
temperature program. This is the rate in degrees Centigrade per minute the GC
oven is ramped up or down from the initial temperature or the previous level’s
final ramp temperature. Clicking on the Down arrow automatically adds a ramp
level after the last one listed. Clicking on the Up arrow deletes the highest level or
the one being displayed on the bottom

Chapter 3
Initial / Temp Text Box

The initial temperature the oven is set at the beginning of the temperature
program. For isothermal runs, this is the oven temperature for the entire run. After
Preready or Prep Run this is the temperature the oven will be at.
Initial / Hold Time text box

The amount of time to maintain the initial temperature.
Ramp / Rate Text Boxes

The rate of change of the temperature when increasing it from one value to the
next. Described in degrees Celsius per minute (°C/min). The ramp begins at the
previous step’s final temperature value and proceeds to the current step’s final
temperature at the specified rate.
Ramp / Temp Text Boxes

The temperature the oven is set at for the next ramp of the temperature program.
For isothermal runs, this is the oven temperature for the run. After Prep Run this is
the temperature the oven will be at.
Ramp / Hold Time Text Boxes

The time to maintain the temperature specified in the Final Value control box.
Oven Group Box

This group box allows you to control the following functions:

Chapter 3
Oven Parameters Column Oven
Max Temp Text Box

Specify the maximum temperature for this run. The GC has a maximum
temperature of 350°. The maximum allowable temperature for the column being
used in the method is automatically set.
PrepRun Timeout
Specify how long the GC should remain in the Ready to Inject mode before
returning to Stand By. If the START button is not pressed within the prep run
timeout period, then the GC will return to Stand By mode. This feature is a
protective measure to keep the GC from being in the Ready to Inject mode too
long. For example, this will prevent accumulation of contaminants on the
analytical column when doing splitless injections.
Equilibration Time (min) text box

Specify how much time the GC should wait after the initial conditions are met
before going to standby.

Chapter 3

Split/Splitless Injector
4
(S/SL)
This chapter describes the Split/Splitless (S/SL) injector and contains operating
sequences for the different split/splitless operating modes.
S/SL Overview .....................................................................................................58
S/SL Injection Techniques....................................................................................67
S/SL Inlet Parameters ...........................................................................................73
Operating Sequences
Installing a Liner and a Septum............................................................................65

Chapter 4
Split/Splitless Injector (S/SL) S/SL Overview
S/SL Overview
The S/SL injector, shown in Figure 4-1, is optimized for either split or splitless
applications to ensure effective sample transfer into the column, minimizing
heavy component discrimination.
1. Septum Cap 7. Graphite Column Ferrule

2. Septum 8. Capillary Column
3. Graphite Liner Seal A. Carrier Gas Inlet
4. Glass Liner B. Split Line
5. Fixing Nut C. Septum Purge Line
6. M4 Retaining Nut
Figure 4-1. Split/Splitless Injector

Chapter 4
S/SL Overview Split/Splitless Injector (S/SL)
For both split and splitless applications, the sample is injected through a septum
into a glass liner in the vaporization chamber.
The technique used, either split or splitless, determines the choice of the glass
liner. You can control the injector temperature from ambient to 375 °C, although
the actual injector temperature you use depends on the solvent choice and thermal
stability of the samples.
The Digital Pressure Flow Control (DPFC) controls the split flow, while the
septum purge flow is kept constant by a calibrated flow regulator.
The S/SL injector is also equipped with electronically actuated On/Off valves for
split and septum purge lines. See Figure 4-2
10 9 8 7 6 Purge
C Split
5 4
B
3 1
A
2
1. Flow Sensor 1 2. Proportional Valve 1

3. Pressure Sensor 4. Fixed Flow Regulator 5 mL/min
5. On/Off Valve 1 6. Flow Sensor 2
7. Proportional Valve 2 8 Trap
9. On/Off Valve 2 10. Split Line Filter
A. Carrier Gas Inlet B. Septum Purge Line Outlet
C. Split Line Outlet
Figure 4-2. Gas Control

The septum purge system continually purge the septum with a flow of gas. This
prevents the volatile components given off by the septum from entering the
column. Figure 4-3 shows the septum purge system.

Chapter 4
1. Spring 6. Graphite Liner Seal

2. Septum 7. Glass Liner
3. Septum Holder A. Carrier Gas Inlet
4. Septum Support B. Septum Purge Line
5. Liner Cap C. Split Line
Figure 4-3. Septum Purge System

Figure 4-4 shows the S/SL injector components.

Chapter 4
3
4
12
5 9
6
13
14
15
7 10
16
11
1. Septum Cap 9. Injector Body

2. Spring 10. Metal Ring
3. Septum Holder 11. Fixing Nut
4. Septum 12. Silver Seal
5. Septum Support 13. Terminal Fitting
6. Liner Cap 14. Fixing Nut
7. Liner 15. Graphite Column Ferrule
8. Graphite Liner Seal 16. M4 Retaining Nut
Figure 4-4. Split/Splitless Injector Components

Chapter 4
Septum
Standard Septum
Always use good quality septa, such as the BTO septa supplied with the FOCUS
GC. Such septa resist deformation, have longer life expectancy, and have a low
bleed level, even at high temperatures.
Microseal™ Valve
S/SL injector is compatible to use Merlin Microseal™ High Pressure Valve
instead of the standard septa.
NOTE To replace the standard septum with the Microseal™ Valve, the relevant installation kit is
required.
Liners
You may install different types of glass liners depending on the injection mode
used. Table 4-1 shows the liner options.
Table 4-1. Liner Sizes and Applications

ID mm OD mm Application
5 8 Glass liner used for split injection
3 8 Glass liner used for split injection
3 8 Glass liner used for splitless injection
5 8 Glass liner used for splitless injection
5 8 Glass liner used for direct injections into a wide-bore
column.
5 8 Glass liner used for split injections at high flow rates or for
the most polar solvents.

Chapter 4
The glass liner used for direct splitless injection into a wide-bore column is
tapered at the bottom. It is used with 0.53 mm ID columns. Figure 4-5 shows the
tapered glass liner.
1. Carrier Gas Inlet 3. Septum Purge Line

2. Split Line
Figure 4-5. S/SL Wide-Bore Injection with a Tapered Liner
A laminar cup liner is used for split injections at high split flow rates or for the
more polar solvents. This glass liner has a mixing chamber with an extended flow
path that allows complete sample vaporization before the sample reaches the split
point.

Chapter 4
Packed Columns
With a special conversion kit, you can install packed columns in the S/SL injector,
as shown in Figure 4-6.

2. Split Line
Figure 4-6. S/SL with a Packed Column

Chapter 4
OPERATING SEQUENCE
Installing a Liner and a Septum
Materials required:
• liner
• septum
• tweezers
• graphite seal
• liner cap wrench (included with the GC)
NOTE The injector fittings may be hot.

This sequence must be performed with the injector at working temperature.
1. Choose the correct liner for your application (see Table 4-1). Slide a graphite
seal onto the liner from the bottom (the bevelled end) and push it to
approximately 8–10 mm from top (the flat end).
CAUTION Be careful not to break the graphite or to allow graphite to enter the liner.
2. Hold the top of the liner with tweezers. Lower it, bevelled end first, into the
injector. The liner should rest on the terminal fitting at the bottom of the
injector.
3. Insert the liner cap and secure it with the liner cap wrench. The liner cap must
be screwed down tight enough to ensure a good seal between the liner and the
injector body.
4. Place the septum support in the injector. The septum support must lie flush
with the top of the injector. If not, the liner cap may not be tight enough.
5. Use tweezers to pick up the septum. Place the septum into the septum holder,
then place the holder on top of the complete injector assembly.
CAUTION To avoid contamination, do not touch the septum with your hands.

Chapter 4
6. Gently screw the septum cap onto the injector assembly until finger-tight to
hold the septum in place.
WARNING! If the injector is hot, use the liner cap wrench to turn the septum cap.
Do not overtighten the septum cap. The septum will deform and may be difficult to
penetrate with the syringe needle.

Chapter 4
S/SL Injection Techniques Split/Splitless Injector (S/SL)
S/SL Injection Techniques

This paragraph describes the different sample injection techniques.
Split Injection Technique

In split injection, only a part of the sample transfers into the column. The rest
discharges through the split line.
The ratio of the split flow to the column flow (the split ratio) determines the
amount of sample that enters the chromatographic column. Figure 4-7 illustrates
the gas flows for the split injection technique.
You inject the sample into a glass liner inside the heated vaporization chamber. In
the chamber, the sample undergoes rapid vaporization. The relatively high gas
flow through the injector carries the vaporized sample rapidly down toward the
head of the column.
At the column head, the sample splits in the split ratio. A portion of the sample
goes into the column, while the remainder is carried out the split line. You set the
column flow in the CARRIER menu and the split flow in the INLET menu.
Narrow bore columns, which have inherently low column flows, can produce
relatively high split ratios.
NOTE Hot Empty Needle Injection Technique

Using conventional syringes in hot injectors may cause discrimination of higher boiling
point components. This is due to partial sample vaporization within the hot syringe needle.
We recommend you use a hot empty needle injection technique. This technique consists of
drawing the sample volume into the syringe barrel followed by a small air gap, which
ensures the syringe needle is empty. You insert the empty needle into the injector, wait a
few seconds, inject the sample rapidly, and immediately remove the syringe.
Split injection is suitable for high-concentration sample analysis, headspace

analysis, and isothermal analysis.

Chapter 4
Split/Splitless Injector (S/SL) S/SL Injection Techniques

2. Split Line
Figure 4-7. Split Injection Technique
The major advantages of split injection are simplicity and the ability to introduce
samples over a wide range of concentrations. Peak shapes in the chromatogram
are generally very sharp due to the rapid sample introduction into the column.

Chapter 4
Splitless Injection Technique

Splitless injection is suitable for the analysis of compounds present in very low
concentrations.
The splitless technique allows the entire sample to enter the column without
splitting. This offers better sensitivity than the split technique.
With splitless injection, the split line is closed during sample injection and
transfer to the column. Once the transfer is over, the split line reopens to flush the
vaporization chamber of any remaining sample vapors. Figure 4-8 shows the
split/splitless injector used for splitless injection.
During splitless injection, when the split valves are closed, the flow of gas through
the injector is relatively low. It is equal to the column flow—only a few mL/min.
The vapor cloud generated by the vaporization of the liquid sample expands
upward from the point of vaporization and can fill the liner.
The injector can accept and quantitatively transfer to the column sample volumes
of up to 5 μL.
With injection volumes higher than 4 μL, the recovery of the sample injected can
be improved by closing the septum purge together with the split valve during the
splitless period.
You can program this in the INLET menu when you select the Splitless mode.
Condensation and subsequent loss of higher molecular mass compounds in the top
region of the injector liner is prevented by effective heating over the whole length
of the injector.

Chapter 4
1. Carrier Gas Inlet 3. Split Line

2. Septum Purge Line
Figure 4-8. Splitless Injection Technique
The transfer of the vaporized sample from the injector to the column takes place
very slowly due to the relatively low column flows involved. With typical carrier
gas flow rates of 1–4 mL/min, the transfer can take between 30 and 90 seconds,
depending on a variety of circumstances.
This transfer time is the splitless time. You can set the splitless time in the INLET
menu when you select Splitless mode. For narrower diameter columns (< 0.22
mm) with inherently lower flows (< 1.0 mL/min), the transfer might never be

Chapter 4
completely achieved due to back diffusion of sample vapors in the injector at a

higher rate than transfer into the column.
You can counter this by using the splitless surge pressure mode. In this mode, the
pressure in the injector temporarily increases during the splitless period to
increase the flow into the column. You set the surge pressure, which activates
during the Prep Run stage.
At the end of the splitless period, the split valve reopens and the split flow flushes
the injector of any remaining sample vapors. In splitless injection, the absolute
split flow is not important. It needs only be sufficient to purge the injector.
Normally 40–50 mL/min is adequate.
Refocusing the Sample

The sample vapors enter the column over an extended period of time and produce
very broad starting bands. To maintain column efficiency, some form of
refocusing must take place in the column inlet before chromatography begins.
To achieve this, keep the oven temperature to a sufficiently low value during the
transfer of the sample to trap it on the column head by condensation or solvent
effect.
This technique’s efficiency is greatly enhanced by correctly choosing conditions

for column character, carrier gas flow rates, splitless time, column temperature,
and injector liner internal diameter. All of these conditions can affect the transfer
efficiency and refocusing.
• Solvent Effect
To refocus the compounds that elute at low temperature, the so-called solvent
effect is used. It consists of the volatile compounds trapping in the solvent
recondensed in column. It is obtained cooling the column to 20–25 °C below
the solvent boiling point, combined with injection volumes of at least 1 μL.
Isothermal analysis or temperature programming can then continue.
• Temperature Effect
You can refocus later eluting compounds without solvent effects by cooling
the oven sufficiently during the transfer. The trapping temperature effect traps
and refocuses the sample compounds.

Chapter 4
Flooding
Splitless injections may occasionally exhibit an effect known as flooding, which
can result in peak distortion due to the solvent condensation.
NOTE Hot Empty Needle Injection Technique

Using conventional syringes in hot injectors may cause discrimination of higher boiling
point components. This is due to partial sample vaporization within the hot syringe needle.
We recommend you use a hot empty needle injection technique. This technique consists of
drawing the sample volume into the syringe barrel followed by a small air gap, which
ensures the syringe needle is empty. You insert the empty needle into the injector, wait a
few seconds, inject the sample rapidly, and immediately remove the syringe.

Chapter 4
S/SL Inlet Parameters Split/Splitless Injector (S/SL)
S/SL Inlet Parameters

This page is the method editor for setting up the injector parameters.
S/SL Inlet page is accessible from the Roadmap-Home Page by clicking

icon.
Figure 4-9. S/SL Inlet Page
This page contains four group boxes.

• Mode List Box
• Inlet Group Box
• Purge Group Box
• Surge Group Box

Chapter 4
Split/Splitless Injector (S/SL) S/SL Inlet Parameters
Mode List Box

Use this list box to select one of the following inlet operating mode.
Split
The carrier flow is split in the injection port with the bulk going out the split vent.
Use this injection type when analyzing high concentration or neat samples, or in
instances where sensitivity is less important. The split vent remains open all the
time. This method yields the sharpest peaks, if the split gas is properly mixed.
Additionally, this technique can improve peak shape and resolution.
Splitless
The split vent is closed during the injection to drive most of the sample into the
column. Solvent effect is required to refocus the analytes, especially most volatile
components. You can achieve solvent effect by keeping the oven 20 °C below the
solvent boiling point. Splitless times of ~ 1 minute are typical.
Splitless w/surge
A surge is applied during the splitless time to reduce residence time of the
analytes in the inlet. This will reduce band broadening and may sharpen peaks,
especially for more volatile components, which are not improved by cold trapping
effects on the column. Usually this technique involves an oven temperature 50° C
below the BP of analyte.
Inlet Group Box

Use this group box to set the following inlet operating parameters.

Chapter 4
S/SL Inlet Parameters Split/Splitless Injector (S/SL)
Temperature check box and text box

The setpoint for the inlet's temperature. Depending on the mode of injection, it
should be set at a temperature appropriate to vaporize the sample and solvent.
Split Flow check box and text box

Specify the total split flow coming out of the inlet. This is the total flow out of the
inlet when the split valve is open.
Split Ratio text box

The ratio of split vent flow to the column flow. Calculate the split ratio as shown:
Split Ratio = (column flow + split vent flow) / (column flow).
Splitless Time text box

The amount of time after the injection at which the split vent opens.
Purge Group Box

This group controls the septum purge for the inlet.

Chapter 4
Split/Splitless Injector (S/SL) S/SL Inlet Parameters
Constant Septum Purge check box

The septum purge may be turned off during a splitless injection. Checking this
box will keep the septum purge valve open continuously. By leaving this box
unchecked, the analyst may close this valve during the injection splitless time.
Stop Purge Time text box

Enter the time (in minutes) for the septum purge valve to close after beginning the
injection. The Constant Septum Purge check box has to be unchecked for this
option to be used. This is usually set to the same time as the splitless time.
Surge Group Box

This box is available when in Mode box splitless with surge injection option has
been selected.
Surge Pressure
The pressure applied during the splitless time to produce a surge of flow in the
inlet to speed transfer of the sample. It may be used, depending upon the analysis,
to sharpen peaks closer to the solvent’s boiling point where cold trapping is
ineffective and solvent effect is the main refocusing mechanism. Try adding 8 psi
or 55.157 kPa to the inlet and observe early peaks after the solvent to see if peak
tailing is reduced.
Surge Duration
The amount of time a pressure surge is administered after the injection. Typically,
set to coincide with the splitless time.

Column
5
This chapter describes the analytical column installed in the column oven.
Introduction ..........................................................................................................78
Installation ............................................................................................................79
Keeping Leaks Under Control..............................................................................82
Column Conditioning ...........................................................................................91
Operating Sequences
How to Connect a Capillary Column ...................................................................79
Manual Checking for Leaks .................................................................................83
Performing a Column Evaluation.........................................................................84
Performing an Automatic Leak Check .................................................................89

Chapter 5
Column Introduction
Introduction
The capillary column should be positioned inside the oven on the column support.
Using Correct Fittings

To connect a capillary column to the injector and MS transfer line, you must use
the proper column ferrules and retaining nuts.
Column Ferrules
Encapsulated graphite ferrules are used to connect the capillary column to the
S/SL injector.
Vespel ferrules are used to connect the capillary column to the MS interface.
Refer to the MS Manual.
CAUTION Overtightening compression ferrules does not necessarily produce a stronger,

leak-free joint. In fact, very often the reverse is true. Too much pressure can cause a
leak in the joint and make it very difficult to reseal that particular joint when
changing columns.
Table 5-1 lists the graphite ferrules to use depending on the capillary column
external diameter. Ferrules that are the wrong size may cause leaks and
contamination.
Table 5-1. Ferrules

Capillary Column Graphite Ferrules
0.1 mm ID 0.25 mm ID / 0.35 mm ID1
0.25 mm ID 0.35 mm ID
0.32 mm ID 0.45 mm ID
0.53 mm ID 0.8 mm ID
1. Depending on column manufacturer
Retaining Nuts
M4 split retaining nuts are used to connect capillary columns to injector. The nuts
are split to allow easy installation and removal.

Chapter 5
Installation Column
Installation
The column is installed in the GC oven and connects the injector to the detector.
CAUTION Each column has a maximum recommended operating temperature. To protect the
column from excessively high temperatures, remember to set the Max temp
parameter for the column oven in the Oven Group Box as described in Chapter 3.
OPERATING SEQUENCE
How to Connect a Capillary Column
To install the capillary column, the following sequential steps should be
performed:
• Installing the Column Support
• Preparing a Capillary Column
• Connecting to an S/SL Injector
• Connecting to a MS Transfer Line
Installing the Column Support

To install the column support into the GC oven, insert the four pins into the
corresponding button-holes on the ceiling of the GC oven.
Preparing a Capillary Column

To prepare metal or fused silica capillary column operate as follows:
CAUTION Wear safety glasses to protect your eyes from flying particles while handling,
cutting, or installing columns. Be careful handling columns to avoid accidental hand
injuries.
Fused Silica Capillary Column

To obtain a correct cut of fused silica capillary column, use ceramic scoring wafer
or sapphire scribe.

Chapter 5
Column Installation
Materials required:
• ceramic scoring wafer or sapphire scribe.
1. Hold the capillary column between your thumb and index finger with the
column extending past the tip of your index finger.
2. Score the column very gently. Excessive force could crush the column end.
3. Snap off the end of the column.
4. Inspect the column end for an even, flat cut.
Metal Capillary Column

To obtain a correct cut of metal capillary column, use a triangular file.
Materials required:
• Triangular file
1. Hold the capillary column between your thumb and index finger with the
column extending past the tip of your index finger.
2. Score all round the column very gently.
3. Snap off the end of the column.
4. Inspect the column end for an even, flat cut.
Connecting to an S/SL Injector

Before connecting the column, make sure the injector has been properly
assembled and programmed and the column support has been installed in the GC
oven. For more information about split/splitless injectors, refer to Chapter 5.
Materials required:
• M4 column retaining nut
• graphite ferrule
• typewriter correction fluid or a felt-tipped pen

Chapter 5
Installation Column
• 6 mm wrench
1. Slide the graphite ferrule onto the capillary column with the beveled end
facing the injector. Be careful to avoid damaging the graphite ferrule when
inserting the column.
2. Cut at least 1 cm from the column end.
3. Place the column on the column support.
4. Use typewriter correction fluid or a felt-tipped pen to mark the correct

position of the ferrule from the end of the column depending on the injection
technique. The correct positions are as follows:
— 40 mm for split injection
— 64 mm for splitless injection
5. Insert the column about 2 cm into the injector and slide the ferrule on the
column up to the injector base, then slide the retaining nut onto the column
through the side cut. The FOCUS GC retaining nuts have a slotted design that
makes them easy to add and remove.
6. Finger-tighten the column retaining nut until it starts to grip the column.
7. Adjust the column position so that the mark is even with the column retaining
nut.
8. Use the 6 mm wrench to tighten the retaining nut using no more pressure than
is necessary to obtain a good seal (1/4 to 1/2 turn).
9. Conduct a leak check of the column installation, as described in the paragraph

Keeping Leaks Under Control on page 82.
Connecting to a MS Transfer Line

Before connect the outlet end of the column to the MS detector transfer line, refer
to the FOCUS DSQ manual.

Chapter 5
Column Keeping Leaks Under Control
Keeping Leaks Under Control

FOCUS GC features a series of automatized operations that make easier the task
of keeping under control the tightness of your system.
The sequence Manual Check for Leaks - Column Evaluation - Automatic Leak
Check is the key for minimizing troubles related to leaks.
After you install a column you must perform a manual leak check and column
evaluation then you can use the automatic leak function at any time in the future to
check for leaks
Column Evaluation
Once the leak has been removed and the tightness of the system is reasonably
sure, you should perform the Column Evaluation automatic control and compare
the response with the K Factor values reported in K Factor Tables. Refer to
Performing a Column Evaluation operating sequence.
If the value obtained does not agree with the one reported on the card, this means
that the leaks have not been repaired.
Performing the Column Evaluation is the necessary condition for the success of
any subsequent Automatic Leak Check.
Identifying and Removing Leaks

If the Automatic Leak Check (or any significant symptom) has notified a possible
leak in the system, you should:
• Check the whole system for leaks, from the carrier gas inlet to the MS transfer
line.
• Check the accessible, critical connections (column to injector, column to MS
transfer line, split and purge valves, septum caps).
A possible leaks source may be the gas bottles/gas chromatograph connections.

Check these lines before the others, if specific symptoms indicate that the leak is
outside the gas chromatograph.
Refer to Performing an Automatic Leak Check

Chapter 5
Keeping Leaks Under Control Column
OPERATING SEQUENCE
Manual Checking for Leaks
Before you begin this sequence, you must install the column into the injector, but
not into the MS trasfer line.
Materials needed:
• silicon rubber septum of any dimension
Proceed as follows:
1. Carefully push the detector end of the capillary column into the rubber septum
to seal it.
2. Close off splitting and purge valves on the injector (by using the virual
keypad as described in chapter 8 Use of the Virtual Keypad)
3. Increase the carrier gas pressure to 150–200 kPa and allow the column and
injector pressure to stabilize. This can take up to 30 seconds.
4. Reduce the pressure to 50 kPa.
5. Observe the actual pressure. In a leak-tight system, the pressure should not
drop more than 1 kPa/minute.
6. If your installed column is leak tight, remove the septum and prepare the end
of the column for installation into MS Transfer line.
7. If it is not leak tight, check the tightness of the column ferrule and repeat the
leak check sequence.

Chapter 5
OPERATING SEQUENCE
Performing a Column Evaluation
The column flow control in the FOCUS GC is indirect. This means that the GC
regulates pressure to control the flow of gas through the column. To do this, the
GC relies on a column constant. The column constant is a measure of the columns
pneumatic resistance. Use the FOCUS GC’s column evaluation feature to
automatically calculate the column constant.
To perform the column evaluation, the system uses the correlation between the
applied pressure to the flow and the column temperatures. This operation must be
carried out every time a new column is installed. Before performing the column
evaluation, a manual checking for leaks of the system must be carried out.
The GC must not be performing a run and must be isothermally stable before you
can perform a column evaluation.
1. In the Instrument Setup window, select the FOCUS Pull-up menu then the
option Column Evaluation. The following dialog windows appears:
2. To start Column Evaluation press . You can visualize the actual

values of Oven temperature, Pressure and Column flow.
NOTE To exit column evaluation menu without performing column evaluation, press

Chapter 5
3. The GC automatically performs column evaluation.
NOTE To abort column evaluation press
4. After e few minutes a response message appears. Compare the response with
the K Factor values, reported in paragraph Expected K Factor, according to
the carrier gas used.
5. If the value obtained does not agree with the one reported on the k Factor
Tables, this means that the leaks have not repaired.
CAUTION Column Evaluation can be performed also by using the virtual keypad as described
in paragraph How to perform a Column Evaluation in Chapter 8.
Expected K Factor
The following tables indicate the expected K factors for columns of ideal
dimensions when using helium, hydrogen, or nitrogen as a carrier gas.
Use this information when interpreting results from a Column Evaluation.
Deviations from this chart will occur due to dimensional tolerances.
For example, a 30 m x 0.25 mm column will typically give K factors of 1.5–2.0.

Large deviations from the expected values will indicate leaks in the septum or
column ferrule or a plugging of the column at the inlet or exit points.
K Factor Tables
• Helium Carrier Gas Theoretical K Factor
• Nitrogen Carrier Gas Theoretical K Factor
• Hydrogen Carrier Gas Theoretical K Factor

Chapter 5
Helium Carrier Gas Theoretical K Factor
COLUMN ID (mm)
0.10 0.15 0.18 0.20 0.22 0.25 0.32 0.53
2.5 5.55 1.095 0.53 0.347 0.237 0.142 0.053
5 11.1 2.19 1.06 0.694 0.474 0.284 0.106 0.014
6 13.3 2.63 1.27 0.833 0.569 0.341 0.127 0.017
7 15.5 3.07 1.48 0.971 0.663 0.398 0.148 0.020
8 17.8 3.51 1.69 1.11 0.758 0.455 0.169 0.022
9 20.0 3.95 1.90 1.25 0.853 0.511 0.191 0.025
10 22.2 4.39 2.11 1.39 0.948 0.568 0.212 0.028
15 6.58 3.17 2.08 1.42 0.852 0.318 0.042
20 8.77 4.23 2.78 1.90 1.14 0.423 0.056
25 11.0 5.29 3.47 2.37 1.42 0.529 0.070
30 13.2 6.34 4.16 2.84 1.70 0.635 0.084
COLUMN LENGTH (m)
35 15.3 7.40 4.86 3.32 1.99 0.741 0.098

40 17.5 8.46 5.55 3.79 2.27 0.847 0.113
45 19.7 9.52 6.24 4.26 2.56 0.953 0.127
50 21.9 10.6 6.94 4.74 2.84 1.06 0.141
55 24.1 11.6 7.63 5.21 3.13 1.16 0.155
60 12.7 8.33 5.69 3.41 1.27 0.169
65 13.7 9.02 6.16 3.69 1.38 0.183
70 14.8 9.71 6.63 3.98 1.48 0.197
75 15.9 10.4 7.11 4.26 1.59 0.211
80 16.9 11.1 7.58 4.55 1.69 0.225
85 18.0 11.8 8.06 4.83 1.80 0.239
90 19.0 12.5 8.53 5.11 1.91 0.253
95 20.1 13.2 9.00 5.40 2.01 0.267
100 21.1 13.9 9.48 5.68 2.12 0.281
105 22.2 14.6 9.95 5.97 2.22 0.295

Chapter 5
Nitrogen Carrier Gas Theoretical K Factor
COLUMN ID (mm)
0.10 0.15 0.18 0.20 0.22 0.25 0.32 0.53
2.5 4.95 0.98 0.471 0.309 0.2155 0.126 0.047
5 9.90 1.96 0.943 0.619 0.423 0.253 0.094 0.012
6 11.9 2.35 1.13 0.743 0.507 0.304 0.113 0.015
7 13.9 2.74 1.32 0.866 0.592 0.355 0.132 0.017
8 15.8 3.13 1.51 0.990 0.676 0.406 0.151 0.020
9 17.8 3.52 1.70 1.11 0.761 0.456 0.170 0.022
10 19.8 3.91 1.89 1.24 0.845 0.507 0.189 0.025
15 29.7 5.87 2.83 1.86 1.27 0.760 0.283 0.037
20 7.82 3.77 2.48 1.69 1.01 0.378 0.050
25 9.78 4.72 3.09 2.11 1.27 0.472 0.063
30 11.7 5.66 3.71 2.54 1.52 0.566 0.075
COLUMN LENGTH (m)
35 13.7 6.60 4.33 2.96 1.77 0.661 0.088

40 15.6 7.54 4.95 3.38 2.03 0.755 0.100
45 17.6 8.49 5.57 3.80 2.28 0.850 0.113
50 19.6 9.43 6.19 4.23 2.53 0.944 0.125
55 21.5 10.4 6.81 4.65 2.79 1.04 0.138
60 11.3 7.43 5.07 3.04 1.13 0.151
65 12.3 8.04 5.49 3.29 1.23 0.163
70 13.2 8.66 5.92 3.55 1.32 0.176
75 14.1 9.28 6.34 3.80 1.42 0.188
80 15.1 9.90 6.76 4.06 1.51 0.201
85 16.0 10.5 7.18 4.31 1.61 0.213
90 17.0 11.1 7.61 4.56 1.70 0.226
95 17.9 11.8 8.03 4.82 1.79 0.238
100 18.9 12.4 8.45 5.07 1.89 0.251
105 19.8 13.0 8.87 5.32 1.98 0.263

Chapter 5
Hydrogen Carrier Gas Theoretical K Factor
COLUMN ID (mm)
0.10 0.15 0.18 0.20 0.22 0.25 0.32 0.53
2.5 2.49 0.492 0.237 0.155 0.106 0.063 0.023
5 4.98 0.984 0.474 0.311 0.213 0.127 0.047
6 5.98 1.18 0.569 0.374 0.255 0.153 0.057
7 6.97 1.38 0.664 0.436 0.298 0.178 0.066
8 7.97 1.57 0.759 0.498 0.340 0.204 0.076
9 8.96 1.77 0.854 0.560 0.383 0.229 0.085
10 9.96 1.97 0.949 0.623 0.425 0.255 0.095 0.012
15 14.9 2.95 1.42 0.934 0.638 0.382 0.142 0.019
20 19.9 3.93 1.90 1.25 0.850 0.510 0.190 0.025
25 24.9 4.92 2.37 1.56 1.06 0.637 0.237 0.031
30 5.90 2.85 1.87 1.28 0.765 0.285 0.037
COLUMN LENGTH (m)
35 6.89 3.32 2.18 1.49 0.892 0.332 0.044

40 7.87 3.80 2.49 1.70 1.02 0.380 0.050
45 8.85 4.27 2.80 1.91 1.15 0.427 0.057
50 9.84 4.74 3.11 2.13 1.27 0.475 0.063
55 10.8 5.22 3.42 2.34 1.40 0.522 0.069
60 11.8 5.69 3.74 2.55 1.53 0.570 0.076
65 12.7 6.17 4.05 2.76 1.66 0.617 0.082
70 13.7 6.64 4.36 2.98 1.78 0.665 0.088
75 14.7 7.12 4.67 3.19 1.91 0.712 0.095
80 15.7 7.59 4.98 3.40 2.04 0.760 0.101
85 16.7 8.06 5.29 3.61 2.17 0.807 0.107
90 17.7 8.54 5.60 3.83 2.29 0.855 0.114
95 18.6 9.01 5.91 4.04 2.42 0.902 0.120
100 19.6 9.49 6.23 4.25 2.55 0.950 0.126
105 20.6 9.96 6.54 4.46 2.68 0.997 0.133

Chapter 5
OPERATING SEQUENCE
Performing an Automatic Leak Check
When you perform an automatic leak check of the FOCUS GC system, the GC
measures the column flow with a true mass flow sensor and compares it to a
calculated flow value obtained from the original column constant to see if the
numbers match. The instrument detects a gas leak if there is a significant
difference between the two values.
To start the leak check operate as follows:
1. In the Instrument Setup window, select the FOCUS Pull-up menu then the
option Leak Check. The following dialog windows appears.
2. To start leak check press . You can visualize the actual

values of Oven temperature, Pressure and Column flow.
NOTE To exit leak check menu without performing leak check, press .
3. The system is automatically pressurized with carrier gas and sealed to

perform leak check.
NOTE To abort leak check press

Chapter 5
4. At the end of the leak check, if the system is free of leaks the Leak Check
Passed message will be visualized.
5. If leaks are found, an error message will be displayed. In this case, eliminate
leaks and repeat the leak check procedure.
Note that only a previous Column Evaluation, performed in a condition of true

tightness, can ensure the validity of the subsequent Automatic Leak Check
responses.
CAUTION An automatic leak check can be performed also by using the virtual keypad as
described in paragraph How to Perform a Leak Check in Chapter 8.

Chapter 5
Column Conditioning Column
Column Conditioning
To ensure optimum analytical performance, a new column must be conditioned to
remove contaminants and unwanted volatile compounds.
Column conditioning is required to remove volatile contaminants adsorbed from
the air.
Column conditioning consists of passing a carrier gas flow through the column
and heating the column to a temperature 20–50 °C above the maximum
temperature that will be used for running analyses, provided that temperature is
within the operating range of the column.
For detailed information on column conditioning of your specific column, refer to
the column manufacturer’s instructions.
CAUTION With the column already installed, before starting column conditioning, disconnect
the column outlet from the MS detector. With the column not already installed,
connect only the column inlet to the injector.

Chapter 5
Column Column Conditioning

Getting Started
6
This chapter contains instructions to configure, set operating parameters and
control your FOCUS GC Version for MS through Xcalibur software.
Configuring the FOCUS GC ................................................................................94
Use Roadmap-Home Page....................................................................................96
FOCUS GC Setup.................................................................................................99
FOCUS GC Pull-up Menu..................................................................................102
Method Editing...................................................................................................103
Oven ...................................................................................................................104
Inlet SSL.............................................................................................................108
Carrier................................................................................................................. 114
MS Transfer Line................................................................................................ 117
Run Table............................................................................................................ 118
Virtual Keypad....................................................................................................122
Valves Manual Activations.................................................................................124
Instrument Start-up .............................................................................................125
Operating Procedures
Setting Up a Single Ramp Temperature Program ..............................................106
Setting Up Multiple Ramp Temperature Program..............................................107
Programming the Split Mode ............................................................................. 111
Programming the Splitless Mode ....................................................................... 112
Programming the Surge Splitless Mode ............................................................. 113
Programming The Carrier Gas Parameters......................................................... 116
How to Start-up the Instrument ..........................................................................125

Chapter 6
Getting Started Configuring the FOCUS GC
Configuring the FOCUS GC

This paragraph contains the instruction to configure your FOCUS GC.
On the PC desktop, click twice on the Instrument Configuration icon to

enter Instrument Configuration Dialog Window.
Figure 6-1. Instrument Configuration Dialog Window
1. Select the FOCUS GC from the Available Device box.
2. Pressing ADD, the FOCUS GC moves to the Configure Device box.
3. After the FOCUS GC or DSQ is in the Configure Device box, you can enter
configuration information by pressing CONFIGURE.
4. The following Page appears

Chapter 6
Configuring the FOCUS GC Getting Started
Figure 6-2. FOCUS GC Configuration Page
where:
Connections Group Box
Parameter Description
Serial Port Select the Com Port where you have the FOCUS GC
connected.
Option Group Box
Pressure Unit Select the pressure units to display in the Instrument Setup
Pages (kPa, Bar, PSI).
Selecting different pressure units does not affect the GC.
5. Press OK to return Instrument Configuration Dialog Window, then press DONE

to exit Instrument Configuration Dialog Window.

Chapter 6
Getting Started Use Roadmap-Home Page
Use Roadmap-Home Page

From the Roadmap–Home Page, shown in Figure 6-3, you may display dialog
windows to set FOCUS GC parameters and to display the current GC status and
actual values.
On the PC desktop, click twice on the Excalibur icon to enter Excalibur

program.
Figure 6-3. Roadmap-Home Page
GC Status and Actual Values

Status pages for your FOCUS GC are located on your Xcalibur Roadmap-Home
page. Just highlight FOCUS GC from the Roadmap Status tab scroll list and see
the following pages (status, temperatures, flows, and pressures) display the
current GC status.

Chapter 6
Use Roadmap-Home Page Getting Started
Status Page
In the Status window the message indicating the current status of the GC, the
elapsed time and the remaining time of the analytical run are displayed.
General Group Box
Status Indicates if instrument is communicating to Xcalibur.
Run Group Box
Elapsed time The amount of time that has elapsed since the run started.
Remaining time The amount of time that remains before the run finishes.
Emergency Conditions Group Box

When an emergency condition occur, a mark appears in the relevant box or in
more boxes depending of the nature of the error.

Chapter 6
Getting Started Use Roadmap-Home Page
Emergency Your Xcalibur software automatically checks this box if an error
Shutdown condition like a leaking hydrogen sensor or something is
malfunctioning internally in your FOCUS GC. The software
automatically shuts the FOCUS GC off.
Over This box is checked only when Xcalibur software detects the
temperature temperature is over the recommended level.
Shorted RTD This detected problem requires certified technical support.
Contact your local Thermo Tech Support office for service.
Shorted oven This detected problem requires certified technical support.
RTD Contact your local Thermo Tech Support office for service.
Actual Values Page

The Actual Status page displays the actual and the setpoint values of the FOCUS
GC parameters set in the Instrument Setup dialog window.

Chapter 6
FOCUS GC Setup Getting Started
FOCUS GC Setup
This paragraph contains instruction to set the carrier gas type to use, the signal
selection (Handshake) to allows the correct cooperation between FOCUS GC and
MS detector, and to configure external valves or devices.
On the Roadmap-Home Page, click on icon. The FOCUS Instrument Setup

dialog window will be displayed visualizing all configuration tabs such as Oven,
Inlet SSL, Carrier, MS Transfer Line and Run Table, required to set the GC
parameters. Refer to paragraph Method Editing.
To return Roadmap-Home Page from each configuration tab press the

button.
To setup FOCUS GC, select Focus menu then the option Instrument Setup.
NOTE For further details about Focus menu, refer to paragraph FOCUS GC Pull-up Menu.
The following FOCUS GC Setup Page will be displayed:
Figure 6-4. FOCUS GC Setup Page

Chapter 6
Getting Started FOCUS GC Setup
Carrier Box
Gas Type Select the type of carrier gas to use for the analyses (He, N2, H2).
Verify that the carrier gas used has been properly connected to the
GC.
WARNING! Hydrogen is a potentially dangerous gas.
Handshake Group Box

The FOCUS GC cooperates with a MS detector during the analysis. To allow the
device to run properly, you must indicate how the signal will change.
Parameter Range Description

Remote Pulse High to Low (default) This parameter allows another device
Start IN to start the FOCUS GC.
Pulse Low to High
Inhibit When Low (default) This parameters delays readiness until
Ready the GC receives a signal from another
When High
device.
End of Pulse High to Low (default) This parameter signals another device
Run OUT that the run has ended.
Pulse Low to High
Autostart On/Off Check this box to turn on auto start
execution.
Start of Pulse High to Low (default) This parameter signals another device
RUN OUT that the run has started.
Pulse Low to High
GC Ready When Low (default) This parameter signals another device
OUT that the GC is ready.
When High
Prep-Run Pulse High to Low (default) This parameter signals another device
OUT that the GC is preparing for a run.
Pulse Low to High

Chapter 6
FOCUS GC Setup Getting Started
Valves Group Box

In this box you can configure two gas sampling valves, when present, and
program two external events to be the default condition for an external device. See
also Run Table.

Valve #1 None - Sampling Select in this box Sampling only if a gas sampling
valve is present and connected to the GC.
Otherwise, select none.
Valve #2 See Valve #1 Select the external event default condition. The
EV #1 On - Off external device will return to the condition
default specified by the external event you have
EV #2 See EV #1 programmed to be the default whenever the GC’s
default in Standby mode.
Buttons
Button Description
DONE Click this button to exit
GET Click this button to get the current configuration from the GC.
SEND Click this button to send the current configuration to the GC.

Chapter 6
Getting Started FOCUS GC Pull-up Menu
FOCUS GC Pull-up Menu

The FOCUS menu, shown in Figure 6-5, is located on the Instrument Setup-menu
bar
Figure 6-5. FOCUS GC Pull-up Menu
Option Description
Instrument Allows to perform instrument setup. Refer to paragraph
Setup Method Editing in this Chapter.
Send Method to Downloads the GC portion of the current method from the
GC Instrument Setup window to the GC.
Get Method from Uploads the current method from the GC to the Instrument
GC Setup window.
Start GC / Prep Allows starting the GC run.
Run
Stop GC Allows stopping the GC run.
Keypad Allows accessing the GC control panel. Refer to paragraph
Virtual Keypad in this chapter.
Column Allows to perform a column evaluation. Refer to Performing a
Evaluation Column Evaluation in Chapter 5.
Leak Check Allows to perform an automatic leak check. Refer to
Performing an Automatic Leak Check in Chapter 5.

Chapter 6
Method Editing Getting Started
Option Description
Valves Allows valves manual activation. Refer to paragraph Valves
Manual Activations in this chapter
Flow Calculator Useful to determine column pressure settings and flow rates
through a capillary column.
Vapor To rapidly calculate the expansion volume using several
Calculator factors.
Method Editing
From the Roadmap-Home Page, click on icon. The Instrument Setup
dialog window will be displayed where all the configuration tabs required to set
the GC parameters are available:
• Oven
• Inlet SSL
• Carrier
• MS Transfer Line
• Run Table
To return Roadmap-Home Page from each configuration tab click the

button.

Chapter 6
Getting Started Oven
Oven
This page is the method editor for setting up parameters in the GC run.
Figure 6-6. The Oven Page
See also:
• Setting Up a Single Ramp Temperature Program
• Setting Up Multiple Ramp Temperature Program
To return Roadmap-Home Page click the button.

Chapter 6
Oven Getting Started
Ramps Group Box

Initial From 30 °C to 350 °C In this box set the temperature in °C at which the oven is set
Temperature in step of 1°C and conditioned before the GC enters the sampling phase.
Initial Hold Time From 0 to 99.99 In this box set the time in minutes, the oven will be kept at the
minutes initial temperature.
Ramp 1 From 0.1 to 120 °C/min Rate for the temperature ramp from Initial Temperature to
Rate (°C/min) In step of 0.1 °C/min Temperature 1. In this box set the rate increment to reach the
temperature set in Temperature 1.
Temperature 1 From 30 to 350 °C Temperature for second temperature program level.
In step of 1 °C In this box set the target temperature in °C the oven must
reach at the end of the Ramp 1 phase.
Hold Time 1 From 0 to 99.99 Duration of the second temperature program level
minutes Temperature 1. In this box set the time in minutes the oven
will be kept at the Temperature 1.
Ramp 2 From 0.1 to 120 °C/min Rate for the temperature ramp from Temperature 1 to
Temperature 2 From 30 to 350 °C Temperature for third temperature program level. In this box
In step of 1 °C set the target temperature in °C the oven must reach at the
end of the Ramp 2 phase.
Hold Time 2 From 0 to 99.99 Duration of the third temperature program level Temperature
minutes 2. In this box set the time in minutes the oven will be kept at
the Temperature 2.
Ramp 3 From 0.1 to 120 °C/min Rate for the temperature ramp from Temperature 2 to
Temperature 3 Form 30 to 350 °C Temperature for forth temperature program level. In this box
In step of 1 °C set the target temperature in °C the oven must reach at the
end of the Ramp 3 phase
Hold Time 3 From 0 to 99.99 Duration of the forth temperature program level Temperature
minutes 3. In this box set the time in minutes the oven will be kept at
the Temperature 3.

Chapter 6
Getting Started Oven
Oven Group Box

Auto Prep On -Off Check this box for the GC to automatically go to the Ready state
Run when the initial conditions are met.
If this box is not checked, you will have to press the START key
located on the FOCUS GC virtual keypad or to select the option
StartGC/PrepRun in Focus menu.
Max Temp From 50 °C to 350 °C Specify the maximum temperature for this run.
(°C) The software automatically sets the maximum allowable
In step of 1 °C
temperature for the column being used in the method.
Prep Run From 0 to 99.00 Enter the duration of the Prep Run.
Timeout minutes The injection must occur within this time or the timeout will
return the GC to Standby condition.
Equilibrium From 0 to 99.00 In this box set the time in minutes the GC has to wait before
Time (min) minutes entering the sample phase. This time is used for conditioning the
oven at the temperature specified in Initial Temperature box.
OPERATING SEQUENCE
Setting Up a Single Ramp Temperature Program
This program raises the initial oven temperature to a specified final temperature at
a specified rate and maintains the final temperature for a specified time.
1. Enter in Initial Temp°C box the initial temperature.
2. Enter in Initial Hold Time (min) box the time you want the oven to
maintain the initial temperature.
3. Enter in Ramp 1 Rate (°C/min) box the ramp rate for the oven to reach
the ramp’s Ramp 1 Temp °C.
4. Enter in Ramp 1 Temp °C box the final temperature for the ramp.
5. Enter in Ramp 1 Hold Time (min) box the time the oven will maintain the
final Ramp 1 Temp °C.

Chapter 6
Oven Getting Started
OPERATING SEQUENCE
Setting Up Multiple Ramp Temperature Program
This program raises the initial oven temperature to a specified final temperature
through up to seven ramps, each having a specified ramp rate, time, and
temperature.
1. Enter in Initial Temp°C box the initial temperature.
2. Enter in Initial Hold Time (min) box the time you want the oven to
maintain the initial temperature.
4. Enter in Ramp 1 Temp °C box the final temperature for the ramp.
5. Enter in Ramp 1 Hold Time (min) box the time the oven will maintain the
final Ramp 1 Temp °C.
6. Press the up button to add a new ramp level.
8. Enter in the Ramp 2 Temp °C box the final temperature for the ramp.
9. Enter in the Ramp 2 Hold Time (min) box the time the oven will maintain
the final Ramp 2 Temp °C.
To add additional oven ramps, repeat the steps 6 through 9.

Chapter 6
Getting Started Inlet SSL
Inlet SSL
This page is the method editor for the Split/Splitless inlet injector.
Figure 6-7. The Inlet SSL Page
See also:
• Programming the Split Mode
• Programming the Splitless Mode
• Programming the Splitless Mode
• Gas Saver
• Valves Manual Activations

Chapter 6
Inlet SSL Getting Started
Mode List Box

Mode Description Set:
Split Use this injection mode when analyzing high concentration or neat Split Flow
samples, or in instances where sensitivity is less important. The split vent Split Ratio
remains open all the time. This method yields the sharpest peaks if the
split gas is properly mixed.
Splitless The split vent is closed during the injection to drive most of the sample Split Flow
into the column. The solvent effect is required to refocus the analytes, Splitless Time
especially more volatile compounds. You can achieve the solvent effect by
keeping the analytical column or guard column slightly below the
solvent's boiling point. Splitless times of about 1 minute are typical.
Splitless Same as Splitless but can also program a surge during an injection. Surge Split Flow
w/Surge starts at Prep Run and continues until the surge duration time is finished. Splitless Time
Surge is further defined in the Surge group Box.
Surge Pressure
Surge Duration
Inlet Group Box

Temperature From 100 °C to 375 °C Specify in this box the injector temperature setpoint.
(°C)
In steps of 1 °C
0 = Off
Split Flow From 10 to 100 ml/min Check in this box to turn On the split flow. Specify the split
(ml/min) flow coming out of the injector. Set 0, to close the split valve
In steps of 1 ml/min
and to turn Off the split flow.
0 = No Split
Split Ratio From 1 to 1000 It is displays only when Split mode is Selected. Specify the
In steps of 1 ratio of split flow compared to the column flow.
Splitless From 0 to 9.99 minutes Specify the length of time the split valve remains closed after a
Time (min) splitless injection.
In steps of 0.01 minutes
The timer begins at the start of the run.

Chapter 6
Purge Group Box

Constant Yes - No Check this box to activate a constant septum purge to
Septum Purge continuously flush the septum with a purge flow of 5 ml/min
when using helium or nitrogen as carrier gas or 10 ml/min when
using hydrogen as carrier gas. When the Constant Septum
Purge checkbox is unchecked, the following parameter needs to
be programmed.
Stop Purge From 0 to 9,99 minutes This option may be used only when the Constant Septum Purge
Time: (min) In steps of 0.01 minutes checkbox is unchecked. Specify the length of time the purge
valve remains closed after a splitless injection. This is usually
set to the same time as the splitless time.
Surge Group Box

Surge From 10 to 1000 kPa Specify the surge pressure to accelerate the transfer process of
Pressure the substances from the injector to the column. The pressure
In steps of 1 kPa
(kPa) surge starts in the Prep Run phase and ends at the end of the
Surge Duration you program.
Surge From 0 to 9.99 minutes Specify the duration of the surge pressure after run start.
Duration
In steps of 0.01 minutes
(min)

Chapter 6
OPERATING SEQUENCE
Programming the Split Mode
In split injection, only a portion of the sample transfers to the column. Most of it
discharges through the splitting line. The ratio between the split flow and the
column flow defines the amount of sample that enters the chromatographic
system. The split and column flows must be set to obtain the correct split ratio
necessary for the analysis.
Before you begin programming, do the following:

• Verify that a column is correctly installed, the correct liner is in the injector,
and the system is free of leaks.
• Program the carrier gas flow as described in paragraph Carrier.
Proceed as follows:
1. I.n the Mode box select Split.
2. Set the appropriate Inlet Temperature.
3. Specify the split flow or the split ratio. To set Split Flow enter the value in
the relevant box. The split ratio will be calculated for you.
To set Split Ratio, enter the value in the relevant box. The split flow will
be calculated for you.

Chapter 6
OPERATING SEQUENCE
Programming the Splitless Mode
In splitless analyses, the splitting line is closed during the sample transfer onto the
column. The time during which the splitting valve remains closed is called the
splitless time. When the sample transfer ends, the split line reopens to purge the
residual sample components, essentially solvent, out of the vaporization chamber.
You can activate a constant septum purge, if necessary, to continuously flush the
septum with a purge flow. The septum purge prevents septum bleed components
from entering the column.

Proceed as follows:
1. In the Mode box select Splitless
3. Set the Split Flow and enter the desired value.
4. Specify the Splitless Time.
5. If constant septum purge is required, check the Constant Septum Purge

box to activate a constant septum purge.
If constant septum purge is not required, uncheck the Constant Septum
Purge. box
In the Septum Purge Time box enter the time the purge flow should be
interrupted.

Chapter 6
OPERATING SEQUENCE
Programming the Surge Splitless Mode
Proceed as follows:
1. In the Mode box select Splitless w/surge
3. Set the Split Flow and enter the desired value.
4. Specify the Splitless Time.
5. In the Surge Pressure box enter the value of the pressure surge.
6. In the Surge Duration box enter the duration of the pressure surge.
7. If constant septum purge is required, check the Constant Septum Purge

box to activate a constant septum purge.
If constant septum purge is not required, uncheck the Constant Septum
Purge.
In the Septum Purge Time box enter the time the purge flow should be
interrupted.

Chapter 6
Getting Started Carrier
Carrier
This page is the method editor for setting the carrier gas for the FOCUS GC inlet.
Figure 6-8. The Carrier Page
See also:
• Programming The Carrier Gas Parameters

Chapter 6
Carrier Getting Started
Flow Group Box

Flow Mode Constant Flow Set the operating mode required.
Constant Pressure Selecting Constant Flow, the column flow is kept constant
throughout the analysis. The pressure at the column head will
change with the column temperature to maintain a consistent
flow. See Flow.
Selecting Constant Pressure, the pressure at the column
head is kept constant throughout the analysis. During a
temperature program, the column flow decrease due to the
increase of the carrier gas viscosity. See Pressure.
Flow From 0.1 to 50.0 ml/min It is displayed when Constant Flow is selected in Flow
(ml/min) In steps of 0.1 ml/min Mode box.
Enter a column flow for the analytical column. When using
0 = Flow Off
an oven temperature program, run the GC to automatically
increase the pressure constant flow on the column: This
compensates a gas’s increased viscosity due to an increase of
temperature.
Pressure From 7 to 700 kPa It is displayed when Constant Pressure is selected in Flow
(kPa) Mode box. Enter inlet pressure for the analytical run.
In step of 1 kPa
0 = Pressure Off
Vacuum Yes - No Check this box to compensate for a vacuum at the end of the
Compensation analytical column. When the box is not checked calculation
are made considering the detector, which at atmospheric
pressure.
Yes –No Checking this box enables flow to the inlet. When this box is
not checked gas flow is cut off to the inlet.
Gas Saver
Gas saver controls reduce carrier gas consumption, especially when a large split
flow is used. The gas saver options are set to come on at some point well after the
injection to conserve gas. Checking the box will activate the feature of gas saver.

Chapter 6
Getting Started Carrier

Enable On – Off Check this box to activate gas saver function to the inlet. The
Gas Saver Flow and Gas Saver Time parameters must be
programmed.
When this box is nor checked, gas saver function is not
activated.
Flow (ml/min) From 10 to 500 ml/min Enter the desired flow after the injection or in Standby.
In step of 1 ml/min
Time (min) From 0 to 9.99 minutes Enter the time after the injection when gas saver flow will be
In steps of 0.01 min activated.
OPERATING SEQUENCE
Programming The Carrier Gas Parameters
Before you begin this procedure, do the following:
• Check that the carrier gas type is correct for the analysis.
NOTE When you install a new column, you must perform a Column Evaluation.
1. Select the Carrier Constant Flow or Constant Pressure mode.
2. Enter the initial Flow or Pressure.

If you selected Constant Flow mode, enter in the Flow (ml/min) box the
desired value. The GC calculates the pressure necessary and adjusts the
pressure as necessary to maintain the constant flow.
If you selected Constant Pressure mode, then in the Pressure (kPa) box
enter the desired value.
3. Activate the Gas Saver if required checking the Enable check button.
Check the Gas Saver box to activates the gas saver control.
In Flow (ml/min) and Time (min) boxes type the desired values.

Chapter 6
MS Transfer Line Getting Started
MS Transfer Line
This page is the method editor for setting and control the temperature of the MS
transfer line.
Figure 6-9. The MS Transfer Line Page
MS Transfer Line Group Box

Check this box to activate the temperature control when required.
Ms Transfer Set the desired temperature value from 0 to 450 °C.

Line (°C)

Chapter 6
Getting Started Run Table
Run Table
This page allows you program events to happen prior to or during a run. For
example, a valve could open two minutes into a run. Listed in the run table page
are settings entered prior to the run in the Run Time Event dialog box. Time,
item, and settings display in this run table. Control listed in the Initial Values
group box is for switching external device On/Off.
Figure 6-10. Run Table Page
See Also:
• Add/Edit Run-Time Event Screen

Chapter 6
Run Table Getting Started
Time, Item, and Settings Group Box

All selections made in the Add/Edit Run-Time Event screen display in this table.
The categories display items important during a run-time event.
Option Description
Time Displays the time at which the run time event will occur.
Item Displays which event (Valve, or External) was configured in the Add/Edit Run Time Event
screen.
Setting Displays if the Valve event or the External event settings are On or Off.
Initial Values Group Box

Controls listed in the Initial Values group box are for setting default values for
external events. After External events are made in the Add/Edit Run-Time Event
screen, they display in the Run Table. Use the External event parameter to activate
or deactivate the event.
Option Description
External Event #1 On Located on the back of your FOCUS GC is a port with two contacts that can be
External Event #2 On programmed to turn external devices On or Off. Pre-run conditions for
External events are set on the Run Table page under the Initial Values group.
From the Run Table page during a specific run time, you can change the status
of these external switches
Buttons
Button Description
ADD Select this button to add a run-time event and to display the Add/Edit Run-Time Event screen.
Run-time events selected from the Add/Edit Run-Time Event screen are displayed on the Run
Table page (under the Time, Item, and Setting columns.)
EDIT Select this button to edit a current run-time event and to edit items selected in the Add/Edit Run
Time Event screen. Before selecting this button, select a run-item listed in the Time, Item, and
Setting table. Then click the Edit button to display the Add/Edit Run-Time Event screen.
REMOVE Select this button to delete a current run-time event: First, select an item listed in the Time, Item,
and Setting table, then click the Remove button to remove the selected run item.

Chapter 6
Getting Started Run Table
Add/Edit Run-Time Event Screen

Select the ADD or EDIT from the Run Table page to display the Add/Edit Run-
Time Event screen. Events displayed on the Run Table page are from selections
made in this screen
Figure 6-11. ADD/Edit Run-Time Event Screen
Event Time Group Box

Use the parameters listed in this group box to determine when to activate the
event.
Option Description
Prep Run This option makes the selected event (Valve, or External)
happen before the run begins.
Run Time This option makes the selected event (Valve, or External)
happen at the time specified during the run.
Valve Event
This group of parameters contains configuring options for valve events.

Chapter 6
Run Table Getting Started
Option Description
Valve number Select from one to two pneumatic valves for each external
event to turn on from the Run Table page. If you use all two
then none is available for other events.
Valve Type Sampling is available only. Sampling is a valve used to inject a
volume of sample into the carrier stream.
Inject for This parameter is only available after selecting Sampling for a
valve type. Specify how many minutes to inject the sample.
Setting For Sampling the settings are Load or Inject.
External Event Group Box

This group of parameters contains options for external events. Each event selected
here is displayed on the Run Table page.
Option Description
External Number Select which of the two-(2) external events to program. The
GC has two available open collector outputs, which can be
configured to switch external valves, switches, and other
options. Select the numbered event matching the GC
connection number.
Setting Select On or Off to set the external event at the specified
programmed run time.

Chapter 6
Getting Started Virtual Keypad
Virtual Keypad
To display the keypad, from Instrument Setup dialog windows, select Focus
then Control Panel option. See also FOCUS GC Pull-up Menu.
For detailed information about the FOCUS GC Virtual Keypad refer to Chapter 8
Use of the Virtual Keypad
Figure 6-12. Control Panel - Virtual Keypad
Move your cursor across any region located in this illustration. Your cursor
becomes a hand when a region has related popup topic. Use these topics to learn
how the FOCUS GC keypad is functionally organized.
Description
Display Panel
The display panel displays the settings currently in use. Listed top to bottom on
the display panel is typically a menu title bar, parameters, scroll indicators, and a
cursor indicating your current position.
Use the data-entry keys to navigate up or down the menu and to enter values.
GC Status LEDs
This region contains light emitting diodes, which indicate the FOCUS GC
operating status. Observe the GC status periodically to determine what stage the
GC is in during the run.

Chapter 6
Virtual Keypad Getting Started
Action Keys
Use these keys to start or interrupt activities, to display the instrument status and
to open menus. Listed left to right are Start, Stop, Status, Home, Dec/Inc and
Enter.
Data Entry Keys

Use these keys to enter information into a displayed menu: Listed left to right: On/
Yes, Clear, Off/No, Enter, (press to move up or down in menu), and the numerical
keypad.
Keypad Menu
File Menu
This menu permits to access the following functions:
Get Method from GC

This function allows to transfer method data from GC to data system.
Send Method to GC
This function allows to transfer method data from data system to GC.
Close
This function allows to close FOCUS GC virtual keypad.

Chapter 6
Getting Started Valves Manual Activations
Valves Manual Activations

To display the relevant page, from Instrument Setup dialog windows, select
Focus then Valve option. See also FOCUS GC Pull-up Menu.
Figure 6-13. Valves Dialog Window
Inlet SSL Valves Group Box

Check in the relevant box to open or close the inlet valve of interest before or
during a run.
Valve Vents Group Box

Set the Load or Inject position of the sampling valve (when present):
Set On/Off the Event Valve #1 checking the relevant check box.

Chapter 6
Instrument Start-up Getting Started
Instrument Start-up
This start-up sequence contains the instructions which combines the analytical
procedure with the use of the Excalibur program.
OPERATING SEQUENCE
How to Start-up the Instrument
The sequence of instructions begins with the assumption that all the instruments
of the system are ON, set and ready to initiate the analyses.
Preliminary Check
Before start the GC, verify that the following operations have been already carried
out:
• The carrier gas supply line is correctly connected to the DPFC module and the
inlet pressure is set at the required value as described in Chapter 1.
• The FOCUS GC is properly electrically connected and configured.
• The carrier gas type is correctly set.
• The analytical column is correctly installed and conditioned.
• The correct liner is the SSL injector.
• The system is free of leak.
• The column evaluation has been carried out.
Setting the GC Parameters
1. In the Instrument Setup dialog window program the required Oven, Inlet
SSL, Carrier, MS Transfer line and Run Table parameters as described in this
chapter.
2. In the sequence set-up, program a sample run. Refer to Xcalibur manual for
more information.

Chapter 6
Getting Started Instrument Start-up
Performing an Injection
3. The FOCUS GC will automatically perform the PressRun operations.

Depending on the SSL operating mode you have programmed, the FOCUS
GC will perform the following operations:
• When the gas saver function is programmed, Prep Run ends the gas saver
mode and resets the split flow to the flow used during the injection.
• In Splitless mode, Prep Run closes the split valve and will close the
septum purge valve as programmed.
• In Surge Splitless mode, Prep Run initiates the surge pressure.
4. When the Ready to Inject LED is lit, insert the syringe into the injector, wait
for approximately 2 seconds, inject the sample rapidly, and rapidly remove
the syringe from the injector. (This is the Hot Empty Needle technique).
5. To start the run, press START button in Control Panel or again selecting
Start GC/Preprun option in the FOCUS menu or again by pressing the
optional remote Start button.
The GC will complete the analysis as programmed.

Maintenance and
7
Troubleshooting
This chapter contains information and operating sequences to perform the
necessary maintenance of the instrument and also information concerning
troubleshooting in case of malfunctioning.
Maintenance .......................................................................................................128
Maintaining a SSL Injector ................................................................................131
Troubleshooting..................................................................................................140
Error Messages ...................................................................................................142
Guide to Solve Analytical Problems ..................................................................143
Operating Procedures
Replace the Standard Septum .............................................................................133
Replace or Clean the Liner when a Standard Septum is Installed......................135

Chapter 7
Maintenance and Troubleshooting Maintenance
Maintenance
This paragraph provides information on the maintenance of the instrument. It also
contains the instructions for the instrument shutdown.
WARNING! Before performing any operation of maintenance that requires the closure of the
carrier gas, it is necessary to shut down the MS detector. Refer to the FOCUS DSQ
manual.
How To Perform Maintenance

Thermo Fisher Scientific authorized technical personnel under the instrument
warranty or, when this has expired, possibly under a Service Contract Program
will normally perform full instrument servicing. To ensure that your FOCUS GC
always performs to its full potential, the operator must carry out a certain amount
of routine maintenance on a regular basis.
Suggested Maintenance Schedule

Preventive maintenance keeps your instruments running at peak performance.
The recommended maintenance schedule, shown in the Maintenance Schedule
Table, is based on a GC running multiple samples in an 8-hour day.
You may need to adapt the schedule to your situation depending on:
• The number of analyses per day
• How clean the samples are
• The condition of the syringe needle
• Environmental conditions such as dirt and ambient temperature
Septa
Septa degrade over time. Different types will degrade at varying rates. Factors
affecting septa life include:
• Number of samples injected
• Injector temperature
• Condition of the syringe needle

Chapter 7
Maintenance Maintenance and Troubleshooting
Ferrules and Seals

Ferrules and seals should be replaced when they are too flat to produce a good
seal.
NOTE Unless required applications necessitate frequent dismantling and replacement of columns
and accessories, seals and ferrules normally need to be disturbed only when dismantling is
required. However, the FOCUS GC should be periodically leak-tested and the seal
tightened or replaced as necessary.
Traps
Internal and external traps in the gas line must be periodically serviced. It is
advisable to check the state of the traps every time gas cylinder is replaced..
Detector Unit
To ensure optimum performance of the detector, refer to the relevant manual.
Make sure you not only perform each scheduled item, but that you record it as
well, along with any observation about instrument performance. Your records and
notes can be invaluable when trying to trace a service problem.
In addition to the routine and preventive maintenance that you perform, we
recommend annual inspections by Thermo Fisher Scientific customer service
engineers. These yearly checkups ensure that your instrument remains in peak
condition.
Maintenance Schedule Table

.
Table 7-1. Standard Maintenance Schedule
Frequency Task
Daily Run Automatic Leak Test.
Run performance check standard as required by method.
Run calibration curve as required by method.
Note gas pressure when the weekly pressure check shows it to be
below 5000 kPa (50 bar or 750 psig).

Chapter 7
Maintenance and Troubleshooting Maintenance
Table 7-1. Standard Maintenance Schedule (Continued)

Weekly Change injector liner.
Check pressure of gas cylinders. Replace the cylinder when its
pressure drops below 3500 kPa (35 bar or 500 psi).
Monthly Check for leaks from the primary gas supply to the GC.
Semiannually Regenerate the S/SL inlet vent line trap.
Recondition or replace internal and external traps if present.
Instrument Cleaning
WARNING! Cleaning must be performed with the instrument off and the power cord discon-
nected.
Normal usage of the FOCUS GC can cause the exterior to get dirty.
Externally clean the instrument with a cloth dampened with soap and water
solution, or with a household non-abrasive product, carefully avoid seeping of the
products used inside the instrument.
If you just suspect that a substance used for cleaning or a product submitted to
analysis has infiltrated inside the instrument, immediately shut down the
instrument and call an authorized customer support engineer for proper actions.
The service engineer must be fully informed on the nature of the concerned
substance. In the event that a hazardous material is spilled on or in the instrument,
clean the spill according to the procedures in the Material Data Sheet for that
substance.
WARNING! It is your responsibility to avoid that dangerous liquids and/or materials seeping
inside the GC during operation and maintenance.

Chapter 7
Maintaining a SSL Injector Maintenance and Troubleshooting
Maintaining a SSL Injector

The S/SL (Split/Splitless) injector will normally be serviced by Thermo Fisher
Scientific authorized technical personnel. In order to operate, the injector requires
periodic maintenance from the user. This maintenance includes:
• The replacement of the septum
• The cleaning or replacement of the liner
• The maintenance of the Merlin Microseal Valve when used instead of the
standard septum.
When Replacing the Septum

The septum should be replaced at least after every 200 injections, or every time a
problem related to septum damage or wear occurs.
It is a good practice to change the septum with a new one every time the liner is
replaced.
CAUTION Use original Thermo Fisher Scientific standard septum. Septa from other
manufacturers may show different rates of degradation.
When Cleaning or Replacing the Liner

The liner must be replaced periodically, depending on the number of injections
performed and the characteristics of the samples injected. Typical symptoms will
indicate that the liner must be replaced. The most common is the appearance of
tailing peaks in the chromatogram, particularly for polar compounds.
It is good practice to replace the septum every time the liner is replaced.
You can replace the liner with a new one or clean the liner and reinstall it.
The following table shows the available types of liners and the indications for the
correct choice.

Chapter 7
Maintenance and Troubleshooting Maintaining a SSL Injector
Liner PN
Split injections, 3 mm 453 200 31
Split injections, 5 mm 453 200 30
Splitless injections, 3 mm 453 200 32
Splitless injections, 5 mm 453 200 33
Liner for direct injections into wide bore column 453 003 10
Laminar cup liner for split injections at high split flow rates or 453 003 20
for the most polar solvents.
If the Glass Liner Breaks Inside the Injector

When replacing or removing a glass liner, it might break inside the injector. In this
case the broken parts of the liner must be removed from the injector, including the
glass splinters that might fall into the lower part of the vaporization chamber.
Refer to Removing a Broken Liner for instructions.
The following Operating sequences help you to maintain properly the SSL
injector.
• Replace the Standard Septum
• Replace or Clean the Liner when a Standard Septum is Installed
NOTE To replace a standard septum with the Microseal Valve, refer to the relevant Installation
Guide.

Chapter 7
OPERATING SEQUENCE
Replace the Standard Septum
Material needed
• Non metallic sharp tool
• Septum
• Tweezers
WARNING! This operation must be carrier out at low temperature to avoid burns. Therefore,
before beginning the sequence, the injector must be cooled to room temperature.
Preliminary Operations
1. Vent the MS system referring to the DSQ Manual.
2. While in Standby condition, in OVEN page set the initial oven temperature to
30 °C.
3. In INLET SSL page set the inlet temperature to 0 (0 = Off).
4. When the inlet reaches the room temperature, enter in CARRIER page and
uncheck the flow box to cut off the gas flow to the inlet.
Removing the Septum
5. Unscrew the septum cap.
6. Remove the septum holder with septum, then the septum support. See A of
Figure 7-1.
7. Remove the septum from the septum holder (use non-metallic tools). See B of
Figure 7-1.
8. Insert a new septum into the septum holder. See B of Figure 7-1.
CAUTION Use tweezers to avoid touching the septum with your fingers.

Chapter 7
Figure 7-1. Replace the Septum
Replacing the Septum
9. Clean the septum support from possible fragments left by the septum and
reinsert it into the injector.
10. Place the septum holder on the top of the septum support (see C of
Figure 7-1).
11. Tighten the injector cap to finger tight.
CAUTION Do not overtighten the injector cap. You could damage the septum and affect
performance.
Restart the GC Conditions
12. In CARRIER, OVEN and INLET pages set the normal working conditions.
13. Perform an automatic leak check.

Chapter 7
OPERATING SEQUENCE
Replace or Clean the Liner when a Standard Septum is Installed
Material needed
• Liner cap removal tool
• Glass liner
• Graphite seal
• Ultrasonic bath
• Methanol/acetone mixture (1:1)
• Non metallic sharp tool
• Standard Septum
• Tweezers
WARNING! This operation must be carrier out at low temperature to avoid burns. Therefore,
before beginning the sequence, the injector must be cooled to room temperature.
When handling organics solvents you must take precautions to avoid health
hazards.
Preliminary Operations
1. Vent the MS system referring to the DSQ Manual.
2. While in Standby condition, in OVEN page set the initial oven temperature to
30 °C.
3. In INLET SSL page set the inlet temperature to 0 (0 = Off).
4. When the inlet reaches the room temperature, enter in CARRIER page and
uncheck the flow box to cut off the gas flow to the inlet.
Removing the Septum
5. Unscrew the septum cap.

Chapter 7
6. Remove the septum holder with septum, then the septum support. See A of
Figure 7-2.
Figure 7-2. Replace and Clean the Liner (1)
7. Use the liner cap wrench provided with the GC to remove the injector liner
cap. See B of Figure 7-2.
8. Use tweezers to remove the liner with the graphite seal. See C of Figure 7-2.
CAUTION Be careful not to break the glass liner inside the injector when removing it. Glass
splinters might fall into the lower part of the vaporization chamber. If the liner
breaks, refer to Replace a Broken Liner.
• If you are going to use a new liner, go to the step Cleaning the liner then
continue from the step Replacing the Liner.
• If you are going to clean the liner go to step Cleaning the liner then continue
from the step Replacing the Liner.
• If you are going to remove a broken liner go to step Removing a Broken Liner
then continue from the step Replacing the Linerr.

Chapter 7
Cleaning the liner
a. Put the dirty liner into an ultrasonic bath filled with a methanol/acetone
mixture (1:1) and sonicate it for about half an hour.
b. Using tweezers, remove the liner from the bath and dry it with
compressed clean air.
NOTE For trace analysis, you should pre-treat the liner with a suitable silylating reagent prior to
re-inserting it into the injector.
Removing a Broken Liner
a. Unscrew the nut that retains the analytical column, there move the
analytical column with its ferrule. See D of Figure 7-3.
b. Unscrew the retaining nut at the bottom of the injector, the remove the
terminal fitting with its silver seal. See E of Figure 7-3.
CAUTION Glass splinters from the broken liner will fall from the injector.
Figure 7-3. Replace a Broken Liner
c. With the aid of a pipe cleaner, remove the possible glass fragments from
the vaporization chamber.

Chapter 7
d. Reinsert the silver seal and the terminal fitting, and then tighten the nut
that retains the terminal fitting. See F of Figure 7-3.
e. Insert the analytical column with its ferrule into the bottom of the injector
in its previous position, then tighten the M4 retaining nut to hold the
column in place. See G of Figure 7-3.
Replacing the Liner
9. Holding the new (or cleaned) liner with tweezers, place a graphite seal over
the liner, making sure to leave a distance of about 10 mm between the seal and
the liner end.
10. Using tweezers, insert the liner into the injector and push it gently towards the
bottom fitting. See D of Figure 7-4.
CAUTION Make sure you insert the beveled end of the liner towards the bottom of the injector.
Be careful not to damage the graphite seal or allow graphite to entering the liner.
Should this occur, clean the liner with an inert gas.
11. Tighten the liner cap using the liner cap wrench provided with the GC. See E
of Figure 7-4.

Chapter 7
12. Remove the septum from the septum holder (use non-metallic tools).
13. Insert a new septum into the septum holder. See F of Figure 7-5.
CAUTION Use tweezers to avoid touching the septum with your fingers.
14. Clean the septum support from possible fragments left by the septum and
reinsert it into the injector.
15. Place the septum holder on the top of the septum support (see G of
Figure 7-5).
16. Tighten the injector cap to finger tight.
CAUTION Do not overtighten the injector cap. You could damage the septum and affect
performance.
Restart the GC Conditions
17. In CARRIER, OVEN and INLET pages set the normal working conditions.
18. Perform an automatic leak check.

Chapter 7
Maintenance and Troubleshooting Troubleshooting
Troubleshooting
This paragraph contains instructions for the instrument troubleshooting and a brief
guide for the analytical troubleshooting.
Systematic approach is required to cause identification and problem solving. For
this is purpose, a method as the following one is suggested.
Electrical Connections
• Ensure that the electrical line is grounded and the voltage supply stable.
• Verify that all the electrical connections between GC and eventual subsidiary
units are correct.
Gases
• Verify that the carrier gas line is turned on.
• Verify that the detector gases are set to the correct flow rate.
• Check that leaks are not present in the system.
Injection
• Use syringe for gas chromatography having appropriate volume.
• The sample must be prepared and diluted correctly.
• Always inject the same sample volume.
• The split ratio must remain constant.
• If present, verify the autosampler performance.
• When an autosampler is used, the sample vials must be correctly crimped.
Chromatographic column
• The column must be compatible with the analysis to be carried out; correctly
installed and conditioned before use.
• Verify that the column-to-inlet ferrule is not leaking.
• Verify the presence of gas leaking.

Chapter 7
Troubleshooting Maintenance and Troubleshooting
• Check the column efficiency periodically.
Detector
• Ensure that the detector parameters are correctly set.
• Check for eventual detector contamination.
Data System
• Check that the Data System in use is properly connected.
Instrument Troubleshooting
The control unit of the GC performs a number of test routines to monitor and
report on the status of the major chromatographic and control functions.
Instrument malfunctioning, due to a component failure or to abnormal operating
condition is identified by the red lighting of the Not Ready/Error LED located on
the GC Status Panel.
The control unit of the GC performs a number of test routines to monitor and
report on the status of the major chromatographic and control functions.
Instrument malfunctioning, due to a component failure or to abnormal operating
condition is identified by the red lighting of the Not Ready/Error LED located on
the GC Status Panel.
When lit, this LED indicates that the injector and oven power has been cut off for
safety reasons and an error message indicating the possible cause of error appears
on the display. See Error Messages.

Chapter 7
Maintenance and Troubleshooting Error Messages
Error Messages
The following table reports the error messages and the explanation of the relevant
correlated problem
Table 7-2. Error Messages

Message Description
TEMP SHUTDOWN This message appears in two cases the carrier supply is
Loss of carrier missing and the actual pressure value is 0, or the actual
pressure cannot reaches the setpoint value.
HARDWARE SHUTDOWN The oven temperature exceeds the temperature limits (350 °C).
Oven T over limits Error may be due to a probe malfunctioning.
HARDWARE SHUTDOWN The inlet temperature exceeds the temperature limits (375 °C).
Inlet T over limits Error may be due to a probe malfunctioning.
HARDWARE SHUTDOWN The MS transfer line temperature exceeds the temperature
Det T over limits limits (375 °C). Error may be due to a probe malfunctioning.
HARDWARE SHUTDOWN This message appears when a MS detector is connected to the
X line T over limits GC instead of FID. The MS detector transfer line detector
temperature exceeds the temperature limits. Refer to the
relevant MS detector manual.
TEMP SHUTDOWN The oven is not heating.
Oven not heating
TEMP SHUTDOWN The inlet not heating.
Inlet not heating
TEMP SHUTDOWN The detector is not heating.
Det not heating
TEMP SHUTDOWN The MD detector transfer line not heating. Refer to the relevant
X-line not heating MS detector manual.
TEMP SHUTDOWN Hydrogen flows inside the column oven. Probably leaks in the
Hydrogen alarm column connections or column breakage.
HARDWARE SHUTDOWN Voltage supply to electric circuits is too low.
Undervoltage alarm

Chapter 7
Guide to Solve Analytical Problems Maintenance and Troubleshooting
Guide to Solve Analytical Problems

Rectifying faults in a chromatographic system is relatively simple, provided a
logical and systematic problem-finding procedure is adopted.
Most faults can be identified from the chromatogram especially for test mixtures
and we strongly recommend that a test mix be injected periodically to test the
efficiency of the chromatographic system as well as the detector performance.
Additionally, a leak must be performed should any part of the system be
disturbed.
Finally, routine cleaning of injector and detector units will help to avoid problems
occurring in the chromatographic system.

Chapter 7
Maintenance and Troubleshooting Guide to Solve Analytical Problems
Baseline
Behavior Characteristics Cause Remedy

Accumulation of stationary Replace the end section of the
phase column.
Carrier gas cylinder Replace the carrier gas cylinder
pressure too low to allow or increase the pressure.
control
Drifting carrier gas or Check the gas controllers.
combustion gas flows
Accumulation of impurities Check impurity levels in the gas
in column source. Use correct gas purity.
Carrier gas leak in the Perform a leak test and ensure
system the tightness of the connections
Drifting
Falling on the carrier gas line.
Column is baking out Allow enough time for the
column to stabilize.
Accumulation of impurities Check impurity levels in the gas
Rising in column source. Use correct gas purity.
Contaminated detector Refer to detector Manual
Rising under Column contaminated Recondition the column.
temperature
program
operation
Carrier gas flow rate too Reduce the carrier gas flow.
high
Contaminated column Recondition the column.
High-standing current
Contaminated gases Replace gas cylinders or gas
filters.

Chapter 7
Guide to Solve Analytical Problems Maintenance and Troubleshooting

Excessive column Check the oven temperature,
stationary phase bleeding ensuring it doesn't exceed the
column upper limit.
High-standing current
Recondition the column.
(continued)
Replace the column.
Loose connections Ensure all interconnections and
screw connections are tight.
Dip after solvent Detector contaminated Bake out or clean the detector.
peak
Excessive column bleed Reduce the upper column
during column temperature temperature.
programming Bake out the column. Install a
high temperature column.
Oxygen contamination is Install oxygen filters in carrier
Irregular S-shaped
decomposing the stationary gas line.
shape
phase Check pneumatic and inlet
systems for leaks.
Use correct gas purity with low
oxygen content.
Large AC power Use a dedicated clean AC line of
Square waves fluctuations; heavy sufficient amperage
equipment on same line
Contaminated detector Isolate the detector from
electronics. If noise disappears,
clean the detector.
Contaminated column Condition the column.
High-frequency
Noise Contaminated detector gas Check the gas purity and install
noise
supply appropriate filters
Detector temperature higher Reduce the detector temperature
than column maximum to the column temperature upper
temperature limit.

Chapter 7
Maintenance and Troubleshooting Guide to Solve Analytical Problems

External electrical Attach an AC line monitor and
interference check purity of the AC supply
Noise High-frequency
Loose column fittings Tighten fittings accordingly.
(Continued) noise
Loose detector electrical Make sure the leads are properly
connections connected.
Spiking External electrical Attach an AC line monitor and
interference check the purity of the AC
supply

Use of the Virtual
8
Keypad
This chapter provides basic information about of the functions and menus of the
FOCUS GC Version for MS virtual keypad.
Overview ............................................................................................................148
Virtual Keypad Main Menu................................................................................152
Time....................................................................................................................157
Valves .................................................................................................................158
Run Time Events ................................................................................................159
Run-Log..............................................................................................................160
Configuration......................................................................................................162
Info/Diagnostics .................................................................................................167

Chapter 8
Use of the Virtual Keypad Overview
Overview
The virtual keypad of the FOCUS GC has three components:
• a line-line display
• display LEDs showing the instrument’s status
• a keypad for data entry.
Each component is discussed in order from the top down. Figure 8-1 illustrates the
complete FOCUS GC virtual keypad.
Figure 8-1. The Virtual Keypad
The Display
The display shows the menus you use to control the GC parameters, settings, and
configuration options. The data entry keys allow you to scroll through, set, and
modify the menu information.
Figure 8-2 shows the components of a typical menu display.
Setpoint Value
Menu Title Scroll Indicator

Parameter Line
Actual Value
Figure 8-2. Components of the Menu Display

Chapter 8
Overview Use of the Virtual Keypad
The following are the menu display components:
Menu Title—This is the first line of each menu. The menu title remains at the top
of the display and does not move, even when you scroll up and down the menu
items.
Cursor—The cursor indicates the currently selected menu item. Use the
UP ARROW and DOWN ARROW keys to move the cursor.
Setpoint Value and Actual Value—Many parameters display two values. The first
value is the actual value of the GC parameter. You enter the second value, which is
the setpoint.
Scroll Indicator—This item is found in the upper right corner of the display. It
indicates when not-currently visible menu items exist. It appears in three ways:
• ↓, indicating that you can scroll downward
• ↑ , indicating that you can scroll upward
• , indicating that you can scroll in either direction
↔
Currently Visible Menu Parameters—The display shows four lines of a menu at a

time. Because the menu title always takes up the first line, three lines show menu
items.
Not Currently Visible Menu Parameters—The display shows three menu items at
a time. If a menu contains more than three lines, you can use the arrow keys to
scroll through the rest of the menu items.
The Display LEDs

The LEDs (Light Emitting Diodes) on the left side of the display screen indicate
the FOCUS GC’s operating status.
The status LEDs indicate the current operating mode and special settings activated
by the operator. Table 8-1 lists and explains each status LED.

Chapter 8
Use of the Virtual Keypad Overview
Table 8-1. Status LED Descriptions

LED Description
Not Ready/Error This LED lights when the GC is not ready to make a run, usually
because the specified oven temperature has not been reached. It
remains lit if any additional equilibration time has been configured. It
blinks when the GC has one or more error conditions.
Standby/Prep Run This LED lights when the GC is in Standby, waiting to be advanced to
the Ready status.
It blinks links while the GC prepares for a run, for example, while
opening or closing valves as required by the method or waiting for an
external device such as a mass spectrometer.
Ready to Inject This LED lights when the prep run has finished, indicating you can
inject a sample or start an autosampler.
Run This LED lights when a run is in progress.
The FOCUS GC Virtual Keypad

The following Table lists and describe the keys on the FOCUS GC virtual keypad.
Table 8-2. Keypad Descriptions

Key Description
The blue START key is a double function key. When pressed a first time it starts
the PREP RUN function. When pressed a second time, it starts a run with
programmed parameters after you manually inject a sample into the inlet. When
a remote start by another device, such as an autosampler, has been programmed,
the system automatically starts after injection.
The red octagonal STOP key has the following functions:
- stops a run in progress
- resets the FOCUS GC from READY to NOT READY
STATUS key displays the instrument status and any reasons the GC is in Not
Ready mode.

Chapter 8
Overview Use of the Virtual Keypad
Table 8-2. Keypad Descriptions (Continued)

Key Description
HOME key opens Main Menu and returns precedent page menu. The data entry
keys allow you to scroll through, set, and modify the menu information.
Use the SCROLL UP and SCROLL DOWN arrow keys to scroll through a list of
menus or to move the cursor to an editable field.
INC key (increase) allows increasing the parameter value.
DEC key (decrease) allows decreasing the parameter value.
ENTER key confirms changes to a selected menu item
Parameters Entry
The user points to any of the parameter navigating with the keys HOME, SCROLL
UP and SCROLL DOWN.
Only the bottom line is dedicated to parameters editing, first line is only for menu
title and doesn’t scroll. Once you have reached the line related to the parameter to
change, type the number with the numeric kaypad or increase or decrease the
value by the INC and DEC keys. During parameter editing the value is blinking.
.
OVEN Title Line
Temp 100 100 Editing Line
When the set value is the desired one, by pressing the key ENTER, the value is
accepted.
Any key different from ENTER, INC, DEC will escape parameter editing without
variation.

Chapter 8
Use of the Virtual Keypad Virtual Keypad Main Menu
Virtual Keypad Main Menu

To open main menu, press HOME key. Main menu contains the following page
menus available sequentially by pressing the SCROLL UP and SCROLL DOWN
arrow keys.
FOCUS GC
OVEN
INLET
CARRIER
DETECTOR
SIGNAL
AUTOSAMPLER
OTHERS
To open a page menu move the cursor up to the menu of interest, then press
ENTER key. To return precedent page menu press HOME key.
Oven
Use the Oven page to set temperatures, times and ramp rates. You can program up
to seven temperature ramps per run.
OVEN
Temp 100 100

Initial time 90.00
Ramp 1 120.0
Final temp 1 100
Final time 1 60.00
Ramp 2 Off

Chapter 8
Virtual Keypad Main Menu Use of the Virtual Keypad
Inlet
Use this page to set inlet parameters such as temperature and split flow.
The Mode menu items displays the current operating mode. Use INC and DEC keys
to modify the selection.
INLET
Mode Split
The items in the inlet menu vary depending on the operating mode you select in
the INLET menu. The following table shows the split/splitless inlet menu for the
operating modes.
Split Mode Splitless Mode Surge Splitless Mode

INLET INLET INLET
Temp 200.. 200 Temp 200..200 Temp 200..200

Mode Split Mode Splitless Mode Surge Splitless
Total flow (150.0) Total flow (150.0) Total flow (150.0)
Split flow 100 100 Split flow 100 100 Split flow 100 100
Split ratio 1000.0 Splitless time 1.00 Splitless time 1.00
Const sept purge Off Surge pressure 100
Stop purge for 1.00 Surge duration 1.00
Const sept purge Off
Stop purge for 1.00
Carrier
Use this page to display in the carrier menus vary with the pressure and flow
modes you select.
CARRIER
Flow mode Const flow

Chapter 8
You have a choice of two flow modes:

• Constant pressure mode, which sets pressure only
• Constant flow mode which maintains a specific flow rate through the column.
The items in the carrier menu vary depending on the operating mode you select in
the CARRIER menu. The following table shows carrier menu for the operating
modes.
CARRIER (He) CARRIER (He)
Pressure (100) Pressure 100 100

Col.Flow 12.0 12.0 Col.Flow (10.0)
Flow mode Const flow Flow mode Const Pres
Gas saver flow 100 Gas saver flow 100
Saver time 1.00 Saver time 1.00
Vacuum comp. Off Vacuum comp. Off
Leak check Leak check
Column evaluation Column Evaluation
Carrier Menu in Carrier Menu in
Constant Flow Mode Constant Pressure Mode
How to Perform a Leak Check

1. Scroll to Leak check and press ENTER to open Leak Check menu.
LEAK CHECK
Run leak check

Exit w/o leak check
2. To start the leak check, scroll to Run leak check and press ENTER

Chapter 8
Virtual Keypad Main Menu Use of the Virtual Keypad
How to perform a Column Evaluation

1. Scroll to Column evaluation and press ENTER to open COLUMN
EVALUATION menu.
COLUMN EVALUATION
Run column eval.

K = 100.0000
Exit w/o column eval
2. To start column evaluation, scroll to Run column eval and press ENTER
Detector
Use this page to display the MS detector menu.
DETECTOR
MS Line Temp 100 100
Signal
This page is not available.
Autosampler
Autosampler is controlled only by Xcalibur System.
When the autosampler is not present or when the GC is connected to the data
system, the following messages are respectively displayed.
.
AUTOSAMPLER AUTOSAMPLER
Not present Locked by Data System

Chapter 8
Others
.
OTHERS
Configuration
Use this page to entry the following submenu:

• Time
• Valves
• Run Time Events
• Run-Log
• Configuration
• Info/Diagnostics
For details refer to the relevant paragraphs in this chapter.

Chapter 8
Time Use of the Virtual Keypad
Time
This option allows you to visualize the following parameter
• Time
• Date
• Last run time
• Next run time
• Elapsed time and time remaining during the current run
• The column flow calculator
In Main Menu move the cursor until the Others page is selected, then press
ENTER. Scroll to Time then press ENTER
OTHERS
Time
When the GC is not running a menu appears as the following:
TIME
Next routine 15.00

Last routine 120.00
We 13 Mar 2002 12:03
V=100 F=100.0 01:00
Flowmeter volume 100
When the GC is running a menu appears as the following:

Chapter 8
Use of the Virtual Keypad Valves
TIME
Elapsed time 5.00

Time left 110.00
We 13 Mar 2002 12:03
V=100 F=100.0 01:00
Measured volume 100
Valves
Use this feature to specify and control up to four valves, as well as to manually
change the state of inlet valves. For instance you can manually:
• Open or close the S/SL inlet valves before or during a run
• Switch a gas sampling valve from load to inject position
• Activate or deactivate an external event
ENTER. Scroll to Valves then press ENTER
OTHERS
Valves
When a gas sampling valve is not present a menu appears as the following:
VALVES
Split valve Off

Sept purge valve On
EV#1 Off
EV#2 Off

Chapter 8
Run Time Events Use of the Virtual Keypad
When a gas sampling valve is present and configured (refer to Valves

Configuration Menu in paragraph Configuration) a menu appears as the
following:
VALVES
Split valve Off

Sept purge valve On
GSValve#1 Load
EV#2 Off
Run Time Events

This options allows you to program events to happen prior to or during a run. For
instance, a valve could open two minute into a run.
You can program:
• An output signal adjustment, such as autozero.
• A valve to open or close.
• An external event from another device.
In Main Menu move the cursor until Others page is selected, then press ENTER.
Scroll to Run time event then press ENTER.
OTHERS
Run Time Events
The first time you program a time event (Run Time Events empty) the following
menu appears:
RUN TIME EVENTS
<None>
Add run time event

Chapter 8
Use of the Virtual Keypad Run-Log
In RUN TIME EVENTS menu scroll to Add run time events and press ENTER:
The following menu appears:
.
EDIT EVENTS
Event EV#1
Run time Pre run
Setpoint 2
Next event
Run-Log
This function displays the run log, which records error or the method
modifications that happens during run time. It display the time and description
any deviation that occur.
The run log keeps track of any errors or deviations during the run.
This information can be used to meet good laboratory practice (GLP) standards.
For example, if you interrupt the run for any reason, the run log will record the
time the run stopped and an interpretation of the event. The Run-log is cleared and
reset at the beginning of the next run.
When the run log contains entries, it is shown in the STATUS menu.
To see the journal of events, in Main Menu move the cursor until the Others page
is selected, then press ENTER. Scroll to Run-log then press ENTER
OTHERS
Run-log
An example of Run-log is shown below.

Chapter 8
Run-Log Use of the Virtual Keypad
RUN LOG (XofY) 1

Itime 200.00 ’ 220.00 2
at run time 0.50
ITemp 120 ’ 100
at run time 2.00
Ftime 1.00 ’ 10.00
at run time 2.50
Ramp2 50.0 ’ 120.0
at run time 3.10
Oven T is 105 (110)
at run time 3.40

(continue)

Chapter 8
Use of the Virtual Keypad Configuration
Configuration
This paragraph describes how to configure your FOCUS GC.
When to Configure
The FOCUS GC has few special set up sequences. After you first install and
configure the instrument, you will need to reconfigure only after you make
changes to the components. You must configure the system when:
• using the FOCUS GC for the first time
• changing carrier gases
• changing column types (to set the appropriate maximum oven temperature)
For details refer to Configuration Menu.
Configuration Menu
In Main Menu move to cursor until the Others page appears, then press ENTER.
.
OTHERS
Configuration
Scroll to Configuration and press ENTER. The following table describes the
items in the Configuration menu. Each item has a submenu.
Table 8-3. Configuration Menu

Menu Description
CONFIGURATION This line is the title bar
Oven Controls preparatory actions such as an automatic prep
run, timeout, equilibration time.
Carrier This parameter controls the type of carrier gas.
Autosampler Not active

Chapter 8
Configuration Use of the Virtual Keypad
Table 8-3. Configuration Menu (Continued)

Menu Description
General This parameter controls the RS 232 Baud rate for the
communication with an external device and the Main
supply frequency
Keyboard and This parameters controls keypad and display preferences.
Display
Handshake This parameter configures the polarity of signals from
external device
Time This parameter sets the time and data
Valves This parameter controls an eventual gas sampling valve
Oven Configuration Menu

The FOCUS GC oven provides great flexibility in controlling and programming
temperatures. In the CONFIGURE OVEN menu you can set various preparatory
parameters.
CONFIGURE OVEN
Max temperature 300

Equilib. Time 10.00
Auto prep run Off
Auto start Off
Prep-run timeout 10
Carrier Configuration Menu

Commonly used gases are Helium, Nitrogen and Hydrogen.
You specify the type of carrier gas in the CONFIGURE CARRIER menu by using
the INC and DEC key.

Chapter 8
CONFIGURE CARRIER
Gas Type Helium
WARNING! You cannot choose hydrogen as a carrier gas unless your instrument has a
hydrogen sensor. See Using Hydrogen.
Autosampler Configuration Menu

The autosampler is controlled by the data system. When the autosampler is not
present or if the GC is connected to the data system the following messages are
respectively displayed:
CONFIG AUTOSAMPLER CONFIG AUTOSAMPLER
Not present Locked by Data System
General Configuration Menu

Use this item to set the mains supply frequency of the country where the GC is
installed. Use the INC and DEC key the select the required value.
GENERAL CONFIG
Baud rate 38400

AC mains freq. 50
Keyboard & Display Configuration Menu

This menu allows you to customize your keyboard and display.
Keyboard beep leads to a submenu where you can specify when you want the GC
to alert you with a keyboard sound. To move to the submenu, select Keyboard
beep and press ENTER.

Chapter 8
Configuration Use of the Virtual Keypad
CONFIG KEYB. & DISP.
Keyboard lock Off

Keyb. Beep Enter key
Delimeter type “.”
Pressure unit kPa
Brightness 3
Keyb. Beep causes the GC to beep when you press the key specified in the
submenu.
Beep Submenu
KEYBOARD BEEP:
All keys
Enter key press
On invalid key
Never
Handshake Configuration Menu

The FOCUS GC can cooperate with other instruments, such as an autosampler or
mass spectrometer, during analysis. To allow other devices to run properly, you
must indicate how the signal will change. For example, the menu specifies that
another device will start the GC when the remote start signal changes from high to
low.

Chapter 8
CONFIG HANDSHAKE
Remote start in H L
Inhibit ready High
End of run out H L
Start of run out H L
GC ready out High
Prep run out High
Time Configuration Menu

The current date and time are displayed. You can set this time from the
CONFIGURE menu. When you open the CONFIGURE TIME menu, the following
items appear:
CONFIGURE TIME
Time: 18:14:11
Date: Mon 11/Mar/2002
NOTE Time is set on a 24-hour clock.
Valves Configuration Menu

You can configure two gas sampling valves, when present, and program two
external events to be the default condition for an external device. See also Run
Time Events
CONFIGURE VALVES
Valve#1 Gas sampling

Valve#2 none
EV#1 default Off
EV#2 default On

Chapter 8
Info/Diagnostics Use of the Virtual Keypad
Info/Diagnostics
Use this feature to bring up hardware, software and diagnostic information
ENTER. Scroll to Info/Diagnostics then press ENTER
OTHERS
Info/Diagnostics
A menu appears as the following:
INFO/DIAGNOSTICS
Serial #: 12345678
FW ver: 2.00.31
DPFC ver: 0.27
BOOT ver: 1 B.0
Manufact.: 1/Jan/02
Total runs 1234567
Ambient press 103.0
OV 31.8 F= 27 S=off
IN 41.8 F= 30 S=off
DT 25.3 F= 25 S=off
OVPL 3 10°C 0.7%
Table 8-4. Info/Diagnostics

INFO/DIAGNOSTICS This line is the title bar
Serial # T The number (eight figures) indicates the product code.
FM ver: Indicates the version of the firmware
DPFC ver: Indicates the version of the DPFC module

Chapter 8
Use of the Virtual Keypad Info/Diagnostics
Table 8-4. Info/Diagnostics

BOOT ver: Data for Thermo Electron authorized technical
personnel only.
Manufact.: Indicates the manufacturing date of your GC.
Total runs The number (seven figures) Indicates the performed
analyses.
Ambient press Indicates the ambient pressure expressed in kPa.
OV, IN, DT, OVPL Diagnostics data for Thermo Electron authorized
technical personnel only.

Customer
A
Communication
This appendix contains contact information for Thermo Electron offices
worldwide. This appendix also contains one-page Reader Survey. Use this survey
to give us feedback on this manual and help us improve the quality of our
documentation.
How To Contact Us
Thermo Electron provides comprehensive technical assistance worldwide and is
dedicated to the quality of our customer relationships and services. Use this list to
contact your local Thermo Electron office or affiliate.
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Appendix A
How To Contact Us
FINLAND FRANCE
Oy G.W. Berg & Co. AB Thermo Fisher Scientific France SA
PO Box 12 Hightec Sud 12 Avenue des Tropiques – Z.A. de Courtaboeuf
Finn 02201 Espoo BP 141 - 91944 Les Ulis Cedex
Tel: (9) 88664600 Fax: (9) 88664699 Tel:(01) 6918 8810 Fax:: (01) 6929 9382
GERMANY GREECE
Thermo Fisher Scientific GMBH Rigas Labs
Im Steingrund 4-6 5, Salaminos Str.
63303 Dreieich 546 26 Thessaloniki - Greece
Tel: 6103-408-0 Fax: 6103-408-1111 Tel: (031) 550669/540410 Fax: (031) 550073
IRELAND ITALY
Thermo Fisher Scientific U.K. Thermo Electron S.p.A.
19 Trentham Lake South Strada Rivoltana
Imex Technology Park, Trentham 20090 Rodano (Milan)
ST4 8JF, Stoke on Trent, STAFF Tel: (02) 95059226 Fax: (02) 95059256
Tel: (1782) 645136 Fax: (1782) 645121
NETHERLANDS NORWAY
Interscience B.V. IT Instrument Teknikk
Tinstraat 16, Postbus 2148, 4800 CC Breda Skandinavia A/S – PO Box 14
Tel: (076) 5411800 Fax: (076) 5420088 Grins Naeringspark 1 N-1345 Østerås
Tel: (67) 149303 Fax: (67) 149302
PORTUGAL SPAIN
Unicam Sistemas Analiticos, Lda. Thermo Fisher Scientific Scientific-Thermo Instruments S.A.
Estrada da Rocha, 2-A-Sala C Avenida Valdelaparra 27
2799-508 Linda A Velha Edifico Alcor – 2a Planta
Tel: +351 (21) 4153740 Fax: +351 (21) 414 2006 28108 Alcobendas – Madrid
Tel: +34 (91) 6574930 Fax: +34 (91) 6574937
SWEDEN SWITZERLAND
Thermo Fisher Scientific AB - Sweden Brechbühler AG
Pyramidbacken 3 Steinviesenstrasse 3, CH 8952 Schlieren
SE 14175 Kugens Kurva Tel: (01) 732 3131 Fax: (01) 730 6141
Tel: (8) 55646800 Fax: (8) 55646808
TURKEY UNITED KINGDOM
Dolunay Teknik Cihazlar Ltd. Thermo Fisher Scientific U.K.
Darulaceze Cad. No 43/A 19 Trentham Lake South
80290 Okmeydani Imex Technology Park, Trentham
Istanbul ST4 8JF, Stoke on Trent, STAFF
Tel: +90 (212) 2105435 Fax: +90 (212) 2105434 Tel: (1782) 645136 Fax: (1782) 645121

Appendix A
How To Contact Us
AFRICA, ASIA AND OCEANIA
AUSTRALIA EGYPT
Thermo Fisher Scientific Australia PTY LTD Scientic Services
Unit 14, 38-46 South Street 20, Shehab Street, El Mohandeseen
Rydalmere, NSW 2116 Dokki, Cairo
Tel: 02 9898 9000 Fax:: 02 9898 9800 Tel: (2) 3600482 Fax:: (2) 3481424
INDIA ISRAEL
Nulab Equipment Co. Pvt. Ltd. Bargal Analytical Instruments & Software Ltd.
Labhouse Plot No. F-13 4 Wallenberg Raoul Street
Opp. Seepz, Marol M.I.D.C. Tel Aviv 69719
Andheri (East) Mumbay 400 093 Tel: +972 (3) 6490823 Fax: +972 (03) 6490826
Tel: +91 (22 28376701 Fax:: +91 (22) 28368275
JAPAN JORDAN
Thermo Fisher Scientific K.K. Hijaz Electronic & Scientific Supplies Est
Nishi-Shinjuku, Toyokuni Building P.O. Box 925133
2-5-8 Hatsudai, Shibuya-ku, Tokyo 151-0061 Amman 11110
Tel: (03) 3372 3001 Fax: (03) 3372 7051 Tel: + 0962 (6) 5359761 Fax: + 0962 (6) 5359761
KOREA LEBANON
InSung Chromatech Co., Ltd. LaboTech Engineering
InSung Bldg 89-111, Shinjung 2-dong Ashrafieh, Monot Street, P.O. Box 16
Yangcheon-Ku – Seoul 7186 Beirut
Tel: (02) 2644 1991 Fax: (02) 2644 1996 Tel: (1) 332707 Fax: (1) 333707
NEW ZEALAND PAKISTAN
Alphatech Systems Ltd & Co. Total Technology
P.O. Box 37583 Parnell 1st floor, 4-Singhar Centre, 16 Mc Lagan Road
Auckland Lahore 54000
Tel: (09) 3770392 Fax: (09) 3098514 Tel: +92 (42) 7236496/7224459 Fax: +92 (42) 7234689
PEOPLES REPUBLIC OF CHINA SINGAPORE
Thermo Beijing Office CE Instruments Enterprise Singapore
Room 912-916, Ping-an Mansion no 23 c/o Sintech Scientific S.E.A. Pte Ltd
Finance Street No. 196 Pandan Loop #02-18
Xi Cheng District Pantech Industrial Complex
Beijing Singapore 128384
Tel: +86 (10) 66210852 / 66210839 Fax: +86 (10) 6610851Tel: +656 4646302 Fax: +656 2346252
Also serving INDONESIA, MALAYSIA, THAILAND, PHILIPPINES, HONG KONG

Appendix A
How To Contact Us
SOUTH AFRICA TAIWAN R.O.C.

Premier Technologies E Hong Instruments Co, Ltd.
P.O Box 173 2FL, No.157, Sec 2, Fu Hsing S. Road
Northriding 2162 Taipei 106
South Africa Taiwan R.O.C.
Tel: (011) 4661410 Fax: (011) 4661313 Tel: +886 (02) 2755 2266 Fax: +886 (02) 2707 7693
U.A.E
BDH Middle East
P.O. Box 28637
Dubai
Tel: (4) 2852211 Fax: (4) 2861331
NORTH, CENTRAL AND SOUTH AMERICAS
CANADA U.S.A.
Thermo Fisher Scientific Americas Thermo Fisher Scientific Americas
Tel: (732) 981-0390 Fax: (732) 981-0029. Tel: (732) 981-0390 Fax: (732) 981-002

Reader Survey
Product: FOCUS GC Version for MS
Manual: Instruction Manual
Part No.: 317 094 27
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Fax or mail this form to:
Thermo Electron S.p.A.
Strada Rivoltana km 4
20090 Rodano (MI)
ITALY
Fax: 39 02 95059388
Glossary
This section contains an alphabetical list and descriptions of terms used in this guide and the help
diskette. It also includes abbreviations, acronyms, metric prefixes, and symbols.
A
A ampere
ac alternating current
ADC analog-to-digital converter
B
b bit
B byte (8 b)
baud rate data transmission speed in events per second
C
ºC Celsius
CIP Carriage and Insurance Paid To
cm centimeter
CPU central processing unit (of a computer)
CSE Customer Service Engineer
D
d depth
DAC digital-to-analog converter
dc direct current
DS data system

Glossary
E
ECD Electron Capture Detector
EMC electromagnetic compatibility
ESD electrostatic discharge
F
ºF Fahrenheit
FID Flame Ionization Detector
FOB Free on Board
FPD Flame Photometric Detector
ft foot
G
g gram
gain A measure of the ability of an electronic circuit or device to
increase the magnitude of an electronic input parameter.
GC gas chromatograph
GND electrical ground
H
h height
h hour
harmonic A high-frequency disturbance that appears as distortion of the
distortion fundamental sine wave.
HOT OC High Oven Temperature Cold On-Column Injector
HV high voltage

Glossary
Hz hertz (cycles per second)
I
ID inside diameter
IEC International Electrotechnical Commission
impulse See transient
in inch
I/O input/output
K
k kilo (103 or 1024)
K Kelvin
kg kilogram
kPa kilopascal
L
l length
l liter
lb pound
LED light-emitting diode
LVOCI Large Volume On-Column Injector
M
m meter (or milli [10-3])
M mega (106)
µ micro (10-6)
MBq megabecquerel

Glossary
mCi millicurie
meniscus The curved upper surface of a column of liquid.
min minute
mL milliliter
mm millimeter
m/z mass-to-charge ratio
N
n nano (10-9)
negative polarity The inverse of a detector signal polarity.
nm nanometer
NPD Nitrogen Phosphorous Detector
O
OCI On-Column Injector
OD outside diameter
Ω ohm
P
p pico (10-12)
Pa pascal
PCB printed circuit board
PDD Pulsed Discharge Detector
PID Photoionization Detector
PKD Packed Column Injector
PN part number

Glossary
PPKD Purged Packed Column Injector

psi pounds per square inch
PTV Programmable Temperature Vaporizing Injector
R
RAM random access memory
RF radio frequency
ROM read-only memory
RS-232 industry standard for serial communications
S
s second
S/SL Split/Splitless Injector
sag See surge
slow average A gradual, long-term change in average RMS voltage level,
with typical durations greater than 2 s.
source current The current needed to ignite a source, such as a detector
lamp.
surge A sudden change in average RMS voltage level, with typical
duration between 50 µs and 2 s.
T
TCD Thermal Conductivity Detector
transient A brief voltage surge of up to several thousand volts, with a
duration of less than 50 µs.

Glossary
V volt
V ac volts, alternating current
V dc volts, direct current
VGA Video Graphics Array
W
w Width
W Watt
NOTE The symbol for a compound unit that is a quotient (for example, degrees Celsius per
minute or grams per liter) is written with a negative exponent with the denominator.
For example:
° C min-1 instead of ° C/min
g L-1 instead of g/L

Index
A E
About This Manual xiii Electrical Connections 35
Conventions Used xv Electronic Compartment 27, 32
Overview xiii Error Messages 142
Analytical Problems 143 Event Time Group Box 120
Analytical Unit 26 Expected K Factor 85
Exterior
C cleaning xxiv
Capillary Column External Devices
How to connect 79 Autosamplers 30
Carrier Gas External Event Group Box 121
Control 27
Inlet Port 35 F
Carrier Page 114 Ferrules 78
Cleaning xxiv, 130 FOCUS GC version for MS
Cleaning the unit 27 Components 26
Column 77 Configuration 94
Conditioning 91 Description 25
Installation 79 Document Set xx
Keeping Leaks Under Control 82 Front Panel 30
Column Evaluation 82 Instrument
Column Ferrules 78 Overview 26
Column Oven 28, 31 Setup 99
Column oven 26 Pull-up Menu 102
Columns 28
Fittings 78 G
Ferrules 78 Gas Control 27
Retaining Nuts 78 Carrier 27
Configuring the FOCUS GC 94 GC Left Hand-side Panel 38
Control Panel 27, 31 GC Parts
GC User Interface 39 Description 30
Conventions Used xv Getting Started 93
Column Glass Liner
Using Correct Fittings 78 Breakage 132
Guide to Solve Analytical Problems 143
D
Decontaminating the unit 27 H
Decontamination xxiv Hazardous material
Detector 29 decontamination xxiv
Detector compartment 26 spills xxiv
Display 27, 148 High Voltage Section 33
Display LEDs 149 High-voltage compartment 27
DPFC Module 27 Hot Empty Needle Injection 67, 72
How To Perform Maintenance 128
Hydrogen

Index
Sensor M
Use xxiv Maintanance
Use xxiii SSL Injector 131
Hydrogen Sensor xxiv Maintenance 127, 128
FID 140
I Schedule Table 129
Initial Values 119 Suggested Schedule 128
Injector 28 Markings xviii
Injector compartment 26 Material Safety Data Sheets xxiv
Inlet Parameters 73 Method Editing 103
Inlet SSL Page 108 Methods and Sequences 30
Instrument Microseal™ Valve 62
Automation 29 MS Detector 29
Classification xxi MS Transfer Line Page 117
Markings xviii
Symbols xviii N
Instrument Automation 29 Not Ready/Error LED 32, 150
Instrument Cleaning 130
Instrument Overview 26 O
Instrument Troubleshooting 141 OCI. See On-Column Injector
Item 119 On-Column Injector 28
Oven Exhaust Vent 37
K Oven Page 104
K Factor 85
Tables 85 P
Keypad 150 Pneumatic Compartment 26
Pneumatic compartment 26
L Preliminary Check 125
Leak
Identifying 82 R
Manual Checking 83 Rear Panel 34
Removing 82 Replace the Standard Septum 133
Leal Check Retaining Nuts 78
Performing an Automatic 89 Roadmap-Home Page 96
LEDs Run Table 118
Display 149
Not Ready/Error 32, 150 S
Standby/Prep Run 32, 150 S/SL
Liner 65 Constant Septum Purge 76
Cleaning 131 Injection Technique 67
Replacing 131 Injection Techniques 67
Liners 62 Inlet Parameters 73
Low Voltage Section 33 Packed Column 64
Parameters
Inlet 74

Index
Prameters Gas Control 59

Purge 75 Septum Purge System 60
Split Flow 75 Standard Septum 62
Split Ratio 75 Cleaning 135
Splitless Time 75 Replacement 133, 135
Stop Purge Time 76 Replacing 131
Surge Duration 76 Standby/Prep Run LED 32, 150
Surge Pressure 76 Symbols xviii
Temperature 75
Wide-Bore Injection with a Tapered Liner 63 T
S/SL Overview 58 Technical Features xxi
S/SL Parameters Temperature Effect 71
Mode 74 Time 119
Surge 76 Top Panel 37
S/SL. See Split/Splitless Injector Troubleshooting 127, 140
Safety Information xxii Instrument 141
Use of Gases xxii
safety symbols xv–xix U
Sample Use of Gases xxii
Refocusing 71 user interface 27
Septum 65 Using Hydrogen xxiii
Settings 119 Using the Hydrogen Sensor xxiv
Solve Analytical Problems 143
Solvent Effec 71 V
Split 74 Valve Event 120
Split Injection Technique 67 Valves Manual Activations 124
Split/Splitless Virtual Keypad 122
Injector Components 61
Split/Splitless Injector 57, 58
Liners 62
Menus 65
Overview 58
Packed Columns 64
Septum 62
Split Injection Technique 67
Splitless Injection Technique 69
cold trapping 71
flooding 72
sample refocusing 71
solvent effect 71
Split/Splitless Injector (S/SL) 57
Splitless 74
Splitless Injection Technique 69
Splitless w/surge 74
SSL

Index

Operating Sequences
Configuring the Carrier Gas ..............................................................................................................43
Configuring the Pressure Unit ...........................................................................................................43
Installing a Liner and a Septum .........................................................................................................65
How to Connect a Capillary Column .................................................................................................79
Manual Checking for Leaks ...............................................................................................................83
Performing a Column Evaluation ......................................................................................................84
Performing an Automatic Leak Check ..............................................................................................89
Setting Up a Single Ramp Temperature Program .............................................................................106
Setting Up Multiple Ramp Temperature Program .............................................................................107
Programming the Split Mode .............................................................................................................111
Programming the Splitless Mode .......................................................................................................112
Programming the Surge Splitless Mode ............................................................................................113
Programming The Carrier Gas Parameters ........................................................................................116
How to Start-up the Instrument .........................................................................................................125
Replace the Standard Septum ............................................................................................................133
Replace or Clean the Liner when a Standard Septum is Installed .....................................................135
List of Figures
Figure 1-1. FOCUS GC Components .............................................................................................26
Figure 1-2. Front Panel....................................................................................................................30
Figure 1-3. Column Oven Internal View ........................................................................................31
Figure 1-4. Status Panel ..................................................................................................................31
Figure 1-5. Electronic Compartment...............................................................................................33
Figure 1-6. Rear Panel.....................................................................................................................34
Figure 1-7. Electrical Connections..................................................................................................36
Figure 1-8. Rear Panel.....................................................................................................................37
Figure 1-9. GC Left Hand-side Internal View ................................................................................38
Figure 1-10. User Interface ...............................................................................................................39
Figure 2-1. DPFC Module...............................................................................................................44

Figure 2-2. Carrier Gas Page...........................................................................................................45
Figure 3-1. The Column Oven ........................................................................................................50

Figure 3-2. Oven Air Circulation ....................................................................................................51
Figure 3-3. Oven Page.....................................................................................................................52
Figure 4-1. Split/Splitless Injector ..................................................................................................58

Figure 4-2. Gas Control...................................................................................................................59
Figure 4-3. Septum Purge System...................................................................................................60
Figure 4-4. Split/Splitless Injector Components .............................................................................61
Figure 4-5. S/SL Wide-Bore Injection with a Tapered Liner .........................................................63
Figure 4-6. S/SL with a Packed Column.........................................................................................64
Figure 4-7. Split Injection Technique .............................................................................................68
Figure 4-8. Splitless Injection Technique .......................................................................................70
Figure 4-9. S/SL Inlet Page .............................................................................................................73
Figure 6-1. Instrument Configuration Dialog Window...................................................................94

Figure 6-2. FOCUS GC Configuration Page ..................................................................................95
Figure 6-3. Roadmap-Home Page...................................................................................................96
Figure 6-4. FOCUS GC Setup Page................................................................................................99
Figure 6-5. FOCUS GC Pull-up Menu............................................................................................102
Figure 6-6. The Oven Page .............................................................................................................104
Figure 6-7. The Inlet SSL Page.......................................................................................................108
Figure 6-8. The Carrier Page...........................................................................................................114
Figure 6-9. The MS Transfer Line Page .........................................................................................117
Figure 6-10. Run Table Page.............................................................................................................118
Figure 6-11. ADD/Edit Run-Time Event Screen ..............................................................................120
Figure 6-12. Control Panel - Virtual Keypad ....................................................................................122
Figure 6-13. Valves Dialog Window ................................................................................................124
Figure 7-1. Replace the Septum ......................................................................................................134

Figure 7-2. Replace and Clean the Liner (1) ...................................................................................136
Figure 7-3. Replace a Broken Liner ................................................................................................137
Figure 8-1. The FOCUS GC Versione for MS Virtual Keypad......................................................148

Figure 8-2. Components of the FOCUS GC Menu Display ...........................................................148
List of Tables
Table 1-1. Status LED Descriptions ..............................................................................................32
Table 4-1. Liner Sizes and Applications........................................................................................62
Table 5-1. Ferrules .........................................................................................................................78
Table 7-1. Standard Maintenance Schedule...................................................................................129

Table 7-2. Error Messages .............................................................................................................142
Table 8-1. Status LED Descriptions ..............................................................................................150

Table 8-2. Keypad Descriptions ....................................................................................................150
Table 8-3. Configuration Menu .....................................................................................................162
Table 8-4. Info/Diagnostics ...........................................................................................................167

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Thermo Scientific

FOCUS GC Version For MS

Printing History: First Edition, released September 2003

have been carried out by authorized personnel and if:

Thermo Electron S.p.A.

FOCUS GC MS Version -Instruction Manual iii

FOCUS GC Version for MS - Instruction Manual v

GC Left Hand-side Panel............................................................................................ 38

vi FOCUS GC Version for MS - Instruction Manual

FOCUS GC Version for MS - Instruction Manual vii

Expected K Factor ...................................................................................................... 85

viii FOCUS GC Version for MS - Instruction Manual

Initial Values Group Box .......................................................................................... 119

FOCUS GC Version for MS - Instruction Manual ix

Error Messages ...................................................................................................................... 142

x FOCUS GC Version for MS - Instruction Manual

FOCUS GC Version for MS - Instruction Manual xi

xii FOCUS GC Version for MS - Instruction Manual

Chapter 1, FOCUS GC Version for MS Description, provides a basic overview of

Chapter 2, Gas Control, contains information on controlling and programming the

Chapter 4, Split/Splitless Injector (S/SL), describes the Split/Splitless (S/SL)

Chapter 5, Column, describes the analytical columns installed in the FOCUS GC

Chapter 6, Getting Started, This chapter contains instructions to configure, set

Chapter 7, Maintenance and Troubleshooting, contains information and operating

FOCUS GC Version for MS - Instruction Manual xiii

Appendix A, Customer Communication, contains contact information for Thermo

xiv FOCUS GC Version for MS - Instruction Manual

Conventions Used in This Manual

Bold Bold text indicates names of windows, dialog boxes, and

This symbol alerts you to important information related to the

This symbol alerts you to an action or sequence that, if

This symbol indicates an electric shock hazard.

FOCUS GC Version for MS - Instruction Manual xv

This symbol indicates danger from hazardous chemicals.

This symbol indicates danger from high temperature surfaces

This symbol indicates a fire hazard.

This symbol indicates an explosion hazard.

This symbol indicates a toxic hazard.

This symbol indicates the presence of flammable materials.

This symbol indicates the presence of radioactive material.

This symbol indicates an operation or sequence that must not

This symbol indicates an eye hazard. Eye protection must be

This symbol indicates the user must wear a protective screen

xvi FOCUS GC Version for MS - Instruction Manual

This symbol indicates the user must wear protective shoes

This symbol indicates the user must wear protective clothing

This symbol indicates the user must wear gloves when

FOCUS GC Version for MS - Instruction Manual xvii

Instrument Markings and Symbols

Both direct and alternating current

Three-phase alternating current

Earth (ground) terminal

Protective conductor terminal

Frame or chassis terminal

xviii FOCUS GC Version for MS - Instruction Manual

Caution, hot surface