Rev A - Text - USB

Alliance 2695
Table of Contents
Section Title
1 Alliance Overview
2 Theory of Operation
3 Configuration
4 Direct Functions
5 Injector rebuild
6 Alliance Diagnostics
7 Alliance Other Tests 1
10 Alliance Head Rebuild
11 Syringe & Drive
12 Method Development
13 Cleaing the Sample Compartment
Appendix A Selected Error Codes
Appendix B Priming procedures
Appendix C PM Kit Contents

Chapter One: Alliance Separations Module
Alliance Separations Module
Rev. 27510 Waters Confidential and Proprietary Information

Chapter 1: Page 1 of 14
 This course introduces you to the Waters™ 2695 Separations Module.

 The Separations Module is an integrated solvent and sample
management platform.
 The two primary configurations are as follows:
— 2695 - Provides quaternary solvent, high performance solvent delivery, a four-
channel in-line vacuum degasser, a sample heater/cooler, and an integral
plunger seal-wash system, 120-vial capacity sample management system, liquid
crystal
t l di
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 Cut away view of the 2695 showing the location of various

assemblies.

 Sample heater / cooler - can maintain sample compartment at

temperatures from 4 °C to 40 °C.
 Type I Column heater - can maintain column temperature from 5 °C
above ambient temperature (minimum 20 °C) to 60 °C.
 Type II Column heater - can maintain column temperature from 5 °C
above ambient temperature to 65 °C.
 Column heater / cooler – can maintain column temperature from 4 °C
C
to 65 °C
 Column switching valves - a motorized valve that allows flow to be
switched to one of several columns, 4 types available
Description Software Controlled by

Detection
2 Column (6port, 2 position) No I/O
3 Column Yes 2695 Software
6 Column Yes 2695 Software
2 Column – Regeneration Yes 2695 Software
(10 port, 2 position
 Barcode reader - can read bar code 128C labels attached to the vial

 The Alliance Separations Module uses a switching power supply, it

senses whether it is connected to 120 V or 240 V and configures itself
automatically.
 The power supply is short circuit protected and does not have
external replacement fuses. The power supply is reset by power
cycling the instrument.
 See Making Power Connections, in the Operator’s Guide.

 Analog I/O - Input; stop flow, hold inject and output; inject start,
chart out,4 switches, run stop.
 RS-232 - Two ports:

— A connects to a Waters 746 Data Module or serial printer.
— B connects to a non Waters or non-Micromass data system to control the
Separations Module.
 IEE-488 - Connects to a Waters detector (PDA, 2487, 486, 410 or

2410), Millennium or Empower data station, or Micromass MassLynx
computer.
 See Digital Signal Connections

Connections, in the Operator’s Guide

 The Analog Input / Output connections are the same on all the
Alliance Separations Modules.
 See I/O Signal Connections, in the Operator’s Guide.

 See Making Fluid Connections, in the Operator’s Guide.

 Solvent Lines: clear 1/8 inch OD tubing with stainless steel

sinker/filter
— Yellow Tag = Solvent A
— Blue Tag = Solvent B
— Red Tag = Solvent C
— Green Tag = Solvent D
 Plunger Wash: clear 1/8 inch OD tubing

— Green Tag with plastic sinker/filter
 Needle Wash: Green 1/16 inch OD tubing

 Degasser Vent: Clear 1/4 inch OD
 Plunger Wash: Clear 1/8 inch OD
 Purge / Vent: Clear 1/16 inch OD
 Needle Wash: Yellow 1/16 inch OD

 Outlet to Column: 1/16 inch, OD, 0.009 inch ID stainless steel, Red
Tag

 When the Alliance Separations module is powered ON, several

diagnostic routines are performed. Once these electronic tests are
complete, the front panel screen displays the results.



Chapter Two: Alliance Theory of Operation
Alliance Theory of Operation

Chapter 2 Page 1 of 25


 Degassing efficiency is based upon the solvent gas load and the
length of time the solvent remains in the chamber. Degassing
efficiency drops off above 4.5 ml/minute flow rate through a chamber.

 The solvent degasser has an internal volume of approximately 500 ul.

 The Gradient Proportioning Valve (GPV) has 4 solenoid valves, one for
each solvent reservoir (A,B,C,D). When a solvent valve is open, flow
from that solvent reservoir is allowed through the manifold to the
common outlet. From the common outlet the flow travels to the inlet
check valve of the Primary Head.
 The line from the degasser to the “D” port has been removed to show
the threaded fitting.

 1. Serial Flow Path – Solvent blending in piston chamber

 2. Independent Piston Drive – Dual drive motors
 3. Dual Pressure Transducers – Two point performance monitoring
 4. Variable Piston Volume – Balanced with flow rate
 5. Gradient Proportioning Valve – Low volume design

 1. High pressure fluid path (solid black)
 2. Seal wash tubing
 3. Head nut
 4. Locking ring

 FIFO - First in, first out results in mixing in heads. Gradients run
smoothly.

 The above slide shows the relative piston velocities for the primary
and accumulator pistons in the solvent management system for the
2695. The solvent management system components work together to
deliver solvent in the following sequence.
 The accumulator plunger (left plunger) moves forward delivering

solvent, while the primary plunger (right plunger) moves backwards
filling with solvent.
 While the accumulator continues to deliver solvent, the primary
plunger waits. The primary pressure transducer then measures the
pressure and matches it to the system pressure by moving the
primary plunger forward, pre-compressing the solvent.
 When the accumulator pplunger
g reaches the end of its stroke,, it slows
down and reverses direction. Simultaneously, the primary plunger
moves forward delivering solvent.
 While the accumulator plunger moves backwards, the primary plunger
moves forward slightly faster which allows the primary plunger stroke
to both fill the accumulator piston chamber and to deliver solvent to
the rest of the system

 The sample carrier includes the carousels. Its function is to position

the vials under the injector so samples can be withdrawn.
 The injector, and associated valves, withdraws the sample at

atmospheric pressure and inserts it into the high pressure solvent
stream.

 1 - Carousel Carrier Motor
 2 - Sample Carousel Motor
 3 - Sample Carousel
 4 - Carousel Carrier
 5 - Position Sensors
 6 – Z-axis motor

 1 - Injector Motor
 2 - Needle
 3 - Seal Pack
 4 - Position Sensors
 5 - Outlet Tube to Column

 Beginning in October 2005, a new injector design was implemented in the

2695 and 2695D instruments.
 The new injector assembly is compatible with earlier 2690/5 instruments, no
firmware upgrade is required to make use of this new style injector
assembly.
 All 2695’s and 2695D’s beginning with the following serial numbers have the
new Phase 2 injector.
Serial # Type
J05 SM4 035M 2695 with sample heater/cooler
J05 SM7 373M 2695 without sample heater/cooler
J05 SD6 228M 2695D, 6-sample
J05 SD8 225M 2695D, 8-sample
New Injector Assembly

P/N 700002789 Injector only
New Injector Upgrade Kit
P/N 70000279 Includes sample &
restrictor loop, bracket &
cable assemblies
New Seal Pak P/N 700002791 Pre-assembled

seal pak, compatible
with all earlier injectors

 The 2695 needle wash uses approximately 0.8 ml per injection.

 When the High Pressure Motorized Valve (HPMV) is closed, the cross
port in the spool is outside the flow path.
 When the valve opens, the cross port in the spool is pulled back
between the valve seals and flow can exit through the nose cap.

 The normal valve configuration is Valve 1 (inject) open, Valve 2

(syringe) closed, Valve 3 (vent) closed, Valve 4 (needle wash) closed.
 Because of the restrictor loop between Valve 1 and the injector, 95%
of the flow will go through the sample loop and 5 % will go through
the restrictor.
 For the next set of slides,

— Valve 1 = V1
— Valve 2 = V2
— Valve 3 = V3
— Valve 4 = V4

 At the start of the purge cycle,

— V1 closes,
— V3 opens,
— V2 opens, flow goes up the sample loop and out to waste.
— The syringe drives to its upper limit (Empty position).
 The Sample Loop Volumes applies only to this part of the purge cycle.
cycle

 In the second part of the purge cycle, V1 opens, 95% of the flow goes
through the connection from V1 to V2.
 The syringe drives to its lower limit (Full position), reverses direction
again and drives to its upper limit (Empty position), then returns to
its Home position.

 The third part of the purge cycle is optional.

 If you select to do a Compression Check;
— V1 closes.
— The needle lowers till the port is in the lower seal.
— V3 closes.
— The syringe is driven up to compress the mobile phase.
— The p
pressure limit can be set between 30 and 300 p
psi.

 The injection cycle starts from the Normal valve configuration.

100% flow
 At the injection start,

— V1 closes, all flow now passes through the restrictor.
— The needle lowers till the port is in the lower seal.
— V3 opens,
— V2 opens venting the pressure in the sample loop.
— V3 closes to prevent siphoning.
— The needle wash pump starts. V4 opens.

 With V3 closed,
— the needle lowers into the vial.
— V4 closes. The needle wash pump stops.
— The syringe plunger lowers pulling sample into the needle (27 motor steps / µL
for the 250 µL syringe).

 If the sample volume is greater than the syringe can draw (60% of
full capacity),
— V2 closes,
— V3 opens,
— The syringe expels the drawn volume,
— V3 closes,
— V2 opens and the syringe draws the remaining volume.
 If large sample volumes are being drawn, be sure to attach an

appropriate size auxiliary sample loop.

 When the total sample volume has been drawn into the sample loop,
— the needle rises until the port is in the lower seal,
— V3 opens,
— V2 closes,
— the syringe expels the drawn volume.
— V3 closes.
— The needle rises until the port is between the upper and lower seals. The sample
loop pressurizes.
— V1 opens, 95% of the flow goes through the sample loop delivering the sample
to the column.

Chapter Three: Alliance Configuration
Configuration

Configuration
 Before using the Separations Module, a variety of operating

parameters may need to be configured. The Configuration screen is
used to:
— Set up the Separations Module for the first time

— Change the configuration of the Separations Module
— Add, change, or delete a user
— Reset the clock
— Press Config, the configuration page is displayed

Configuration
 Syringe Size dialog box - Select the syringe size installed in the
Separations Module.
 The 250 µL syringe is standard. Optional sizes are 25 µL and 2500

µL.
 Verify the volume of the physical syringe and the volume displayed in
the Syringe Size: match.

Configuration
 The Loop Size: will accept any value from 0 to 999999 µL.

Configuration
 System dialog box - Select the appropriate operating mode.

 No Interaction - Use for standalone operation.
 System Controller - Use for standalone operation when controlling
Waters detectors over the IEEE-488 interface.
 Controlled by Empower - Use when Empower software controls the
HPLC system.
 Controlled by Millennium32 - Use when Version 3.2
3 2 or higher controls
the HPLC system.
 Controlled by MassLynx - Use when MassLynx software (Version 3.5
or higher) controls the HPLC system.
 Controlled by Millennium 2.XX - Use when Version 2.xx, controls the
HPLC System.
 Operate Gradient by Event In - Use when an auto sampler (external
to the Separations Module) initiates a chromatographic run by contact
closure.

Configuration
 Controlled via RS232 (binary) - Use when a non-Waters or non-

Micromass data system controls the Separations Module by RS-232
communications, using binary protocol.
 Controlled via RS232 (ASCII) - Use when a non-Waters or non-

Micromass data system controls the Separations Module by RS-232
communications, using ASCII protocol.

Configuration
 IEEE 488 Address: dialog box.
Note: Address #1 is not recognized as a valid IEEE-488 address by

Millennium.

Configuration
 Printer dialog box - Selects the type of printer and the baud (data
transfer) rate.
Note: If you set the printer to “None”, you must select “Disable
Reporting” in the Report Options dialog box.

Configuration
 The Baud rate is selectable between 1200, 2400, or 9600.
 The baud rate set on your printer and the Alliance must match.

Configuration
 Report Options dialog box. - Select any option and press any numeric
key to enable or disable the option
 Press Enter. An “X” in the box indicates the option is enabled.

Configuration
 Date Format dialog box - Select either month-day-year (USA style) or

day-month-year (rest of world)

Configuration
 Set Clock Dialog Box - Set current date and time.
Note: Time is set by 24 hour clock but displayed as a 12 hour clock.
 Press Set

Configuration
 Pressure Units dialog box - Pressure can be displayed in psi, bar, or

kPascal.
 14.5 psi = 1 bar

 1 psi = 6.895 kPascal

Configuration
 Alarm Sound dialog box - Select Beep once or Continuous

Configuration
 User names screen. User name is only helpful in the standalone

mode.
 Press Add, the text entry screen is displayed.

Configuration
 To enter a name, press the screen key for the appropriate letter
group, that group expands.
 For example, press the GHIJKL screen key.

Configuration
 The expanded GHIJKL screen.
 Press the appropriate letter, you will return to the text entry page.

Configuration
 The letter K was entered and the screen returned to the first text
entry page.
 Press the More screen key.

Configuration
 This screen allows you to backspace, overstrike, or use lowercase

letters in a text field.

Configuration
 Installed Options screen. This is a display only screen.
 Displays a list of the hardware options installed in the Separations

Module.

Configuration
 Events In Dialog Box - Specifies the external signal conditions to

enable Stop Flow and Inject Hold.
 Choices on pull down menus are Ignore, High, Low (TTL Logic).
 Logic choices are AND, OR
 Press OK, More and Compression Check.

Configuration
 Compression Check Dialog Box - Specifies criteria for the compression

check.
Function Range Typical
Compression
Pressure 30 - 300 psi 100 psi
Compressible Volume -
25 µL syringe 1 -15 µL 15 µL
250 µL syringe 5 - 30 µL 20 µL
2500 µL syringe 5 - 100 µL 50 µL
Decay Time - 0.1 - 5.0 min 1.0 min

Maximum Delta Decay -
10 - 100 psi <50 psi
 Press OK

Configuration
 Status Page Layout dialog box - Allows you to enable (see) or disable
(hide) various status boxes on the Status Page. Boxes can be raised
or lowered as to placement on the Status Pages.
 Highlighting a status box using the cursor arrows on the front panel
and press a numeric key to toggle enable/disable.

Configuration
 The Status page Layout menu scrolled to see the last two choices.

Configuration
 Auto-Shutdown dialog box - Select the separation method to be used

while the Separations Module is shut down.
Note: Only the initial conditions in the method you select are used.
 Press OK, then Exit.

Configuration
 When you exit from Configuration, this message appears.

Chapter Four: Direct Functions
Direct Functions

Direct Functions
In this section we cover Dry Prime, system Prime, Wet Prime, and
Purge Injector in detail.
Equilibrate - Brings the Separations Module to the initial conditions of

a specified separations method.
Condition Column - Runs the gradient in a specified separations

method without making an injection.
Inject Samples - Makes a series of injections from a specified vial

range.

Direct Functions

Direct Functions
2695 Status (1) Page
Press Direct Function

Direct Functions
Select the Dry Prime function, then press OK.

The Dry Prime screen allows you to prime each solvent line
individually, without delivering solvent. When you press one of the
“Prime” keys you should hear a click as the corresponding gradient
valve opens.
1. Open the draw off valve by turning it counter clockwise 1/2 turn and firmly
insert the Luer of the syringe into the valve.
2. While holding the syringe in place with one hand, draw back on the syringe with
the other hand to create the vacuum necessary to draw the
air out of the line.
3. Repeat this process until the solvent starts to flow into the syringe.
4. Repeat these steps to prime all 4 solvent lines.
5. Press a screen key corresponding to the solvent with which you wish to prime
the system.
Press Enter.
Note: You do not enter a flow rate for the dry prime. The module
gradually ramps up to a preprogrammed flow rate of 3 mL/min.
Attention: While the solvent is flowing, this is a good time to check all
fluid connections at the Gradient Proportioning Valves and the
Degasser to make sure there are no solvent leaks.

Direct Functions
Dry Prime Screen
Press Continue.

Direct Functions
Status screen (1st Page)
The timer in the upper right of the window shows the time remaining
until the dry prime flow ends.
The Direct Function is grayed out, indicating that function is not

available at this time.
time

Direct Functions
System Prep Screen
Press OK.

Direct Functions
Select an appropriate
Flow rate
% composition of mobile phase(s)
Press Next

Direct Functions
Select the desired solvents

Press Next

Direct Functions
Read the information on the screen to continue

Press Start (or cancel to return to main screen)

Direct Functions
Wet Prime screen

Press OK.
Wet Prime after dry priming the instrument. It is important to
perform a wet prime to remove any air bubbles that may be
potentially caught in either the vacuum degasser chamber or sparge
tubing. A wet prime is also performed when the fluidic path in the
solvent management system contains fluid and you want to change
reservoirs or solvents. The wet prime replaces fluid in the path from
the reservoirs to V1 and then to waste.
waste
Note: To avoid damage to the plunger seals, perform a wet prime only
when there is solvent in the solvent management system fluidic path.
Enter the flow rate and duration to prime (using the composition
entered in the Status screen), then press OK. The solvent
management system begins to operate. The duration of the prime
depends on the option installed in the Separations Module:
Option: Flow Rate (mL/min) Duration (min)

Performance Plus Degasser 7.5 2
Degasser Option 7.5 6
Sparge option 7.5 2
At the end of the specified time the flow stops and the unit returns to
the idle mode
mode.
Allow the degasser to run for 5 - 10 minutes with no solvent flow.

Direct Functions

Direct Functions

Direct Functions
At this point you can either press the Resume Prime key to continue
the Wet Prime or press the Abort Prime key to end the Wet Prime.
Press Next Page, the Status (2) screen is displayed.

Direct Functions
The Status (2) screen.
Press Direct Function.

Direct Functions
Once the Fluid Handling Unit has been primed, turn the Degasser ON.
The 2690 degasser modes are Disabled (Off), Normal (timed cycle),
and Continuous. A 2690 Separations Module with a Performance+
degasser should be run only in Continuous mode.
The 2695 (Performance Plus) degasser modes are ON and OFF.

OFF
Leave the degasser ON for 15 minutes with no solvent flow to allow

the solvent to become thoroughly degassed.

Direct Functions
Direct Functions screen
Select Purge Injector
Press OK.

Direct Functions
Purge Injector screen
Enter a minimum of 6 loop volumes
Select Compression check
Press Question Mark key.

Direct Functions
Help Message displayed for compression check box.
Press OK, the next help screen is displayed.

Direct Functions
Second help screen for “Compression check?”
Press the ?, an additional help screen is displayed.

Direct Functions
Additional help screen for “Compression check?”giving as brief

definition of a purge.
Press Exit and then press any Numeric Key, an “X” will fill the
“Compression check?”? box.

Direct Functions
Select Purge Injector dialog box with compression check?
Press OK.

Direct Functions
Status page (1) during Purge Injector.
This shows the first step of the purge, note the positions of the
valves.

Direct Functions
This shows the empty syringe step of the purge, note the positions
of the valves.

Direct Functions
The Separations Module is preparing for the compression check by

testing the column resistance.
Note: A column needs to be present in order to run the compression

check If there is no column resistance the compression test will fail.
check. fail

Direct Functions
Status page (2) during Compression Check

Direct Functions
Status page (2) during normal running.

Chapter Five: Injector Rebuild
Injector Rebuild

Chapter 5 : Page 1 of 49
Injector Rebuild
This section covers removing the injector, rebuilding the Seal Pack,
replacing the needle, and re-installing the injector into the
Separations Module.

Injector Rebuild
Removing Seal Pack

Power down the 2690/2695 Separations Module and disconnect
external power.
Remove the cover and right side panel to access the injector
assembly.
Disconnect the injector motor and sensor cables from the Fluidics
Driver board.
Disconnect the Green needle wash line from the upper seal wash
body tube (runs to V4) and the CLEAR needle wash line from the
lower seal wash body tube (runs to needle wash pump)
Remove the column from the RED line
Disconnect the yellow sample loop from the transducer.
Using a long flat
flat-blade
blade screwdriver, loosen the two captive mounting
screws securing the injector to the floor of the compartment.
Lift injector up and tilt slightly back to remove it from the instrument.
Disconnect stainless steel restrictor loop from the seal pack.
Remove RED line from the seal pack.

Injector Rebuild
Before removing the injector, power down the unit and remove the
power cord from the back of the instrument. This will protect the
PCB’s.

Injector Rebuild
Remove the cover by loosening the captive Phillips screw in the upper
left corner of the syringe compartment. (left photo above)
Slide the cover back and lift it off.

Injector Rebuild
Remove the right side panel by removing the two Phillips screws in
the dimples near the front edge of the side panel.

Injector Rebuild
With the right side panel removed, the injector and valves are visible.
This photo shows a 2690 Separations Module with an early Degasser

Module

Injector Rebuild
Remove the needle wash lines. They are press fit over the stainless
steel tubes.
Note: The needle wash inlet line (green) is connected to the upper
needle wash housing.

Injector Rebuild
Disconnect the sample loop (yellow) from the transducer.

Injector Rebuild
The power and sensor cables for the injector are dressed along the
2695 chassis to prevent their interfering with moving parts. The
cables are held in place with nylon clips.
Start at the injector and follow the cables to their connectors on the
driver PCB.

Injector Rebuild
Disconnect the sensor cable from the front edge of the PCB.
Disconnect the motor cable from the top of the PCB.
Both cables are keyed and have locking mechanisms holding them in
their respective connectors.

Injector Rebuild
The motor and sensor cables have latches on them to prevent the
connector from coming loose due to vibration.
The locking mechanism must be depressed to remove the connector

from the circuit board.

Injector Rebuild
Using a long flat-bladed screwdriver, loosen the two captive mounting

screws on the base of the injector assembly. These screws hold the
assembly to the compartment floor.
Lift the injector up and slightly back to remove it from the instrument.
Note: Do not lift the assembly too high or the restrictor loop will bend
out of shape. Although this will not effect the injector’s functioning,
the bent tubing may make re-installing the assembly into the
instrument difficult.

Injector Rebuild
Tip the injector assembly down as illustrated in the photo above.

Disconnect the restrictor loop from the seal pack.

Injector Rebuild
Remove the outlet (red) line from the seal pack.

Injector Rebuild
The Phase II injector restrictor loop and outlet line can be removed
without removing the injector from the chassis.
The Phase II injector is held in place by two captive Phillips head

screws. The sample loop fitting must also be loosened.

Injector Rebuild
Removing Seal Pack

Remove the injector from the instrument following the procedure on
previous page.
Turn injector assembly over and place on its motor end to position
seal pack up.
Drive the needle to the lowest position (towards motor) by manually
turning the worm gear
gear.
Note: Reposition the tab to between the sensors before re-installing and
trying to initialize.
On Performance PLUS seal wash housing, remove the frit retainer.
Remove the three screws with washers that secure the seal pack to
the injector baseplate.
Manually turn the motor shaft to drive the needle up until seal pack
assembly just lifts away from injector baseplate.
Hold onto seal pack and turn needle down to free seal pack from
injector needle.

Injector Rebuild
Turn the injector assembly over and place it on its motor to position
the seal pack up.
Pull the needle back by turning the lead screw until the slide is
touching the connector on the motor shaft.

Injector Rebuild
You must remove the frit retainer on the 2695 (Performance Plus or
Phase II) needle wash housing before removing the mounting screws.
With a Phillips screwdriver, remove the three screws with washers

that secure the seal pack to the injector base plate.
The Phase II Seal Pack can be mounted to the Phase I Injector

mechanism with no modifications required.
The Seal Pack is mounted to the Phase II Injector by four (4) M3 T10
TORX bolts.

Injector Rebuild
This view shows the three assemblies which make up the seal pack.
The Guide Tube is inserted through the center hole of three (3) on the
Performance Plus seal body and the center hole of five (5) on the
Phase II seal body.

Injector Rebuild
Manually turn the motor shaft to drive the needle forward until the
seal pack just lifts away from the injector base plate.
Hold onto the seal pack and turn the motor shaft to pull the needle
out of the seal pack.

Injector Rebuild
All Alliance Separations Modules manufactured since January 2001

have the Performance Plus needle wash housing and have the
following spare parts.
— WAT271019, Seal Pack Rebuild Kit
— WAT270942, Seal Pack Replacement Kit
— WAT270944, Performance Maintenance kit

Injector Rebuild
The new needle wash filter installed in the new frit retainer.
Remove the frit retainer from the lower needle wash body and
remove the needle wash filter.
Insert a new needle wash filter (415000230) into the retainer.

Injector Rebuild
Place the lower seal wash body frit retainer side down and, using the
plastic side of the seal removal tool (WAT039802) remove the seal.

Injector Rebuild
The seal insertion tool is used to install the plunger seal.
The tool on the left is as it comes from the molder. The tool on the
right has been “field modified” so it can be used to install the plunger
wash seals.

Injector Rebuild
Wet the new seal (WAT270668) and seal wash body thoroughly with
methanol or IPA and insert seal into the lower seal wash body, spring
side facing in using a modified seal insertion tool (WAT270969).

Injector Rebuild
Using the metal end of the seal removal tool (WAT039802), remove
the high pressure seals from the seal body.
It will be necessary to insert the removal tool at least two full turns
into the seal. These seals require a strong tug to remove them from
the body.

Injector Rebuild
Tools for installing the seals (WAT034497) are in the 715 valve rebuild
kit (WAT045427)
— Seal Punch - WAT045458
— Seal Guide - WAT045459

Injector Rebuild
Wet the seal (WAT033276) with methanol or isopropyl alcohol (IPA).

Injector Rebuild
Place the seal on the Punch, spring side visible.

Injector Rebuild
Place the seal guide on the seal body and wet with methanol or IPA

Injector Rebuild
Insert the seal into the seal guide and press down. It takes a
considerable amount of force to seat the seal in the seal body.

Injector Rebuild
Here the seal is fully seated in the seal body.
Repeat the process for the other side.

Injector Rebuild
Remove the frit retainer from the upper seal wash body and remove
the needle wash filter and TFE washer from the frit retainer.
Using the metal end of the seal removal tool (WAT039802) remove
the upper spacer from the upper seal wash body.
Part Part Number

Alignment Tube WAT031956
Teflon Washer WAT077321
Frit WAT072324
Upper Spacer WAT031957
Frit Retainer WAT212043 (not in PM Kit)

Injector Rebuild
Wet the new upper spacer (WAT031957) thoroughly with methanol or

compatible solvent and press into place in the upper seal wash body
using the flat end of a pen to seat the spacer.

Injector Rebuild
Insert a new TFE washer (WAT077321) and needle wash filter frit
(WAT072324) into the frit retainer.

Injector Rebuild
Turn the upper needle wash housing upside down and screw the
assembled parts into the upper seal wash body finger tight.

Injector Rebuild
Insert the guide tube into the housing after wetting it with Mesh or
IPA.

Injector Rebuild
Use a 5/16” wrench to loosen the compression screw and remove the
old needle.

Injector Rebuild
Use the old needle as a guide. Place the new compression screw
(WAT025313) and ferrule (WAT022330) onto the pointed end of the
old needle.
NOTE: Do not put the compression screw or ferrule over the pointed end
of the new needle.

Injector Rebuild
Insert the pointed end of the old needle into the fitting in the injector
slide and tighten finger tight. Remove the old needle.

Injector Rebuild
Holding the new needle by the blunt end, insert the blunt end into the
compression screw and ferrule which are aligned. Ensure the blunt
end is bottomed out in the fitting.
Tighten the compression screw one full turn to seat the ferrule onto
the needle.
Loosen the compression screw to align the needle.

Injector Rebuild
Align the needle by rotating the needle so the port in the needle is
aimed at the edge of the notch in the injector base plate for the seal
pack/injector.
This will ensure the port in the needle is aligned with the outlet port
of the seal pack to minimize band spreading.

Injector Rebuild
Use two 5/16 inch wrenches to loosen or tighten the needle fitting on
the Phase II injector assembly.
Insert the new needle in the Phase II injector the same way as in the
standard injector (pages 40-43)

Injector Rebuild
Align the needle by rotating the needle so the port in the needle is
aimed at the edge of the notch in the injector base plate for the
Phase II seal pack/injector.
This will ensure the port in the needle is aligned with the outlet port
of the seal pack to minimize band spreading.

Injector Rebuild
Wet the seal pack with methanol or IPA and slide it over the needle.
Install the three screws holding the seal pack to the injector base
plate.

Injector Rebuild
The new Phase II seal pack can be mounted to the old style injector
assembly using the three Phillips head screws that held the old seal
pack in place.

Injector Rebuild
Screw the frit retainer, with the new filter frit, into the lower seal
wash housing finger tight.

Injector Rebuild
Turn the lead screw to re-set the sensor flag between the upper and
lower sensors.
Reinstall the injector into the 2690/2695. Follow pages 5:16 to 5:8
(reverse of removing)
Helpful hint: Leave the cover and side panel off until all testing has
been successfully completed.

Chapter Six: Alliance Diagnostics
2695 Diagnostics

2695 Diagnostics
Prime Seal Wash - Fill/flush seal (plunger) wash system
Compression test - Checks low pressure side of injection system
Prime Needle Wash - Fill/flush needle wash system
Adjust Seals - Calibrates injector seal pack to the system
Service Utilities - Password protected
Other Tests - Most diagnostic tools located here

2695 Diagnostics
Main Screen
Press Diag, the diagnostics menu screen is displayed.

2695 Diagnostics
Diagnostics menu screen
Serial number is entered in Service Utilities
Lifetime Counters: Helpful to determine service intervals based on use

rather than by calendar. They cannot be reset.
Transducers:
— System = accumulator pump
— Primary = primary pump
— Sample = sample loop of injector
Press Prime SealWsh, the Prime Seal Wash dialog box is displayed.

2695 Diagnostics
Prime Seal Wash dialog box
Press Start.

2695 Diagnostics
Prime Seal Wash dialog box (Running)
Seal wash pump cycles once per second. Each pulse is 200 ml.
Priming may require applying a vacuum to the seal wash outlet.
Press Halt, then Close.

2695 Diagnostics
Return to Diagnostics screen
Note: All tests performed with degassed methanol.
Press Comp Check, the Compression Check idle screen is displayed.

2695 Diagnostics
Compression Check dialog box
Press Start
Note: The values seen were generated when the Purge Injector was
done in the Status-Direct page in this course.

2695 Diagnostics
Compression Check dialog box (Running)
The 2690 / 2695 require approximately 500 psi to perform a

compression check. The unit will determine flow rate to obtain the
required pressure.
If there is insufficient system pressure,

pressure the unit will not perform the
test and a “Restriction Missing” warning message will appear.

2695 Diagnostics
Compression Check dialog box
Press Close to accept the new values and return to the Diagnostics
screen.
Press Prime NdlWsh, the Needle Wash dialog box is displayed.

2695 Diagnostics
The Prime Needle Wash dialog box
Press Start, the function starts and runs for 0.5 minutes. It may be
necessary to elevate the needle wash reservoir and run the test more
than once to prime the needle wash. A spray of liquid will come out
the yellow line when the needle wash pump is primed.
At the end of the priming, press Close to return to Diagnostics page,
Press Adjust Seals, the Adjust Seals dialog box is displayed.

2695 Diagnostics
The Adjust Seals dialog box
The unit will generate approximately 1000 psi to perform this

procedure. The flow rate should be between 0.3 and 1.5 ml/min when
performing this procedure. Too slow a flow and the pressure may not
rise fast enough for the unit to find the seal edge. Too fast a flow can
damage the seal. If you cannot generate this pressure, the system
reports a “Restriction Missing” error.
When you first start the 2690 / 2695, after you change or rebuild the
seal pack, or as a check if you get a compression failed error.
Press Start.
Start

2695 Diagnostics
The test is performed on the Adjust Seal dialog box (Running)

After approximately 10 minutes, the adjustment is complete and the
seal pack numbers will be displayed in the Diagnostic screen.
Acceptable ranges for the Adjust Seal Pack diagnostic are as follows:
— Top 30 - 80 30 - 50 typical
— Bottom 80 - 200
— Width(Bottom - Top) 50 - 120 70 - 90 typical

2695 Diagnostics
The Adjust Seals dialog box (idle) screen showing the new and
previous values.
Press the Accept Results key; then, after returning to the

Diagnostics screen.
Press Service Utilities,

Utilities the Service Utilities dialog box is displayed.
displayed

2695 Diagnostics
The service utilities are password protected.

Chapter Seven: Alliance Diagnostics and Tests
Alliance Diagnostics
and Tests

and Tests

and Tests
Diagnostics screen
Press Other Tests key.

and Tests
Other Diagnostics menu screen
Select Motors and Valves
Press OK, the Motors and Valves diagnostic screen is displayed.

and Tests
Motors and Valves diagnostic screen
Place “X”, by typing any number, in the Needle Wash Pump block to
turn it on.(Valve and Needle Wash Pump states changed by pressing a
number key.)
Note: V3 must be open for V2 to open.

open

and Tests
Needle Position menu

— Stream - Port in needle is between the two seals in the seal pack. (normal
position)
— Seal - Port in needle is in the middle of the lower seal pack seal.
— Vial - Needle is in the sample vial.
— Wet - Needle is in the seal wash position
Press Exit key.

and Tests
Syringe Position menu

— Home - Plunger approximately 40 ml’s below upper limit switch
— Empty - Plunger at upper limit switch
— Full - Plunger at lower limit switch

and Tests
GPV menu
— GPV - Can be set to Solvent A, B, C, or D

and Tests
Sensors menu
If the instrument continually gives a “Missing Vial” error, the vial
sensor may be adjusted for greater sensitivity
To make this adjustment:
— 1. Remove the top cover.
— 2. Go to the Sensor Page ( Main Page, Diag, Other Tests, Sensors)
— 3.Observe the two LED
LED’s
s on the encoder box on the Fluidics PCB.
• The Green LED should be blinking continuously.
• The Yellow LED should blink when it sees light (no vial) and OFF when the light beam
is broken.
— 4. Remove the carousel and place your hand in the sample compartment to
break the light beam.
— 5. Turn the adjustment pot slowly counter-clockwise until the Yellow LED begins
to blink.
Note: This adjustment is effective to increase the vial sensor sensitivity
to consistently sense vials, however, the opposite is not true. You
cannot decrease the sensitivity so the device will not sense a vial
when the unit always sees a vial.

and Tests
Select Static Leak Test.

Press OK.
Note: Perform the static leak test whenever
— you suspect leakage in the inlet check valves or plunger seals
— you perform maintenance on the solvent management system
— you replace high pressure fluid path fittings internal to the 2690/2695 Solvent
g System
Manager y
before doing this test, run the system at 4500 psi for 5 minutes to energize the
seals
Required Materials
— Pin plug (WAT025566)
— Wrench, 5/16-inch, open end
— Wrench, 5/8-inch, open end (or adjustable)
— Waste container

and Tests
Step 1 of the Static Leak test
Note: Follow all directions as prompted on the display. DO NOT

jump ahead of or lag behind the directions.
Loosely does not mean finger tight.

and Tests

— Allow solvent to drip from the loose fitting.

and Tests

— Tighten using wrenches.

and Tests
Accumulator Test screen
Accumulator pressure ramped to 5000 psi. Pressure must reach this

level with 20% of the max stroke length of the plunger.
Maximum decay rate 300 psi/min (below rev.2.02), 600 psi/min (rev.
2 02 and higher) taken from 1 to 1.4
2.02 1 4 minutes after the pump arrives
at 5000 psi. (Cannot be under 4400 psi at the end of 1.4 min.)
While acquiring the decay rate the pressure in the primary may not
rise above 100 psi. This would indicate a leak in the accumulator
check valve.

and Tests
Primary Test Screen
At the end of 1.4 minutes, if the accumulator passes, the primary test
starts.
The pressure must reach 4000. Pressure must reach this level using
20% of the max stroke length of the plunger.
Maximum decay rate 300 psi/min (below rev 2 2.02),
02) 600 psi/min
taken from 2.5 to 2.9 minutes after the pump arrives at 5000 psi.
(Can not be under 3400 psi at the end of 2.9 min.)
During the primary test the pressure in the accumulator may not drop
below that in the primary.

and Tests
Test Passed screen
Remove the pin plug
Press Continue.

and Tests
Test results screen
Press Close, then return to Diagnostics screen.

and Tests
Select Valve Leak Test
Perform the valve leak test whenever you suspect leakage in the
sample management valves or the seal pack, or you perform
maintenance on the valves.
Required Materials
— Pin plug (WAT025566)
— Union (WAT097332)
— Wrenches, 5/16-inch, open end, two (or one 5/16-inch and one adjustable)
— Waste container

and Tests
Valve Leak Test screen, V1, in Other Diagnostics.
For the Valve Leak tests the pressure limit can be set by the operator.

and Tests
Valve Leak Test options menu
Option Components Tested

V1 Valve 1, the inject valve and the seal pack
V2 Valve 2, the syringe valve and the seal pack
Above seal Seal Pack, the upper part of the lower seal
Below seal Seal Pack, the lower part of the lower seal

and Tests
Step 1 of the Static Leak Test
Note: Follow all directions as prompted on the display. DO NOT jump

ahead of or lag behind the directions.
Attention: The following information is missing from the instructions on

the screen
screen, “attach a union (WAT097332) to the outlet end of the red
line”.
Loosely does not mean finger tight.
Press Continue.

and Tests
Step 2 of the Valve Leak Test

— Tighten the pin plug with wrenches, then press Continue.

and Tests
Valve Leak Test status screen for V1

and Tests
Valve Leak Test results screen
Maximum decay rate 600 psi/min

and Tests
Valve Leak Test screen for V2

and Tests
Valve Leak Test screen for “Above seal”
This test option checks for solvent leaking by the upper portion of the
lower seal of the injector.

and Tests
Valve Leak Test screen for “Below seal”
This test option checks for solvent leaking by the lower portion of the
lower seal of the injector.

Chapter Eight: Alliance Diagnostics and Tests (2)
Rev. 27510 Waters Confidential and Proprietary Information Chapter 8: Page 1 of 19


From the Main Page, select Diag, select Other Tests,
Scroll to Inputs and outputs, the inputs and outputs diagnostics

screen is displayed.

The Inputs and Output diagnostic allows you to view the status of
input and output connections.
See Diagnostics section in the Operator’s Guide.

Scroll to Keypad, the keypad diagnostic screen is displayed.

The Keypad diagnostic allows you to test the keys on the front panel
of the Separations Module. The corresponding key in the diagnostic
changes appearance when the front panel key is pressed.

Scroll to Carousel, the Carousel test screen is displayed.
The Carousel test allows you to test the:

— Vial sensor
— Carousel ID sensor
— Carousel drive
— Bar code reader, if installed
Use this test if you experience problems with the carousel carrier
system.

Carousel Test screen
Type in a New Vial number and press Go To Vial.

If there is no vial in the position the carousel is sent to, the above
message is displayed.

Scroll to Sample heater/cooler, the Sample Heater/Cooler test screen

is displayed.

The Sample Heater/Cooler test screen.
Press the ? Key on the front panel.

Help message for the Sample Heater/Cooler test.

Sample Heater/Cooler test, equilibrating the thermal devices.

Sample Heater/Cooler test, cooling the sample chamber.

Sample Heater/Cooler test, results.

Scroll to Defrost sample cooler, the Sample heater/cooler, Defrost

dialog screen is displayed.

Sample Heater/Cooler Defrost dialog screen.
Press Start.

Defrost instruction screen.

Sample Heater/Cooler Defrost screen, function running.

Chapter Nine: Alliance Diagnostics and Tests (3)


The valve rebuild kit contains:
Description Part # Qty
Assy, Nut & Spool WAT045266 1
M715 Seal WAT045454 2
O-Ring, Teflon WAT097387 1
Seal Insert WAT021132 1

HPMV - High Pressure Motorized Valve.


From the Main Page

Select Diag,
Select Other Tests
Scroll to Rebuild injector valves, the Rebuild injector valves utility

screen is displayed.

Injector Valve Rebuild Utility screen
Materials required
— Rebuild kit WAT45426 (contains seal body with seals) or
— Kit WAT45427 (1 time) and WAT45424 rebuild kit (w/o SS seal body) that
contains just the seals, spool, and O ring.
— Torx screwdriver (T-10)
( )
— Wash bottle with MeOH or IPA
— Waste container

Remove the cover from the Separations Module.
Use the 5/16 inch open end wrench to remove the three fluid fittings
on the valve to be rebuilt. This picture shows Valve 2.
The solvent line to Valve 3 has been removed for photography

purposes.
purposes

There are 4 Torx screws (T-10) holding the valve assembly together.

Pull the Nose Cap straight off.

Pull the seal body and backing plate straight off.

With these removed, the spool is visible.

Drive the spool out of the valve by pressing Reverse.

This photo shows the alignment pin in the valve housing and the
groove in the spool assembly. The pin and groove prevent the spool
from rotating when the motor turns.

This photo shows the alignment guide in the new polymeric valve
housing and the groove in the spool assembly. The guide and groove
prevent the spool from rotating when the motor turns.

Press Forward while gently against the spool to help engage it into
the valve.

Retract the spool by pressing Forward again.

Remove both old seals from the valve body by turning the seal
removal tool (#4 brass wood screw) one full turn into the seal and
pulling the seal out.
Wash the valve body with methanol or isopropyl alcohol to remove

any particulate matter.

Place the seal guide (WAT045458) over the valve body.
Place the seal (WAT045454) on the seal punch (WAT045459) so you

can see the internal spring.
Wet the seal guide and seal with methanol (MeOH) or isopropyl
alcohol (IPA).
(IPA)

With the valve body on a smooth, hard, flat surface (bench top)
carefully insert the seal into the seal guide and press down to seat
the seal in the valve body.
Turn the valve body over and repeat for the second seal.

Install the backing plate.

Install the shaft of the seal insert into the spool.

Wet the seals with MeOH or IPA.

Being careful not to exert any side force, slide the valve body over the
seal insert and spool.
Note: The through ports on the seal body are vertical. The valve will
work if the ports are horizontal, but the fitting tubing will not reach
the ports.

IMPORTANT! Remove the seal insert from the spool. If you do not
remove the insert, the controlled valve outlet will be plugged once the
valve is re-assembled.

Remove the Teflon O-ring from the nose cap of the valve. Be careful
not to scratch the sealing surfaces.
Wet the new O-ring (WAT097387) with methanol or isopropyl alcohol

and press it into the grove in the nose cap.
Slide the nose cap over the spool

spool. Make sure the O-ring
O ring stays in the
groove.

Align the 4 mounting holes in the Nose Cap, Seal Body, and Backing
Plate to install the mounting screws.

Re-connect the three fluid fittings, and tighten them.
Purge the system to remove air from the lines.

Scroll to Turn off GPV, the GPV is off screen is displayed.

All 4 valves in the GPV are now closed.
Pressing OK will return the GPV to the normal state.

Select Create GPV Test Method, then Press OK, the Diagnostics page
is displayed.
Press Exit to return to the Main Page, press Develop Methods.

The GPV Method Set is shown on the Methods page.

Scroll to Firmware checksum, the Firmware checksum screen is

displayed

The Firmware checksum for Version:

— 1.20 (2690) = 11E55753H
— 1.21 (2690) = BED5D6C7H
— 1.22 (2690) = 16E65888H
— 2.00 (2695) = 48ED5EFH
— 2.01 (2695) = not released to field
— 2.02 (2695) = 387B4E11H

Chapter Ten: Alliance Head Rebuild
Alliance Head Rebuild


From the Main Screen
Press Diag, the Diagnostics screen is displayed.

From the Diagnostics menu screen
Press Other Tests, the Other Diagnostics menu is displayed.

On the Other Diagnostics menu, scroll down to
Head removal & replacement, Press OK or Enter, the Head Removal

& Replacement screen is displayed.

Select the primary (right side) head
Press Start.

Page 2 of instructions
Follow the instructions, do not get ahead of, or fall behind the
instructions .
Press Continue.

Once you have removed the head and plunger assembly from the
instrument, press Continue.

Remove the check valve housing from the Primary (right pump) and
replace the check valve cartridge ( part #:WAT270941).
Be sure to insert the check valve cartridge with the arrow pointing up,
as installed in the pump manifold.
Note: The outlet (top) of the check valve has two holes.

Open the solvent conditioning system and the solvent delivery system
doors.
Loosen the captive retaining screws on the trays and pull the trays
forward. This will make it easier to work on the heads.

The 2695 now comes with Performance PLUS check valve housings.

The arrow indicates the outlet of the check valve.

If you have problems with the check valves sticking, there is an
optional ceramic check valve for those applications.
The C identifies the ceramic check valve
Part number 700002399 package of 2.

Standard Housings
— Using a ½” open end or an adjustable wrench, hold the check valve housing and
loosen & remove the compression fitting.
— Loosen the check valve housing and remove the check valve assembly.
Performance Plus Housings

— Using
g a ¼” open
p end wrench,, hold onto the center of the housing.
g
— Using a ½” or an adjustable wrench, loosen the housing.

Pull the housing from the head and remove the check valve assembly.

Install the new check valve assembly in the housing.
Reinstall the housing back into the manifold and tighten.

Note: This is properly installed with the Check Valve extending out of
the housing.
The seal surface is on the top and bottom, the extended portion does
not effect the functionality.

This is how the assembly looks when it is removed from the pump.

Gently separate the pump head, plunger wash, and plunger

assemblies.

The PM kit contains two new plunger assemblies (WAT270488), one

for each pump.

Exploded view of the head assembly with seals.

The center seal is the plunger seal (WAT270789)
The two seals at the edge of the head are the face seals
(WAT270163).

Remove the plunger seal using the plastic end of the seal removal tool
(WAT039802).

Remove the face seals using the plastic end of the seal removal tool.

Wet the face seals with methanol or IPA and insert the new face seals
into the head. There is no orientation to the face seals.
Use the edge of a credit card or ID badge to press the seal into the
head. Be careful not to scratch or leave any particles on the seals
when installing them

Wet the plunger seal, head and tool with methanol or IPA and install
the seal into the head.

Push the seal in until the tool is against the head.

The seal wash face seal (WAT270481) is not replaced as part of a

routine performance maintenance.

Front (lower right) and back (upper left) views of the plunger wash
assembly.
The stainless steel plunger wash body and washer are re-used.

Use the plastic end of the seal removal tool to pull the plunger wash
seals from the plunger wash body.

Use a modified seal insertion tool to insert new seals in the plunger
wash body.
Wet the seals and plunger wash body with MeOH or IPA before
inserting the seals.

Wet the plunger seal, plunger wash seal, and the plunger with
methanol or IPA before re-assembling them.
Hold the plunger near the end, as shown above, to help prevent
breaking the plunger while installing it through the seals.

Make sure you see this page before re-inserting the head and plunger
assembly into the instrument.
Do as instructed and press Continue.

Do as instructed and press Continue.
You will return to the first Head Removal & Replacement screen.

Select the Accumulator (left side)

Press Start.
Repeat the steps on pages 7 through 27 to rebuild the Accumulator

head.
Note: Do not get ahead or fall behind the directions on the screen.
When you have completed rebuilding the accumulator head,

Press Close, the exiting screen is displayed.

The exiting head removal mode screen.
When the instrument has exited the head removal mode, the
Diagnostics screen will be displayed.
A Static Leak Test or flow rate accuracy test should be performed

after rebuilding the pump heads.
heads Wet Prime the Separations Module
before beginning the test.
Before performing the Static Leak Test, run the Separations Module at
4500 PSI for 5 minutes to “energize” the seals.

Chapter Eleven: Alliance Syringe and Drive
Alliance Syringe and Drive

Rev. 27510 Chapter 11: Page 2 of 13

Syringe size is set on the CONFIG page.
Draw rate is set on page 2 of the Separations Method editor on the

2690/5 or in the Instrument Method editor in Millennium32 or
Empower.

There are two versions of the syringe drive. They are

interchangeable.

Set the flow to 0 ml/min
Remove the knurled lock nut that holds the plunger to the
syringe guide mounting bracket.

From the Main Menu:

Press the Diag key,
Press the Other Tests key,
Press the Motors and Valves key
— Open Valve 3
— Select Syringe Position: Full
The syringe guide bracket will move down, the plunger will not move
since the knurled knob has been removed.

Unscrew the syringe from the mounting block.

Wet the plunger tip in mobile phase.
Insert the plunger into the barrel of the syringe.
Note: Do not push the plunger all the way into the syringe body. Doing
so may push the end seal out of the syringe, damaging the device.

Draw some mobile phase into the syringe.
Remove the air from the syringe so the plunger tip is wet and any air
bubbles are at least 1/2 inch (1cm) above the plunger tip.

Screw the syringe into the mounting block, but do not tighten it yet.
Slide the plunger down until the threaded end is through the guide
bracket.
Tighten the syringe finger tight.

Select Syringe Position: Empty.
The syringe will move to the top position expelling the air from the
top of the syringe.

Place and tighten the knurled knob on the threaded end of the
plunger.

Select Syringe Position: HOME
The syringe will move down to its home position.
Press Normal States, the instrument will re-initialize all the valves.
Go to the Status page, press Direct Function.
Run a purge with compression check to verify the syringe has been
installed properly.

Chapter Twelve: Alliance Develop Methods
Alliance Develop Methods
Rev. 27510 Waters Confidential and Proprietary Information Chapter 12 : Page 1 of 38


Main Screen
Press Develop Methods.

To view Develop Methods

Press Edit (at bottom left of screen)
Press Exit
Note “Delete” is grayed out (can’t delete default)
See the Operator’s Manual for proper use of the AutoStartPLUS

sample set and separations methods.
Press More.

Methods Screen (2nd page) at bottom left
Note:“Rename” and “Make Tpl” are blanked out (not available) Tpl
= Template
Press More.

Arrive at Methods Screen with “Export” and “Import”
Press More,
Return to 1st Methods screen
Press New.

Arrive at New Method screen editor
Press Separation Method key

Type in a name
Press Enter.

1st of 6 pages which shows bubble defect options
Press Gradient key.

Gradient Table screen
Fill-in information as needed
Press Exit.

Return to 1st screen of Separation Methods

Press Degas key,
Read Degas Editor and make choices (default = ON)
Press OK.

From 1st screen
Press Strk Vol/Seal Wash

Press Enter
Choose Stroke Volume (130μL)
Press OK
Pump Seal Wash Period (leave at default)
Note: The module is shipped with the stroke volume set at 130 μL
stroke volume does not affect flow rate

Press “?” (help)

Press “?” and read “Seal Wash Pump” help
Press Exit to leave help,
Press OK to leave Other Parameters Editor
Press Next.

Sample screen (page 2)
Sample temperature range: 4 °C – 40 °C
Press “?”

Help Message for “On Error”
Press EXIT to return to (2).

Syringe Draw Rates screen

Select Normal
Press Enter

Help for “Draw Rates”

Help for “Needle Depth”
A depth of 0 is 3 mm from needle tip to bottom of vial and 5 mm

above point for hole depth which = 8 mm to start.
Set Needle Depth to 2 mm for LVI’s,
Press Exit, then Next.

Arrive at screen 3, Autosampler parameters

Help for “Pre-Column Volume”
Press Exit

Select Needle Wash

Press Enter
Settings are:
— Normal – (default value) Needle wash runs for 13 seconds, ~800 μL of wash
solvent used per injection
— Double – Needle wash runs for 26 seconds, ~ 1600 μL of wash solvent used
per injection
— Extended – Needle wash runs for 52 seconds, ~ 3200 μL of wash solvent
used per injection
Press Enter to leave settings at default (=normal)

Help on Needle Wash

Press Exit
Press Next

Column screen (4)
Press Next.

Switch choices are:

— On
— Off
— Toggle
— Pulse
— No Change (default)
Leave at default
Select Chart Output

I/O screen 5 of 6
Chart Output menu, top half

I/O screen 5 of 6
Chart Output menu, bottom half
Press Next.

Screen 6 of 6 Detectors
Absorbance Detector choices are

— Not used
— 486
— 2487
Refractive Index Detector choices are

— Not used
— 410/2410.
— A 2414 controlled by an Alliance Separations Module will be seen as a 410.
Press Exit.

Parameter dialog boxes for the UV/Vis and R/I detectors.

Save Changes screen
Press Yes,
Return to Methods screen
Press Run.

Arrive at Run Samples Methods screen
Functional View, top half of function list

Sample Set screen, filled table; Auto Standards row highlighted
Press Row Details.

Run Samples screen, Auto Standards menu
Press OK.

Run Samples screen
Press Next View

Run Samples screen, shows Carousel Loading View
Press Exit.

Save Changes screen
Press Yes.

Save As Sample screen
Press Enter.

Run samples screen, Quit view
Push Yes.

Return to Methods View
See New Sample Set
Press Exit.

Chapter Thirteen: Cleaning the Sample Compartment
Cleaning the Sample Compartment

Open the solvent conditioning, solvent delivery, and syringe

compartment doors.
Open the sample compartment door and remove the carousels from
the compartment using the carousel advance function on the display
window.
After removing all the carousels, bring the carrier to the “A” position

There are two captive Allen screws (see above) that hold the
front panel in place.

Loosen the captive screws using a 3 mm Allen wrench.

Pull the bottom of the front panel forward and lower it away from the
instrument

Press down on both sides of the metal bar as indicated above.
Slide the carrier towards you.

Once the carrier is removed, the carrier and compartment can be

cleaned using an appropriate cleaning solvent.
After cleaning the sample compartment and carrier, replace the

carrier.
The “A” carousel position must be facing the front of the

compartment.

Press down on both sides of the metal bar indicated above and slide
the carrier over the carrier drive axel.

Place the top of the front panel in place and swing the bottom in
towards the instrument.
Note: It may require some wiggling to get the front panel over the
diskette drive.

Tighten both captive 3 mm Allen screws to secure the front panel to

the instrument.
Replace the carousels.

Appendix A: Selected 2690/5 Error Codes
Error Codes

Appendix A: Page 1 of 22
Error Codes
Selected Alliance Error Codes

1 Bubble
1. B bbl found
f d on compression
i 2
2. Carousel Z axis malfunction 5
3. Clearing Memory 6
4. Column temp h/w fault
— (1= communications, 2= watchdog, 3=h/w over temp, 4= internal fan, 5= not
implemented,
p , 6 thermistor)) 7
5. Compression check failed 7
6. Compression leak test failed 7
7. Degasser pressure fault 8
8. Fatal Error 9
9. Lost Prime 10
10.Missing Vial 11
11.Needle Malfunction 12
12.Sample syringe over pressure 12
13.Sample temp h/w fault
— (1=communications, 2=watchdog, 3=h/w over temp, 4=internal fan,
5=externall ffan, 6=thermistor
6 h i high,
hi h 7=thermistor
h i llow))
13
14.Seal pack geometry fault (1=seal too high, 2=seal too low, 3=seal too
wide, 4=seal too narrow) 13
15.Solvent delivery h/w fault 14
16.Solvent delivery
y motor lost sync
y
(0=Primary, 1=Accumulator) 14
17.Transducer range (volts) 15

Error Codes
1. Bubble found on compression

The 2690/5/ has a diagnostic
g feature to detect the p
presence of g
gas ((bubbles)) in
the fluid stream of the Solvent Management System. This diagnostic feature
can also be used to troubleshoot when a bubble detection error occurs.
Once a bubble is detected, the Solvent Management System implements a

recovery sequence that increases the stroke volume while maintaining the
flow rate and composition. During this process, pressure ripple as high as
40% may be observed. Although composition is maintained, the increase in
stroke volume draws in larger packets of mobile phase. Therefore, shifting
off retention
t ti ti
times may bbe noticed
ti d ddue tto a difference
diff iin mobile
bil phase
h
mixing at the time of the recovery sequence. Successful recovery results in
full restoration of the programmed stroke volume and continuation of the
separation. Unsuccessful recovery is dependent upon the programmed
bubble detect alarm setting.
Bubble detection is based on sensing the ratio of Compression to

Decompression volume, which can be viewed in Service Utilities. If the C/D
ratio exceeds the threshold,
threshold a "Bubble Detection" error will occur.
occur When this
occurs, the gas-to-liquid content of the mobile phase is beyond the
instrument's ability to accurately meter the solvent mixture.
Monitoring the C/D ratio will give a good indication of the gas-to-liquid content.
This reference list shows the C/D ratio and expectations of conditions.
C/D Ratio Description

1.1 Theoretically perfect
(physically impossible to attain perfection)
1.1 Exceptionally great values
1.2 - 1.4 Normal values
1.5 - 1.7 Gas-to-liquid content increasing
1.8 Bubble Detection occurs
Definitions:
Compression - Compression value of the Primary Piston Cycle. Compression
(forward movement of the plunger) of the mobile phase to bring the Primary
operational pressure from 0psi to System operating pressure prior to
delivery stroke.
Decompression - Decompression value of the Primary Piston Cycle.

Cycle
Decompression (reverse movement of the plunger) of the mobile phase to
bring the Primary operational pressure from System operating pressure
back to 0psi to following the delivery stroke.
C/D Ratio - The calculated ratio value of the Compression/Decompression

values.
The criteria for a bubble to be detected is:

Error Codes
1. If the System pressure is above 650psi in the first cycle in which the C/D ratio is
greater than 1.8 and the C/D ratio remains above 1.8 for the next five consecutive
pump cycles
l (f
(for a ttotal
t l off 6 cycles).
l )
An excessive ratio value suggests that either the intake stroke has a bubble or that the
mobile phase has a higher than normal gas content.
It is important to understand the amount of time it takes to fully recover from a

detected bubble. There are several steps that contribute to the time it takes to
complete this process.
process The time to clear a bubble is dependent on: (1) Programmed
flow rate setting. (2) Programmed piston stroke volume. (3) Bubble
detection/recovery sequence.
1. Armed - always monitoring at C/D ratio value.

2. Detected - C/D value of 1.8 or above is detected, waits then rechecks to eliminate
false detection. 6 cycles
3. Recovery - steps to 135ul-stroke volume, one step up stroke sequence per cycle.
10 cycles
4. Restore - steps back to original set stroke volume, (example: from 135ul back to
25ul = 4 cycles) X # cycles
5. Waits - wait state buffer before being Armed. 6 cycles
Bubble detection is method specific. It is programmed in the Mobile Phase screen of the
method.
h d Programming off this
h alarm
l will
ll d
determine iff this
h ffunction is active.
Alarm Response Description
Disable - Recovery will not be performed when a bubble is detected, the error will not
be logged.
Log Quietly -No audible or visual display alert, reports to error log only, bubble
recovery will
ill b
be automatically
t ti ll performed.
f d
Alert User - Audible alert and visual display notification box will occur, reports to error
log, bubble recovery will be automatically performed.
Stop Function - Current operation will be suspended following completion, audible
alert and visual display notification box will occur, reports to error log, recovery
sequence will not occur.
Stop Flow - Solvent delivery flow is stopped, current operation will be suspended,
audible alert and visual display
p y notification box will occur,, reports
p to error log,
g,
recovery sequence will not occur.
Note: Bubble Detection is always active. After a bubble has been detected, the alarm
setting will determine if the solvent delivery system must continue to the recovery
stage. Or if this alarm is disabled, do not continue to the recovery stage. If "Log
Quietly" or "Alert User" is programmed and a bubble continues to be detected, the
Detection/Recovery algorithm will continue indefinitely.

Error Codes
The C/D Ratio can be used for troubleshooting and diagnosing symptoms that
relate to a Bubble Detection error. First, y
you must ensure all the solvent
lines have been primed in the proper fashion. For a proper comparison it is
best to have all four solvent lines contain the same mobile phase. You must
also ensure proper solvent conditioning has been programmed and verify
that there is no related solvent conditioning errors logged. Once this criteria
is met this diagnostic can now be used.
1. Program Solvent Conditioning (for example Degasser=Continuous,

S
Sparge=100%),
100%) then
th let
l t restt att 0mL
0 L for
f 5 minutes.
i t
2. Set the composition to 100% Solvent Line A
3. Program a 1mL-flow rate.
4. Go to Service Utilities. Main Page-Diag-Service Util-Password=1147.
5. Monitor the C/D Ratio for 5 minutes. Record the average C/D ratio for
Solvent Line A.
6 Change the composition to 100% Solvent Line B.
6. B
Solvent Line B.
8. Change the composition to 100% Solvent Line C.
Solvent Line C.
10.Change the composition to 100% Solvent Line D.
11.Monitor the C/D Ratio for 5 minutes. Record the average C/D ratio for
Solvent Line D.
After the C/D ratios for each solvent line has been recorded, the next step is to
use the C/D ratios as an indicator to help determine the cause of failure.
A solvent line with C/D ratios at 1.8 or above should be targeted to determine
failure. It can be any fluidic path component failure for those specific solvent
lines with elevated C/D ratios. Including improperly primed solvent lines,
restricted solvent sink filters, solvent tube failure, loose fittings to/from
degasser chambers, inefficient degasser chambers, and GPV leakage.
If all the solvent lines have elevated C/D ratios then the problem is most likely
do to some component in common with all the solvent lines. Targeting the
tubing connections at the output of the GPV, GPV outlet tubing connections,
primary inlet check valve, check valve housing tightness, Primary Head
Plunger Seal, Primary Head Face Seals, head and head nut tightness could
also be suspect to cause this failure.
Rather than allowing the system to drive the plungers in the “auto” mode,
bubbles may be more effectively cleared by forcing the system to operate
with a stroke length of 100 μL.

Error Codes
L e n g t h
135 135u l B u b b le R eco very M o d e
130 130u l
120 120u l
100 100u l
S t r o k e
50 50u l
25 25u l (25ul only with degas ser)
0 0.53 1.23 3.03 5.0 10.0

F l o w R a t e
2. Carousel Z axis malfunction
Optical fence
Carousel Drive Operation Each time a carousel is in the LOAD position, the adjacent
carousel is located under the carousel dog pin shaft assembly. Just as the carrier
rotates to position and identify carousels,

Error Codes
The individual sample carousels must be rotated to locate specific sample vials. This is
accomplished by two stepper motors within the carousel drive mechanism and is a
multistep
lti t process. Fi
First,
t th
the sample
l carousell mustt b
be engageddb by th
the carousell
RAM shaft assembly. This is accomplished by a linear actuator motor located at the
top of the carousel drive mechanism and a dog-pin shaft at the bottom of this
mechanism. The linear actuator motor drives the entire carousel motor lift housing
and dog pin shaft down and engages the sample carousel. The dog pin shaft is so
named because of the right-angled pin at the bottom, which fits into a similarly
shaped slot in the center of each sample carousel. When the dog pin engages a
sample carousel, an optical fence, attached to the dog-pin shaft, drops into a
sensor within the carousel drive mechanism. The corresponding
p g DOG PIN LED -
DS38 on the Fluidics Driver PCB lights.
If you get a Z axis malfunction:

1. Inspect the optical fence and insure that it is parallel to the base of the carousel
drive. If the fence has gone into the sensor and wobbles so that light is detected
when it shouldn’t be seen you get the error.
2. The sensor may be too low.
3. The optical fence may be hitting the top of the sensor bracket.
4. Insure that the adjacent cables haven’t migrated under the fence.
3. Clearing Memory
For diagnostic purposes, the 2690/5 has a set of key sequences to allow the clearing of
specific data.
Upon power up the 2690/5 will perform an initialization routine. Approximately 21
seconds after power up, the instrument will give three quick audible beeps. Then,
the Alliance logo appears.
Immediately after the three audible beeps are heard, press the appropriate Clear key
combination
bi ti sequentially.
ti ll A clear
l message will
ill th
then b
be di
displayed.
l d
The following key sequences must be performed:

Clear 8 – Erases all methods, user and instrument configuration data, (including seal
pack data). This will not clear the instrument serial number or set the seal wash
pump option to be present.
Clear + Softkey1 – Zeros all lifetime data
Cl
Clear + Softkey2
S ftk 2 – Erases
E error llog d
data
t
Clear + Softkey3 – Erases trace log data
Clear + 0 (zero) – Clears everything, equivalent to performing all four sets of
above key sequences.
Note: Softkey1 is the leftmost softkey under the main menu, softkey2 is to the right
of 1 , and so forth.
Caution: Use these codes with caution
caution. It is impossible to recover cleared data.
data

Error Codes
4. Column temp h/w fault (1= communications, 2= watchdog, 3=h/w

over temp, 4= internal fan, 5= not implemented, 6 thermistor)
1. Errors 1 and 2 are both communications errors. Power down and check for
loose cables and connectors.
2. To correct error 3, open up the temperature window. The value may be set
from 1 to 20 degrees C.
3. Error 4: The software monitors the circulating fan motor amperage. If

there is a problem with the motor the amperage rises and the error is
displayed and the heater is shut off.
4. Error 6, Thermistor, the RTD has failed.
5. Compression
i check
h k ffailed
il d
The default compression parameters are 300 psi and 20 l. If the system can
not achieve the 300 psi using 20 l of volume or less this error is displayed.
Things that could cause this error are:
1. Undegassed solvent
2 Leaking
2. L ki syringe
i plunger
l
3. Leaking V3
4. Air in the sample management system
5. A leak in the sample management system
6. Improperly adjusted seals
7. Allowable volume (5 – 30 μL ) too small
6 Compression
6. C i leak
l k test
t t failed
f il d
This error is displayed after the system passes the compression check. The
second half of the check is monitoring the pressure decay once the system
arrived at pressure. The default value is wait 1 minute and the pressure
shouldn’t have fallen more than 50 psi. Causes for failure:
1 Undegassed solvent
1.

Error Codes
2. Leaking syringe plunger
3. Leaking V3
4. Too much time after the system reaches pressure (.1 to 5 minutes)
and/or too small a pressure decay allowed (10 to 100 psi)
5. A leak
l k in the
h sample
l management system
6. Improperly adjusted seals
7. Degasser pressure fault
On the older type 2690/5’s (pre 11/98) the pressure in the degassing
chambers had to get below –9.8 psig and maintain an acceptable leak
rate in the “normal” configuration. In the newer 2690/5’s (after
3/99) the systems use absolute pressure and these systems must
drop below 4 psi.
Vacuum pump
PCB
Bleed valve
Vacuum chambers
To troubleshoot the vacuum system:

1. Clip a hemostat to the plastic tubing to the chambers between the
valve/PCB. See if the system will generate a vacuum. If it does,
move the hemostat and isolate a pair of the chambers.
chambers If a vacuum
results the problem must lie in the tubing associated with and/or the
other pair of chambers.
2. If no vacuum is detected on just the pump, valve, and PCB use a

syringe to pull a vacuum on just the PCB. If there is no reaction, the
PCB is bad.

Error Codes
3. If the PCB is OK check all of the tubing and the vacuum pump and bleed
valve. One way to check this combination is to jump out the valve and
simply check the pump and PCB combination.
combination
The new chambers are effective up to 5 ml/min where the older design are
effective up to 2 ml/min. When priming the degasser chambers, you should
flush with a minimum of 5 volumes of solvent. The new chambers with .024
ID tubing, now have an internal volume of 10 mL’s. This means that there
should be a minimum of 50 mL’s of solvent flushed through each channel of
the degasser.
Good laboratory practice is important. If buffers are in use, always remove the
buffers if the instrument is not going to be used for extended time periods.
Replace the buffers with filtered water, then follow with an aqueous/organic
mix.
Do not allow the degasser to operate for extended periods of time when the
flow rate is at 0 ml. Organic
g solvents will super
p degas,
g , resultingg in solvent
vapor condensing outside the tubular membranes.
Always "Wet Prime" after an overnight shut down or any long periods of non-
use. Program a low flow rate (0.1-0.5) for 10 minutes after the Wet Prime
to allow degassed solvent to flow into the system.
When connecting the threaded tubes to the chamber, do not overtighten the
fitting The fittings should be finger tight only
fitting. only. Be sure to use the Tefzel
(purple) ferrule. This ferrule is softer and seals with less force. Less force
is used to eliminate the need for overtightening and the possibility of
cracked fittings or chambers.
The new style Chambers are fully backward compatible for replacement into
instruments with the original style chambers. It is acceptable to have a
combination of old and new style chambers in the same 2690/5 or stand
alone vacuum degasser.
degasser If it becomes necessary to replace a chamber,
chamber only
the failed chamber should be replaced. It is not necessary to replace all
four. Customers should be informed that the flush volume is slightly higher.
It would be simpler to recommend that all chambers be flushed with 50
mL’s of solvent, even if there is a combination of chambers in the system.
A information sheet describing this memo in brief form and an installation

guideline will be included with each spare chamber ordered. The new part
number for this chamber is 700000269.
8. Fatal Error
This error is displayed when a low level operating system program on the CPU
PCB has occurred. It will lock up the instrument and be display as "Fatal
Error in VRTX In addition to the previous Tip & Trick Technique dated
1/16/97 consider the full list of ideas.

Error Codes
Use this list at your discretion, since some ideas are more severe than others.
1. Power On/Off the instrument.

2. Reseat all proms and cables on the CPU PCB.
3. Clean the battery contacts, check the voltage, and replace battery.
4. Check power supply voltages (with all options running, for max load)
5. Press the reset button on the CPU PCB.
6. Reload the software.
7
7. Cl
Clear RAM
RAM. (b
(back
k up previous
i methods,
th d they
th will
ill be
b deleted!)
d l t d!)
8. Replace the CPU. (back up methods previous CPU for transfer)
9. Delete some methods stored in memory to a manageable amount, only if a
large amount are present. Reference to the "Release Notes, 2690/5 Version
1.00 & 1.01" discuss instrument memory capacity, it states:
Instrument Memory Capacity
The Waters 2690/5 contains sufficient nonvolatile memory capacity for storage
of up to 60 methods,
methods sample sets and sample templates.
templates As the memory
capacity is approached, the time required to create and save programs is
extended from a few seconds to over 30 seconds. Saving long, complex
programs can also reduce capacity. Waters recommends that no more than
30 programs be stored at any one time.
One case to date we have found an instrument with 52 saved methods showed
an error, which occurred while editing a running method.
9 Lost Prime
9.
The 2690/5 has an internal diagnostic that monitors the system transducer
backpressure to protect the system from running dry. The diagnostic is
totally independent of the bubble detection and clearing algorithm. This
diagnostic is called the Loss Of Prime Shutdown (LOPS). If this occurs the
2690/5 will display a “Loss off of Prime” error message.
The LOPS diagnostic monitors the system backpressure of each delivery cycle.
The flow delivery will automatically be given a stop flow command, and shut
down if the instrument detects a low pressure limit threshold of 25 psi or
below for 50 consecutive (primary/accumulator) delivery cycles.
Alarm Response Description
Stop Flow Solvent delivery flow is stopped
Current operation will be suspended
Audible alert and visual dialog
notification box
Error will be logged
LOPS is always active through all flow rates for the normal flow mode. LOPS is
not active during any priming sequence.

Error Codes
10. Missing Vial
With use of clear or translucent vial caps the alarm message "missing
vial" may occur.
The vial detection system consists of an optical control box (located on

the fluidics driver pcb) and fiber optics cables leading to/from the
carousel compartment. A vial is detected when a vial cap breaks the
light path. If a vial cap is not present or does not break the light path
when the "Verify vial presence" is enabled (located in the config
screen) a "missing vial" alarm will occur.
Vial Present Sensor Maintenance

Over time, the sensing ability of the device may be diminished due to
accumulation of debris on the ends of the fibers or a melting of the
fibers due to solvents such as Methylene Chloride and other
chlorinated solvents. If vials are not being sensed, this may be the
case. This can be remedied by squarely cutting off up to 1/4” at the
end of the fibers and reinserting the fibers into place.
A decrease in transmitted light can also occur if the fibers are bent
and/or broken. In this case the fibers must be replaced. The fibers
are available as a spare part that includes a 25
25” length and a fiber
optic cable cutter.
To replace or repair a fiber optic cable:

1. Remove the top and right side covers from the instrument. This will
provide easy access to the cable at the right of the sample
compartment.
p The cable ppositioned at the top
p of the sample
p
compartment will require removal of the injector for easy access.
2. The fiber optic cable is secured in the sample compartment housing
by a metal cable holder. While holding the cable holder firmly, loosen
the epoxy around the cable and pull it out of the holder.

Error Codes
3. Cut 1/4” from the end of the cable using the cutter provided with the spare
fiber optic cable or, if a cutter is not available, use a brand new razor blade.
Note: A clean cut is necessary for proper light transfer. The cable cutter
allows you to make four cuts. Do not reuse the same position in the
cable cutter.
4. Blow out the cable holder with house air to remove any dust or debris
before inserting cable.
5. Bottom out new or cleanly cut fiber optic cable in the holder and secure in
place with silicone.
Vial Present Sensor Adjustment
When the instrument is continually giving Missing Vial errors, the vial sensor
require adjustment for greater sensitivity. This adjustment is made as
follows:
1. Go to Sensor Page.
2. Observe the two LEDs on the encoder box on the Fluidics PCB.
a. The Green LED should be blinking continuously.
b. The Yellow LED should blink when it sees light and go OFF whenever the light beam is
broken.
3. Remove the carousel and place your hand in the sample compartment to
break the light path.
4. Increase sensor sensitivity by turning the pot slowly counter-clockwise until
the Yellow LED begins to blink.
Note: This adjustment is effective to increase sensitivity to consistently sense

vials, however the opposite is not true. For example, you cannot decrease
the sensitivity to fool the sensor into not sensing a vial in cases where the
2690/5 is always seeing a vial.
11. Needle Malfunction
The injector sensor (top or bottom) did not see an appropriate change in state
when expected.
Check motor function
Check sensors (flag with a business card)
The most common report is after a long period of non-use (also if a buffer has
been used in the needle wash).. The dry injector seals grab the needle.
Washing out the needle wash frits with clean water or repowering the
system will cure the problem
12. Sample syringe over pressure
A pressure exceeding 350 psig was detected in the sample loop when V2 was
open. The system has automatically stopped solvent delivery to prevent
damage to the syringe. This can be caused by:
Blockage in the waste line
Bad V1, V2, or V3

Error Codes
Seal pack seals out of adjustment
13. Sample temp h/w fault (1=communications, 2=watchdog, 3=h/w

over temp, 4=internal fan, 5=external fan, 6=thermistor high,
7=thermistor low)
1 and 2 are both communications errors. Power down the system and check all
of the heater/chiller cables and connectors.
3 h/w is over temp. Try opening up the temperature range window.
4 Software monitors the amperage to the motors. If amperage goes high, the
motor is defective and the system shuts down the device.
5 There are three external motors on the H/C. If amperage goes high on at
least two of the motors you get the code and the system shuts down the
device.
6 & 7 possible bad thermistor RTD probe.
14. Seal pack geometry fault (1=seal too high, 2=seal too low, 3=seal
too wide, 4=seal too narrow)
Technical Discussion: This error occurs after a seal pack adjustment has
been performed an result parameters fall outside of acceptable range limits.
Parameter Acceptable Range Typical Range
Top 30 – 80 40 +/- 10
Width 50 – 120 80 +/- 10
Bottom 80 – 200 Top + Width
Testing: Perform the Adjusting the seal procedure in the operator’s manual.
I
Insure that:
th t
There is a restriction that will generate 1000 psig within 3 ml/min.

Flow should be 1 – 1.5 ml/min for best results
The system has been purged twice before you start
The methanol has been thoroughly sparged or degassed
If the error appears:
pp
1. Check that the flow is between 1 and 1.5 ml/min.

2. Assure the Methanol is degassed
3. Stop the flow and check the transducer values on the display. They should
be near zero and stable.
4. Pin plug the outlet of the system and drive the pressure up to 4500 psi for
at least two minutes. This will energize
g the seal p
pack and valve seals. Re-
do the seal pack adjustment.

Error Codes
5. Check the Sensor bracket for proper adjustment. The gap between the bottom of the top of the
sensor bracket and the injector motor baseplate should be approximately 5/16 of an inch. It may be
necessary to adjust the bracket UP.
To Adjust:
1. Loosen the holding screw at the base of the bracket.
2. Turn the adjusting screw on top of the bracket ¼ turn counter-clockwise.
Note: Each ¼ turn of the screw is equal to approximately 5 motor steps.
3. Re-tighten the holding screw.
15. Solvent delivery h/w fault
Failure of some component connected to the piston drive PCB.

1. Power supply 24V
2. Piston drive
3
3. Piston drive PCB or 7A fuse (PN WAT 290188)
4. With a H/C, 2 out of the three external fans failing or with no H/C the single external fan failing.
Check the fan connections for oxidation etc.
5. Check all cable connections to the piston drive PCB.
6. Check the gray cable connection CPU to piston drive PCB.
16. Solvent delivery motor lost sync (0=Primary, 1=Accumulator)
Full list of any possible component failure.:

1. Cables, loose connections or bad cables.
2. Faulty Acc. or Prim. Transducer or Pressure not vented.
3. Piston Drive Failure, encoder, motor, or mechanical failure.
4. Piston Drive PCB, electronic component failure.
5. Power Supply, voltages may be dropping out of range.
6. CPU PCB,, inability
y to properly
p p y translate encoding
g device.
Troubleshooting
DOES THE 2690/5 INITIALIZE PROPERLY?

NO,
Cables - Reseat all related cables to and from the Piston Drives, CPU PCB, Piston Drive PCB and Power
Supply. Check continuity for cables end to end. Pay close attention to the "Y" power cable from the
Piston Drive PCB to the Primary and Accumulator,
Accumulator remove the connector from the motor and remove
the protective cover. Press the wires into the displacement pins to assure proper contact. Also pay
attention to the large gray cable ensuring the sliding lock is connected on both ends.
Pressure on transducers - Ensure pressure is properly vented, open vent valve, re-initialize. If
transducer fault occurs, swap connections on CPU to determine cause of failure due to bad
transducer or CPU PCB.

Error Codes
Power Supply - Check voltages during initialization, if possible check with all
p
options "ON" after initialization to ensure full p
power draw. Check directly
y on
the power cable to the Piston Drive PCB, orange wire=24VDC, red
wire=5VDC, black wire=common, green=ground.
Piston Drive - A mechanical tolerance may be the cause. When initializing, the
plunger is gently driven to touch the head, motor steps are then counted to
determine the home position and travel of the piston. A mechanical
tolerance may cause the plunger to bounce back when it touches the head
th
therefore
f falsely
f l l causing
i th
the motor
t hhoming
i tto b
become iinaccurate.
t TTo
determine this theory, loosening the head nut before initialization will
eliminate bounce back.
Ensure that the motor is mounted securely to the piston cylinder by checking
the mounting screws for a tight fit.
YES,
DOES THE FAILURE OCCURE AT LOW FLOW RATE AND LOW
PRESSURES? Follow troubleshooting ideas listed above.
YES,
DOES THE FAILURE OCCUR AT HIGH FLOW RATE AND HIGH PRESSURE,
DURING WET OR DRY PRIMINGPRIMING, OR DURING BUBBLE DETECTION
AND CLEARING?
The piston driving the plunger into the head, due to mechanical problems could
cause this. Also, could be caused by torque problems with the motor or a
voltage inconsistency or lack of proper voltage from the power supply, bad
connections or pin contacts. Note all voltages should be checked with all
options "ON" under full load.
Follow troubleshooting ideas listed above.
17. Transducer range (volts)
Are all 3 transducers the same? Yes, all the transducers are common in style.
The replacement part can be ordered using WAT270966.
The most common failure will be identified upon initialization. If the software
can not electronically zero the transducer an "Out of range" error will occur.
When electronically zeroing there is a specified window of zeroing range, if
outside the range an error will occur. This range can be viewed in the
Service Utilities page, a box containing all the voltage offsets will be
displayed. A perfect transducer will have a reading of 0.5V.

Error Codes
The range of electronic zeroing capability is 0.5V +/-0.2V (0.3V to0.7V),

if outside this range an "Out
Out of range
range" error will occur
occur. A reading of 4
volts signifies a dead transducer.
Swapping connections at the CPU board location can be used to

troubleshoot and verify a specific transducer has failed. If the error
follows the transducer connector that was swapped, the failed
transducer cable or connections is suspect.
transducer, suspect
If backpressure is present on the transducers this may also produce this

same error. Verify all pressure has been bled from the fluid
components while troubleshooting this failure.
Adjustments of fine zero for the transducers can be attempted to

manually re-zero the transducer to bring it in acceptable range for the
electronic zeroing. Removal of the black rubber stopper on the
transducer will allow access to the adjustment potentiometer.

Error Codes

Error Codes
2695 System Error Messages
MESSAGE ACTION STEPS
Accumulator over pressure Locate restriction... guard column /

column / inline filter / blocked tubing.
Bubble found on intake Wet prime and allow system to sit at zero flow
with the degasser
g in continuous mode for approx.
pp
10 min. prior to starting the run. If the flow
rate is greater than 1 mL/min. install extended
flow inlet tube.
Carousel malfunction Cycle power. If message persists call Waters

Service Representative.
Carousel Z axis malfunction Cycle power

power. If message persists call Waters
Compression check failed Solvent not degassed properly. Check for bubble
on syringe plunger. Test seal pack and valve 3.
Perform appropriate maintenance.
Degasser pressure fault Replace faulty degasser chamber or vacuum

pump. Call Waters Service Representative.
Lost prime Solvent not degassed properly. Change check

valves. If the flow rate is greater than 1 ml/min.
install extended flow inlet tube.
Missing vial The missing vial should be placed in the correct

llocation
ti iin th
the ttray. Di
Disable
bl th
the vial
i l sensor
[Main>>Config>>Highlight] "Verify vial presence"
press clear. Call Waters Service Representative.
Needle malfunction Check needle wash reservoir. Prime needle wash.

Cycle power. If message persists call Waters
Plunger homing fault Cycle power. Change inline filter. If message

persists call Waters Service Representative.
Primary transducer range Call Waters Service Representative.

(volts) Sample

Error Codes
A2695 System Error Messages
MESSAGE ACTION STEPS
Solvent delivery h/w fault Cycle power. If message persists call Waters Service
Representative.
Solvent delivery motor Cycle power. Change inline filter. If message

lost sync persists call Waters Service Representative.
Syringe Movement malfunction Cycle power

power. If message persists call Waters Service Representative
Representative.
System over pressure Locate restriction... guard column / column / inline filter /
blocked tubing.
System under pressure Connect column. Locate leak. 50 psi is needed to run the
system.
Chromatographic Errors
SYMPTOMS POSSIBLE CAUSES CORRECTIVE ACTI0N
Erratic retention times

Air bubble Wet prime the unit.
Degas all solvents.
Malfunctioning check valves Clean/ replace check

valves.
Solvent leak Check all fittings. Replace

seals.
Chemistry Check mobile phase,

column, Gradient
Proportioning Valve.
Clogged solvent filters Replace filters.

filters
Temperature Use column oven.
Increased retention times

Incorrect flow rate Malfunctioning check
valve.
Solvent leak.
Incorrect Mobile Phase Change solvent

solvent.
Column Contaminated. Clean/replace the column.

Error Codes
Reduced retention times Incorrect flow rate Change flow rate.
Incorrect solvent composition Change composition. Check gradient

proportioning valve.
High column temp. Change column temp.
Column contamination Clean/ replace column.
Solvent not degassed Degas solvent.
Reproducibility errors Solvent not degassed Degas solvent.
Air in syringe Purge solvent management system.
Incompatible vial septa Switch to approved vial and septa.
Sample management Contact Waters Service

system Representative.
Baseline drift Column not equilibrated Equilibrate column.
Detector not equilibrated Allow detector to warm up. Time will

vary with wavelength and sensitivity.
Solvent contaminated Use fresh solvent.
Solvent not properly degassed Degas solvent.
Flow/ Pressure fluctuations Prime system. Replace check valves,

pump seals.
Temperature fluctuations Stabilize operating environment.
Leaking flow cell Repair leak.
Dirty flow cell Clean flow cell.
Baseline noise
Flow fluctuations Malfunctioning check valve. Leaks,
Seals, fittings.
Radio frequency noise Eliminate interference.
Air in detector Purge detector.
Solvent not degassed Degas solvent.

Error Codes
Baseline noise Solvents contaminated Use fresh solvents.
Column contaminated Clean/ replace column.
Electronic Call Waters Service Representative.
Sensitivity loss Solvent leak Check all fittings
Degraded, contaminated, or Use fresh sample.

improperly prepared sample.
Column contaminated Clean/ replace column.
Loss of column efficiency Clean/ replace column.
Leak in flow cell Repair leak.
Change in mobile phase Correct mobile phase. (i.e. pH or ionic

composition)
iti )
Contaminated solvents Use fresh mobile phase.
Old L
Lamp R l
Replace llamp
Split peaks Needle wash solvent Prime needle wash solvent.

Solvent not appropriate for samples.
Column Clean/ Replace column.

Appendix B: Priming Procedures
Appendix B
Rev. 27510 Waters Confidential and Proprietary Information Appendix B : Page 1 of 6

Appendix B
Priming as New or Dry system using undegassed solvents.
1. Fill the solvent bottles with Mobile Phase
2. From the Status Page turn the degasser On.*
3 Perform a dry prime until solvent flows from each of the four lines.
3. lines
4. Starting with the organic solvent, perform a 3 minute Wet Prime on

each line separately at a flow rate of 5.0 mL/min.**
5. Once all lines are p

primed,, set the flow rate to 0.0 mL/min with the
degasser on for 10 minutes.
6. Start the flow with the initial conditions of your chromatographic

method. Equilibrate with 10 column volumes of solvent.
7 Ch
7. Checkk the
th Pressure
P Ripple
Ri l on page twot off the
th Status
St t Page.
P Th
The
ripple should be less than 2% of the system pressure. (For systems
pressures above 1000 psi, repeat Wet Prime if the ripple is too high)
8. After the column is equilibrated, Purge the autosampler. (Initial

conditions)
9. Run samples.
* The degasser should never be left on with no flow for long periods of
time (I.e. overnight)
** Caution: To avoid precipitating salts in the Separations Module, use an

intermediate solvent such as water when you change from buffers to
high-organic content solvents.

Appendix B
Priming an idle system using existing mobile phase
1. From the Status Page turn the degasser on. *
2. For each line that will be used, starting with the organic solvent, perform a
1.5 minute Wet Prime at a flow rate of 5.0 mL/min. **
3. Once all lines are primed, set flow rate to 0mL/min with degasser on
continuous for 10 minutes.
4. Start the flow with the initial conditions of your chromatographic method.
Equilibrate with 10 column volumes of solvent.
5. Check the Pressure Ripple on page two of the Status Page. The ripple
should be less than 2% of the system pressure. (for system pressures
above 1000psi, repeat Wet Prime if the ripple is too high)
6. After the column is equilibrated, Purge the autosampler. (initial

conditions)
7. Run Samples.
* The degasser should never be left on with no flow for long periods of time.
(i.e. overnight)
** Caution: To avoid precipitating salts in the Separations Module use an

intermediate solvent such as water when you change from buffers to high-
organic content solvents.

Appendix B
Changing the Mobile Phase
1. Fill all of the solvent bottles with mobile phase.

2. For each line that will be used, starting with the organic solvent, perform a
3 minute Wet Prime at a flow rate of 5.0 mL/min. **
3. Once all of the lines are primed, set the flow rate to 0 mL/min with the
degasser on for 10 minutes. *
4. Start the flow with the initial conditions of your chromatographic method.
Equilibrate with 10 column volumes of solvent.
5. Check the Pressure Ripple on page two of the Status Page. The ripple
should be less than 2% of the system pressure. (for system pressures
above 1000psi, repeat wet prime if the pressure is too high)
6 After the column is equilibrated,
6. equilibrated Purge the autosampler
autosampler. (initial conditions)
7. Run Samples.
* The degasser should never be left on with no flow for long periods of time.
(i.e. overnight)
** Caution: To avoid precipitating salts in the Separations Module use an

intermediate solvent such as water when you change from buffers to high-
organic content solvents.
Note: When first starting to equilibrate your column, one or two Bubble
Detects is normal
normal. The system is detecting any small bubbles and using its
its’
automatic algorithm to clear the bubbles.
Note: The volume of each solvent line in a 2695 including the vacuum
degasser chamber is 5.5 mL. This volume must be considered when priming
the system and changing to a different mobile phase.
Note: The degasser can be turned off, the flow rate stopped and the lamp
turned off (if controlling the detector through the Alliance) in a Shutdown
Method.

Appendix B
Priming the Seal Wash Pump (when needed)
1. Press the Diag screen key in the Main Menu screen. The Diagnostic
screen appears.
2. Attach the syringe adapter (from the Start-up Kit) to the syringe.
3. Remove the solvent filter from the plunger seal wash inlet or remove
the plunger seal wash waste line from the waste container. (Either
pushing solvent through it or drawing solvent through it can be used to
prime the plunger seal wash pump)
4 Fill the s
4. syringe
inge with
ith pl
plunger
nge seal wash
ash solvent*
sol ent* and attach the syringe
s inge
adapter to the end of the plunger seal wash line.
5. Press the Prime Sealwash Screen key and then press the Start screen
key. The plunger seal wash procedure begins. Push on the syringe to
push seal wash solution through the system or draw on the syringe to
pull
ll solvent
l t th
through
h th
the plunger
l seall wash
h pump.
6. When solvent flows out of the plunger seal wash line or into the syringe
(the pump will run quieter when it is primed) press the Halt screen key.
7 Reinstall the solvent filter and place the seal wash inlet line back into
7.
the plunger seal wash reservoir or place the plunger seal wash waste
line back into the waste container. To finish the priming, press the Start
screen key again.
8. Press Close to return to the diagnostics screen.
* Choose a Seal Wash solution that has high solubility with salts and /or
buffers used in the mobile phase. (Usually a solution of 80 - 90%
aqueous, 20 - 10% methanol)

Appendix B
Priming the Needle Wash Pump (daily or weekly)
1. Make sure Needle Wash line (Green Line) is in its appropriate bottle.
2. Press the Diag screen key in the Main screen. The Diagnostics screen
appears.
3. Press the Prime NdlWsh screen key. The 30-second needle wash
procedure begins. If solvent does not flow out of the waste line (the
yellow line) press the Start Again screen key.
Note: Choose a Needle Wash solution that your sample is soluble in.
B ffe ed solutions
Buffered sol tions or
o a mobile phase modifier
modifie such
s ch as TFA are
a e not
recommended. If these solutions are necessary they must be flushed
from the instrument.

Appendix C: 2695 PM Kit Contents
PM Kit Contents

Appendix C: Page 1 of 2
PM Kit Contents
Part Part # Qty.
Seal 1/8” Fluoroloy-G mini WAT270789 2
Plunger WAT270488 2
Solvent Filter WAT)25531 4
Check Valve: Cartridge Assy 289000144 2
Face Seal WAT270163 4
Syringe WAT073109 1
Filter Insert Assy WAT088084 1
*Seal Wash Tube Seal WAT270668 5
Seal Wash Plunger Seal Wash WAT270160 2
Assy, Diffuser WAT007272 1
WAT025313 1
* Screw, Compression
*Ferrule 410001125 1
*Spacer Upper Seal Wash WAT031957 1
Battery, Lithium 484 WAT080443 1
*Needle Wash Frit WAT072324 1
*Teflon Washer WAT077321 1
*Tube, Cut Seal Wash Injector WAT031956 1
*Needle 405001338 1
*Needle Seal WAT033276 2
*Needle
Needle Wash Filter 415000230 1
*Retainer, Filter 405001171 1
Tubing, Teflon AWG 9 Thin Wall WAT024036 1
*Glove, Powder Free, 2/pk WAT241050 1
The 2695 PM kit contains all the parts subject to normal wear to be
p
replaced in one instrument.
It comes with a 7 language protocol outlining instrument diagnostic
tests, accuracy calibration, and tables for recording results.
Items marked with an asterisk (*) are also found in the Seal Pack
Rebuild Kit,
P/N
/ WAT271019.
The kit contains one Seal Wash Tube Seal, P/N WAT270668.

Appendix C: Page 2 of 2

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7 Alliance Other Tests 1

8 Alliance Other Tests 2

9 Alliance Other Tests 3

10 Alliance Head Rebuild

11 Syringe & Drive

13 Cleaing the Sample Compartment

Appendix A Selected Error Codes

Appendix B Priming procedures

Appendix C PM Kit Contents

Rev. 27510 Waters Confidential and Proprietary Information

 This course introduces you to the Waters™ 2695 Separations Module.

Rev. 27510 Waters Confidential and Proprietary Information

 Cut away view of the 2695 showing the location of various

Rev. 27510 Waters Confidential and Proprietary Information

 Sample heater / cooler - can maintain sample compartment at

Description Software Controlled by

Rev. 27510 Waters Confidential and Proprietary Information

 The Alliance Separations Module uses a switching power supply, it

 See Making Power Connections, in the Operator’s Guide.

Rev. 27510 Waters Confidential and Proprietary Information

 RS-232 - Two ports:

 IEE-488 - Connects to a Waters detector (PDA, 2487, 486, 410 or

 See Digital Signal Connections

Rev. 27510 Waters Confidential and Proprietary Information

 See I/O Signal Connections, in the Operator’s Guide.

Rev. 27510 Waters Confidential and Proprietary Information

 See Making Fluid Connections, in the Operator’s Guide.

Rev. 27510 Waters Confidential and Proprietary Information

 Solvent Lines: clear 1/8 inch OD tubing with stainless steel

 Plunger Wash: clear 1/8 inch OD tubing

 Needle Wash: Green 1/16 inch OD tubing

 See Making Fluid Connections, in the Operator’s Guide.

Rev. 27510 Waters Confidential and Proprietary Information

 Degasser Vent: Clear 1/4 inch OD

 Plunger Wash: Clear 1/8 inch OD

 Purge / Vent: Clear 1/16 inch OD

 Needle Wash: Yellow 1/16 inch OD

 See Making Fluid Connections, in the Operator’s Guide.

Rev. 27510 Waters Confidential and Proprietary Information

 See Making Fluid Connections, in the Operator’s Guide.

Rev. 27510 Waters Confidential and Proprietary Information

 When the Alliance Separations module is powered ON, several

Rev. 27510 Waters Confidential and Proprietary Information

Rev. 27510 Waters Confidential and Proprietary Information

Rev. 27510 Waters Confidential and Proprietary Information

Rev. 27510 Waters Confidential and Proprietary Information

Rev. 27510 Waters Confidential and Proprietary Information

Rev. 27510 Waters Confidential and Proprietary Information

Rev. 27510 Waters Confidential and Proprietary Information

 The solvent degasser has an internal volume of approximately 500 ul.

Rev. 27510 Waters Confidential and Proprietary Information

Rev. 27510 Waters Confidential and Proprietary Information

 1. Serial Flow Path – Solvent blending in piston chamber

Rev. 27510 Waters Confidential and Proprietary Information

 1. High pressure fluid path (solid black)

 2. Seal wash tubing

Rev. 27510 Waters Confidential and Proprietary Information

Rev. 27510 Waters Confidential and Proprietary Information