User Manual GC Ms System 7250 Qtof G7250 90007 en Agilent

Agilent 7250 Accurate-Mass Quadrupole
Time-of-Flight GC/MS System

Troubleshooting and Maintenance Manual
Notices
© Agilent Technologies, Inc. 2019 Warranty
No part of this manual may be repro- WAR N IN G
The material contained in this docu-
duced in any form or by any means ment is provided “as is,” and is subject
(including electronic storage and to being changed, without notice, in
A WARNING notice denotes a
retrieval or translation into a foreign lan-
future editions. Further, to the maxi- hazard. It calls attention to an
guage) without prior agreement and operating procedure, practice,
mum extent permitted by applicable
written consent from Agilent Technolo-
gies, Inc. as governed by United States
law, Agilent disclaims all warranties, or the like that, if not correctly
either express or implied, with regard performed or adhered to, could
and international copyright laws.
to this manual and any information
contained herein, including but not lim-
result in personal injury or
Manual Part Number death. Do not proceed beyond a
ited to the implied warranties of mer-
G7250-90007 chantability and fitness for a particular WARNING notice until the
purpose. Agilent shall not be liable for indicated conditions are fully
Edition errors or for incidental or consequen- understood and met.
First Edition, January 2019 tial damages in connection with the
furnishing, use, or performance of this
Printed in USA
document or of any information con-
Agilent Technologies, Inc. tained herein. Should Agilent and the
5301 Stevens Creek Boulevard  user have a separate written agree-
Santa Clara, CA 95052 ment with warranty terms covering the
material in this document that conflict
with these terms, the warranty terms in
the separate agreement shall control.
Safety Notices
C AU T I O N
A CAUTION notice denotes a 
hazard. It calls attention to an
operating procedure, practice,
or the like that, if not correctly
performed or adhered to, could
result in damage to the product
or loss of important data. Do
not proceed beyond a CAUTION
notice until the indicated
conditions are fully understood
and met.
7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual

Contents
1 Introduction
Abbreviations Used 10
The 7250 Accurate-Mass Quadrupole Time-of-Flight GC/MS
System 11
7250 Accurate-Mass Q-TOF GC/MS Description 13
Side Panel AC Power Connectors 14
Back Panel Connectors 15
Interfacing Start Events to External Devices 16
Remote control processor 16
Remote start signals 16
System ready 16
Start run input 17
Important Safety Warnings 18
Safety and Regulatory Certifications 21
Intended Use 24
Cleaning/Recycling the Product 24
Accidental Liquid Spillage 24
Moving or Storing the MS 24
2 General Troubleshooting
Troubleshooting Tips and Tricks 26
General Symptoms 27
Chromatographic Symptoms 29
Mass Spectra General Symptoms 34
Pressure Symptoms 36
7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 3

Temperature Symptoms 38
Error Messages 40
Air Leaks 45
Contamination 46
3 CI Troubleshooting
Common CI-Specific Problems 50
Air Leaks 52
How do I know if I have an air leak? 52
Special NCI notes 53
How do I find the air leak? 53
Pressure-Related Symptoms 55
Poor vacuum without reagent gas flow 56
High pressure with reagent gas flow 56
Pressure does not change when reagent flow is
changed 57
Signal-Related Symptoms 58
No peaks 58
No reagent gas peaks in PCI 58
No PFDTD peaks in PCI 59
No reagent gas peaks in NCI 59
No PFDTD calibrant peaks in NCI 59
No sample peaks in NCI 59
Large peak at m/z 238 in NCI OFN spectrum 60
No or low reagent gas signal 60
No or low PFDTD signal, but reagent ions are normal 61
Excessive noise or low signal-to-noise ratio 62
Peak at m/z 32 63
Tuning-Related Symptoms 64
4 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual

Reagent gas ion ratio is difficult to adjust or unstable 64
Cannot complete Autotune 65
The CI ion source is dirty 65
Air leak 65
4 General Maintenance
Before Starting 68
Scheduled maintenance 68
Tools, spare parts, and supplies 69
High voltage precautions 69
Dangerous temperatures 69
Chemical residue 70
Electrostatic discharge 71
To Refill the EI Calibration Vial 73
To Connect the GC Nitrogen Gas Source to the Collision
Cell 75
To Separate the GC from the MS 76
To Position the GC Next to the MS 78
To Move or Store the MS 79
To Access the Left Side Lifting Handle 82
5 CI Maintenance
To Minimize Rotary Vane Foreline Pump Damage from
Ammonia 86
To Replace the Chemical Ionization Gas Purifier 88
To Clean the Reagent Gas Supply Lines 89
To Refill the CI Calibration Vial 90
6 Vacuum System
Overview 94

Maintaining the Vacuum System 95
Periodic maintenance 95
Other procedures 95
More information is available 95
Vacuum System Components 96
Common Vacuum System Problems 97
Foreline Pump 98
To connect the foreline hose to the foreline pump 98
To disconnect the foreline hose from the foreline
pump 99
To check the rotary vane pump oil mist filter 99
To check the rotary vane foreline pump fluid level 100
To add oil to the rotary vane foreline pump 100
To replace the oil in the rotary vane foreline pump 101
The oil pan under the foreline pump can be a fire
hazard 103
To remove the exhaust silencer filter 103
To install the exhaust silencer filter 104
To replace the IDP-15 dry pump tip seal 105
To replace the IDP pump HEPA filter cartridge 107
To change the exhaust silencer filter cartridge 107
To install the IDP pump ballast 108
To remove the IDP pump ballast 109
Side Plate 110
Vacuum Seals 110
EI Calibration Valve 111
CI Calibration Valve 112
7 Replacement Parts
To Order Parts 114

Electronics 115
Vacuum System 118
Analyzer 121
GC/MS Interface 126
Consumables and Maintenance Supplies 128
Additional CI Parts 131

1 Introduction
Abbreviations Used 10
The 7250 Accurate-Mass Quadrupole Time-of-Flight GC/MS System 11
7250 Accurate-Mass Q-TOF GC/MS Description 13
Side Panel AC Power Connectors 14
Back Panel Connectors 15
Interfacing Start Events to External Devices 16
Important Safety Warnings 18
Safety and Regulatory Certifications 21
Intended Use 24
Cleaning/Recycling the Product 24
Moving or Storing the MS 24
This chapter provides general information about the Agilent 7250 Accurate-Mass
Quadrupole Time-of-Flight (Q-TOF) GC/MS System, including a hardware
description and general safety warnings.

1 Introduction
Abbreviations Used
The abbreviations in Table 1 are used in discussing this product. They are
collected here for convenience.
Table 1 Abbreviations
Abbreviation Definition
AC Alternating current
ALS Automatic liquid sampler
CC Collision cell
CI Chemical ionization
DC Direct current
EI Electron impact
EPC Electronic pneumatic control
eV Electron volt
GC Gas chromatograph
GC/MS Gas chromatograph mass spectrometer
id Inside diameter
IDP Isolated dry pump
LAN Local Area Network
LE-EI Low energy EI
m/z Mass-to-charge ratio
MFC Mass flow controller
MS Mass spectrometer
MS1 Quadrupole
OFN Octafluoronaphthalene (sample)
PFTBA Perfluorotributylamine (calibrant)
Q-TOF Quadrupole time-of-flight
Quad Quadrupole mass filter
RF Radio frequency
RFPA Radio frequency power amplifier
TOF Time-of-flight
Torr Unit of pressure, 1 mm Hg
Turbo Turbomolecular vacuum pump

1 Introduction
The 7250 Accurate-Mass Quadrupole

Time-of-Flight GC/MS System
The 7250 Accurate-Mass Quadrupole Time-of-Flight (Q-TOF) GC/MS System is a
standalone capillary GC detector for use with Agilent 8890 and 7890 Series gas
chromatographs. The 7250 Q-TOF features:
• Three turbomolecular vacuum pumps
• Foreline pump
• Rotary vane pump
• Optional isolated dry pump (IDP)
• Independently MS-heated LE-EI ion source
• Independently MS-heated hyperbolic quadrupole mass filter, which can be
heated to high temperatures, minimizing the contamination typical with low
temperature analyses
• Single hexapole collision cell
• Ion-focusing slicer
• Vacuum-insulated flight tube with dual-stage ion mirror
• Fast electronics, allowing fast sampling rates
• Analog-to-digital detector
• Independently GC-heated GC/MS interface
Physical description
The 7250 Q-TOF GC/MS is approximately 53.5 cm high, 69 cm wide, and 92 cm
deep. The flight tube extends 136 cm up over the top of the instrument.
The turbo pump mainframe weighs 159 kg. The weight of the attached foreline
(rotary) pump is 25 kg for the DS202 rotary vane pump model, and 45 kg for the
IDP model.
The basic components of the instrument are the:
• Frame/cover assemblies
• Vacuum system
• GC/MS interface

1 Introduction
• Ion source
• Flight tube electronics
• Collision cell
• Detector
• Analyzer
Vacuum gauge
The 7250 Q-TOF GC/MS is equipped with three ion vacuum gauges:
• Vacuum manifold chamber
• TOF vacuum manifold chamber
• Turbomolecular vacuum pumps exhaust
The MassHunter Workstation can be used to read the pressure (high vacuum) in
the vacuum manifold, at the turbomolecular vacuum pump discharge, and the
flight tube.
Ionization modes
The 7250 Accurate-Mass Q-TOF GC/MS can operate in EI mode using the
standard LE-EI ion source or in CI mode using the optional CI MS system. In
electron impact mode, the Q-TOF can operate in standard or low-energy modes.

1 Introduction
7250 Accurate-Mass Q-TOF GC/MS

Description
Figure 1 is an overview of a typical 7250 Accurate-Mass Q-TOF GC/MS system.
Flight tube
ALS
8890 GC
Q-TOF
MS power Front right Source GC power Oven door Drawer

switch grill window cover switch latch
Figure 1. 7250 Accurate-Mass Q-TOF and 8890 GC/MS System

1 Introduction
Side Panel AC Power Connectors
Figure 2. Side panel power supply
Main power cord receptacle (top)

The AC power cord located on the left side of the MS brings in all electrical power
for the MS. The power cord can be detached from the MS.
Foreline pump power receptacle (bottom)

The foreline pump power cord receptacle located on the left side of the MS
provides AC power for the foreline pump. If the power switch is off, no power is
supplied to the foreline pump.

1 Introduction
Back Panel Connectors
Figure 3. Back panel connections
Remote start connector

The remote start connector is the external connector for the remote start
circuitry on the LAN/MS control card. It receives remote start signals from the
GC.
LAN (I/O) connector

The LAN cable from the data system is a dedicated LAN line that is connected to
the LAN communications connector. It carries all data communication between
the PC and the MS.
Directly connect a single dedicated LAN cable between the PC and the 7250
C AU T I O N Q-TOF. Do not use a LAN switch, router, or other device between the PC and
the Q-TOF.

1 Introduction
Interfacing Start Events to External Devices

Remote control processor
The remote control processor on the LAN/MS control card synchronizes
start-run signals with GCs and other devices. The functions of the remote control
processor are extended to the remote start (Remote) connector on the back
panel of the MS. (See Figure 4.) The remote start cable connects the GC and the
MS. An optional cable can extend these events to another instrument.
Remote start signals

It is often necessary to communicate with external devices (for example, a
purge-and-trap) during a run. Typically, these communications are requests to
send a system-ready signal. They also include:
• Receive a start run signal from an external device
• Program the timing of events during a run
Start Ground
Ready
Figure 4. Remote start connector
System ready
When interfacing to an external device, it is often desirable to send a
system-ready signal to the device. In the case of a multisample Tekmar
purge-and-trap, each sample is purged onto a trap where it waits for a ready
signal. On receipt of the ready signal, the desorption cycle begins. When a
specific temperature is reached, the purge-and-trap closes a contact to indicate
the run has started.

1 Introduction
The ready pin on the remote start connector on the GC is held low at all times
except when the GC, MS, and data system are all ready. On system ready, a logic
high of 5 VDC is present between that pin and any ground. This same high can be
detected between the ready and ground pins on the remote start connector on
the MS.
Start run input

The best way to generate a start run signal is to use the remote start connector
on the GC. Since remote start cables are made for most common devices, this is
often the simplest way. A general-purpose remote start cable that terminates in
spade lugs (Y-Remote Start/Stop, APG p/n G1530-61200), is also available.
Ensure that the system is actually ready before the start run signal is sent.
If necessary, the remote start connector on the back of the MS can be used to
send the start run signal. A contact closure between the start and ground pins
will start the run if the system is ready.

1 Introduction
Important Safety Warnings

There are several important safety notices to always keep in mind when using
the MS.
Many internal parts of the MS carry dangerous

voltages
If the MS is connected to a power source, even if the power switch is off,
potentially dangerous voltages exist on:
• The wiring between the MS power cord and the AC power supply
• The AC power supply itself
• The wiring from the AC power supply to the power switch
With the power switch on, potentially dangerous voltages also exist on:
• All electronics boards in the instrument
• The internal wires and cables connected to these boards
• The wires for any heater (oven, detector, inlet, or valve box)
All these parts are shielded by covers. With the covers in place, it should be
WAR N IN G difficult to accidentally make contact with dangerous voltages. Unless
specifically instructed to, never remove a cover unless the detector, inlet, and
oven are turned off.
If the power cord insulation is frayed or worn, the cord must be replaced.
WAR N IN G Contact your Agilent service representative.
Electrostatic discharge is a threat to MS

electronics
The printed circuit boards in the MS can be damaged by electrostatic discharge.
Do not touch any of the boards unless it is absolutely necessary. If you must
handle them, wear a grounded wrist strap, and take other antistatic precautions.

1 Introduction
Precautions to take to prevent an explosion
The use of hydrogen gas is specifically prohibited with this product.

WAR N IN G
You MUST make sure the top thumbscrew on the analyzer side plate is fastened
WAR N IN G finger-tight. Do not overtighten the thumbscrews; this can cause air leaks.
You MUST leave the collision cell chamber top plate shipping brackets
fastened. Do not remove the shipping brackets from the top plate for normal
operation; they secure the top plate in the event of an explosion.
Failure to secure your MS as described above greatly increases the chance of

WAR N IN G personal injury in the event of an explosion.
Many parts are dangerously hot

Many parts of the GC/MS operate at temperatures high enough to cause serious
burns. These parts include, but are not limited to the:
• Inlet
• Oven and its contents
• Valve box
• Column nuts attaching the column to an inlet, detector, or GC/MS interface
• Foreline pump
• GC/MS interface
• Quadrupole
• Ion source
Always cool these areas of the system to room temperature before working on
them. They will cool faster if you first set the temperature of the heated zone to
room temperature. Turn the zone off after it has reached the setpoint. If you
must perform maintenance on hot parts, use a wrench and wear gloves.
Whenever possible, cool the part of the instrument that you will be maintaining
before you begin working on it.

1 Introduction
Be careful when working behind the instrument. During cool-down cycles, the
WAR N IN G GC emits hot exhaust that can cause burns.
The foreline pump can cause burns if touched when operating.

WAR N IN G
The insulation around the inlets, detectors, valve box, and the insulation cups
WAR N IN G is made of refractory ceramic fibers. To avoid inhaling fiber particles, we
recommend the following safety procedures: ventilate your work area; wear
long sleeves, gloves, safety glasses, and a disposable dust/mist respirator;
dispose of insulation in a sealed plastic bag in accordance with local
regulations; wash your hands with mild soap and cold water after handling the
insulation.
The oil pan under the rotary vane foreline

pump can be a fire hazard
Oily rags, paper towels, and similar absorbents in the oil pan could ignite and
damage the pump and other parts of the MS.
Combustible materials (or flammable/nonflammable wicking material) placed

WAR N IN G under, over, or around the foreline (roughing) pump constitutes a fire hazard.
Keep the pan clean, but do not leave absorbent material such as paper towels
in it.

1 Introduction
Safety and Regulatory Certifications

The 7250 Q-TOF GC/MS conforms to the following safety standards:
• Canadian Standards Association (CSA): CAN/CSA-C22.2 No. 61010-1-04
• CSA/Nationally Recognized Test Laboratory (NRTL): UL 61010–1
• International Electrotechnical Commission (IEC): 61010–1
• EuroNorm (EN): 61010–1
The 7250 Q-TOF GC/MS conforms to the following regulations on
Electromagnetic Compatibility (EMC) and Radio Frequency Interference (RFI):
• CISPR 11/EN 55011: Group 1, Class A
• IEC/EN 61326-1
• AUS/NZ
This ISM device complies with Canadian ICES-001. Cet appareil ISM est
conforme a la norme NMB—001 du Canada.
The 7250 Q-TOF GC/MS is designed and manufactured under a quality system
registered to ISO 9001.
The 7250 A-TOF GC/MS is RoHS compliant.
South Korean Class A EMC Declaration

A 급 기기 ( 업무용 방송통신기자재 )
This equipment is Class A suitable for professional use and is for use in
electromagnetic environments outside of the home.
이 기기는 업무용 (A 급 ) 전자파적합기기로서 판 매자 또는 사용자는 이 점을 주 의하
시기 바라 며 , 가정외의 지역에서 사용하는 것을 목적으 로 합니다 .
Information
The Agilent Technologies 7250 Accurate-Mass Q-TOF GC/MS meets the
following International Electrotechnical Commission (IEC) classifications:
Equipment Class I, Laboratory Equipment, Installation Category II, and Pollution
Degree 2.

1 Introduction
This unit has been designed and tested in accordance with recognized safety
standards, and is designed for use indoors. If the instrument is used in a manner
not specified by the manufacturer, the protection provided by the instrument
may be impaired. Whenever the safety protection of the MS has been
compromised, disconnect the unit from all power sources, and secure the unit
against unintended operation.
Refer servicing to qualified service personnel. Substituting parts or performing
any unauthorized modification to the instrument may result in a safety hazard.
Symbols
Warnings in the manual or on the instrument must be observed during all phases
of operation, service, and repair of this instrument. Failure to comply with these
precautions violates safety standards of design and the intended use of the
instrument. Agilent Technologies assumes no liability for the customer’s failure
to comply with these requirements.
See accompanying instructions for more information.
Indicates a hot surface.
Indicates hazardous voltages.
Indicates earth (ground) terminal.
Indicates potential explosion hazard. or
Indicates radioactivity hazard.
Indicates electrostatic discharge hazard.
Indicates that you must not discard this

electrical/electronic product in domestic household waste.

1 Introduction
Electromagnetic compatibility
This device complies with the requirements of CISPR 11. Operation is subject to
the following two conditions:
• This device may not cause harmful interference.
• This device must accept any interference received, including interference
that may cause undesired operation.
If this equipment does cause harmful interference to radio or television
reception, which can be determined by turning the equipment off and on, the user
is encouraged to try one or more of the following measures:
• Relocate the radio or antenna.
• Move the device away from the radio or television.
• Plug the device into a different electrical outlet, so that the device and the
radio or television are on separate electrical circuits.
• Ensure that all peripheral devices are also certified.
• Ensure that appropriate cables are used to connect the device to peripheral
equipment.
• Consult your equipment dealer, Agilent Technologies, or an experienced
technician for assistance.
Changes or modifications not expressly approved by Agilent Technologies could
void the user’s authority to operate the equipment.
Sound emission declaration

Sound pressure
Sound pressure Lp < 70 dB according to EN 27779:1991 and EN ISO 3744:1995.
Schalldruckpegel
Schalldruckpegel LP < 70 dB nach EN 27779:1991 und EN ISO 3744:1995.

1 Introduction
Intended Use
Agilent products must only be used in the manner described in the Agilent
product user guides. Any other use may result in damage to the product or
personal injury. Agilent is not responsible for any damages caused, in whole or in
part, by improper use of the products, unauthorized alterations, adjustments or
modifications to the products, failure to comply with procedures in Agilent
product user guides, or use of the products in violation of applicable laws, rules
or regulations.
Cleaning/Recycling the Product

To clean the unit, disconnect the power and wipe down with a damp, lint-free
cloth. For recycling, contact your local Agilent sales office.
Accidental Liquid Spillage

Do not spill liquids on the MS. If liquid is accidentally spilled on the MS, first, cut
the power. Once the MS is disconnected from all power sources, dry all affected
parts. If the liquid spillage affects the electronics, wait at least 24 hours,
depending upon the ambient humidity. While waiting for the parts to dry, please
call your local Agilent service representative.
Moving or Storing the MS

The best way to keep your MS functioning properly is to keep it pumped down
and hot, with carrier gas flow. If you plan to move or store your MS, a few
additional precautions are required. The MS must remain upright at all times; this
requires special caution when moving. The MS should not be left vented to
atmosphere for long periods. For more information, see “To Move or Store the
MS” on page 79.

2 General Troubleshooting
General Symptoms 27
Chromatographic Symptoms 29
Mass Spectra General Symptoms 34
Pressure Symptoms 36
Temperature Symptoms 38
Error Messages 40
Air Leaks 45
Contamination 46
This is a quick reference to symptoms and possible causes of the most common
problems experienced by users. For each symptom, one or more possible
causes are listed. In general, the causes listed first are the most likely causes or
the easiest to check and correct.
Help with problems specific to operating in chemical ionization (CI) mode are
covered in Chapter 3, “CI Troubleshooting,” starting on page 49.
This chapter does not include corrective actions for the possible causes listed.
Some of the corrective actions required may be dangerous if performed
incorrectly. Do not attempt any corrective actions unless you are sure you know
the correct procedure and the dangers involved. See the other chapters in this
manual for more information.
If the material in this chapter and in the online help proves insufficient to help you
diagnose a problem, contact your Agilent Technologies service representative.

2 General Troubleshooting
Troubleshooting Tips and Tricks

Rule 1: “Look for what has been changed.”
Many problems are introduced accidentally by human actions. Every time any
system is disturbed, there is a chance of introducing a new problem.
• If the MS was just pumped down after maintenance, suspect air leaks or
incorrect assembly.
• If carrier gas or helium gas purifier was just changed, suspect leaks or
contaminated or incorrect gas.
• If the GC column was just replaced, suspect air leaks or a contaminated or
bleeding column.
Rule 2: “If complex isn’t working, go back to

simple.”
A complex task is not only more difficult to perform, but also more difficult to
troubleshoot. If you’re having trouble detecting your sample, verify that autotune
is successful.
Rule 3: “Divide and conquer.”

This technique is known as “half-split” troubleshooting. If you can isolate the
problem to only part of the system, it is much easier to locate.
To determine whether an air leak is in the GC or the MS, vent the MS, remove the
column, and install the blank interface ferrule. If the leak goes away, it was in the
GC.

General Symptoms
This section describes symptoms you might observe when first turning on the
GC/MS system. All of these symptoms would prevent operation of the system.
GC does not turn on

Nothing happens when the GC is switched on. The GC fans do not turn on and
the control display does not light.
• Disconnected GC power cord
• No voltage or incorrect voltage at the electrical outlet
• Failed fuse in the GC
• GC power supply is not working correctly
MS does not turn on

Nothing happens when the MS is switched on. The foreline pump does not start.
The cooling fan for the high-vacuum pump does not turn on.
• Disconnected MS power cord
• No voltage or incorrect voltage at the electrical outlet
• Failed primary fuses - Not user replaceable
• MS electronics are not working correctly
Foreline pump is not operating

The MS is receiving power (the fan is operating) but the foreline pump is not
operating.
• A large air leak (usually the analyzer door open) has caused pumpdown
failure. You must power cycle the MS to recover from this state.
• Disconnected foreline pump power cord
• Malfunctioning foreline pump
• Check power switch on foreline pump

MS turns on but then the foreline pump shuts

off
The MS will shut down both the foreline pump and the turbo pumps if the system
fails to pump down correctly. This is usually because of a large air leak or the
side plate has not sealed correctly. This feature helps prevent the foreline pump
from sucking air through the system, which can damage the analyzer and the
turbo pumps.
You must power cycle the MS to recover from this state.

Chromatographic Symptoms
These are symptoms you may observe in the chromatograms generated by data
acquisition. In general, these symptoms do not prevent you from operating your
GC/MS system. They indicate, however, that the data you are acquiring may not
be the best data obtainable. These symptoms can be caused by instrument
malfunctions, but are more likely caused by incorrect chromatographic
technique.
Two of the symptoms also apply to mass spectral data. (See “Poor
sensitivity” on page 32 and “Poor repeatability” on page 33.)
No peaks
If an analysis shows no chromatographic peaks, only a flat baseline or minor
noise, run the automated tune program. If the MS passes tune, the problem is
most likely related to the GC. If the MS does not pass tune, the problem is most
likely in the MS.
Passes tune
• Incorrect sample concentration
• No analytes present
• Syringe missing from the ALS or not installed correctly
• Injection accidentally made in split mode instead of splitless mode
• Empty or almost empty sample vial
• Dirty GC inlet
• Leaking GC inlet*
• Loose column nut at the GC inlet*
* This could cause a fault condition in the GC that would prevent the GC
from operating.
Does not pass tune

• Calibration vial is empty
• Excessive foreline or analyzer chamber pressure
• Very dirty ion source
• Calibration valve is not working correctly

• Bad signal cable connection

• Filament has failed or is not connected correctly
• Bad ion source wiring connection
• Bad detector wiring connection
• Failed MS detector
Peaks are tailing

• Active sites in the sample path
• Injection is too large
• Incorrect GC inlet temperature
• Insufficient column flow
• GC/MS interface temperature is too low
• Ion source temperature is too low
Peaks are fronting

• Column film thickness mismatched with analyte concentration (column
overload)
• Initial oven temperature is too low
• GC inlet pressure too high
• Insufficient column flow
Peaks have flat tops

• Insufficient solvent delay
• Incorrect scale on the display

Peaks have split tops

• Bad injection technique
Baseline is rising
• Column bleed
• Other contamination
Baseline is high
• Column bleed
• Other contamination
Baseline is falling
A falling baseline indicates contamination is being swept away. Wait until the
baseline reaches an acceptable level. Common causes include:
• Residual air and water from a recent venting
• Column bleed
• Septum bleed
• Splitless injection time too long (inlet is not properly swept, resulting in
excess solvent on the column and slow solvent decay)

Baseline wanders
• Insufficient carrier gas supply pressure*
• Malfunctioning flow or pressure regulator*
• Intermittent leak in the GC inlet*
from operating.
Retention times for all peaks drift – shorter

• Column has been shortened
• Initial oven temperature was increased
• Column is getting old
Retention times for all peaks drift – longer

• Column flow has been reduced
• Initial oven temperature was decreased
• Leaks in the GC inlet*
from operating.
Poor sensitivity
• Incorrect tuning, or tune file that does not match the type of analysis
• Repeller voltage is too low
• Incorrect temperatures (oven, GC/MS interface, ion source, or mass filter)
• Incorrect sample concentration
• Dirty GC inlet
• Incorrect split ratio
• Purge-off time in splitless mode is too short

• Excessive pressure in the analyzer chamber

• Dirty ion source
• Air leaks between chambers
• Poor filament operation
• Detector is not working correctly
• Incorrect mass filter polarity
• Collision cell voltage
from operating.
Poor repeatability
• Dirty syringe needle
• Dirty GC inlet
• Loose column connections
• Variations in pressure, column flow, and temperature
• Loose connections in the analyzer
• Ground loops
from operating.

Mass Spectra General Symptoms

This section describes symptoms you might observe in mass spectra. Some of
these symptoms will appear in the mass spectra of samples. Others you will
observe only in a tune report. Some of these symptoms have causes that can be
corrected by the operator. Others, however, require service by an Agilent
Technologies service representative.
Two of the chromatographic symptoms, also apply to mass spectral. (See “Poor
sensitivity” on page 32 and “Poor repeatability” on page 33.)
No peaks
• Ion source cables not connected
• Bad connections to or from the detector
• Detector power supply output cable has failed
• Collision cell voltages
• Collision cell gas flow
• Other electronics failure
• Incorrect tune file (inappropriate parameters)
Isotopes are missing or isotope ratios are

incorrect
• Wrong precursor or wrong product ion was selected
• MCP or PMT voltage is too low
• Repeller voltage is too high
• Wrong ions are chosen
• High background
• Collision cell voltage

High background
• TOF vacuum or Quad vacuum
• Air leak
• Contamination

Pressure Symptoms
This section describes unusual pressure readings and their possible causes. At
typical column flow rates (0.5 to 2.0 mL/minute), the foreline pressure will be
approximately 16 to 18 mTorr. The Quad pressure with collision cell gas on or off
will be approximately 1 × 10-4 to 2 × 10-4 Torr. These pressures can vary widely
from instrument to instrument so it is very important that you are familiar with
the pressures that are typical for your instrument at given carrier and collision
gas flows.
Table 2 Influence of carrier and collision cell gas flows on vacuum
CC Gas On  
N2 = 1 mL/min 
He = 4 mL/min CC Gas Off
Column flow Rough Vac Quad Vac TOF Vac Rough Vac Quad Vac TOF Vac
(mL/min) (mTorr) (Torr) (Torr) (mTorr) (Torr) (Torr)
0.7 1.25 E+02 3.50 E-05 2.61 E-07 2.70 E+01 5.78 E-07 1.58 E-07
1 1.30 E+02 3.49 E-05 2.61 E-07 3.61 E+01 6.21 E-07 1.58 E-07
1.2 1.34 E+02 3.49 E-05 2.61 E-07 4.13 E+01 6.55 E-07 1.58 E-07
2 1.48 E+02 3.51 E-05 2.61 E-07 6.18 E+01 8.09 E-07 1.59 E-07
3 1.63 E+02 3.52 E-05 2.61 E-07 8.45 E+01 9.99 E-07 1.60 E-07
Foreline pressure is too high

If the pressure you observe for a given column flow has increased over time,
check the following:
• Column (carrier gas) flow is too high
• Collision cell gas flow is too high
• Air leak (usually the side plate is not pushed in or vent valve is open)
• Rotary foreline pump oil level is low or oil is contaminated
• IDP foreline pump tip seal is worn down and needs replacing
• Foreline hose is constricted
• Foreline pump is not working correctly

Foreline pressure is too low

If the foreline pressures you observe are below 20 mTorr, check for the following:
• Column (carrier gas) flow is too low
• Column plugged or crushed by an overtightened nut
• Collision gas flows are too low
• Empty or insufficient carrier gas supply*
• Bent or pinched carrier gas tubing*
• Foreline gauge is not working correctly
* This could create a fault condition in the GC that would prevent the GC
from operating.
Quad pressure is too low

If the quad pressure you observe is below 1 × 10-6 Torr with the collision cell gas
on or off, check for the following:
• Column (carrier gas) flow is too low
• Collision gas flows are too low
• Column plugged or crushed by overtightened nut
• Empty or insufficient carrier gas supply*
• Bent or pinched carrier gas tubing*
* This could create a fault condition in the GC that would prevent the GC
from operating.
High vacuum pressure is too high

If the high vacuum pressure you observe is above 2 × 10-6 Torr, check for the
following:
• Turbos are not up to speed
• Too much water is in the system
• Did not wait long enough for system to pump down
• Poor carrier gas quality
• System is not leak tight, check fittings

Temperature Symptoms
The MS has three heated zones:
• Ion source
• Mass filter
• GC/MS interface
Each heated zone has a heater and temperature sensor. The ion source and
mass filter are powered and controlled by the MS. The GC/MS interface is
powered and controlled by the GC.
Ion source will not heat up

• High-vacuum pump is off or has not reached normal operating conditions*
• Incorrect temperature setpoint
• Ion source has not had enough time to reach temperature setpoint
• Ion source heater cartridge is not connected*
• Ion source temperature sensor is not connected*
• Ion source heater failed (burned out or shorted to ground)*
• Ion source temperature sensor failed*
• Source power cable is not connected to the quadrupole board*
* This will cause an error message.
Mass filter (quad) heater will not heat up

• High-vacuum pump is off or has not reached normal operating conditions*
• Incorrect temperature setpoint
• Mass filter has not had enough time to reach temperature setpoint
• Mass filter heater cartridge is not connected*
• Mass filter temperature sensor is not connected*
• Mass filter heater failed (burned out or shorted to ground)*
• Mass filter temperature sensor failed*

• Cable is not connected to the quadrupole board*

* This will cause an error message.
GC/MS interface will not heat up

• Incorrect setpoint(s)
• Setpoint entered in wrong heated zone
• GC/MS interface has not had enough time to reach temperature setpoint
• GC is off
• GC experienced a fault and needs to be reset*
• GC/MS interface heater/sensor cable is not connected*
• GC/MS interface heater failed (burned out)*
• GC/MS interface sensor failed*
• GC electronics are not working correctly*
* This will cause a GC error message. GC error messages are described in
the documentation supplied with your GC.

Error Messages
Sometimes a problem in your MS will cause an error message to appear in the
MassHunter Workstation software. Some error messages appear only during
tuning. Other messages may appear during tuning or data acquisition.
Some error messages are “latched.” These messages remain active in your data
system even if the condition that caused the message has corrected itself. If the
cause is removed, these messages can be removed by checking instrument
status through the data system.
Difficulty in mass filter electronics

• Pressure in the analyzer chamber is too high
• RFPA is not adjusted correctly
• Mass filter (quad) contacts are shorted or otherwise not working correctly
• Mass filter is not working correctly
Difficulty with the photo multiplier or

microchannel device
• Broad peaks, such as the solvent peak, eluted while the analyzer was on
Difficulty with the fan

If a cooling fan fault occurs, the vacuum control electronics automatically shut
off the high-vacuum pump, the ion source, and mass filter heaters. Therefore, the
message: “The system is in vent state” may also appear. It is important to note
that even though the high-vacuum pump is off, the analyzer chamber may not
actually be vented. See “The system is in vent state” on page 43 in this section
for precautions to take.
• The fan is disconnected
• The fan has failed

Difficulty with the high vacuum pump(s)

If the pump failed to reach 50% of full speed within 10 minutes, or experienced a
fault.
You must switch the MS off and back on to remove this error message. Ensure
the turbo pump has slowed down before switching off the MS. The message will
reappear if the underlying problem has not been corrected.
• Large vacuum leak is preventing the turbo pump from reaching 50% of full
speed
• Turbo pump(s) is not working correctly
High foreline pressure

• Excessive carrier gas flow (typically > 5 mL/min)
• Excessive solvent volume injected
• Large vacuum leak
• Severely degraded foreline pump oil
• Collapsed or kinked foreline hose
Internal MS communication fault

Lens supply fault

• Electrical short in the analyzer
• MS cannot maintain the voltage setpoint

No peaks found
• Emission current was set to 0
• PMT or MCP voltage is too low
• Calibration vial(s) empty or almost empty
• Air leak
• Signal cable is not connected
• Electrical leads to the MCP are not connected correctly
• Electrical leads to the ion source are not connected correctly
• Filament to the source body is shorted
Temperature control disabled

• One of the heater fuses has failed
Temperature control fault

This indicates that something has gone wrong with the temperature control of
either the ion source or the mass filter (quad) heater:
• Source temperature sensor is open
• Source temperature sensor is shorted
• Mass filter (quad) temperature sensor is open
• Mass filter (quad) temperature sensor is shorted
• No heater voltage (heater fuse has probably failed)
• Heater voltage is too low
• Temperature zone has timed out (heater failed, bad heater wiring, or loose
temperature sensor)
• Problem with the temperature control electronics
• Source heater is open
• Source heater is shorted
• Mass filter heater is open
• Mass filter heater is shorted

The high-vacuum pump is not ready

• One of the three Turbo pumps could have failed
• Turbo pump is on but has not had enough time (10 minutes) to reach 80% of
its normal operating speed
• Turbo pump is not working correctly
• Foreline pump has not reached its target of 10 Torr after 10 minutes
The system is in vent state

The message says the system is vented, but if the fault has just occurred it may
still be under vacuum and the turbo pump may still be at high speed. Wait at least
30 minutes after seeing this message before you actually vent the MS.
Venting the MS too soon after this message appears can damage a turbo
C AU T I O N pump.
• System was vented purposely (no problem)

• Fan fault has turned off the high-vacuum pump (power cycle the MS to clear
the fault)
• Fuse for the high-vacuum pump has failed
There is no emission current

• Check tune file to be certain that emission current is not = 0
• Filament is not connected properly; try the other filament
• Filament has failed; try the other filament
There is not enough signal to begin tune

• Corrupted tune file
• Poor mass axis calibration
• Width gain or offset is too high

• Calibration vial empty or almost empty

• Air leak
• MCP or PMT voltage is too low
• Signal cable is not connected
• Electrical leads to the detector are not connected correctly
• Electrical leads to the ion source are not connected correctly
• Filament shorted to the source body
• Collision cell voltages

Air Leaks
Air leaks are a problem for any instrument that requires a vacuum to operate.
Leaks are generally caused by vacuum seals that are damaged or not fastened
correctly. Symptoms of leaks include:
• Higher than normal analyzer chamber pressure or foreline pressure
• Higher than normal background
• Peaks characteristic of air (m/z 18, 28, 32, and 44 or m/z 14 and 16)
• Poor sensitivity
• Low relative abundance of m/z 502 (this varies with the tune program used)
Leaks can occur in either the GC or the MS. The most likely point for an air leak is
a seal you recently opened.
In the GC, most leaks occur in:
• GC inlet septum
• GC inlet column nut
• Broken or cracked capillary column
Leaks can occur in many more places in the MS:
• GC/MS interface column nut
• Side plate O-rings (all the way around)
• Calibration valve
• GC/MS interface O-ring (where the interface attaches to the analyzer
chamber)
• End plate O-ring
• Turbo pump O-rings
• Collision cell cover O-ring

Contamination
Contamination is usually identified by excessive background in the mass
spectra. It can come from the GC or from the MS. The source of the
contamination can sometimes be determined by identifying the contaminants.
Some contaminants are much more likely to originate in the GC. Others are more
likely to originate in the MS.
Contamination originating in the GC typically comes from one of these sources:
• Column or septum bleed
• Dirty GC inlet
• GC inlet liner
• Contaminated syringe
• Poor quality carrier gas
• Dirty carrier gas tubing
• Fingerprints (improper handling of clean parts)
Contamination originating in the MS typically comes from one of the following
sources:
• Air leak
• Cleaning solvents and materials
• Rotary foreline pump oil
• IDP foreline pump tip seal
• Fingerprints (improper handling of clean parts)
Table 3, “Common contaminants,” on page 47 lists some of the more common
contaminants, the ions characteristic of those contaminants, and the likely
sources of those contaminants.

Table 3 Common contaminants
Ions (m/z) Compound Possible source
18, 28, 32, 44 or 14, 16 H2O, N2, O2, CO2 or N, O Residual air and water, air leaks,
outgassing from Vespel ferrules
31, 51, 69, 100, 119, 131, PFTBA and related ions PFTBA (tuning compound)
169, 181, 214, 219, 264, 376, 414,
426, 464, 502, 576, 614
31 Methanol Cleaning solvent
43, 58 Acetone Cleaning solvent
78 Benzene Cleaning solvent
91, 92 Toluene or xylene Cleaning solvent
105, 106 Xylene Cleaning solvent
151, 153 Trichloroethane Cleaning solvent
69 Foreline pump oil or PFTBA Foreline pump oil vapor or

calibration valve leak
73, 147, 207, 221, 281, 295, 355, Dimethylpolysiloxane Septum bleed or methyl silicone
429 column bleed
149 Plasticizer (phthalates) Vacuum seals (O-rings)

damaged by high temperatures,
vinyl gloves
Peaks spaced 14 m/z apart Hydrocarbons Fingerprints, foreline pump oil


3 CI Troubleshooting
Common CI-Specific Problems 50
Air Leaks 52
Pressure-Related Symptoms 55
Signal-Related Symptoms 58
Tuning-Related Symptoms 64
This chapter outlines the troubleshooting of the Agilent 7250 Accurate-Mass

Q-TOF GC/MS System equipped with the chemical ionization (CI) source. Most
of the troubleshooting information in the previous chapter also applies to CI
Q-TOFs.

3 CI Troubleshooting
Common CI-Specific Problems

Because of the added complexity of the parts required for CI, there are many
potential problems added. By far the greatest number and most serious
problems with CI are associated with leaks or contamination in the reagent gas
introduction system. NCI is especially sensitive to the presence of air; leaks small
enough to cause no problems in PCI can destroy NCI sensitivity.
As with EI, if the MS tunes well and no air leak is present, sample sensitivity
problems should be addressed by GC inlet maintenance first.
• Wrong reagent gas
• Reagent gas not hooked up or hooked up to wrong reagent gas inlet port
• Wrong ions entered in tune file
• Wrong tune file selected
• Not enough bakeout time has elapsed since vent (background is too high)
• Wrong column positioning (extending > 4-5 mm past tip of interface)
• Interface tip seal not installed
• EI source installed in CI mode
• EI filament or other EI source parts in CI ion source
• Air leaks in reagent gas flow path
• CI filament has stretched and sagged:
• High emission current
• High temperature
• Filament was defective
• Linear (no inflection point) electron energy (EIEnrgy) ramp

Troubleshooting Tips and Tricks

Rule 1: “Look for what has been changed.”
Many problems are introduced accidentally by human actions. Every time any
system is disturbed, there is a chance of introducing a new problem.
• If the MS was just pumped down after maintenance, suspect air leaks or
incorrect assembly.
• If the reagent gas bottle or gas purifier were just changed, suspect leaks or
contaminated or incorrect gas.
• If the GC column was just replaced, suspect air leaks or contaminated or
bleeding column.
• If you have just switched ion polarity or reagent gas, suspect the tune file you
have loaded in memory. Is it the appropriate file for your mode of operation?
Rule 2: “If complex isn't working, go back to

simple.”
A complex task is not only more difficult to perform, but also more difficult to
troubleshoot as well. For example, CI requires more parts to work correctly than
EI does.
• If you are having trouble with NCI, verify that PCI still works.
• If you are having trouble with other reagent gases, verify that methane still
works.
• If you are having trouble with CI, verify that EI still works.
Rule 3: “Divide and conquer.”

This technique is known as “half-split” troubleshooting. If you can isolate the
problem to only part of the system, it is much easier to locate.
• To isolate an air leak, select Shutoff valve. If abundance of m/z 32 decreases,
the problem is not in the flow module.

Air Leaks
How do I know if I have an air leak?
Run an air and water check. See the software online help for additional
information.
Large air leaks can be detected by vacuum symptoms: loud gurgling noise from
the foreline pump, inability of the turbo pumps to reach 95% speed, or, in the case
of smaller leaks, high pressure readings on the high vacuum gauge controller.
The mass flow controller is calibrated for methane and the high vacuum gauge
controller is calibrated for nitrogen, so measurements are not accurate in
absolute terms:
Familiarize yourself with the measurements on your system under operating
conditions. Watch for changes that may indicate a vacuum or gas flow problem.
There should not be any peak visible at m/z 32 (O2). This almost always indicates
an air leak.
Figure 5. Looking for air leaks

Special NCI notes

Since NCI is so extremely sensitive, air leaks that are not detectable in EI or PCI
can cause sensitivity problems in NCI. To check for this kind of air leak in NCI,
inject OFN. The base peak should be at m/z 272. If the abundance of m/z 238 is
much greater than that of m/z 272, you have an air leak.
How do I find the air leak?

1 See Figure 6, “Schematic of CI flow control,” on page 54 and Table 4, “Flow
module valve state diagram,” on page 54.
2 Look for the last seal that was disturbed.
• If you just pumped down the MS, press on the side plate to check for
proper seal. Poor alignment between the front analyzer and the GC/MS
interface seal can prevent the side plate from sealing.
• If you just replaced the reagent gas bottle or gas purifier, check the fittings
you just opened and refastened.
3 Check for tightness of seals at GC inlet and GC/MS interface column nuts.
Ferrules for capillary columns often loosen after several heat cycles. Do not
overtighten the interface nut.
4 If any of the fittings inside the flow module (VCR fittings) were loosened and
then retightened, the gasket must be replaced. These gaskets are good for
one use only.
Do not loosen the nuts on any VCR fittings unless you intend to replace the
C AU T I O N gaskets. Otherwise, you will create an air leak.
5 Remember that most small air leaks visible in CI mode are located in either
the carrier gas or reagent gas flow paths. Leaks into the analyzer chamber
are not likely to be seen in CI because of the higher pressure inside the
ionization chamber.
6 Half-split the system.
• Close valves starting at the gas select valves (Reagent gas and Carrier gas
purge), then close the shutoff valve. See Figure 6, “Schematic of CI flow
control,” on page 54 and Table 4, “Flow module valve state diagram,” on
page 54.
• Cool and vent the MS, remove the GC column, and cap off the interface.

If you use argon or other introduced gas to find air leaks, this does not work well
for the reagent gas flow system. It takes as long as 15 minutes for the peak to
reach the ion source if the leak is at the inlet to the flow module.
Flow control module

Gas A
FC
CI cal
valve
FT
Shutoff
valve MFCV
NC
Gas B
To ion source PFDTD
Figure 6. Schematic of CI flow control
Table 4 Flow module valve state diagram
      Standby,
   Purge with Purge with Pump out  vented, or
Result Gas A flow Gas B flow Gas A Gas B flow module EI mode
Gas A Open Closed Open Closed Closed Closed
Gas B Closed Open Closed Open Closed Closed
MFCV On (at setpoint) On (at setpoint) On (at 100%) On (at 100%) On (at 100%) Off (at 0%)
Shutoff valve Open Open Open Open Open Closed

Pressure-Related Symptoms
The following symptoms are all related to high vacuum pressure. Each symptom
is discussed in more detail in the following pages.
The mass flow controller is calibrated for methane and the high vacuum gauge
controller is calibrated for nitrogen, so these measurements are not accurate in
absolute terms (Table 5). They are intended as a guide to typical observed
readings. They were taken with the following set of conditions:
Source temperature 300 °C

Quad temperature 150 °C
Interface temperature 280 °C to 320 °C
Helium carrier gas flow 1 mL/min
Table 5 Typical analyzer vacuum with reagent gas flow
Collision cell gas flow on Collision cell gas flow off

N2 = 1.5 mL/min N2 = 0 mL/min
  Quadrupole Flight tube Rough pump Quadrupole Flight tube

MFC (%) Rough pump (Torr) (mTorr) (mTorr) (Torr) (Torr)
0 1.36e+02 3.62e-05 3.35e-07 9.13e+01 5.98e-07 1.64e-07
10 1.36+02 3.62e-05 3.37e-07 1.14e+01 1.27e-06 1.65e-07
15 1.43+02 3.66e-05 3.37e-07 1.23e+01 1.62e-06 1.67e-07
20 1.5+02 3.71e-05 3.39e-07 1.31e+01 1.96e-06 1.67e-07
25 1.57+02 3.73e-05 3.41e-07 1.39e+01 2.32e-06 1.70e-07
30 1.63+02 3.77e-05 3.41e-07 1.46e+01 2.64e-06 1.71e-07
35 1.69+02 3.81e-05 3.41e-07 1.52e+01 3.00e-06 1.71e-07
40 1.74+02 3.83e-05 3.43e-07 1.58e+01 3.34e-06 1.72e-07

Poor vacuum without reagent gas flow

Excess water
Allow the instrument to bake out more and flow reagent gas through the lines to
purge any accumulated water.
Air leak
information.
The foreline pump is not working properly

For the standard foreline pump, replace the pump oil. If that does not help,
contact your local Agilent Technologies service representative.
The turbo pumps are not working properly

Check the pump speed. It should be at least 95%. Contact your local Agilent
Technologies service representative.
Use of ammonia as reagent gas can shorten the life of the foreline pump oil
C AU T I O N (with standard pump) and possibly of the foreline pump itself. See “To
Minimize Rotary Vane Foreline Pump Damage from Ammonia” on page 86.
High pressure with reagent gas flow

The reagent gas flow rate is too high
On the flow controller, turn down reagent gas flow as appropriate. Verify that
reagent ion ratios are correct.
Air leak
information.
Interface tip seal is not installed

Check the source storage box. If the seal is not in the box, vent the MS and verify
that the seal is correctly installed.

Pressure does not change when reagent flow

is changed
The reagent gas regulator is closed
Check and, if necessary, open the reagent gas regulator.
The reagent gas regulator is set to the wrong pressure

Set the reagent gas regulator to 20 to 25 psi (138 to 172 kPa) for methane or to
3 to 10 psi (21 to 69 kPa) for isobutane or ammonia.
The valve on the reagent gas bottle is closed

Check and, if necessary, open the valve on the reagent gas bottle.
The reagent gas supply is empty

Check and, if necessary, replace the reagent gas supply.
Reagent lines kinked, bent, pinched, or disconnected

Inspect the reagent lines and repair any defects. Ensure the reagent line is
connected to the rear of the flow module. Ensure the methane line is connected
to the Gas A inlet.
GC/MS interface clogged or damaged

Check for flow and repair or replace components as indicated.

Signal-Related Symptoms
This section describes symptoms related to the signal. The symptom may be
too much signal, too little signal, a noisy signal, or an incorrect signal.
Signal-related symptoms are generally observed during tuning but may also be
observed during data acquisition.
Error messages in autotune due to insufficient signal may vary. The following
symptoms are covered in more detail in this section:
• No peaks. See page 58.
• No or low reagent gas signal. See page 60.
• No or low PFDTD signal. See page 61.
• Excessive noise. See page 62.
• Low signal-to-noise ratio. See page 62.
• Peak at m/z 32. See page 63.
No peaks
When troubleshooting “no peaks”, it is important to specify what mode of
operation is being used and what expected peaks are not being seen. Always
start with methane PCI and verify presence of reagent ions.
No reagent gas peaks in PCI

If MS has been working well and nothing seems to have been changed
• Wrong tune file loaded, or tune file corrupted
• Wrong ion polarity (there are no reagent ions visible in NCI)
• No reagent gas flow; look for background ions and check pressure
• Wrong reagent gas selected for the tune file (looking for wrong ions)
• Large air leak
• Poor vacuum (pump problem). See page 56.

If MS was recently switched from EI to CI

• No reagent gas flow
• Analyzer not sealed (big air leak)
• Wrong tune file loaded or tune file corrupted
• Ion source not assembled or connected correctly
• Wrong reagent gas selected for the tune file (looking for wrong ions)
No PFDTD peaks in PCI

• Incorrect reagent gas. There are no PCI PFDTD peaks created with isobutane
or ammonia. Switch to methane.
• Analyzer not sealed (big air leak)
• No calibrant in vial
• Defective calibration valve(s)
• Air leak in carrier or reagent gas path
No reagent gas peaks in NCI

• Reagent gases do not ionize in NCI; look for background ions instead
• Verify tune parameters
• If no background ions are visible, go back to methane PCI
No PFDTD calibrant peaks in NCI

• Look for background ions: 35 (Cl-), and 235 (ReO3-)
• Verify tune parameters
• Go back to methane PCI
No sample peaks in NCI

• Go back to methane PCI
• Poor quality reagent gas (purity less than 99.99%)

Large peak at m/z 238 in NCI OFN spectrum

• Find and fix your small air leak
No or low reagent gas signal

If you have just installed the CI ion source and have an air leak or large amounts
of water in the system and have run one or more autotunes, the ion source is
probably dirty now.
Fix the air leak. Clean the ion source. Then bake out for two hours before tuning.
See the Agilent 7250 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operating Manual.
The wrong reagent gas is flowing.

Turn on the correct reagent gas for your tune file.
Ion polarity is set to Negative. No reagent gas ions are formed in NCI.
Switch to Positive ionization mode.
The reagent gas flow is set too low.

Increase the reagent gas flow.
Reagent gas supply tubing is blocked, kinked, pinched, or disconnected.

Inspect and, if necessary, repair or replace the reagent gas supply tubing.
Carbon has built up on the filament or filament has sagged out of

alignment.
Inspect the filament. If necessary, replace the filament.
Too much air or water in the system.

information.
The signal cable is not connected.

Check and, if necessary, reconnect the signal cable.

The filament or filament support is shorted to the ion source body or

repeller.
Inspect the filament. If necessary, realign the filament support arms.
The electron inlet hole is blocked.

Inspect the electron inlet hole. If necessary, clean the hole with a clean toothpick
and a slurry of aluminum oxide powder and methanol. If the electron inlet hole is
that dirty, the entire ion source probably needs to be cleaned.
Saturated methane/isobutane gas purifier

Replace the gas purifier.
Poor quality methane (purity below 99.99%)

Replace the methane with high-purity methane. If necessary, clean and purge the
reagent gas lines and clean the ion source.
No or low PFDTD signal, but reagent ions are

normal
You are using any reagent gas but methane in PCI.
Switch to methane.
Wrong or corrupted tune file loaded

Check your tune file.
No PFDTD in the calibrant vial

Inspect the calibration vial on the GC side of the MS. If necessary, fill the vial with
PFDTD. Do not fill the vial completely; keep the level at least 0.5 cm from the top
of the vial.
The pressure of the methane entering the flow controller is too high.
Make sure the regulator on the methane supply is set to 20 to 25 psi (138 to
172 kPa).

The CI ion source is dirty.

Clean the ion source. See the Agilent 7250 Accurate-Mass Quadrupole
Time-of-Flight GC/MS System Operating Manual.
The calibration valve was not purged after the vial was refilled.
Purge the calibration valve as described in “To Refill the CI Calibration Vial” on
page 90. Then clean the ion source.
The calibrant vial was overfilled. Excess PFDTD can quench the chemical
ionization reactions.
Check the level of the PFDTD in the calibration vial. It should be below the end of
the inside tube in the vial.

Excessive noise or low signal-to-noise ratio

The GC inlet needs maintenance.
Refer to the GC manual.

Time-of-Flight GC/MS System Operating Manual for more information.
Poor vacuum
Check the pressure on the high vacuum gauge controller.
Air leak
information.

Replace the gas purifier. See “To Replace the Chemical Ionization Gas
Purifier” on page 88.


Reagent gas flows too high (in EI/PCI MSs)

Verify that the reagent gas setup is correct.
Peak at m/z 32
A visible peak at m/z 32 in methane pretune often indicates air in the system.
New or dirty reagent gas supply tubing

Purge the reagent gas supply lines and flow module for at least 60 minutes. See
the Agilent 7250 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operating Manual for more information.
Air leak
Check for leaks and correct any that you find. See “Air Leaks” on page 52. After
all leaks have been corrected, clean the ion source.
Contaminated reagent gas supply. Suspect this if you have recently

replaced your gas tank, and you have ruled out air leaks.
Replace the reagent gas supply.
The capillary column is broken or disconnected.

Inspect the capillary column. Make sure it is not broken and it is installed
correctly.

Replace the gas purifier.

Tuning-Related Symptoms
This section describes symptoms related to tuning. Most symptoms involve
difficulties with tuning or with the results of tuning. The following symptoms are
covered in this section:
• CI ion ratio is difficult to adjust or unstable
• Cannot complete autotune
Reagent gas ion ratio is difficult to adjust or

unstable
The interface tip seal is incorrectly placed, damaged, or missing.
Inspect the interface tip seal. If necessary, remove and reinstall it to ensure a
good seal with the CI ion source. Replace it if it is damaged. Install it if it is
missing.
Residual air in the MS or in the reagent gas supply lines

information.
Air leak
information.
The reagent gas supply is at the wrong pressure.

Check the regulator on the reagent gas supply. It should be adjusted to 20 psi
(138 kPa).
A leak in the reagent gas delivery path. This is especially likely if you have
set the methane flow much higher than normal and the ratio is still too low.
Check the reagent gas path. Tighten fittings.


Cannot complete Autotune

Wrong or corrupted tune file
Check the tune parameters.
The m/z 28/27 ion ratio (for methane) is incorrect. The correct ratio should
be between 1.5 and 5.0.
If the ion ratio is incorrect, adjust it. See the Agilent 7250 Accurate-Mass Q-TOF
GC/MS System Operating Manual for more information.

Clean the ion source. See the Agilent 7250 Accurate-Mass Q-TOF GC/MS System
Operating Manual for more information.
Too much air or water in the system

See “Air Leaks” on page 52. After eliminating these problems, clean the ion
source.
The CI ion source is dirty

Air leak
information.


4 General Maintenance
Before Starting 68
To Refill the EI Calibration Vial 73
To Connect the GC Nitrogen Gas Source to the Collision Cell 75
To Separate the GC from the MS 76
To Position the GC Next to the MS 78
To Move or Store the MS 79
To Access the Left Side Lifting Handle 82
This chapter describes maintenance procedures and requirements that are used
with all Agilent 7250 Accurate Mass Q-TOF GC/MS Systems.

4 General Maintenance
Before Starting
For your safety, read all of the information in this introduction before performing
any maintenance tasks.
Scheduled maintenance
Common maintenance tasks are listed in Table 6. Performing these tasks when
scheduled can reduce operating problems, prolong system life, and reduce
overall operating costs.
Keep a record of system performance (tune reports) and maintenance
operations performed. This makes it easier to identify variations from normal
operation and to take corrective action.
Table 6 Maintenance schedule
Task Every Every 6 Every As

week months year needed
Check the foreline pump oil level X
Check the calibration vial(s) X

Replace the foreline pump oil* X
Replace the tip seals on the optional IDP X
Replace the filters on the optional IDP X
Clean the ion source X
Check the carrier gas trap(s) on the GC and MS X
Replace the worn out parts X

Replace GC gas supplies X
Replace CI reagent gas supplies X
Check the foreline pump X
Tune the MS X
Leak check the system X

†
Lubricate side plate or vent valve O-rings X
* Or as needed, every 3 months if ammonia is being used as CI reagent gas.

† Vacuum seals other than the side plate O-ring and vent valve O-ring do not need to be lubricated.
Lubricating other seals can interfere with their correct function.

Tools, spare parts, and supplies

Some of the required tools, spare parts, and supplies are included in the GC
shipping kit, MS shipping kit, or MS tool kit. You must supply others yourself.
Each maintenance procedure includes a required materials list.
High voltage precautions

When the MS is plugged in, even if the power switch is off, dangerous voltage
(200/240 VAC) exists on the wiring and fuses between where the power cord
enters the instrument and the power switch.
When the power switch is on, dangerous voltages exist on:
• Electronic circuit boards
• Toroidal transformer
• Wires and cables between these boards
• Wires and cables between these boards and the connectors on the back
panel of the MS
• Some connectors on the back panel (for example, the foreline power
receptacle)
Normally, all of these parts are shielded by safety covers. As long as the safety
covers are in place, it should be difficult to accidentally make contact with
dangerous voltages.
Do not perform maintenance with the MS turned on or plugged into its power
WAR N IN G source, unless you are instructed to do so by one of the procedures in this
chapter.
Some procedures in this chapter require access to the inside of the MS while the
power switch is on. Do not remove any of the electronics safety covers in any of
these procedures. To reduce the risk of electric shock, follow the procedures
carefully.
Dangerous temperatures
Many parts in the MS operate at, or reach, temperatures high enough to cause
serious burns. These parts include, but are not limited to:
• GC/MS interface

• Analyzer parts
• Vacuum pumps
The foreline pump can cause burns if touched when operating.

WAR N IN G
Never touch these parts while your MS is on. After the MS is turned off, give
WAR N IN G these parts enough time to cool before handling them.
The GC/MS interface heater is powered by a heated zone on the GC. The
WAR N IN G interface heater can be on, and at a dangerously high temperature, even
though the MS is off. The GC/MS interface is well insulated. Even after it is
turned off, it cools very slowly.
The GC inlets and GC oven also operate at very high temperatures. Use the same
caution around these parts. See the documentation supplied with your GC for
more information.
Chemical residue
Only a small portion of your sample is ionized by the ion source. The majority of
any sample passes through the ion source without being ionized. It is pumped
away by the vacuum system. As a result, the exhaust from the foreline pump will
contain traces of the carrier gas and your samples. Exhaust from the rotary vane
foreline pump also contains tiny droplets of foreline pump oil.
An oil mist filter is supplied with the rotary vane foreline pump. This filter stops
only pump oil droplets. It does not trap any other chemicals. If you are using toxic
solvents or analyzing toxic chemicals, install a hose from the mist filter outlet to
the outdoors or into a fume hood vented to the outdoors. Comply with your local
air quality regulations.
The oil mist filter supplied with the rotary vane foreline pump stops only
WAR N IN G foreline pump oil. It does not trap or filter out toxic chemicals. If you are using
toxic solvents or analyzing toxic chemicals, vent the exhaust to a safe
location.
The oil in the rotary vane foreline pump also collects traces of the samples being
analyzed. All used pump oil should be considered hazardous and handled
accordingly. Dispose of used oil as specified by your local regulations.

When replacing pump oil, use appropriate chemical-resistant gloves and

WAR N IN G safety glasses. Avoid all contact with the oil.
The optional dry scroll foreline pump may contain significant quantities of
WAR N IN G dust. This dust can contain traces of the chemicals analyzed by the mass
spectrometer. Do NOT use compressed air to blow out this dust. Using
compressed air will contaminate your laboratory with potentially hazardous
dust.
Always perform any maintenance procedures using hazardous solvents under

WAR N IN G a fume hood. Operate the MS in a well-ventilated room.
Electrostatic discharge
All of the printed circuit boards in the MS contain components that can be
damaged by electrostatic discharge (ESD). Do not handle or touch these boards
unless absolutely necessary. In addition, wires, contacts, and cables can conduct
ESD to the electronics boards to which they are connected. This is especially true
of the mass filter (quadrupole) contact wires, which can carry ESD to sensitive
components on the quadrupole board. ESD damage may not cause immediate
failure, but it will gradually degrade the performance and stability of your MS.
When you work on or near printed circuit boards, or when you work on
components with wires, contacts, or cables connected to printed circuit boards,
always use a grounded antistatic wrist strap and take other antistatic
precautions. The wrist strap should be connected to a known good earth ground.
If that is not possible, it should be connected to a conductive (metal) part of the
assembly being worked on, but not to electronic components, exposed wires or
traces, or pins on connectors.
Take extra precautions, such as a grounded antistatic mat, if you must work on
components or assemblies that have been removed from the MS. This includes
the analyzer.

To be effective, an antistatic wrist strap must fit snugly (not tight). A loose
C AU T I O N strap provides little or no protection.
Antistatic precautions are not 100% effective. Handle electronic circuit boards
as little as possible and then only by the edges. Never touch components,
exposed traces, or pins on connectors and cables.

To Refill the EI Calibration Vial

Materials needed
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• PFTBA (05971-60571)
  Procedure
1 Stop any tuning or data acquisition.
2 Turn off the MS electronics.
3 Remove the source window cover. See the Agilent 7250 Accurate-Mass
Q-TOF GC/MS System Operating Manual.
4 Turn the calibration vial collar counterclockwise to loosen it. (See Figure 7.)
Do not remove the collar.
5 Pull the calibration vial out. You may feel some resistance due to the O-ring
around the vial tube section.
Calibration vial Collar
Figure 7. Removing the EI calibration vial

6 Syringe or pipette PFTBA into the vial. With the vial vertical, the liquid should
be just below the end of the internal tube, approximately 70-120 µL of
sample.
7 Push the calibration vial into the valve as far as possible.
8 Withdraw the vial 1 mm. This prevents damage when you tighten the collar.
9 Turn the collar clockwise to tighten it. The collar should be snug but not
overly tight. Do not use a tool to tighten the collar. It does not require that
much force.
10 Reinstall the source window cover.
After removing a calibrant vial, you must purge the calibration valve. Failure to
C AU T I O N do so will result in damage to the filament, microchannel plate, and the
photomultiplier.
11 In the Instrument Control panel, select the MS Tune icon to display the
GC-Q-TOF Tune dialog box. Select the Manual Tune tab then select the Ion
Source tab to display the ion source parameters.
12 Turn off the Emission by selecting the check box.
13 Purge the calibration valve by selecting the EI Cal Valve check box to open
the calibration valve. Close the EI Cal Valve after 30 seconds.

To Connect the GC Nitrogen Gas Source to

the Collision Cell
Materials needed
• Wrench, open-end, 1/4-inch × 5/16-inch (8710-0510)
• Ferrule
• Swagelock nut
  Procedure
1 With the MS vented, use a 5/16 in. wrench to remove the cap from the
nitrogen connection located on the side of the instrument near the transfer
line.
Nitrogen connection
Figure 8. Collision cell nitrogen gas connection
2 Place Swagelok nut and ferrule on the end of the nitrogen line tubing from the
GC.
3 Connect the nitrogen line to the instrument.

To Separate the GC from the MS

This procedure is used for relocating or storing the instrument.This procedure
applies to Agilent 8890 and 7890 GCs.
Materials needed
• Ferrule, blank (5181-3308)
• Self-tightening column nut (recommended, 5190-5233), or interface column
nut (05988-20066)
Ensure the GC/MS interface and the analyzer zones are cool (below 100 °C)
WAR N IN G before you vent the MS. A temperature of 100 °C is hot enough to burn skin;
always wear cloth gloves when handling analyzer parts.

WAR N IN G
Ensure the GC oven and the GC/MS interface are cool before turning off carrier
C AU T I O N gas flow.
Ensure the GC/MS interface, GC inlet, and GC oven have cooled before you
WAR N IN G remove the column. These areas can be hot enough to burn skin.
Procedure
1 Cool down the GC/MS interface, GC inlet, and GC oven.
2 Before separating the GC from the MS, ensure that the capillary column in the
GC oven is either disconnected from the transfer line, or has enough slack
uncoiled from the column hanger. Transportation of either instrument
requires a disconnection of the capillary column.
3 The foreline pump may be located on the floor, on the lab bench next to or
behind the MS, or under the analyzer chamber at the back of the MS. Move it
as needed to provide slack in the tubing and cables.
4 Carefully pull the GC away from the MS until you have access to the GC/MS
interface cable. (See Figure 9, “Separating/connecting the MS and GC,” on

page 77.) The GC is guided as it slides by the spacer bracket underneath both
instruments.
5 Disconnect the GC/MS interface cable. Disconnecting the cable with the GC
on can cause a fault condition.
If you are moving or storing the MS, see “To Move or Store the MS” on page 79.
GC/MS interface
Interface cable
Figure 9. Separating/connecting the MS and GC

To Position the GC Next to the MS

This procedure is used to position the GC next to the MS after moving the GC
away from the MS, or after relocating the instrument.
Ensure the GC/MS interface, GC inlet, and GC oven have cooled. These areas
WAR N IN G can be hot enough to burn skin.
Procedure
1 Slide the units together and ensure you do not damage the capillary column.
2 Before closing the gap between the MS and the GC, connect the interface
cable.
3 Push the GC towards the MS, and close the gap.
4 If needed, connect the column to the transfer line. See the Agilent 7250
Accurate-Mass Q-TOF GC/MS System Operating Manual.
5 Wind the excess column slack in the GC oven around the column basket.
6 Turn on the GC, and start carrier gas flow.

To Move or Store the MS

Materials needed
• Ferrule, blank (5181-3308)
• Self-tightening column nut (recommended, 5190-5233), or interface column
nut (05988-20066)
Procedure
Ensure the GC/MS interface and the analyzer zones are cool (below 100 °C)
WAR N IN G before you vent the MS. A temperature of 100 °C is hot enough to burn skin;
always wear cloth gloves when handling analyzer parts.

WAR N IN G
When the MS is vented, do not put the MassHunter Workstation software into
WAR N IN G Instrument Control view. Doing so will turn on the GC/MS interface heater.
Ensure the GC oven and the GC/MS interface are cool before turning off the
C AU T I O N carrier gas flow.
Never vent the MS by allowing air in through either end of the foreline hose.
C AU T I O N Always use the automated procedure in MassHunter Data Acquisition to vent
the MS.
Do not exceed the maximum recommended total gas flow.
1 Cool down the GC and MS. See the Agilent 7250 Accurate-Mass Q-TOF
GC/MS System Operating Manual.
2 Vent the MS. See the Agilent 7250 Accurate-Mass Q-TOF GC/MS System
Operating Manual.
3 Shut off the carrier gas at the source.
4 Shut off the GC, and unplug the power cord.

5 Disconnect the GC column from the GC/MS interface, and cap the end of the
interface with a blank ferrule. See the Agilent 7250 Accurate-Mass Q-TOF
6 Disconnect the MS power cords on the left side of the instrument.
7 Disconnect the LAN cable, control wires, and carrier gas located on the back
of the instrument. See “Side Panel AC Power Connectors” on page 14.
8 Separate the GC from the MS. See “To Separate the GC from the MS” on
page 76.
9 Disconnect the collision gas supply tubing, and install a plug.
10 Remove the source window cover (see Figure 12, “Remove covers to access
the left side lifting handles,” on page 82), then remove the analyzer cover.
(See Figure 10.)
Figure 10. Analyzer cover
11 Finger-tighten the side plate thumbscrews for the analyzer.
Do not overtighten the side plate thumbscrews. Overtightening will strip the
C AU T I O N threads in the analyzer chamber. It will also warp the side plate and cause
leaks.

Side plate thumbscrews
Figure 11. Side plate thumbscrews
12 Reinstall the analyzer cover and source window cover.

13 Remove the front left grill and left side cover. See “To Access the Left Side
Lifting Handle” on page 82. This uncovers the handles on the left side of the
instrument.
The MS can now be stored or moved. The MS requires three people for lifting.
One for the left side lifting handles, one for the right side lifting handles, and one
for the back side lifting handles.
The MS must remain upright at all times. If you need to ship your MS to another
C AU T I O N location, contact your Agilent Technologies service representative for advice
about packing and shipping.

To Access the Left Side Lifting Handle
Left side cover
Front left grill
Figure 12. Remove covers to access the left side lifting handles
Materials needed
• Screwdriver, Torx T-10 (8710-1623) or T-20 (8710-1615)
The GC/MS interface, the analyzer parts, and the vacuum system operate at
WAR N IN G temperatures high enough to cause serious burns. Give these parts enough
time to cool before accessing them or handling them.
Before performing this procedure, move the GC away from the MS. (See “To
Separate the GC from the MS” on page 76.) Both the GC and MS should be shut
down and disconnected from the building power supply. All gas lines must be
disconnected from the MS.

This procedure demonstrates how to remove the necessary covers to access

the left side lifting handles. The handles on the right and rear sides of the
instrument are not covered, and require no special procedures to access.
  Procedure
1 To remove the front left grill, disengage the two captive screws on the left
side edge of the grill. (See Figure 13.)
Captive screws
Figure 13. Left front grill captive screws
2 Swing the grill open, and remove it by disengaging the cover tabs on the right
side.
3 To remove the left side cover, disengage the two captive screws at the front
edge of the cover. (See Figure 14.)
Captive screws
Figure 14. Left side cover captive screws

4 Slide the left side cover towards the front of the instrument.
5 Remove this cover to access the handle. (See Figure 15.)
Lifting handles
Figure 15. Left side lifting handles

5 CI Maintenance
To Minimize Rotary Vane Foreline Pump Damage from Ammonia 86
To Replace the Chemical Ionization Gas Purifier 88
To Clean the Reagent Gas Supply Lines 89
To Refill the CI Calibration Vial 90
This chapter describes maintenance procedures and requirements that are

unique to an Agilent 7250 Accurate-Mass Q-TOF GC/MS System equipped with
the chemical ionization hardware.

5 CI Maintenance
To Minimize Rotary Vane Foreline Pump

Damage from Ammonia
Air ballasting for an hour every day removes most of the ammonia from the
pump oil. This will greatly increase the life of the pump.
Only perform this procedure if the pump is at normal operating temperature.

C AU T I O N The water vapor in air can cause condensation of the ammonia at the ballast
valve if the pump is cold.
The pump may be dangerously hot. Wear insulating gloves before you touch it
WAR N IN G or the ballast valve.
Procedure
1 Turn the ballast valve on the foreline pump (Figure 16) until the 1s are
aligned. The sound of the pump will get much louder.
Ballast valve
Figure 16. Minimizing ammonia damage
2 Leave the ballast valve open for one hour. You can continue to run samples
while the pump is ballasting.

5 CI Maintenance
3 Close the ballast valve by aligning the 0s. Leaving the ballast valve open all
the time will result in loss of pump oil and damage to the pump.
Always purge the flow module with methane after flowing ammonia. The use
C AU T I O N of ammonia reagent gas also requires that the foreline pump oil be replaced
every two to three months instead of the usual six months.

5 CI Maintenance
To Replace the Chemical Ionization Gas

Purifier
Materials needed
• Chemical ionization gas purifier (5190-9071)
• Front ferrule for 1/8-inch tubing (5180-4110)
• Rear ferrule for 1/8-inch tubing (5180-4116)
• Tubing cutter (8710-1709)
The chemical ionization gas purifier needs to be replaced after four tanks of
reagent gas. This frequency may vary depending on purity of the gas and care
taken in uncapping and installing the gas purifier. A large leak upstream from the
gas purifier can quickly exhaust the reduced metal of the oxygen and moisture
traps.
Procedure
1 Turn off gas flow to the purifier.
Do not remove the caps until you are ready to install the gas purifier. Only
C AU T I O N remove the caps in the gas flow to prevent contamination by air.
Methane is flammable. Extinguish all flames in the area before turning on gas
WAR N IN G flow.
2 Disconnect the fittings on the old purifier.

3 Remove the ferrules from the tubing at the outlet of the gas purifier. Using the
tubing cutter, cut off the end of the tubing with the ferrules.
4 Install the new purifier.
5 Turn on the gas flow, and purge the new purifier.
6 Cap the old purifier, and prepare it to be sent for regeneration. See the
instructions on the label.

5 CI Maintenance
To Clean the Reagent Gas Supply Lines

Materials needed
• Clean, dry nitrogen
• Heat gun
• Tubing cutter (8710-1709)
Do not heat the gas tubing when reagent gas is flowing.

WAR N IN G
Do not put liquids into the tubing. Do not heat the tubing when it is connected
C AU T I O N to the MS.
Procedure
If the reagent gas lines become contaminated, they can be cleaned.
1 Turn off the reagent gas supply.
2 Disconnect the reagent gas tubing from the gas supply, the gas purifier, and
the MS.
3 Cap the gas purifier following the instructions on the label.
4 Connect one end of the tubing to a supply of clean, dry nitrogen and turn on
gas flow.
5 Use the heat gun to warm the tubing, starting at the supply end and working
your way to the free end.
6 Repeat for any other pieces of tubing that need to be cleaned.
7 Reconnect the tubing to the gas supply, gas purifier, and MS. Follow the
instructions on the gas purifier label.
8 Turn on the reagent gas supply.

5 CI Maintenance
To Refill the CI Calibration Vial

Materials needed
• PFDTD calibrant (8500-8510)
• Syringe or pipette, clean
• Large (8610-0300)
• Small (8610-0029)
  Procedure
1 Stop any tuning or data acquisition.
2 Set the reagent gas flow to Gas Off.
3 Turn off the MS electronics.
The analyzers, GC/MS interface, and other components in the analyzer

WAR N IN G chamber operate at very high temperatures. Do not touch any part until you
are sure it is cool.
Always wear clean gloves while handling any parts that go inside the GC or
C AU T I O N analyzer chambers.
4 Cool down the GC/MS transfer line, the GC oven, and the GC inlet to 30 °C.
5 Uncoil enough slack from the capillary column inside the GC oven to allow
the GC to separate from the MS.
6 Move the GC away from the MS. See “To Separate the GC from the MS” on
page 76.
7 The CI vial is located on the side of the instrument near the transfer line.
8 Turn the CI vial collar counterclockwise to loosen it (Figure 17 on page 91).
Do not remove the collar.

5 CI Maintenance
Collar
Calibration vial
Figure 17. Removing the CI calibration vial
Do not rinse the vial with any solvents. Never expose the inside of the vial to
C AU T I O N chlorinated solvents or isopropyl alcohol or water - this will result in severe loss
of CI sensitivity.
9 Pull the calibration vial out. You may feel some resistance due to the O-ring
around the vial tube.
10 Syringe or pipette PFDTD into the vial. With the vial vertical, the liquid should
be just below the end of the internal tube, approximately 70 µL of sample.
11 Push the calibration vial into the valve as far as possible.
12 Withdraw the vial 1 mm. This prevents damage when you tighten the collar.
13 Turn the collar clockwise to tighten it. The collar should be snug but not
overly tight. Do not use a tool to tighten the collar. It does not require that
much force.
14 Position the GC next to the MS. See “To Position the GC Next to the MS” on
page 78.
After removing a calibrant vial, you must purge the calibration valve. Failure to
C AU T I O N do so will result in damage to the filaments and the electron multiplier.

5 CI Maintenance
15 In the Instrument Control panel, select the MS Tune icon to display the GC
Q-TOF Tune dialog box. Select the Manual Tune tab then select the Ion
Source tab to display the ion source parameters.
16 Turn off the Emission by selecting the check box.
17 Purge the calibration valve by selecting the CI Cal Valve check box to open
the calibration valve. Close the CI Cal Valve after 30 seconds.

6 Vacuum System
Overview 94
Maintaining the Vacuum System 95
Vacuum System Components 96
Common Vacuum System Problems 97
Foreline Pump 98
Side Plate 110
Vacuum Seals 110
EI Calibration Valve 111
CI Calibration Valve 112
This chapter describes maintenance requirements of the Agilent 7250 Accurate

Mass Q-TOF GC/MS vacuum system.

6 Vacuum System
Overview
The vacuum system creates the high vacuum (low pressure) required for the
GC/MS to operate. Without the vacuum, the molecular mean free path would be
very short and ions would collide with air molecules before they could reach the
detector. Operation at high pressures also would damage analyzer components.
The Agilent 7250 Accurate-Mass GC/MS System uses four vacuum pumps to
obtain the vacuum levels needed. Three turbomolecular (turbo) pumps create
vacuum in the analyzer. These turbo pumps discharge into a manifold operating
at foreline pump inlet pressure. The foreline pump discharges to near
atmospheric pressure.
Most of the vacuum system operation is automated. Operator interaction and
monitoring is accomplished through the data system.

6 Vacuum System
Maintaining the Vacuum System

Periodic maintenance
As listed in Table 6, “Maintenance schedule,” on page 68, some maintenance
tasks for the vacuum system must be performed periodically. These include:
• Checking the rotary vane foreline pump oil (every week)
• Checking the calibration vial (every 6 months)
• Replacing the rotary vane foreline pump oil (every 6 months)
• Replacing IDP tip seal (yearly)
• Replacing IDP filters (yearly)
Failure to perform these tasks as scheduled can result in decreased instrument
performance. It can also result in damage to your instrument.
Other procedures
Problems with any of the vacuum system seals in the analyzer usually require
the services of Agilent service personnel. See Chapter 2, “General
Troubleshooting” on page 25, and see the online help in the MassHunter
Workstation software for symptoms that indicate this type of maintenance is
required.
More information is available

If you need more information about the locations or functions of vacuum system
components, see the Agilent 7250 Accurate-Mass Q-TOF GC/MS System
Operating Manual.
Most of the procedures in this chapter are illustrated with video clips on the
Agilent GC/MS Hardware User Information & Instrument Utilities and
7250 Q-TOF GC/MS User Information disks.

6 Vacuum System
Vacuum System Components

The parts of the vacuum system are:
• Foreline (rough) pump
• 3 High-vacuum turbo pumps
• Analyzer chambers
• Collision cell connections
• Collision cell plate
• Nitrogen purge and vent system
• Side plate (analyzer door)
• Vacuum seals
• EI calibration valve
• Vacuum control electronics
• Vacuum gauges and gauge control electronics

6 Vacuum System
Common Vacuum System Problems

Air leak symptoms
The most common problems associated with any vacuum system are air leaks.
Symptoms of air leaks include:
• Loud gurgling noise from the foreline pump (very large leak)
• Inability of the turbo pumps to reach 95% speed
• Higher than normal high-vacuum gauge controller readings
The instrument will not pump down successfully unless you press on the side
board (analyzer door) when you turn on the MS power. Continue to press until
the sound from the foreline pump becomes quieter.
Pumpdown failure shutdown

The system will shut down both the high-vacuum and the foreline pump if the
system fails to pump down correctly. It takes approximately 10 minutes for the
foreline pump to achieve 10 Torr, which then allows the turbo pumps to start. If a
turbo pump speed is below 80% after an additional 10 minutes, the system shuts
down.
This is usually because of a large air leak: either the side plate has not sealed
correctly or the electronic vent valve is still open.
To restart the MS, find and correct the air leak, then switch the power off and on.
Press on the side plates when turning on the MS power to ensure good seals.

6 Vacuum System
Foreline Pump
The 7250 can be used with either a standard oil-based rotary vane foreline pump
(DS-202), or a dry scroll pump (IDP-15). Procedures for maintaining these pumps
are provided on the following pages.
Figure 18. Standard rotary vane foreline pump
To connect the foreline hose to the foreline

pump
Materials needed
• Large (8650-0030)
• Small (8650-0029)
  Procedure
This procedure applies to the rotary vane and dry scroll pumps. The dry scroll
pump is shown in the video.

6 Vacuum System
1 Place the o-ring against the hepa filter inlet.

2 Place the foreline hose against the o-ring.
3 Place the clamp over the o-ring, hose flange, and filter flange.
4 Tighten the clamp using the long screw and wing nut.
To disconnect the foreline hose from the

foreline pump
Materials needed
• Large (8650-0030)
• Small (8650-0029)
  Procedure
The foreline pump can cause burns if touched when operating. Make sure it
WAR N IN G has had time to cool.
The MS must be vented and off before the hose is disconnected. Never vent
C AU T I O N the MS by allowing air in through either end of the foreline hose.
1 Unscrew the wing nut on the clamp.

2 While supporting the foreline hose, remove the clamp from the hepa filter
inlet.
3 Remove the hose and o-ring from the filter inlet.
To check the rotary vane pump oil mist filter

Check the oil mist filter weekly for any damage and collected pump fluid.
• If the oil mist filter is damaged, replace it.

6 Vacuum System
• If oil is found in the oil mist filter, open the gas ballast valve counterclockwise
just enough to return the condensed oil back to the pump. Close the gas
ballast valve clockwise.
Do not touch the fluid. The residue from some samples are toxic. Properly
WAR N IN G dispose of the fluid.
When you close the ballast valve, you increase the efficiency of the pump.
NOTE However, you lose oil to the mist filter if you don’t recycle. Check the status of
your oil mist filter at least once per week to ensure that it does not fill with oil.
If you lose too much oil in the foreline pump, the vacuum will not be
maintained, and the MS will vent.
To check the rotary vane foreline pump fluid

level
Check the level and color of the pump fluid weekly.
• Check the fluid level in the window of the foreline pump. The fluid level should
be between the marks for Max and Min.
• Check that the color of the pump fluid is clear or almost clear with few
suspended particles. If the pump fluid is dark or full of suspended particles,
replace it.
Never add or replace the foreline pump fluid while the pump is on.
WAR N IN G
Record this procedure in the Maintenance Logbook, which was supplied with
NOTE your instrument.
To add oil to the rotary vane foreline pump

Add pump oil when the pump oil level is low.
Materials needed
• Funnel

6 Vacuum System
• Large (8650-0030)
• Small (8650-0029)
• Foreline pump oil (Inland 45, 6040-0834)
• Safety glasses (goggles)
Never add pump oil while the pump is on.

WAR N IN G
The fill cap and pump may be dangerously hot. Check that the fill cup and
WAR N IN G pump are cool before you touch them.
Use only foreline pump oil (Inland 45, 6040-0834). Any other fluids can
C AU T I O N substantially reduce pump life and invalidate the pump warranty.
Procedure
1 Vent and turn off the instrument. See the Agilent 7250 Accurate-Mass Q-TOF
2 Unplug the instrument power cord from the electrical outlet.
3 Remove the fill cap on the foreline pump.
4 Add new pump fluid until the fluid level is near, but not over the maximum
mark beside the fluid level window.
5 Reinstall the fill cap.
6 Wipe off all excess oil around and underneath of the pump.
7 Reconnect the power cord.
8 Start up the instrument. See the Agilent 7250 Accurate-Mass Q-TOF GC/MS
System Operating Manual.
To replace the oil in the rotary vane foreline

pump
Replace the pump oil every six months or sooner if the oil appears dark or cloudy.

6 Vacuum System
Materials needed
• Container for catching old pump oil
• Funnel
• Large (8650-0030)
• Small (8650-0029)
• Foreline pump oil (Inland 45, 6040-0834)
• Screwdriver, flat-bladed, large (p/n 8710-1029)
• Safety glasses (goggles)
Never add pump oil while the pump is on.

WAR N IN G
The fill cap and pump may be dangerously hot. Check that the fill cap and
WAR N IN G pump are cool before you touch them.
Do not touch the oil. The residue from some samples are toxic. Properly
WAR N IN G dispose of the oil.
Use only foreline pump oil (Inland 45, 6040-0834). Any other fluids can
C AU T I O N substantially reduce pump life and invalidate the pump warranty.
  Procedure
1 Vent and turn off the instrument. See the Agilent 7250 Accurate-Mass Q-TOF
2 Unplug the power cord from the instrument.
3 Place a container under the drain plug of the foreline pump.
4 Remove the fill cap, then open the drain plug. Drain the fluid completely by
raising the motor end of the pump up.
5 Reinstall the drain plug.
6 Pour in new pump fluid until the fluid level is near, but not above the
maximum mark beside the fluid level window.

6 Vacuum System
7 Reinstall the fill cap.

8 Reconnect the power cord.
9 Start up the instrument. See the Agilent 7250 Accurate-Mass Q-TOF GC/MS
System Operating Manual.
10 Pump down for 30 minutes, then inspect the pump for leaks.
11 Continue pumping down overnight and inspect the pump for leaks the next
day.
The oil pan under the foreline pump can be a

fire hazard
Oily rags, paper towels, and similar absorbents in the oil pan could ignite and
damage the pump and other parts of the MS.
Combustible materials (or flammable/nonflammable wicking material) placed

WAR N IN G under, over, or around the foreline (roughing) pump constitutes a fire hazard. 
Keep the pan clean, but do not leave absorbent material such as paper towels
in it.
To remove the exhaust silencer filter
  Procedure
1 Unscrew the wing nut on the clamp. (See Figure 19 on page 104.)
2 While supporting the silencer filter, remove the clamp.
3 Lift the filter and O-ring from the pump.

6 Vacuum System
Exhaust silencer filter
KF Flange
KF Clamp wing nut
Figure 19. Foreline pump exhaust silencer filter
To install the exhaust silencer filter
  Procedure
1 Place the O-ring against the IDP-15 exhaust. (See Figure 19 on page 104.)
2 Place the exhaust silencer filter against the O-ring.
3 Place the clamp over the O-ring and KF flanges.
4 Tighten the clamp using the long screw and wing nut.

6 Vacuum System
Figure 20. IDP-15 foreline pump
To replace the IDP-15 dry pump tip seal

Materials needed
• Large (8650-0030)
• Small (8650-0029)
• 4 mm hex wrench (8710-2720)
• 5 mm hex wrench (G4514-80524)
• 6 mm hex wrench (8710-1839)
• IDP-15 tip seal maintenance kit (5190-9613)
  Procedure
1 Vent the mass spectrometer (see the Agilent 7250 Accurate-Mass Q-TOF
GC/MS System Operating Manual).
The IDP pump operates at high temperatures. Do not touch any part until you
WAR N IN G are sure it is cool.
2 Using a 4 mm hex wrench, unscrew the six screws securing the front cowl.

6 Vacuum System
3 Rotate the cowl over the exhaust port.

4 Unplug the fan connector at the base of the cowl, and remove the cowl.
5 Set aside the L-bracket.
Wear a face mask. The IDP pump may contain significant quantities of dust
WAR N IN G containing chemicals analyzed by the mass spectrometer. Do NOT use
compressed air to blow out this dust. Using compressed air will contaminate
your laboratory with potentially hazardous dust.
6 Using a 5 mm hex wrench, unscrew the six screws securing the outboard
housing. It may be necessary to raise and support the top console to access
the screws.
7 Remove the scroll housing by lifting it away from the rest of the pump.
8 Remove the O-ring.
9 Remove both tip seals from the orbiting plate and the outboard housing.
10 Use cotton swabs dampened with alcohol to clean all debris from the
orbiting plate, outboard housing, and O-ring groove.
11 Install the new O-ring.
12 Install the new tip seals into the grooves in the orbiting scroll and outboard
housing. The tip seal should be well seated in the grooves, protruding only
slightly from the grooves.
13 Align the outboard housing with the orbiting plate, and reattach it using the
six screws and a 5 mm hex wrench. When tightening the screws, do so in a
crisscross pattern.
14 Reinstall the console.
15 Align the slots in the L-bracket with the holes in the electrical tray.
16 Reconnect the fan connector.
17 Rotate the front cowl over the exhaust port, and align it on the front of the
pump.
18 Reattach the front cowl using the six screws and a 4 mm hex wrench.

6 Vacuum System
To replace the IDP pump HEPA filter cartridge

This procedure applies only to the dry scroll foreline pump.
Materials needed
• Large (8650-0030)
• Small (8650-0029)
• HEPA filter with cartridge (SCRINTRPNW25)
• HEPA filter cartridge (REPLHEPAFILTER1)
The MS must be off and vented, and the foreline pump must be off, before
C AU T I O N performing this procedure.
  Procedure
1 Undo the three latches securing the top of the HEPA filter.
2 Remove the lid, and the filter cartridge from the filter.
3 Insert the new filter cartridge, and replace the lid on top of the filter.
4 Secure the lid using the three latches.
To change the exhaust silencer filter cartridge

Materials needed
• Large (8650-0030)
• Small (8650-0029)
• Exhaust silencer filter cartridge
• large (REPLSLRFILTER1)

6 Vacuum System
The foreline pumps operate at high temperatures. Do not touch any part until
WAR N IN G you are sure it is cool.
  Procedure
1 Unscrew the cap from the exhaust filter.
2 Pull the filter cartridge out of the filter cap.
3 Insert the new filter cartridge.
4 Align the cap onto the filter and twist the cap counter clockwise to lock it in
place.
To install the IDP pump ballast

Materials needed
• 4 mm hex wrench (8710-2720)
• 6 mm hex wrench (8710-1839)
• 14 mm wrench
• Ballast (Contact Agilent for this part)
  Procedure
5 Using a 6 mm hex wrench, remove the ballast plug from the desired gas
ballast port.

6 Vacuum System
6 Screw the ballast into the empty port, and tighten it with a 14 mm wrench.
To remove the IDP pump ballast

Materials needed
• 4 mm hex wrench (8710-2720)
• 6 mm hex wrench (8710-1839)
• 14 mm wrench
• Ballast plug (Contact Agilent for this part)
  Procedure
5 Using a 14 mm wrench, loosen the ballast until it can be removed by hand.
6 Unscrew and remove the ballast.
7 Using a 6 mm hex wrench, install the ballast plug.

6 Vacuum System
Side Plate
The side plate covers the large opening in the side of the analyzer chamber. The
analyzer assembly is attached to the side plate inside the analyzer chamber.
Several electrical feedthroughs are built into the side plate. Wires connect the
feedthroughs to analyzer components.
Thumbscrews are located at each end of the side plate. We recommend that the
thumbscrews be loosely tightened
Fasten the side plate thumbscrews for shipping or storage only. For normal
C AU T I O N operation, both thumbscrews should be loose. Overtightening will warp the
side plate and cause air leaks. Do not use a tool to tighten the side plate
thumbscrews.
When you turn on the power to pump down the MS, press on the side plate to
C AU T I O N ensure good seals.
Vacuum Seals
Several types of Viton elastomer O-ring seals are used to prevent air leaks into
the analyzer chamber. All these O-rings, and the surfaces to which they seal,
must be kept clean and protected from nicks and scratches. A single hair, piece
of lint, or scratch can produce a serious vacuum leak. Three of the O-rings are
lightly lubricated with Apiezon-L vacuum grease: the side plate O-rings and the
vent valve O-ring.
Contact Agilent to have these vacuum seals serviced.

6 Vacuum System
EI Calibration Valve
The EI calibration valve is an electromechanical valve with a vial to hold the
tuning compound. (See Figure 21.) When a calibration valve is opened, tuning
compound in the vial diffuses into the ion source. The valve is controlled by the
MassHunter Workstation software.
The EI calibration valve is held onto the top of the analyzer chamber by two
screws. A small O-ring provides a face seal.
Perfluorotributylamine (PFTBA) is the most commonly used tuning compound
for EI operation. PFTBA is required for automatic tuning of the MS.
EI calibration vial EI calibration valve
Figure 21. EI calibration valve

6 Vacuum System
CI Calibration Valve
The CI calibration valve is part of the reagent gas flow control module supplied
with the optional chemical ionization ion source. The CI calibration valve is an
electromechanical valve with a vial to hold the tuning compound. (See
Figure 22.) It is controlled by the Agilent MassHunter Workstation software. It
opens automatically during CI autotune or manual tuning, allowing the tuning
compound, perfluoro-5,8-dimethyl-3,6,9-trioxidodecane (PFDTD), to diffuse
through the GC/MS interface and into the ion source.
CI Calibration valve
CI Calibration vial
Figure 22. CI calibration valve

7 Replacement Parts
To Order Parts 114
Electronics 115
Vacuum System 118
Analyzer 121
GC/MS Interface 126
Consumables and Maintenance Supplies 128
Additional CI Parts 131
This chapter lists parts that can be ordered for use in maintaining your
7250 Accurate-Mass Q-TOF GC/MS System. It includes most of the parts or
assemblies in the MS. Most of the parts listed are not user-replaceable. They are
listed here for use by Agilent Technologies service representatives.

7 Replacement Parts
To Order Parts
To order parts for your MS, address the order or inquiry to your local 
Agilent Technologies office. Supply them with the following information:
• Model and serial number of your MS, located on a label near the power cord
connections to the mainframe.
• Part number(s) of the part(s) needed
• Quantity of each part needed
Some parts are available as rebuilt assemblies

Rebuilt assemblies pass all the same tests and meet all the same specifications
as new parts. Rebuilt assemblies can be identified by their part numbers. 
The first two digits of the second part of the part number are 69 or 89 (such as
xxxxx-69xxx or xxxxx-89xxx). Rebuilt assemblies are available on an
exchange-only basis. When you return the original part to Agilent Technologies
(after you receive the rebuilt assembly) you will receive a credit.
If you cannot find a part you need

If you need a part that is not listed in this chapter, check the Agilent Technologies
Analytical Supplies Catalog or the online catalog on the Worldwide Web at
http://www.agilent.com/chem. If you still cannot find it, contact your Agilent
Technologies service representative or your Agilent Technologies office.

Electronics
The printed circuit boards in the MS are available only as complete assemblies.
Individual electronic components are not available. This section contains the
following parts: Table 7, “External cables”; Table 8, “Internal cables,” on page 116;
Table 9, “Printed circuit boards,” on page 116; and Table 10, “Fuses and power
switches,” on page 117.
Cables
Table 7 External cables
Description Part number
Remote Start-Stop cable G1530-60930
Y Remote Start-Stop cable G1530-61200
H Remote Start-Stop cable 35900-60800
MS LAN cable 8121-2846
LAN cable 8121-0940
C19 Q-TOF Mainframe
Power cord, Taiwan/S America, C19, 20 A 8120-6360
Power cord, Japan, C19, 20 amp 8120-6903
Power cord, Australia, C19, 16 amp 8120-8619
Power cord, GB/HK/SG/MY, C19, 13 amp 8120-8620
Power cord, Swiss/DK, C19, 16 amp 8120-8622
Power cord, China, C19, 15 amp, fast 8121-0070
Power cord, Israel, C19, 16 amp 8121-0161
Power cord, Argentina, C19, 16 amp 8121-0675
Power cord, India/S.Africa, C19, 15 amp 8121-0710
Power cord, Europe/S Korea, C19, 15 A, 250 V 8121-1222
Power cord, Thai 220 V, 15 A, 1.8 M, C19 8121-1301
Power cord, Brazil, C19, 250 V max 8121-1787
Power cord, US 240 V, C19, 15 amp 8121-0075

Table 8 Internal cables
Cable, Switch board G3850-60819
Cable, Quad driver-1 data G3850-60802
Cable, Collision cell board data G3850-60848
Cable, Filament drive board data G3850-60847
Cable harness, main board 1 G3850-60826
Cable harness, main board 2 G3850-60855
Cable, Gauge 3 extension G3850-60836
Cable, Turbo supply G3850-60810
Cable, Turbo controller module data G3850-60824
Cable, Turbo fan and turbo fan controller G3850-60811
Cable, Turbo pump control module, AC G3850-60825
Cable, Wire lens - 5 G3850-60833
Cable, Rough pump AC output G3850-60837
Printed circuit boards

Table 9 Printed circuit boards
Filament drive board G7250-67018
Collision cell board G7003-65914

Fuses and power switch

Table 10 Fuses and power switches
Fuse - AC Board G1960-6117
Fuse (main frame) metric 8 A 250 V TD FE UL-REC CSA 2110-0969
Fuse (foreline pump) metric 12.5 A 250 V UL-LST CSA 2110-1398
Switch Bd PCA G1960-61000
Power switch button 5041-8381
Switch board cable G3850-60819
Circuit breaker
External fuse
External fuse
Circuit breaker
Figure 23. Fuses and circuit breakers

Vacuum System
This section contains the following parts: Table 11, “O-rings and seals”; Table 12,
“Rotary vane foreline pump and related parts,” on page 119; Table 13, “IDP-15
Pump and related parts,” on page 119; and Table 14, “Turbo pump MS vacuum
system components,” on page 120.
O-rings and seals

Table 11 O-rings and seals
Calibration valve O-ring (1/4-inch) 5180-4182
End plate O-ring (for front and rear end plates) 0905-1441
GC/MS interface O-ring 0905-1405
KF10/16 seal (foreline pump inlet and turbo pump outlet) 0905-1463
KF25 O-ring assembly (turbo pump outlet) 0100-1551
Seal, turbo pump inlet 0100-1879
O-ring, forepump drain plug 0905-1619
Fill plug, forepump 0100-2451
Analyzer ion gauge G1960-80303
Foreline ion gauge G1960-80101
O-ring, standard forepump fill plug 0905-1630
O-ring, ion gauge 0905-1627
O-ring, collision cell feedthrough 0905-1405
O-ring, collision cell plate 0905-1689
Side plate O-ring 0905-1690

Rotary vane foreline pump (DS-202)

Table 12 Rotary vane foreline pump and related parts
Foreline hose assembly (hose and internal spring) 05971-60119
Hose clamp used with 05971-60119 1400-3241
DS 202 foreline pump, 240V G3850-80240
Oil return kit 9499376
Oil mist eliminator kit for KF25 9499392
Oil drain extension 9499375
Aluminum centering ring, with viton o-ring KC25AV
Foreline pump inlet seal (KF10/16) 0905-1463
KF25 Clamp (tp end of hose – not shown) 0100-0549
KF25 Hose adapter (tp end of hose – not shown) G1099-20532
O-ring for oil mist filter and hose barb adapter 0905-1193
IDP-15 dry scroll foreline pump

Table 13 IDP-15 Pump and related parts
IDP-15 tip seal maintenance kit 5190-9613
IDP-15 tip seal replacement kit X3815-67000
IDP-15 pump X3815-64010
HEPA filter SCRINTRPNW25
Exhaust silencer kit EXSLRSH110
Ballast Contact Agilent for this part
Ballast plug Contact Agilent for this part

Turbo pump and related parts

Table 14 Turbo pump MS vacuum system components
Fan (for high-vacuum pump) G1099-60564
Pfeiffer HiPace300, rebuilt G3170-89162
Pfeiffer HiPace300 G3170-80162
KF25 Clamp (for turbo pump outlet) 0100-0549
KF25 O-ring assembly (for turbo pump outlet) 0100-1551
Split flow turbo pump, nEXT200.200D G3850-80010
Split flow turbo pump, nEXT200.200D, rebuilt G3850-89010
ISO100 seals 3150-0962
Claw assembly G3170-60580
• Flat washers 3050-0993
• Lock washers 2190-0669
• Hex nuts 0535-0048
• Half claw clamp G3170-60580
Centering ring, NW25, with o-ring 0100-1551
O-ring, trapped 0905-1463
O-ring 0905-1574
O-ring 0905-1573
O-ring, backup G1969-20082
Hinged clamp with wing nut, NW20/25 0100-1398
Cable, extension G3850-60800
Flex hose, metal, NW 25 G3850-20156
Thermal barrier G1969-20081
Power supply, TMH G3850-60600
CC gas flow module, 3-channel G7002-60044
• GC/MS QQQ flow weldment cap assembly G7000-80500
• 3-Channel QQQ EPC G7000-60506

Analyzer
Table 15 shows the analyzer chambers and associated parts.
Table 15 Analyzer chamber and related parts
Micro Ion Gauge G1960-80303
Ion gauge baffle G7000-20049
O-ring, ion gauge 0905-1627
M3x12L screws 0515-0664
EI Calibration valve assembly G3850-67204
Calibration vial G3170-80002
Collision cell holder G3850-20042
Table 16 shows the replacement parts for the analyzers. Also included in this
section are Table 17, “Analyzer screws,” on page 122; and Table 18, “LE-EI ion
source parts,” on page 122.
Table 16 Analyzer parts
Source PCA and cable assembly G7002-60425
Mass filter cable kit G3170-60130
Mass filter contacts (qty 1) G1099-60142
Mass filter ceramic support, source end G7002-20057
Mass filter heater assembly G1099-60172
Pins for source and detector end mounting G1099-20137

brackets
p-filter bridge G7000-60028
Side plate, weld assembly (support) G7002-67021

Table 17 Analyzer screws
Heater/Sensor (quad) assembly G1099-60172
Ion source thumbscrew G1099-20138
Magnet mounting screws 0515-1046
Screw – magnet bracket to source radiator 0515-1602
Screws – mass filter contact assembly/heater block G3170-20122
Screws – radiator. Mounting brackets quadrupole board 0515-0430
Source radiator screws 0515-1052
Screws for Quad Stop 0515-0221
LE-EI ion source

A list of the replacement parts related to the LE-EI ion source may be found in
Table 18 and an illustration of the parts is also provided in Figure 24, “LE-EI ion
source,” on page 123.
Table 18 LE-EI ion source parts
1 Source finger grip G7002-20008
2 Filament block G7002-20019
3 Extractor lens (5)* , with 3 mm opening G7004-20061
4 Ceramic insulator for extractor G7002-20064
5 Entrance lens (1)* G7250-20075
6 Ion focus lens (2)* G7004-20068
7 Lens insulator/holder G7002-20074
8 M2 x 0.4 screw x 12 mm long gold plated screw G7002-20083
9 Source body G7002-20084
10 Post extractor lens 2 (3)* G7004-20090

*
11 Post extractor lens 1 (4) G7004-20004

Table 18 LE-EI ion source parts (continued)
12 M2 x 6 mm gold plated screw G7002-20109
13 Locking ring lens insulator G7002-20126
14 Filament assembly, HE, single G3850-60021
15 Ring heater/sensor assembly G7002-60043
16 Source mount G7002-60053
17 Repeller assembly G7002-67057
Complete LE-EI Ion Source, Half Ramp G7250-67170
* The number in parenthesis is the number engraved on the lens
12
2
14
8
16
17
15
4
3
11
10
6
5
13
12
Figure 24. LE-EI ion source

Axial CI ion source

A list of the replacement parts related to the Axial CI ion source may be found in
Table 19 and an illustration of the parts is also provided in Figure 25, “Axial CI ion
source,” on page 125.
Table 19 Parts list for Axial CI ion source
Item number Item description Part number
1 Source finger grip G7002-20008
2 Filament block G7002-20019
3 Filament, HES CI G7250-60075
4 5973 Gold Fil Screw (M2 × 0.4 10MM-LG) G1999-20021
5 in-WSHR-Shoulder 0.25 0.37 0.06 Alumina 3050-2670
6 HES CI source mount assembly G7250-60009
7 HES CI repeller assy G7250-60102
8 GCMS Ring heater/sensor assembly G7002-60058
9 HES CI Body G7250-20097
10 Drawout plate G1999-20446
11 HES CI Drawout cylinder G7250-20098
12 HES Ramp CI Ion focus G7250-20096
13 Entrance lens assy, STD, Half-Ramped G7250-20075
14 HES CI Lens insulator G7250-20095
15 Locking ring for lens insulator G7002-20126
16 Screw, M2 × 6 Pan Head Torx, gold plated G7002-20109
Complete assembly Axial CI Ion Source Assy (Support) G7250-67404

16
4
5
1
2
3
4
5
6
8
7
10
11
12
13
14
15
16
Figure 25. Axial CI ion source

GC/MS Interface
A list of the replacement parts related to the GC/MS transferline interface for the
7890 GC and an illustration of the parts is also provided. (See Table 20 and
Figure 26, “GC/MS interface for the 8890 and 7890 GCs,” on page 127.)
Table 20 GC/MS interface for 8890 and 7890 GCs
Item Description Part number
Transferline assembly Contact Agilent for this part
1 Knurled tip seal retainer, threaded G3870-20547
2 1/16 Ferrule no hole graphitized Vespel 0100-0691
2 1/16 Ferrule no hole (qty 10) 5181-3308
3 M3 x 3L Set screw, gold plated G1999-20022
4 Transferline tip base, threaded G3870-20548
5 Tip seal G3870-20542
6 Self-tightening column nut 5190-5233
6 MS interface column nut 05988-20066
7 MS screw G1999-20022
8 M4 X 0.7 16MM-LG 0515-0383
9 Heater clamp G3850-20410
10 Tip seal spring G7005-20024
11 Welded interface assembly G3870-60301
12 Heater/sensor assembly G1099-60107
13 M3 set screw 0515-0236
not shown Fitting-face seal, 1/4 in cap sst 316 0100-2013
not shown VCR gasket, size 4, AG on Ni retainer 0100-1436

8
11 13
2 6
7 5 10
4 9
1
3
12
Figure 26. GC/MS interface for the 8890 and 7890 GCs

Consumables and Maintenance Supplies

This section contains the following parts: Table 21, “EI maintenance supplies”;
Table 22, “Tools”; Table 23, “Ferrules,” on page 129; and Table 24,
“Miscellaneous parts and samples,” on page 130.
Table 21 EI maintenance supplies
Abrasive paper, 30 µm 5061-5896
Aluminum oxide powder, 100 g 393706201
Cloths, clean (qty 300) 05980-60051
Cloths, cleaning (qty 300) 9310-4828
Cotton swabs (qty 100) 5080-5400
Foreline pump oil, Inland 45 6040-0834
Gloves, clean – Large 8650-0030
Gloves, clean – Small 8650-0029
Grease, Apiezon L, high vacuum 6040-0289
Table 22 Tools
Funnel 9301-6461
Hex key, 5 mm 8710-1838
Tool kit G7077-60566
Ball drivers, 1.5-mm 8710-1570
Hex nut driver, 5.5-mm 8710-1220
Pliers, long-nose (1.5-inch nose) 8710-0004
Screwdrivers Flat-blade, large 8730-0002
Screwdrivers Torx, T-10 8710-1623

Table 22 Tools (continued)
Screwdrivers Torx, T-15 8710-1622
Screwdrivers Torx. T-20 8710-1615
MS shipping kit G7077-60502
Gas clean filter kit for carrier gas CP17974
GC-Q-TOF MSD ship kit, EPC-BF G7250-60180
Tweezers, non-magnetic 8710-2460
Wrenches, open-end 1/4-inch × 5/16-inch 8710-0510
Wrenches, open-end 10-mm 8710-2353
Wrist strap, antistatic, small 9300-0969
Wrist strap, antistatic, medium 9300-1257
Wrist strap, antistatic, large 9300-0970
Table 23 Ferrules
For the GC/MS interface
• Blank, graphite-vespel 5181-3308
• 0.3-mm id, 85%/15% for 0.10-mm id columns 5062-3507
• 0.4-mm id, 85%/15%, for 0.20 and 0.25-mm id columns 5062-3508
• 0.5-mm id, 85%/15%, for 0.32-mm id columns 5062-3506
For the GC inlet

Table 24 Miscellaneous parts and samples
Collision cell gas flow module, 3-channel G7002-60044
GC/MS quadrupole flow weldment cap assy G7000-80500
Quadrupole EPC module, 3-channel G7000-60506
Octafluoronaphthalene, OFN, 1 pg/µL 5188-5348
Octafluoronaphthalene, OFN, 100 fg/µL 5188-5348
Benzophenone, 100 pg/µL 8500-5440
PFTBA sample kit 05971-60571
Rough pump oil pan G1946-00034
Eval A, hydrocarbons 05971-60045
Micro-Ion gauge electronics G3170-89001
J20’ 1/8-inch id stainless steel 7157-0210
Wipes (qty 300) 9310-4828
Swagelok ferrule, front, 1/8-inch, 10/package 5180-4110
Swagelok ferrule, rear, 1/8-inch, 10/package 5180-4116
Swagelok nut, for 1/8-inch fitting, 10/package 5180-4104
Swagelok nut and ferrules, 10 set/package 5080-8751
Tubing cutter for SS tubing 8710-1709
Tubing cutter replacement blades 8710-1710

Additional CI Parts
This section shows parts that may be required to maintain the 7250 Q-TOF
GC/MS System with CI. (See Table 25.) The parts in this section are related
directly to the CI accessory and are in addition to the Axial CI ion source parts
listed in Table 19, “Parts list for Axial CI ion source,” on page 124.
Table 25 CI flow control module
CI calibration valve assembly G1999-60452
PFDTD calibrant 8500-8510
Calibration sample vial G3170-80002
Sample vial O-ring, 1/4-inch Viton 5180-4182
Solenoid valve and cable G1999-60452
CI cable from SC to CI flow module G3170-60808
Cable, CI to CI bulkhead G7000-60825
CI Flow control PCA G7000-61025
GF 100 Mass Flow Controller G7000-80030
Shutoff valve G1999-80402
MFC cable G1999-60464
Reagent gas select valve (Gas A and Gas B) G1999-80401
VCR cap, size 4 (1/4-inch) 0100-2013
Plug, size 4 316SS 0100-2014
VCR gasket, 1/4-inch, Ag on Ni retainer 0100-1436
VCR gasket, 1/8-inch 0100-0468
Chemical ionization gas purifier 5190-9071
Stainless steel tubing, 1/8-inch id, 20 feet 7157-0210
Swagelok ferrule, front, 1/8-inch, 20/package 5180-4110
Swagelok ferrule, rear, 1/8-inch, 20/package 5180-4116
Swagelok nut, for 1/8-inch fitting, 20/packages 5080-8751


www.agilent.com
Agilent Technologies, Inc. 2019
First Edition, January 2019
*G7250-90007*
G7250-90007

User Manual GC Ms System 7250 Qtof G7250 90007 en Agilent

Uploaded by

Copyright:

Available Formats

User Manual GC Ms System 7250 Qtof G7250 90007 en Agilent

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

User Manual GC Ms System 7250 Qtof G7250 90007 en Agilent

Uploaded by

Copyright:

Available Formats

Agilent 7250 Accurate-Mass Quadrupole

Time-of-Flight GC/MS System

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 3

4 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 5

6 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 7

The 7250 Accurate-Mass Quadrupole Time-of-Flight GC/MS System 11

7250 Accurate-Mass Q-TOF GC/MS Description 13

Side Panel AC Power Connectors 14

Back Panel Connectors 15

Interfacing Start Events to External Devices 16

Important Safety Warnings 18

Safety and Regulatory Certifications 21

Cleaning/Recycling the Product 24

Moving or Storing the MS 24

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 9

10 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual

The 7250 Accurate-Mass Quadrupole

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 11

12 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual

7250 Accurate-Mass Q-TOF GC/MS

MS power Front right Source GC power Oven door Drawer

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 13

Side Panel AC Power Connectors

Figure 2. Side panel power supply

Main power cord receptacle (top)

Foreline pump power receptacle (bottom)

14 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual

Back Panel Connectors

Figure 3. Back panel connections

Remote start connector

LAN (I/O) connector

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 15

Interfacing Start Events to External Devices

Remote start signals

16 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual

Start run input

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 17

Important Safety Warnings

Many internal parts of the MS carry dangerous

Electrostatic discharge is a threat to MS

18 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual

Precautions to take to prevent an explosion

The use of hydrogen gas is specifically prohibited with this product.

Failure to secure your MS as described above greatly increases the chance of

Many parts are dangerously hot

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 19

The foreline pump can cause burns if touched when operating.

The oil pan under the rotary vane foreline

Combustible materials (or flammable/nonflammable wicking material) placed

20 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual

Safety and Regulatory Certifications

South Korean Class A EMC Declaration

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 21

See accompanying instructions for more information.

Indicates a hot surface.

Indicates hazardous voltages.