Agilent Technologies 7250 User manual

Agilent 7250 Accurate-Mass Quadrupole
Time-of-Flight GC/MS System
Troubleshooting and Maintenance Manual

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual
Notices
© Agilent Technologies, Inc. 2019
No part of this manual may be repro-
duced in any form or by any means
(including electronic storage and
retrieval or translation into a foreign lan-
guage) without prior agreement and
written consent from Agilent Technolo-
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and international copyright laws.
Manual Part Number
G7250-90007
Edition
First Edition, January 2019
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Boulevard 
Santa Clara, CA 95052
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Safety Notices
CAUTION
A CAUTION notice denotes a 
hazard. It calls attention to an
operating procedure, practice,
or the like that, if not correctly
performed or adhered to, could
result in damage to the product
or loss of important data. Do
not proceed beyond a CAUTION
notice until the indicated
conditions are fully understood
and met.
WARNING
A WARNING notice denotes a
hazard. It calls attention to an
operating procedure, practice,
or the like that, if not correctly
performed or adhered to, could
result in personal injury or
death. Do not proceed beyond a
WARNING notice until the
indicated conditions are fully
understood and met.

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

4 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual
Temperature Symptoms 38
Error Messages 40
Air Leaks 45
Contamination 46
3 CI Troubleshooting
Common CI-Specific Problems 50
Troubleshooting Tips and Tricks 51
Air Leaks 52
How do I know if I have an air leak? 52
Special NCI notes 53
How do I find the air leak? 53
Pressure-Related Symptoms 55
Poor vacuum without reagent gas flow 56
High pressure with reagent gas flow 56
Pressure does not change when reagent flow is
changed 57
Signal-Related Symptoms 58
No peaks 58
No reagent gas peaks in PCI 58
No PFDTD peaks in PCI 59
No reagent gas peaks in NCI 59
No PFDTD calibrant peaks in NCI 59
No sample peaks in NCI 59
Large peak at m/z 238 in NCI OFN spectrum 60
No or low reagent gas signal 60
No or low PFDTD signal, but reagent ions are normal 61
Excessive noise or low signal-to-noise ratio 62
Peak at m/z 32 63
Tuning-Related Symptoms 64

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 5
Reagent gas ion ratio is difficult to adjust or unstable 64
Cannot complete Autotune 65
The CI ion source is dirty 65
Air leak 65
4 General Maintenance
Before Starting 68
Scheduled maintenance 68
Tools, spare parts, and supplies 69
High voltage precautions 69
Dangerous temperatures 69
Chemical residue 70
Electrostatic discharge 71
To Refill the EI Calibration Vial 73
To Connect the GC Nitrogen Gas Source to the Collision
Cell 75
To Separate the GC from the MS 76
To Position the GC Next to the MS 78
To Move or Store the MS 79
To Access the Left Side Lifting Handle 82
5 CI Maintenance
To Minimize Rotary Vane Foreline Pump Damage from
Ammonia 86
To Replace the Chemical Ionization Gas Purifier 88
To Clean the Reagent Gas Supply Lines 89
To Refill the CI Calibration Vial 90
6VacuumSystem
Overview 94

6 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual
Maintaining the Vacuum System 95
Periodic maintenance 95
Other procedures 95
More information is available 95
Vacuum System Components 96
Common Vacuum System Problems 97
Foreline Pump 98
To connect the foreline hose to the foreline pump 98
To disconnect the foreline hose from the foreline
pump 99
To check the rotary vane pump oil mist filter 99
To check the rotary vane foreline pump fluid level 100
To add oil to the rotary vane foreline pump 100
To replace the oil in the rotary vane foreline pump 101
The oil pan under the foreline pump can be a fire
hazard 103
To remove the exhaust silencer filter 103
To install the exhaust silencer filter 104
To replace the IDP-15 dry pump tip seal 105
To replace the IDP pump HEPA filter cartridge 107
To change the exhaust silencer filter cartridge 107
To install the IDP pump ballast 108
To remove the IDP pump ballast 109
Side Plate 110
Vacuum Seals 110
EI Calibration Valve 111
CI Calibration Valve 112
7 Replacement Parts
To Order Parts 114

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 7
Electronics 115
Vacuum System 118
Analyzer 121
GC/MS Interface 126
Consumables and Maintenance Supplies 128
Additional CI Parts 131

8 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual

7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 9
1Introduction
Abbreviations Used 10
The 7250 Accurate-Mass Quadrupole Time-of-Flight GC/MS System 11
7250 Accurate-Mass Q-TOF GC/MS Description 13
Side Panel AC Power Connectors 14
Back Panel Connectors 15
Interfacing Start Events to External Devices 16
Important Safety Warnings 18
Safety and Regulatory Certifications 21
Intended Use 24
Cleaning/Recycling the Product 24
Moving or Storing the MS 24
This chapter provides general information about the Agilent 7250 Accurate-Mass
Quadrupole Time-of-Flight (Q-TOF) GC/MS System, including a hardware
description and general safety warnings.

1Introduction
10 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual
Abbreviations Used
The abbreviations in Table 1 are used in discussing this product. They are
collected here for convenience.
Table 1 Abbreviations
Abbreviation Definition
AC Alternating current
ALS Automatic liquid sampler
CC Collision cell
CI Chemical ionization
DC Direct current
EI Electron impact
EPC Electronic pneumatic control
eV Electron volt
GC Gas chromatograph
GC/MS Gas chromatograph mass spectrometer
id Inside diameter
IDP Isolated dry pump
LAN Local Area Network
LE-EI Low energy EI
m/z Mass-to-charge ratio
MFC Mass flow controller
MS Mass spectrometer
MS1 Quadrupole
OFN Octafluoronaphthalene (sample)
PFTBA Perfluorotributylamine (calibrant)
Q-TOF Quadrupole time-of-flight
Quad Quadrupole mass filter
RF Radio frequency
RFPA Radio frequency power amplifier
TOF Time-of-flight
Torr Unit of pressure, 1 mm Hg
Turbo Turbomolecular vacuum pump

1Introduction
7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 11
The 7250 Accurate-Mass Quadrupole
Time-of-Flight GC/MS System
The 7250 Accurate-Mass Quadrupole Time-of-Flight (Q-TOF) GC/MS System is a
standalone capillary GC detector for use with Agilent 8890 and 7890 Series gas
chromatographs. The 7250 Q-TOF features:
•Three turbomolecular vacuum pumps
•Foreline pump
•Rotary vane pump
•Optional isolated dry pump (IDP)
•Independently MS-heated LE-EI ion source
•Independently MS-heated hyperbolic quadrupole mass filter, which can be
heated to high temperatures, minimizing the contamination typical with low
temperature analyses
•Single hexapole collision cell
•Ion-focusing slicer
•Vacuum-insulated flight tube with dual-stage ion mirror
•Fast electronics, allowing fast sampling rates
•Analog-to-digital detector
•Independently GC-heated GC/MS interface
Physical description
The 7250 Q-TOF GC/MS is approximately 53.5 cm high, 69 cm wide, and 92 cm
deep. The flight tube extends 136 cm up over the top of the instrument.
The turbo pump mainframe weighs 159 kg. The weight of the attached foreline
(rotary) pump is 25 kg for the DS202 rotary vane pump model, and 45 kg for the
IDP model.
The basic components of the instrument are the:
•Frame/cover assemblies
•Vacuum system
•GC/MS interface

1Introduction
12 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual
•Ion source
•Flight tube electronics
•Collision cell
•Detector
•Analyzer
Vacuum gauge
The 7250 Q-TOF GC/MS is equipped with three ion vacuum gauges:
•Vacuum manifold chamber
•TOF vacuum manifold chamber
•Turbomolecular vacuum pumps exhaust
The MassHunter Workstation can be used to read the pressure (high vacuum) in
the vacuum manifold, at the turbomolecular vacuum pump discharge, and the
flight tube.
Ionization modes
The 7250 Accurate-Mass Q-TOF GC/MS can operate in EI mode using the
standard LE-EI ion source or in CI mode using the optional CI MS system. In
electron impact mode, the Q-TOF can operate in standard or low-energy modes.

1Introduction
7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 13
7250 Accurate-Mass Q-TOF GC/MS
Description
Figure 1 is an overview of a typical 7250 Accurate-Mass Q-TOF GC/MS system.
Figure 1. 7250 Accurate-Mass Q-TOF and 8890 GC/MS System
Flight tube
Q-TOF
ALS
8890 GC
MS power
switch
Front right
grill
Source
window cover
GC power
switch
Oven door
latch
Drawer

1Introduction
14 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual
Side Panel AC Power Connectors
Main power cord receptacle (top)
The AC power cord located on the left side of the MS brings in all electrical power
for the MS. The power cord can be detached from the MS.
Foreline pump power receptacle (bottom)
The foreline pump power cord receptacle located on the left side of the MS
provides AC power for the foreline pump. If the power switch is off, no power is
supplied to the foreline pump.
Figure 2. Side panel power supply

1Introduction
7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 15
Back Panel Connectors
Remote start connector
The remote start connector is the external connector for the remote start
circuitry on the LAN/MS control card. It receives remote start signals from the
GC.
LAN (I/O) connector
The LAN cable from the data system is a dedicated LAN line that is connected to
the LAN communications connector. It carries all data communication between
the PC and the MS.
Figure 3. Back panel connections
CAUTION
Directly connect a single dedicated LAN cable between the PC and the 7250
Q-TOF. Do not use a LAN switch, router, or other device between the PC and
the Q-TOF.

1Introduction
16 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual
Interfacing Start Events to External Devices
Remote control processor
The remote control processor on the LAN/MS control card synchronizes
start-run signals with GCs and other devices. The functions of the remote control
processor are extended to the remote start (Remote) connector on the back
panel of the MS. (See Figure 4.) The remote start cable connects the GC and the
MS. An optional cable can extend these events to another instrument.
Remote start signals
It is often necessary to communicate with external devices (for example, a
purge-and-trap) during a run. Typically, these communications are requests to
send a system-ready signal. They also include:
•Receive a start run signal from an external device
•Program the timing of events during a run
System ready
When interfacing to an external device, it is often desirable to send a
system-ready signal to the device. In the case of a multisample Tekmar
purge-and-trap, each sample is purged onto a trap where it waits for a ready
signal. On receipt of the ready signal, the desorption cycle begins. When a
specific temperature is reached, the purge-and-trap closes a contact to indicate
the run has started.
Figure 4. Remote start connector
Start Ground
Ready

1Introduction
7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 17
The ready pin on the remote start connector on the GC is held low at all times
except when the GC, MS, and data system are all ready. On system ready, a logic
high of 5 VDC is present between that pin and any ground. This same high can be
detected between the ready and ground pins on the remote start connector on
the MS.
Start run input
The best way to generate a start run signal is to use the remote start connector
on the GC. Since remote start cables are made for most common devices, this is
often the simplest way. A general-purpose remote start cable that terminates in
spade lugs (Y-Remote Start/Stop, APG p/n G1530-61200), is also available.
Ensure that the system is actually ready before the start run signal is sent.
If necessary, the remote start connector on the back of the MS can be used to
send the start run signal. A contact closure between the start and ground pins
will start the run if the system is ready.

1Introduction
18 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual
Important Safety Warnings
There are several important safety notices to always keep in mind when using
the MS.
Many internal parts of the MS carry dangerous
voltages
If the MS is connected to a power source, even if the power switch is off,
potentially dangerous voltages exist on:
•The wiring between the MS power cord and the AC power supply
•The AC power supply itself
•The wiring from the AC power supply to the power switch
With the power switch on, potentially dangerous voltages also exist on:
•All electronics boards in the instrument
•The internal wires and cables connected to these boards
•The wires for any heater (oven, detector, inlet, or valve box)
Electrostatic discharge is a threat to MS
electronics
The printed circuit boards in the MS can be damaged by electrostatic discharge.
Do not touch any of the boards unless it is absolutely necessary. If you must
handle them, wear a grounded wrist strap, and take other antistatic precautions.
WARNING
All these parts are shielded by covers. With the covers in place, it should be
difficult to accidentally make contact with dangerous voltages. Unless
specifically instructed to, never remove a cover unless the detector, inlet, and
oven are turned off.
WARNING
If the power cord insulation is frayed or worn, the cord must be replaced.
Contact your Agilent service representative.

1Introduction
7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual 19
Precautions to take to prevent an explosion
Many parts are dangerously hot
Many parts of the GC/MS operate at temperatures high enough to cause serious
burns. These parts include, but are not limited to the:
•Inlet
•Oven and its contents
•Valve box
•Column nuts attaching the column to an inlet, detector, or GC/MS interface
•Foreline pump
•GC/MS interface
•Quadrupole
•Ion source
Always cool these areas of the system to room temperature before working on
them. They will cool faster if you first set the temperature of the heated zone to
room temperature. Turn the zone off after it has reached the setpoint. If you
must perform maintenance on hot parts, use a wrench and wear gloves.
Whenever possible, cool the part of the instrument that you will be maintaining
before you begin working on it.
WARNING
The use of hydrogen gas is specifically prohibited with this product.
WARNING
You MUST make sure the top thumbscrew on the analyzer side plate is fastened
finger-tight. Do not overtighten the thumbscrews; this can cause air leaks.
You MUST leave the collision cell chamber top plate shipping brackets
fastened. Do not remove the shipping brackets from the top plate for normal
operation; they secure the top plate in the event of an explosion.
WARNING
Failure to secure your MS as described above greatly increases the chance of
personal injury in the event of an explosion.

1Introduction
20 7250 Accurate-Mass Q-TOF Troubleshooting and Maintenance Manual
The oil pan under the rotary vane foreline
pump can be a fire hazard
Oily rags, paper towels, and similar absorbents in the oil pan could ignite and
damage the pump and other parts of the MS.
WARNING
Be careful when working behind the instrument. During cool-down cycles, the
GC emits hot exhaust that can cause burns.
WARNING
The foreline pump can cause burns if touched when operating.
WARNING
The insulation around the inlets, detectors, valve box, and the insulation cups
is made of refractory ceramic fibers. To avoid inhaling fiber particles, we
recommend the following safety procedures: ventilate your work area; wear
long sleeves, gloves, safety glasses, and a disposable dust/mist respirator;
dispose of insulation in a sealed plastic bag in accordance with local
regulations; wash your hands with mild soap and cold water after handling the
insulation.
WARNING
Combustible materials (or flammable/nonflammable wicking material) placed
under, over, or around the foreline (roughing) pump constitutes a fire hazard.
Keep the pan clean, but do not leave absorbent material such as paper towels
in it.