Agilent

7200 Accurate-Mass
Quadrupole
Time-of-Flight GC/MS
System

Operation Manual

Agilent Technologies
Notices
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About This Manual
This manual contains information for operating and maintaining the Agilent
7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS system.

1 “Introduction”
Chapter 1 describes general information about the 7200 Q-TOF GC/MS,
including a hardware description, and general safety warnings.

2 “Installing GC Columns”
Chapter 2 shows you how to prepare a capillary column for use with the MS,
install it in the GC oven, and connect it to the MS using the GC/MS interface.

3 “Operating in Electron Impact (EI) Mode”

Chapter 3 describes routine operations in EI mode such as setting
temperatures, monitoring pressures, tuning, venting, and pumpdown.

4 “Operating in Chemical Ionization (CI) Mode”

Chapter 4 describes additional tasks necessary to operate in CI mode.

5 “Using the Removable Ion Source”

Chapter 5 shows you how to change the removable ion source.

6 “General Maintenance”
Chapter 6 describes general maintenance procedures for the 7200 Q-TOF
GC/MS.

7200 Accurate-Mass QTOF Operation Manual 3

Hardware User Information
Accompanying your hardware and software is a comprehensive collection of
manuals, videos, user applications, and method development tools. These are
located on the:
• Agilent GC and GC/MS User Manuals and Tools DVD set
• Agilent GC/MS Software Information and Manuals memory stick

To Install Your Hardware Library

Version B.01.05
January, 2013
Agilent Technologies
GC/GCMS Hardware User Manuals and Videos

Agilent Technologies
Disk 2/3
Insert Disk 1 into your DVD drive and follow the prompts.
GC/GCMS Hardware User
To install: Manuals and Videos
1. Insert disk into DVD drive
2. Follow the instructions on the screen.
3. If autoplay is not enabled, double-click
"index_xx.html" on the DVD
where xx is:
Version B.01.05 en for English Disk 2/3
ch for 中文
January, 2013 jp for 日本語
To install:
1. Insert disk into DVD drive
2. Follow the instructions on the screen.
© 2013 Agilent Technologies, Inc.3. If autoplay is not enabled, double-click
All rights reserved. "index_xx.html" on the DVD

This can be installed by anyone who has authority to copy

Made in USA where xx is:
en for English

S1
ch for 中文
jp for 日本語

© 2013 Agilent Technologies, Inc.

All rights reserved.
Made in USA

S1
information onto the receiving computer.

To Install Your Software Library

Insert the memory stick into a USB port and follow the prompts.

This can be installed by anyone who has authority to copy

information onto the receiving computer.

See the Agilent 7200 Accurate Mass Q-TOF GC/MS System Quick Start
document (G6845-90014) for more details on how to install this information
on your computer.

4 7200 Accurate-Mass QTOF Operation Manual

Contents
1 Introduction
Abbreviations Used 10
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS
System 12
Hardware Description 14
Important Safety Warnings 15
Safety and Regulatory Certifications 18
Intended Use 21
Cleaning/Recycling the Product 21
Liquid Spills 21
Moving or Storing the MS 21

2 Installing GC Columns
Columns 24
To Install a Capillary Column in a Split/Splitless Inlet 26
To Condition a Capillary Column 29
To Install a Capillary Column in the GC/MS Interface 30

3 Operating in Electron Impact (EI) Mode

Operating the MS from the Data System 34
The GC/MS Interface 35
Before You Turn On the MS 37
Pumping Down 38

7200 Accurate-Mass QTOF Operation Manual 5

 Controlling Temperatures 38
Controlling Column Flow 38
Controlling Collision Cell Flow 39
Venting the MS 39
Typical Vacuum Pressures in EI Mode 40
To Set Monitors for Temperature and Vacuum Status 41
To Set the MS Analyzer Temperature 43
To Set the GC/MS Interface Temperature from the MassHunter Workstation 45
To Calibrate the Column 46
To Configure the Collision Cell Gas 48
To Set the Collision Cell Gas Flow Rate 49
To Autotune the MS for EI Mode 50
To Remove the Upper RIS Cover 52
To Open the Analyzer Cover for Access to the Analyzer Sideplate 53
To Pump Down the MS 54
To Vent the MS 56

4 Operating in Chemical Ionization (CI) Mode

Setting Up Your MS to Operate in CI Mode 58
The GC/MS Interface 59
Operating the CI MS 61
High Vacuum Pressure in CI Mode 62
Other Reagent Gases 63
CI Autotune 65
The Flow Control Module 66
To Switch from the EI Mode to CI Mode 67

6 7200 Accurate-Mass QTOF Operation Manual

 To Operate the Reagent Gas Flow Control Module 69
To Set a Reagent Gas Flow 71
To Perform a CI Autotune 72

5 Using the Removable Ion Source

The Removable Ion Source 76
To Change the Ion Source 78
To Install the RIS Probe Extraction Tool 80
To Remove the Source from the Analyzer Chamber 82
To Change the Ion Source on the RIS Probe Extraction Tool 84
To Install the Ion Source in the Analyzer Chamber 86
To Remove the RIS Probe Extraction Tool from the Instrument 87

6 General Maintenance
Before Starting 90
Maintaining the Vacuum System 94
Maintaining the Analyzer 95
To Disassemble the EI Ion Source 97
To Assemble the EI Ion Source 99
To Disassemble the CI Ion Source 101
To Assemble the CI Ion Source 103
To Clean the Ion Source 105
To Remove a Filament 109
To Install a Filament 111

7200 Accurate-Mass QTOF Operation Manual 7

8 7200 Accurate-Mass QTOF Operation Manual
 Agilent 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual

1
Introduction
Abbreviations Used 10
The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System 12
Hardware Description 14
Important Safety Warnings 15
Safety and Regulatory Certifications 18
Intended Use 21
Cleaning/Recycling the Product 21
Liquid Spills 21
Moving or Storing the MS 21

This section provides general information about the 7200 Accurate-Mass

Quadrupole Time-of-Flight (Q-TOF) GC/MS System, including a hardware
description, and general safety warnings.

Agilent Technologies 9
1 Introduction

Abbreviations Used
The abbreviations in Table 1 are used in discussing this product. They are
collected here for convenience.

Table 1 Abbreviations

Abbreviation Definition

AC Alternating current

ALS Automatic liquid sampler

BFB Bromofluorobenzene (calibrant)

CC Collision cell

CI Chemical ionization

DC Direct current

DFTPP Decafluorotriphenylphosphine (calibrant)

EI Electron impact

EPC Electronic pneumatic control

eV Electron volt

GC Gas chromatograph

id Inside diameter

LAN Local Area Network

m/z Mass to charge ratio

MFC Mass flow controller

MS Mass spectrometer

NCI Negative chemical ionization

OFN Octafluoronaphthalene (sample)

PCI Positive chemical ionization

PFDTD Perfluoro-5,8-dimethyl-3,6,9-trioxydodecane (calibrant)

PFET 2,4,6-tris (Pentafluoroethyl)-1,3,5-triazine

10 7200 Accurate-Mass QTOF Operation Manual

 Introduction 1

Table 1 Abbreviations (continued)

Abbreviation Definition

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

7200 Accurate-Mass QTOF Operation Manual 11

1 Introduction

The 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System

The 7200 Accurate-Mass Quadrupole Time-of-Flight (Q-TOF) GC/MS System is
a standalone capillary GC detector for use with the Agilent 7890 Series gas
chromatograph. The 7200 Q-TOF features:
• Three turbomolecular vacuum pumps
• Rotary vane foreline pump
• Independently MS-heated EI or CI ion source
• Removable ion source (RIS) probe with RIS bayonet and cooling chamber,
which allows quick change from EI to CI ion source with minimal loss of
vacuum in the instrument
• 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 with automatic retraction
during ion source removal

Physical description
The 7200 Q-TOF GC/MS is approximately 48 cm high, 71 cm wide, and 89 cm
deep excluding the flight tube and RIS handle. The flight tube extends 84 cm
over the top of the instrument. The RIS handle, when attached, extends 48 cm
from the front of the instrument.
The weight of the instrument mainframe is 152 kg. The attached foreline
(roughing) pump weighs an additional 21.5 kg.
The basic components of the instrument are: the frame/cover assemblies, the
vacuum system, the GC/MS interface, the removable ion source, the flight tube
electronics, the quadrupole mass filter, the collision cell, and the detector.

12 7200 Accurate-Mass QTOF Operation Manual

 Introduction 1

Vacuum gauge
The 7200 Q-TOF GC/MS is equipped with four ion vacuum gauges. The
MassHunter Workstation can be used to read the pressure (high vacuum) in
the vacuum manifold, the turbomolecular vacuum pump discharge, and the
flight tube.

Ionization modes
The G3851BA 7200 Accurate-Mass Q-TOF GC/MS comes standard with both an
EI source and a CI source.
For the CI system, a methane/isobutane gas purifier is provided and is
required. It removes oxygen, water, hydrocarbons, and sulfur compounds.
The MS CI system has been optimized to achieve the relatively high ion source
pressure required for CI while still maintaining high vacuum in the collision
cell, quadrupole, and TOF tube. Special seals along the flow path of the
reagent gas and very small openings in the ion source keep the ion source
gases in the ionization volume long enough for the appropriate reactions to
occur. The interface has special plumbing for reagent gas. A retractable
insulating seal fits onto the tip of the interface and is used for both CI and EI.
Switching back and forth between CI and EI ion sources takes less than
30 minutes with the new removable ion source (RIS). The RIS allows the
instrument to remain under vacuum, and provides a cooling chamber with N2
purge for rapid ion source cooling without venting the machine. This saves
hours in cycle time over the traditional unit.

7200 Accurate-Mass QTOF Operation Manual 13

1 Introduction

Hardware Description
Figure 1 is an overview of a typical Agilent 7200 Accurate-Mass Q-TOF GC/MS
system.

Flight tube

ALS

7890 GC

Q-TOF

MS power Lower RIS Upper RIS GC power Oven door

switch cover cover switch Drawer latch

Figure 1 7200 Q-TOF GC/MS System

14 7200 Accurate-Mass QTOF Operation Manual

 Introduction 1

Important Safety Warnings

There are several important safety notices to always keep in mind when using
the instrument.

Many internal parts of these instruments carry dangerous voltages

If the instrument is connected to a power source, even if the power switch is
off, potentially dangerous voltages exist on:
• The wiring between the instrument power cord and the AC power supply
• The AC power supply itself
• The wiring from the AC power supply to the power switch
With the power switch on, potentially dangerous voltages also exist on:
• All electronics boards in the instrument
• The internal wires and cables connected to these boards
• The wires for any heater (oven, detector, inlet, or valve box)

All these parts are shielded by covers. With the covers in place, it should be difficult
WA R N I N G
to accidentally make contact with dangerous voltages. Unless specifically
instructed to, never remove a cover unless the detector, inlet, and oven are turned
off.

If the power cord insulation is frayed or worn, the cord must be replaced. Contact
WA R N I N G
your Agilent service representative.

Electrostatic discharge is a threat to instrument electronics

The printed circuit boards in these instruments 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.

7200 Accurate-Mass QTOF Operation Manual 15

1 Introduction

Precautions to take to prevent an explosion

The use of hydrogen gas is specifically prohibited with this product.
WA R N I N G

You MUST ensure the top thumbscrew on the front analyzer side plate and the top
WA R N I N G
thumbscrew on the rear analyzer side plate are both fastened finger-tight. Do not
over-tighten the thumbscrews; this can cause air leaks.
You MUST leave the collision cell chamber top plate shipping brackets fastened.
Do not remove the shipping brackets from the top plate for normal operation; they
secure the top plate in the event of an explosion.

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

WA R N I N G
personal injury in the event of an explosion.

Many parts are dangerously hot

Many parts of these instruments 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 MS interface
• Foreline pump
• GC/MS transfer line
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.

16 7200 Accurate-Mass QTOF Operation Manual

 Introduction 1

Be careful when working behind the instrument. During cooldown cycles, the GC
WA R N I N G
emits hot exhaust that can cause burns.

The foreline pump can cause burns if touched when operating.

WA R N I N G

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

The oil pan under the standard foreline pump can be a fire hazard
Oily rags, paper towels, and similar absorbents in the oil pan could ignite and
damage the pump and other parts of the MS.

Combustible materials (or flammable/nonflammable wicking material) placed

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

7200 Accurate-Mass QTOF Operation Manual 17

1 Introduction

Safety and Regulatory Certifications

The 7200 Q-TOF GC/MS conforms to the following safety standards:
• Canadian Standards Association (CSA): CAN/CSA-C22.2 No. 61010-1-04
• CSA/Nationally Recognized Test Laboratory (NRTL): UL 61010–1
• International Electrotechnical Commission (IEC): 61010–1
• EuroNorm (EN): 61010–1
The 7200 Q-TOF GC/MS conforms to the following regulations on
Electromagnetic Compatibility (EMC) and Radio Frequency Interference
(RFI):
• CISPR 11/EN 55011: Group 1, Class A
• IEC/EN 61326-1
• AUS/NZ
This ISM device complies with Canadian ICES-001. Cet appareil ISM est
conforme a la norme NMB—001 du Canada.

The 7200 Q-TOF GC/MS is designed and manufactured under a quality system
registered to ISO 9001.

Information
The Agilent Technologies 7200 Accurate-Mass Q-TOF GC/MS meets the
following IEC (International Electrotechnical Commission) classifications:
Equipment Class I, Laboratory Equipment, Installation Category II, and
Pollution Degree 2.
This unit has been designed and tested in accordance with recognized safety
standards, and is designed for use indoors. If the instrument is used in a
manner not specified by the manufacturer, the protection provided by the
instrument may be impaired. Whenever the safety protection of the MS has
been compromised, disconnect the unit from all power sources and secure the
unit against unintended operation.
Refer servicing to qualified service personnel. Substituting parts or
performing any unauthorized modification to the instrument may result in a
safety hazard.

18 7200 Accurate-Mass QTOF Operation Manual

 Introduction 1

Symbols
Warnings in the manual or on the instrument must be observed during all
phases of operation, service, and repair of this instrument. Failure to comply
with these precautions violates safety standards of design and the intended
use of the instrument. Agilent Technologies assumes no liability for the
customer’s failure to comply with these requirements.

See accompanying instructions for more information.

Indicates a hot surface.

Indicates hazardous voltages.

Indicates earth (ground) terminal.

Indicates potential explosion hazard. or

Indicates radioactivity hazard.

Indicates electrostatic discharge hazard.

Indicates that you must not discard this

electrical/electronic product in domestic household
waste.

7200 Accurate-Mass QTOF Operation Manual 19

1 Introduction

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

Sound emission declaration

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

Schalldruckpegel
Schalldruckpegel LP < 70 dB nach EN 27779:1991 und EN ISO 3744:1995.

20 7200 Accurate-Mass QTOF Operation Manual

 Introduction 1

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

Cleaning/Recycling the Product

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

Liquid Spills
Do not spill liquids on the MS.

Moving or Storing the MS

The best way to keep your MS functioning properly is to keep it pumped down
and hot, with carrier gas flow. If you plan to move or store your MS, a few
additional precautions are required. The MS must remain upright at all times;
this requires special caution when moving. The MS should not be left vented to
atmosphere for long periods. For more information, see “To Move or Store the
MS” in the Agilent 7200 Q-TOF GC/MS Troubleshooting and Maintenance
Manual.

7200 Accurate-Mass QTOF Operation Manual 21

1 Introduction

22 7200 Accurate-Mass QTOF Operation Manual

 Agilent 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual

2
Installing GC Columns
Columns 24
To Install a Capillary Column in a Split/Splitless Inlet 26
To Condition a Capillary Column 29
To Install a Capillary Column in the GC/MS Interface 30

Before you can operate your GC/MS system, you must select, install, and
condition a GC column. This chapter shows you how to install and condition a
column.

Agilent Technologies 23
2 Installing GC Columns

Columns
Many types of GC columns can be used with the MS, but there are some
restrictions.
During tuning or data acquisition the rate of column flow into the MS should
not exceed the maximum recommended flow. Therefore, there are limits to
column length and flow. Exceeding recommended flow will result in
degradation of mass spectral and sensitivity performance.
Remember that column flows vary greatly with oven temperature. See “To
Calibrate the Column” on page 46 for instructions on how to measure actual
flow in your column. Use the flow calculator in the Agilent Instrument
Utilities software, and Table 2 to determine an acceptable column flow. For
expected column outlet flow pressures, use the values shown in Table 3 for EI
mode and Table 6 for CI mode.

Table 2 Gas flows

Feature 7200 Series

High-vacuum pump 1 Split flow turbo

High-vacuum pump 2 Split flow turbo

High-vacuum pump 3 Turbo

Optimal carrier gas flow, mL/min 1.0 to 1.5

Reagent gas flow, mL/min 1 to 2

Collision cell gas flow 1.5

Maximum recommended gas flow, mL/min* 2.0

Maximum gas flow, mL/min† 2.4

Maximum column id 0.32 mm (30 m length)

* Total gas flow into the MS = column flow + collision cell gas flow + reagent gas flow (if applicable)
+ Agilent Quick Swap flow (if applicable)
† Expect degradation of spectral performance and sensitivity.

24 7200 Accurate-Mass QTOF Operation Manual

 Installing GC Columns 2

Conditioning columns
Conditioning a column before it is connected to the GC/MS interface is
essential.
A small portion of the capillary column stationary phase is often carried away
by the carrier gas. This is called column bleed. Column bleed deposits traces of
the stationary phase in the MS ion source. This decreases MS sensitivity and
makes cleaning the ion source necessary.
Column bleed is most common in new or poorly cross-linked columns. It is
much worse if there are traces of oxygen in the carrier gas when the column is
heated. To minimize column bleed, all capillary columns should be
conditioned before they are installed in the GC/MS interface.

Conditioning ferrules
Heating ferrules to their maximum expected operating temperature a few
times before they are installed can reduce chemical bleed from the ferrules.

Tips and hints

• The column installation procedure for the 7200 Q-TOF GC/MS is different
from that for other MSs. Using the procedure from another instrument may
not work and may damage the column or the MS.
• You can remove old ferrules from column nuts with an ordinary pushpin.
• Always use carrier gas that is at least 99.9995% pure.
• Because of thermal expansion, new ferrules may loosen after heating and
cooling a few times. Check for tightness after two or three heating cycles.
• Always wear clean gloves when handling columns, especially the end that
will be inserted into the GC/MS interface.

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

WA R N I N G

Always wear safety glasses when handling capillary columns. Use care to avoid
WA R N I N G
puncturing your skin with the end of the column.

7200 Accurate-Mass QTOF Operation Manual 25

2 Installing GC Columns

To Install a Capillary Column in a Split/Splitless Inlet

 General Materials
• Gloves, clean
• Large (8650-0030)
• Small (8650-0029)
• Metric ruler
• Septum (may be old, used inlet septum)
• Wrench, open-end, 1/4-inch and 5/16-inch (8710-0510)
Self Tightening column nut materials (Recommended)
• Self Tightening column nut (5190-6194)
• Ferrules, Vespel for Self Tightening column nut
• 5181-3323 Ferrule, 0.4mm VG 0.1-0.25 col 10 pk
• 5062-3514 Ferrule, 0.5mm VG 0.32 col 10 pk
Traditional Universal column nut materials
• 5181-8830 Universal column nut, 2 pk
• Ferrules, Vespel for universal column nut
• 5181-3323 Ferrule, 0.4mm VG 0.1-0.25 col 10 pk
• 5062-3514 Ferrule, 0.5mm VG 0.32 col 10 pk
To install columns in other types of inlets, refer to your gas chromatograph
user information.

Procedure

The GC operates at high temperatures. In order to avoid burns, do not touch any
WA R N I N G
parts of the GC until you are sure they are cool.

1 Cool the oven to room temperature.

26 7200 Accurate-Mass QTOF Operation Manual

 Installing GC Columns 2

Always wear clean gloves while handling any parts that go inside the GC or analyzer
CAUTION
chambers.

2 Wearing clean gloves, slide a septum, column nut, and conditioned ferrule
onto the free end of the column. Figure 2 shows a traditional inlet column
nut but the nut is similarly positioned for a self tightening column nut.

The tapered end of the ferrule should point away from the column nut for
a column attachment to an inlet.

Capillary column

Column cutter

Ferrule

Inlet column nut

Septum

Figure 2 Preparing a capillary column for installation (standard inlet column nut shown)

3 Use the column cutter to score the column 2 cm from the end.
4 While holding the column against the column cutter with your thumb,
break the column against the edge of the column cutter.
5 Inspect the end for jagged edges or burrs. If the break is not clean and
even, repeat steps 3 and 4.
6 Wipe the outside of the free end of the column with a lint-free cloth
moistened with methanol.
7 Position the septum under the column nut so that the column extends
4 to 6 mm past the end of the ferrule (Figure 3).

7200 Accurate-Mass QTOF Operation Manual 27

2 Installing GC Columns

8 Insert the column in the inlet.

9 Slide the nut up the column to the inlet base and finger-tighten the nut.
10 Adjust the column position so the septum is even with the bottom of the
column nut.

Never use a wrench to tighten a self tightening nut. This may result in damage to the
CAUTION
nut or instrument.

11 For the Self Tightening column nut, finger-tighten until it begins to grip
the column then turn an additional 30 to 60 degrees until tight.

For the traditional column nut tighten the nut an additional 1/4 to
1/2 turn. The column should not slide with a gentle tug.
12 Start carrier gas flow.
13 Verify flow by submerging the free end of the column in isopropanol. Look
for bubbles.

Insulation cup
Reducing nut

Capillary column 4 to 6 mm

Ferrule (inside nut)

Inlet column nut

Septum

Figure 3 Installing a capillary column for a split/splitless inlet

The traditional inlet column nut is shown and the recommended self tighten-
ing inlet column nut is also provided but not shown.

28 7200 Accurate-Mass QTOF Operation Manual

 Installing GC Columns 2

To Condition a Capillary Column

 Materials needed
• Carrier gas, (99.9995% pure or better)
• Wrench, open-end, 1/4-inch and 5/16-inch (8710-0510)

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

WA R N I N G

The GC operates under high temperatures. To avoid burns, do not touch any GC parts
WA R N I N G
unless you are certain they are cool.

Procedure

1 Install the column in the GC inlet. (See “To Install a Capillary Column in a
Split/Splitless Inlet” on page 26.)
2 Set a minimum velocity of 30 cm/s, or as recommended by the column
manufacturer. Allow gas to flow through the column at room temperature
for 15 to 30 minutes to remove air.
3 Program the oven from room temperature to the maximum temperature
limit for the column.
4 Increase the temperature at a rate of 10 to 15 °C/min.
5 Hold at the maximum temperature for 30 minutes.

Never exceed the maximum column temperature, either in the GC/MS interface, the
CAUTION
GC oven, or the inlet.

6 Set the GC oven temperature to 30 °C and wait for the GC to become

ready.
7 Attach the column to the GC interface. (See “To Install a Capillary Column
in the GC/MS Interface” on page 30.)
For more information about installing a capillary column, refer to Optimizing
Splitless Injections on Your GC for High Performance MS Analysis, Agilent
Technologies publication number 5988-9944EN.

7200 Accurate-Mass QTOF Operation Manual 29

2 Installing GC Columns

To Install a Capillary Column in the GC/MS Interface

 This procedure is for the installation of a capillary column directly into the
analyzer using the Agilent recommended self-tightening column nut.

Materials needed
• Column cutter, ceramic (5181-8836) or diamond (5183-4620)
• Flashlight
• Magnifying loupe
• Gloves, clean
• Large (8650-0030)
• Small (8650-0029)
• Septum (may be old, used inlet septum)
• Safety glasses
• Column install tool (G3850-60014)
Self Tightening column nut materials (Recommended)
• Self Tightening column nut (5190-5233)
• Ferrules, Vespel for Self Tightening column nut
• 5181-3323 Ferrule, 0.4 mm VG 0.1-0.25 col 10 pk
• 5062-3514 Ferrule, 0.5 mm VG 0.32 col 10 pk
Traditional MS interface nut materials
• MS Interface column nut (05988-20066)
• Ferrules, Vespel for universal column nut
• 5181-3323 Ferrule, 0.4 mm VG 0.1-0.25 col 10 pk
• 5062-3514 Ferrule, 0.5 mm VG 0.32 col 10 pk

30 7200 Accurate-Mass QTOF Operation Manual

 Installing GC Columns 2

Procedure
Always wear clean gloves while handling any parts that go inside the GC or the
CAUTION
analyzer chambers.

1 Condition the column. (See “To Condition a Capillary Column” on

page 29.)

The analyzer, GC/MS interface, and other components in the analyzer chamber
WA R N I N G
operate at very high temperatures. Do not touch any part until you are sure it is cool.

Dangerous voltages exist inside the analyzer chamber, which can result in fatal
WA R N I N G
injury. Do not open the analyzer chamber door for any reason. If access is ever
required, trained service personnel must first disconnect the instrument from the
building power source.

2 Vent the MS. To vent the MS, see “To Vent the MS” on page 56.

The GC operates under high temperatures. To avoid burns, do not touch any GC parts
WA R N I N G
unless you are certain they are cool.

3 Slide the Self Tightening or standard column interface nut and

conditioned ferrule onto the free end of the GC column. The tapered end
of the ferrule must point towards the nut.
4 Insert the column into the column install pre-swaging tool, and allow the
end of the column to project past the end of the tool.
5 Use the column cutter to score the column 2 cm from its end.
6 While holding the column against the column cutter with your thumb,
break the column against the edge of the column cutter.
7 Inspect the end for jagged edges or burrs. If the break is not clean and
even, repeat steps 5 and 6.

7200 Accurate-Mass QTOF Operation Manual 31

2 Installing GC Columns

8 Wipe the outside of the free end of the column with a lint-free cloth
moistened with methanol.
9 Slide the column so that the end projects 4–5 mm past the end of the
column install pre-swaging tool.
10 For the Self Tightening column nut, finger-tighten until it begins to grip
the column then turn an additional 30 to 60 degrees until tight.

For the traditional column nut, tighten the nut an additional 1/4 to
1/2 turn. The column should not slide with a gentle tug.
11 Loosen the column nut and remove the column from the tool.
12 Slide the column into the GC/MS interface.
13 Hand-tighten the nut. Ensure the position of the column does not change
as you tighten the nut.
14 Check the GC oven to be sure that the column does not touch the oven
walls.
15 Check the nut’s tightness after one or two heat cycles; retighten as
appropriate.

32 7200 Accurate-Mass QTOF Operation Manual

 Agilent 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual

3
Operating in Electron Impact (EI) Mode
Operating the MS from the Data System 34
The GC/MS Interface 35
Before You Turn On the MS 37
Pumping Down 38
Controlling Temperatures 38
Controlling Column Flow 38
Controlling Collision Cell Flow 39
Venting the MS 39
Typical Vacuum Pressures in EI Mode 40
To Set Monitors for Temperature and Vacuum Status 41
To Set the MS Analyzer Temperature 43
To Set the GC/MS Interface Temperature from the MassHunter
Workstation 45
To Calibrate the Column 46
To Configure the Collision Cell Gas 48
To Set the Collision Cell Gas Flow Rate 49
To Autotune the MS for EI Mode 50
To Remove the Upper RIS Cover 52
To Open the Analyzer Cover for Access to the Analyzer Sideplate 53
To Pump Down the MS 54
To Vent the MS 56

This chapter will explain how to perform some routine operating procedures
for the 7200 Accurate-Mass Q-TOF GC/MS in EI mode.

Agilent Technologies 33
3 Operating in Electron Impact (EI) Mode

Operating the MS from the Data System

The Agilent MassHunter Data Acquisition Workstation automates tasks such
as pumping down, removing the ion source, monitoring settings, setting
temperatures, tuning, and venting the MS. These tasks are described in this
chapter. Additional information is described in the manuals and online help
supplied with the MassHunter Workstation software.
The software and firmware are revised periodically. If the steps in these procedures do
CAUTION
not match your MassHunter Workstation software, refer to the manuals and online
help supplied with the software for more information.

Your G3851BA 7200 Q-TOF GC/MS provides the capability of operating in

either EI or CI modes, using the new RIS technology. You must specify the type
of ionization you are using in the Acquisition software tune file used by your
method.

34 7200 Accurate-Mass QTOF Operation Manual

 Operating in Electron Impact (EI) Mode 3

The GC/MS Interface

The GC/MS interface (Figure 4) is a heated conduit into the MS for the
capillary column. The interface is bolted onto the right side of the front
analyzer chamber and has an O-ring seal. It has a protective insulated cover
that should be left in place.
One end of the GC/MS interface passes through the side of the gas
chromatograph and extends into the GC oven. This end is threaded to allow
connection of the column with a nut and ferrule. The other end of the
interface fits into the ion source. The last 4 to 5 mm of the capillary column
extends past the end of the guide tube and into the ionization chamber. When
changing the removable ion source, the interface is automatically retracted
from the ion source by the MassHunter software. This allows the ion source to
slide freely in and out of the analyzer chamber.
The GC/MS interface is heated by an electric cartridge heater. Normally, the
heater is powered and controlled by the Thermal Aux #2 heated zone of the
GC. The interface temperature can be set from the MassHunter Workstation or
from the gas chromatograph keypad. A sensor (thermocouple) in the interface
monitors the temperature.
The GC/MS interface generally operates in the 250 to 350 °C range. Subject to
that restriction, the interface temperature should be slightly higher than the
maximum GC oven temperature, but never higher than the maximum column
temperature.

See also
“To Install a Capillary Column in the GC/MS Interface” on page 30.

The GC/MS interface operates at high temperatures. If you touch it when it is hot, it
WA R N I N G
will burn you.

7200 Accurate-Mass QTOF Operation Manual 35

3 Operating in Electron Impact (EI) Mode

Spring-loaded tip
Column nut
seal entrance to
ion source

MS GC oven

IRM calibrant in

Heater sensor assembly

Column end protrudes 4 to 5 mm into the ionization chamber.

Column not shown

Figure 4 The GC/MS interface

36 7200 Accurate-Mass QTOF Operation Manual

 Operating in Electron Impact (EI) Mode 3

Before You Turn On the MS

Verify the following before you turn on or attempt to operate the MS.
• All vacuum seals and fittings must be in place and fastened correctly. The
analyzer plate thumbscrew should be unfastened, unless hazardous carrier
or reagent gases are being used.
• The MS is connected to a grounded power source.
• The GC/MS interface extends into the GC oven.
• A conditioned capillary column is installed in the GC inlet and in the
GC/MS interface.
• The GC is on, but the heated zones for the GC/MS interface, the GC inlet,
and the oven are off.
• Carrier gas of at least 99.9995% purity is plumbed to the GC with the
recommended traps.
• The use of hydrogen gas is specifically prohibited with this product.
• The foreline pump exhaust is properly vented.

The exhaust from the foreline pump contains solvents and the chemicals you are
WA R N I N G
analyzing. The standard foreline pump, also exhausts traces of pump oil. If you are
using toxic solvents or analyzing toxic chemicals, attach a hose (11-mm id) to the
oil mist filter to take the foreline pump exhaust outside or to a fume (exhaust) hood.
Be sure to comply with local regulations. The oil mist filter supplied with the
standard pump stops only pump oil. It does not trap or filter out toxic chemicals.

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

WA R N I N G

7200 Accurate-Mass QTOF Operation Manual 37

3 Operating in Electron Impact (EI) Mode

Pumping Down
Pumping down is only required if the analyzer was vented. It is not required
for changing the ion source.
The data system helps you pump down the MS. The process is mostly
automated. When you turn on the main power switch (while pressing on the
analyzer sideplate), the MS pumps down by itself. The data system software
monitors and displays system status during pumpdown. When the pressure is
low enough, the program turns on the ion source and mass filter heaters and
prompts you to turn on the GC/MS interface heater. The MS will shut down if
it cannot pump down correctly.
Using the MS monitors, the data system can display:
• Motor speed for each MS turbo pump
• Analyzer chamber pressure (vacuum)
• Quadrupole and ion source temperatures

Controlling Temperatures
MS temperatures are controlled through the data system. The MS has
independent heaters and temperature sensors for the ion source and the
quadrupole mass filter. You can adjust the setpoints and view these
temperatures from the data system
The GC/MS interface heater is powered and controlled by the Thermal Aux #2
heated zone of the GC. The GC/MS interface temperature can be set and
monitored from the data system or from the GC keypad.

Controlling Column Flow

Carrier gas flow is controlled by column inlet pressure in the GC. For a given
inlet pressure, column flow will decrease as the GC oven temperature
increases. With electronic pneumatic control (EPC) and the column mode set
to Constant Flow, the same column flow is maintained regardless of
temperature.

38 7200 Accurate-Mass QTOF Operation Manual

 Operating in Electron Impact (EI) Mode 3

The MS can be used to measure actual column flow. You inject a small amount
of air or other unretained chemical and time how long it takes to reach the MS.
With this time measurement, you can calculate the column flow. See “To
Calibrate the Column” on page 46.

Controlling Collision Cell Flow

The collision cell gas flow rate is controlled by an EPC module located in the
GC. The collision cell gas flow consists of nitrogen. The gas pressure at the
EPC outlet controls the flow of the gas. This pressure is controlled by the
MassHunter Data Acquisition Workstation or directly at the GC keypad. See
“To Set the Collision Cell Gas Flow Rate” on page 49.

Venting the MS
A program in the data system automates the venting process. It turns off the
GC and MS heaters and the turbo pump at the correct time.
The Fast Vent feature loads a user-defined GC method that sets an oven
temperature, turns off the transfer line heater and sets the column flow to a
user predefined level.
The MS will be damaged by incorrect venting. A turbo pump will be damaged if
it is vented while spinning at more than 50% of its normal operating speed.

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

WA R N I N G

Never vent the MS by allowing air in through either end of the foreline hose. Use the
CAUTION
vent valve or remove the column nut and column.
Do not exceed the maximum recommended total gas flow. See Table 2.

7200 Accurate-Mass QTOF Operation Manual 39

3 Operating in Electron Impact (EI) Mode

Typical Vacuum Pressures in EI Mode

The largest influences on operating pressure in EI mode are the carrier gas
(column) and collision cell gas flows. Table 3 lists typical pressures for various
helium and nitrogen collision cell gas flows. These pressures are approximate
and will vary from instrument to instrument by as much as 30%.

Table 3 Influence of carrier and collision cell gas flows on vacuum

CC Gas On CC Gas Off

N2 = 1.5 mL/min

Column Flow
(mL/min) Rough Vac Quad Vac TOF Vac Rough Vac Quad Vac TOF Vac

0.5 1.16 * 10-1 3.41 * 10-5 4.20* 10-7 8.29 * 10-2 3.17 * 10-7 2.15 * 10-7

0.7 1.18 * 10-1 3.41 * 10-5 4.20 * 10-7 8.67 * 10-2 3.45 * 10-7 2.15 * 10-7

1 1.22 * 10-1 3.43 * 10-5 4.22 * 10-7 9.17 * 10-2 3.79 * 10-7 2.16 * 10-7

1.2 1.24 * 10-1 3.43 * 10-5 4.22 * 10-7 9.49 * 10-2 4.06 * 10-7 2.16 * 10-7

2 1.32 * 10-1 3.44 * 10-5 4.22 * 10-7 1.07 * 10-1 5.17 * 10-7 2.17 * 10-7

3 1.42 * 10-1 3.44 * 10-5 4.25 * 10-7 1.19 * 10-1 6.51 * 10-7 2.20 * 10-7

4 1.50 * 10-1 3.46 * 10-5 4.27 * 10-7 1.29 * 10-1 7.84 * 10-7 2.21 * 10-7

If the pressure is consistently higher than those listed, refer to the online help
in the MassHunter Workstation software for information on troubleshooting
air leaks and other vacuum problems.

40 7200 Accurate-Mass QTOF Operation Manual

 Operating in Electron Impact (EI) Mode 3

To Set Monitors for Temperature and Vacuum Status

A monitor displays the current value of a single instrument parameter. They
can be added to the standard instrument control window. Monitors can be set
to change color if the actual parameter varies beyond a user-determined limit
from its setpoint.

Procedure
1 Select Instrument > Edit Monitors to display the Select Monitors dialog box.
See Figure 5.

Figure 5 Select Monitors dialog box

7200 Accurate-Mass QTOF Operation Manual 41

3 Operating in Electron Impact (EI) Mode

2 In the Available Monitors column, select a monitor and click the Add button
to move the selected monitor to the Selected Monitors column.
3 Select any other monitors you want and add them to the Selected Monitors
column.
4 Click OK. The new monitors will be stacked on top of each other in the
lower right corner of the Instrument Control window.
5 Select Window > Arrange Monitors, or click and drag each monitor to the
desired position. See Figure 6 for one way of arranging the monitors.

Figure 6 Arranging monitors

6 To make the new settings part of the method, select Save from the Method
menu.

42 7200 Accurate-Mass QTOF Operation Manual

 Operating in Electron Impact (EI) Mode 3

To Set the MS Analyzer Temperature

Setpoints for the MS ion source and quad temperatures are stored in the
current tune file. When a method is loaded, the setpoints in the tune file
associated with that method are downloaded automatically.

Procedure
1 In Instrument Control panel, select the MS Tune icon to display the Tune dialog
box. Select the Manual Tune tab then select the Ion Source tab to display the
ion source parameters.
2 Enter the temperature setpoint in the Source Temp field. See Table 4 for
recommended setpoints.
3 Select the Quadrupole tab to display the MS parameters.
4 Enter the temperature setpoint in the Quad Temp field. See Table 4 for
recommended setpoints.
5 Select the Files and Reports tab then click the Save button to save the tune
file with these changes.

Table 4 Recommended temperature settings

Zone EI operation

MS Source 230 °C

MS Quad 150 °C

7200 Accurate-Mass QTOF Operation Manual 43

3 Operating in Electron Impact (EI) Mode

Figure 7 Setting temperatures

The GC/MS interface, ion source, and the MS quadrupole heated zones
interact. The analyzer heater may not be able to accurately control
temperature if the setpoint for one zone is much different from that of an
adjacent zone.

The software will not allow you to exceed 200 °C for the quadrupole, or 350 °C for
WA R N I N G
the ion source.

44 7200 Accurate-Mass QTOF Operation Manual

 Operating in Electron Impact (EI) Mode 3

To Set the GC/MS Interface Temperature from the MassHunter

Workstation
You can also use the GC Control panel to perform this task.

Procedure
1 Select Instrument > GC Parameters from the Instrument Control panel.
2 Click the Aux Heaters icon to edit the interface temperature (Figure 8). This
example has the GC/MS interface temperature configured as Thermal Aux 2.

Figure 8 Setting the interface temperature

Ensure that the carrier gas is turned on and the column has been purged of air before
CAUTION
heating the GC/MS interface or the GC oven.

7200 Accurate-Mass QTOF Operation Manual 45

3 Operating in Electron Impact (EI) Mode

When setting the GC/MS interface temperature, never exceed the maximum for your
CAUTION
column.

3 Click the heater On check box and enter the setpoint in the Value °C
column. The typical setpoint is 280 °C. The limits are 0 °C to 400 °C. A
setpoint below ambient temperature turns off the interface heater.
4 Click Apply to download setpoints or click OK to download setpoints and
close the window.
5 To make the new settings part of the method, select Save from the Method
menu.

To Calibrate the Column

Capillary columns must be calibrated prior to use with the MS.

Procedure
1 Set Data Acquisition for splitless manual injection and set up a real time
plot to monitor m/z 28.
2 Press [Prep Run] on the GC keypad.
3 Inject 1 µL of air into the GC inlet and press [Start Run]
4 Wait until a peak elutes at m/z 28. Note the retention time.

5 In the Instrument Control panel, select .

6 Select the Configuration tab.
7 Select the Column tab and from the table, then select the column to be
calibrated and click Calibrate.
8 Select the Calc Length button.
9 In the Calculate Column Length dialog box, enter the recorded retention time
in the Holdup Time of an Unretained Peak field.
10 Verify that the other parameters listed (temperature, inlet and outlet
pressures, and gas type) are those used in the method to determine the
holdup time. Change any parameters that are different than those used in
your method.

46 7200 Accurate-Mass QTOF Operation Manual

 Operating in Electron Impact (EI) Mode 3

Figure 9 Calculate Column Length dialog box

11 When the new column length appears, click OK to save the changes.
12 Click OK on the Calibrate Columns screen to save the calibration.

7200 Accurate-Mass QTOF Operation Manual 47

3 Operating in Electron Impact (EI) Mode

To Configure the Collision Cell Gas

1 From the MassHunter Data Acquisition Workstation Instrument Control panel,

select .
2 Click the Configuration icon and select the Modules tab to display the screen.
See Figure 10.

Figure 10 Configure the collision cell gas

3 From the Collision Cell EPC drop-down menu, select N2 as the collision cell
gas.
4 Click OK to save the configuration.

48 7200 Accurate-Mass QTOF Operation Manual

 Operating in Electron Impact (EI) Mode 3

To Set the Collision Cell Gas Flow Rate

1 From the MassHunter Data Acquisition Workstation Instrument Control
panel, select Instrument > GC Parameters.
2 Click the Columns icon to display control parameter entry screen for
column and Aux flow modules. See Figure 11.
3 Select Collision Cell EPC in the Selection list.
4 Enter the required gas flow rates in the appropriate fields.
5 Click the N2 Collision Gas check box to allow the N2 collision gas flow.
6 Click Apply to download the setpoints or OK to download the setpoints and
close the window.
7 To make the new settings part of the method, select Save from the Method
menu.

Figure 11 Setting the collision cell gas flow rate

7200 Accurate-Mass QTOF Operation Manual 49

3 Operating in Electron Impact (EI) Mode

To Autotune the MS for EI Mode

The MS can be tuned using the MassHunter Workstation software.

Procedure
1 Set the system to the same conditions (GC oven temperature and column
flow, and MS analyzer temperature) that will be used for data acquisition.
2 In the Instrument Control panel, click the MS Tune icon to display the
GC/Q-TOF Tune dialog box.
3 The current tune file is displayed in the upper left corner of the
GC/Q-TOF Tune dialog box. Verify that the correct tune file is loaded.
4 If necessary, load a new tune file by clicking on the Files and Report tab then
click on the Load button in the Tune File area. Select a tune file and click the
OK button.
The tune file must match the type of ion source in the analyzer. If you are
using an EI ion source, select a tune file created for an EI ion source.
5 Click the Autotune tab and select the Tune from default settings check box if
you are restarting the system after a system vent, major servicing, or a
power outage. If you clear the Tune from default settings box, the autotune
process starts using the previous tune values.
6 Select Save tune file when done check box to save the new tune parameters
generated by the autotune. Do not select this item if you want to review
the autotune report before saving the newly generated tune parameters.
7 Select the Print autotune report check box to automatically print a tune
report.
8 Click the Autotune button to start the autotune. The Status line displays the
current step in the autotune process and the plot of the tuned parameter
for that step is shown in the top graph. If specified above, at the
completion of the autotune, a Tune Report is printed.
To stop the autotune before it completes the automatic parameter
selection, click the Abort Tune button. The parameters from the last
successful autotune are used.
9 Review the Tune Report. If the results are acceptable and you did not
select the Save tune file when done check box, save the autotune by clicking
the Files and Report tab, then click the Save button.

50 7200 Accurate-Mass QTOF Operation Manual

 Operating in Electron Impact (EI) Mode 3

See the manuals or online help provided with your MassHunter Data
Acquisition Workstation software for additional information about tuning.

Figure 12 EI Autotune

7200 Accurate-Mass QTOF Operation Manual 51

3 Operating in Electron Impact (EI) Mode

To Remove the Upper RIS Cover

 The upper RIS cover is in front of the instrument (Figure 13). Remove it to
access the latches on the analyzer cover, attach the RIS probe, or access the EI
calibration vial. Do not remove the upper RIS cover for any other reasons.

Procedure
1 Grasp the cover by the outside corners.
2 Pull the cover straight up, and remove it from the instrument.

Figure 13 Upper RIS cover

52 7200 Accurate-Mass QTOF Operation Manual

 Operating in Electron Impact (EI) Mode 3

To Open the Analyzer Cover for Access to the Analyzer Sideplate

 Open the analyzer cover (Figure 14) to access the analyzer sideplate only.
This is necessary during pump down or to access the analyzer sideplate
thumbscrews. You should not open the analyzer cover for any other reason.

Procedure

1 Remove the upper RIS cover to expose the analyzer cover latches.
See “To Remove the Upper RIS Cover” on page 52.
2 Open the latches on the analyzer cover at the front of the instrument.
3 Swing the analyzer cover open.

Analyzer cover

Upper RIS cover

Figure 14 Covers

7200 Accurate-Mass QTOF Operation Manual 53

3 Operating in Electron Impact (EI) Mode

To Pump Down the MS

Ensure your MS meets all the conditions listed in the introduction to this chapter
WA R N I N G
before starting up and pumping down the MS. Failure to do so can result in personal
injury.

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

WA R N I N G

Dangerous voltages exist inside the analyzer chamber, which can result in fatal
WA R N I N G
injury. Do not open the analyzer chamber door for any reason. If access is ever
required, trained service personnel must first disconnect the instrument from the
building power source.

Procedure
1 Open the analyzer cover to access the analyzer quad driver board. See “To
Open the Analyzer Cover for Access to the Analyzer Sideplate” on page 53.
2 Plug the power cord into a grounded electrical outlet.
3 Turn on the Q-TOF power switch (Figure 14).
4 Press lightly on the metal box on the quad driver board to ensure a correct
seal.
Do not push on the filament board safety cover while pressing on the analyzer board.
CAUTION
This cover was not designed to withstand this type of pressure.

The foreline pump will make a gurgling noise. This noise should stop
within a minute. If the noise continues, there is a large air leak in your
system, probably at the sideplate seal or the interface column nut.
5 Start the MassHunter Data Acquisition program. If the Q-TOF was
configured for both an EI and a CI ion source, you are prompted for the
ion source type that is currently installed. Click on an EI or CI ion source
type if prompted.
6 Select the MS Tune icon from the Instrument Control panel.
7 Select the Vacuum Control tab.

54 7200 Accurate-Mass QTOF Operation Manual

 Operating in Electron Impact (EI) Mode 3

8 Click the Pumpdown button.

Figure 15 Vacuum Control tab

Do not turn on any GC heated zones until carrier gas flow is on. Heating a column with
CAUTION
no carrier gas flow will damage the column.

Within 10 to 15 minutes, the turbo pump speed should be up to 80%

(Figure 15). The pump speed should eventually reach 95%. If these conditions
are not met, the MS electronics will shut off the foreline pump. In order to
recover from this condition, you must power cycle the MS. If the MS does not
pump down correctly, see the manual or online help for information on
troubleshooting air leaks and other vacuum problems.
9 Turn on the carrier gas flow after the vacuum pumps have been running
for 15 minutes.
10 When prompted, turn on the GC/MS interface heater and GC oven. Click
OK when you have done so. The software will turn on the ion source and
mass filter (quad) heater. The temperature setpoints are stored in the
current autotune file.
11 After the message Okay to run appears, wait 2 hours for the MS to reach
thermal equilibrium. Data acquired before the MS has reached thermal
equilibrium may not be reproducible.
12 Tune the MS. (See “To Autotune the MS for EI Mode” on page 50 or “To
Perform a CI Autotune” on page 72.)

7200 Accurate-Mass QTOF Operation Manual 55

3 Operating in Electron Impact (EI) Mode

To Vent the MS

Procedure

1 Click the MS Tune icon from the Instrument Control panel.

2 Select the Vacuum Control tab. See Figure 15.
3 Set the GC/MS interface heater and the GC oven temperatures to ambient
(room temperature).
4 When the GC temperatures have reached 30 °C, turn off the flow of carrier
gas.
5 Click the Vent button.

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

WA R N I N G

Be sure the GC oven and the GC/MS interface are cool before turning off carrier gas
CAUTION
flow.

6 Turn off the MS by pressing the power switch. (See Figure 1.)
7 Unplug the MS power cord.

Allow the analyzer to cool to near room temperature before touching it.
WA R N I N G

When the MS is vented, do not put the Workstation into Instrument Control view.
CAUTION
Doing so will turn on the interface heater, which can damage the column.

56 7200 Accurate-Mass QTOF Operation Manual

 Agilent 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual

4
Operating in Chemical Ionization (CI)
Mode
Setting Up Your MS to Operate in CI Mode 58
The GC/MS Interface 59
Operating the CI MS 61
High Vacuum Pressure in CI Mode 62
Other Reagent Gases 63
CI Autotune 65
The Flow Control Module 66
To Switch from the EI Mode to CI Mode 67
To Operate the Reagent Gas Flow Control Module 69
To Set a Reagent Gas Flow 71
To Perform a CI Autotune 72

This chapter provides information and instructions for operating the 7200
Q-TOF GC/MS system in Chemical Ionization (CI) mode. Most of the
information in the preceding chapter is also relevant.
Most of the material is related to methane chemical ionization but one section
discusses the use of other reagent gases.
The software contains instructions for setting the reagent gas flow and for
performing CI autotunes. Autotunes are provided for positive CI (PCI) with
methane reagent gas and for negative CI (NCI) with any reagent gas.

Agilent Technologies 57
4 Operating in Chemical Ionization (CI) Mode

Setting Up Your MS to Operate in CI Mode

Setting up your MS for operation in CI mode requires special care to avoid
contamination and air leaks.
• Always use the highest purity methane (and other reagent gases, if
applicable). Methane must be at least 99.9995% pure.
• Always verify the MS is performing well in EI mode before switching to CI.
• Ensure the CI ion source is installed.
• Ensure the reagent gas plumbing has no air leaks. This is determined in PCI
mode, checking for m/z 32 after the methane pretune.
• Ensure the reagent gas inlet line is equipped with gas purifiers (not
applicable for ammonia).

58 7200 Accurate-Mass QTOF Operation Manual

 Operating in Chemical Ionization (CI) Mode 4

The GC/MS Interface

The GC/MS interface (Figure 16) is a heated conduit into the MS for the
capillary column. It is bolted onto the right side of the analyzer chamber, with
an O-ring seal and has a protective insulated cover which should be left in
place.
One end of the interface passes through the side of the GC and extends into
the oven. It is threaded to allow connection of the column with a nut and
ferrule. The other end of the interface fits into the ion source. The last 4 to
5 mm of the capillary column extend past the end of the guide tube and into
the ionization chamber. When changing the removable ion source, the
interface is automatically retracted from the ion source with the MassHunter
software. This allows the source to slide freely in and out of the analyzer
chamber.
For CI operating mode, reagent gas is also plumbed into the interface. A tip
seal keeps reagent gases from leaking out around the tip. The reagent gas
enters the interface body and mixes with carrier gas and sample in the ion
source.
The GC/MS interface is heated by an electric cartridge heater. Normally, the
heater is powered and controlled by the Thermal Aux #2 heated zone of the
GC. The interface temperature can be set from the MassHunter Workstation or
from the gas chromatograph keypad. A sensor (thermocouple) in the interface
monitors the temperature.
This interface is also be used for EI operation.
The interface should be operated in the 250 ° to 350 °C range. Subject to that
restriction, the interface temperature should be slightly higher than the
maximum GC oven temperature, but never higher than the maximum column
temperature.

See Also
“To Install a Capillary Column in the GC/MS Interface” on page 30.

7200 Accurate-Mass QTOF Operation Manual 59

4 Operating in Chemical Ionization (CI) Mode

Never exceed the maximum column temperature, either in the GC/MS interface, the
CAUTION
GC oven, or the inlet.

The GC/MS interface operates at high temperatures. If you touch it when it is hot, it
WA R N I N G
will burn you.

Column nut
Spring-loaded tip
seal entrance to
ion source

MS GC oven

Reagent gas and

IRM calibrant in
Heater sensor assembly

Column not shown

Figure 16 The GC/MS interface

60 7200 Accurate-Mass QTOF Operation Manual

 Operating in Chemical Ionization (CI) Mode 4

Operating the CI MS
Operating your GC/MS in the CI mode is slightly more complicated than
operating in the EI mode. After tuning, gas flow, temperatures (Table 5), and
electron energy may need to be optimized for your specific analyte.

Table 5 Temperatures for CI operation

Ion source Analyzer GC/MS interface

PCI 300 °C 150 °C 280 °C

NCI 150 °C 150 °C 280 °C

Start the system in CI mode

When starting up the system you may begin in either PCI or NCI mode.
Depending upon the application, use the following reagent gas flowrates
during system startup:
• PCI mode set reagent gas flow to 20 (1 mL/min)
• NCI mode set reagent gas flow to 40 (2 mL/min)

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4 Operating in Chemical Ionization (CI) Mode

High Vacuum Pressure in CI Mode

The largest influences on operating pressure in CI mode are the reagent and
collision cell gas flows. Table 6 lists typical pressures for various reagent gas
flows, depending upon the collision cell gas flowrate. Familiarize yourself with
the measurements on your system under operating conditions and watch for
changes that may indicate a vacuum or gas flow problem. Measurements will
vary by as much as 30% from one MS to the next.

Analyzer vacuum with reagent gas flowing

Note that the mass flow controller (MFC) is calibrated for methane and the
vacuum gauge is calibrated for nitrogen, so these measurements are not
accurate, but are intended as a guide to typical observed readings (Table 6).
They were taken with the following set of conditions. Note that these are
typical PCI temperatures:
Source temperature 230 °C
Quad temperature 150 °C
Interface temperature 280 °C
Inlet 250 °C
Oven 100 °C
Helium carrier gas flow 1 mL/min

Table 6 Typical analyzer vacuum with reagent gas flow

Collision cell gas flow on Collision cell gas flow off

N2 = 1.5 mL/min N2 = 0 mL/min

MFC (%) Rough Pump Quadrupole Flight Tube Rough Pump Quadrupole Flight Tube
(mTorr) (Torr) (Torr) (mTorr) (Torr) (Torr)

0 1.36e+02 3.62e-05 3.35e-07 9.13e+01 5.98e-07 1.64e-07

10 1.36+02 3.62e-05 3.37e-07 1.14e+01 1.27e-06 1.65e-07

15 1.43+02 3.66e-05 3.37e-07 1.23e+01 1.62e-06 1.67e-07

20 1.5+02 3.71e-05 3.39e-07 1.31e+01 1.96e-06 1.67e-07

25 1.57+02 3.73e-05 3.41e-07 1.39e+01 2.32e-06 1.70e-07

30 1.63+02 3.77e-05 3.41e-07 1.46e+01 2.64e-06 1.71e-07

35 1.69+02 3.81e-05 3.41e-07 1.52e+01 3.00e-06 1.71e-07

40 1.74+02 3.83e-05 3.43e-07 1.58e+01 3.34e-06 1.72e-07

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 Operating in Chemical Ionization (CI) Mode 4

Other Reagent Gases

This section describes the use of isobutane or ammonia as the reagent gas. You
should be familiar with operating the CI-equipped 7200 Q-TOF GC/MS with
methane reagent gas before attempting to use other reagent gases.

Do not use nitrous oxide as a reagent gas. It radically shortens the life span of the
CAUTION
filament.

Changing the reagent gas from methane to either isobutane or ammonia

changes the chemistry of the ionization process and yields different ions. The
principal chemical ionization reactions encountered are described in general
in the Agilent 7200 Accurate-Mass Q-TOF GC/MS Concept Guide. If you are
not experienced with chemical ionization, we suggest reviewing that material
before you proceed.

Isobutane CI
Isobutane (C4H10) is commonly used for chemical ionization when less
fragmentation is desired in the chemical ionization spectrum. This is because
the proton affinity of isobutane is higher than that of methane; hence less
energy is transferred in the ionization reaction.
Addition and proton transfer are the ionization mechanisms most often
associated with isobutane. The sample itself influences which mechanism
dominates.

Ammonia CI
Ammonia (NH3) is commonly used for chemical ionization when less
fragmentation is desired in the chemical ionization spectrum. This is because
the proton affinity of ammonia is higher than that of methane; hence less
energy is transferred in the ionization reaction.
Because many compounds of interest have insufficient proton affinities,
ammonia chemical-ionization spectra often result from the addition of NH4+
and then, in some cases, from the subsequent loss of water. Ammonia reagent
ion spectra have principal ions at m/z 18, 35, and 52, corresponding to NH4+,
NH4(NH3)+, and NH4(NH3)2+.

7200 Accurate-Mass QTOF Operation Manual 63

4 Operating in Chemical Ionization (CI) Mode

Use of ammonia affects the maintenance requirements of the MS. See Chapter 6,
CAUTION
“General Maintenance”” for more information.

The pressure of the ammonia supply must be less than 5 psig. Higher pressures can
CAUTION
result in ammonia condensing from a gas to a liquid.
Always keep the ammonia tank in an upright position, below the level of the flow
module. Coil the ammonia supply tubing into several vertical loops by wrapping the
tubing around a can or bottle. This will help keep any liquid ammonia out of the flow
module.

Ammonia tends to break down vacuum pump fluids and seals. Ammonia CI
makes more frequent vacuum system maintenance necessary. (See the Agilent
7200 Q-TOF GC/MS Troubleshooting and Maintenance Manual.)

When running ammonia for 5 or more hours a day, the foreline pump must be ballasted
CAUTION
(flushed with air) for at least 1 hour a day to minimize damage to pump seals. Always
purge the MS with methane after flowing ammonia.

Frequently, a mixture of 5% ammonia and 95% helium or 5% ammonia and

95% methane is used as a CI reagent gas. This is enough ammonia to achieve
good chemical ionization while minimizing its negative effects.

Carbon dioxide CI
Carbon dioxide is often used as a reagent gas for CI. It has obvious advantages
of availability and safety.

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 Operating in Chemical Ionization (CI) Mode 4

CI Autotune
After the reagent gas flow is set, the lenses and electronics of the MS should be
tuned which is a good starting point for developing your application settings.
Typical CI application settings are shown inTable 7.
Perfluoro-5,8-dimethyl-3,6,9-trioxidodecane (PFDTD) is used as the calibrant.
Instead of flooding the entire vacuum chamber, the PFDTD is introduced
directly into the ionization chamber through the GC/MS interface by means of
the gas flow control module. There are no tune performance criteria. If CI
autotune completes, it passes.
Always verify MS performance in EI before switching to CI operation.
CAUTION

Table 7 Typical CI application settings

Parameter Methane Isobutane Ammonia EI

Ion polarity Positive Negative Positive Negative Positive Negative N/A
Emission 150 μA 50 μA 150 μA 50 μA 150 μA 50 μA 35 μA
Electron energy 150 eV 150 eV 150 eV 150 eV 150 eV 150 eV 70 eV
Filament 1 1 1 1 1 1 1 or 2
Repeller 3V 3V 3V 3V 3V 3V 30 V
Ion focus 130 V 130 V 130 V 130 V 130 V 130 V 90 V
Entrance lens 20 V 20 V 20 V 20 V 20 V 20 V 25 V
offset
Shutoff valve Open Open Open Open Open Open Closed
Suggested flow 20% 40% 20% 40% 20% 40% N/A
Source temp 250 °C 150 °C 250 °C 150 °C 250 °C 150 °C 230 °C
Quad temp 150 °C 150 °C 150 °C 150 °C 150 °C 150 °C 150 °C
Interface temp 280 °C 280 °C 280 °C 280 °C 280 °C 280 °C 280 °C
Autotune Yes Yes No Yes No Yes Yes
N/A Not available

7200 Accurate-Mass QTOF Operation Manual 65

4 Operating in Chemical Ionization (CI) Mode

The Flow Control Module

The CI reagent gas flow control module regulates the flow of reagent gas into
the CI GC/MS interface. The flow module consists of a mass flow controller
(MFC), gas select valves, CI calibration valve, shutoff valve, control electronics,
and plumbing.
The instrument provides Swagelok inlet fittings for connecting the CI reagent
gas. The software refers to it as CI reagent gas. Supply reagent gases at
20 to 25 psi (138 to 172 kPa) for Methane.

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 Operating in Chemical Ionization (CI) Mode 4

To Switch from the EI Mode to CI Mode

Always verify GC/MS performance in EI before switching to CI operation.

CAUTION

Always wear clean gloves while touching the analyzer or any other parts that go inside
CAUTION
the analyzer chamber.

Procedure
1 Change the source. See “To Change the Ion Source” on page 78.
2 Load a suitable PCI or NCI method for use with the CI source.
3 Click the MS Tune icon in the Instrument Control panel to display the Tune
dialog box and select the Autotune tab.
The method selects PCI or NCI autotune and the correct reagent gas.
4 Select the Tune from default settings check box because you have changed the
ion source.
5 Select Print autotune report check box to automatically print a tune report.
6 Click the Autotune button to start the autotune. At the completion of the
autotune, a Tune Report is printed.
7 Review the Tune Report. If the results are acceptable, save the autotune by
clicking the Files and Report tab, then click the Save button.

Table 8 Default Tune Control Limits, used by CI autotune only

Reagent gas Methane Ammonia

Ion polarity Positive Negative Positive Negative

Abundance target 1x106 1x106 N/A 1x106

Peakwidth target 0.7 0.7 N/A 0.7

Maximum repeller 4 4 N/A 4

7200 Accurate-Mass QTOF Operation Manual 67

4 Operating in Chemical Ionization (CI) Mode

Table 8 Default Tune Control Limits, used by CI autotune only (continued)

Reagent gas Methane Ammonia

Maximum emission current, 240 50 N/A 50

µA

Max electron energy, eV 240 240 N/A 240

Notes for Table 8:

• N/A Not available.
• Abundance target Adjust higher or lower to get desired signal abundance.
Higher signal abundance also gives higher noise abundance.
• Peakwidth target Higher peakwidth values give better sensitivity, lower
values give better resolution.
• Maximum emission current Optimum emission current maximum for NCI
is very compound-specific and must be selected empirically. Optimum
emission current for pesticides, for example, may be about 200 µA.

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 Operating in Chemical Ionization (CI) Mode 4

To Operate the Reagent Gas Flow Control Module

Procedure
1 In Instrument Control panel, select the MS Tune icon to display the GC/Q-TOF
Tune dialog box. Select the Manual Tune tab then select the Ion Source tab to
display the ion source parameters.

Figure 17 CI flow control

7200 Accurate-Mass QTOF Operation Manual 69

4 Operating in Chemical Ionization (CI) Mode

2 Use the parameters in the CI Reagent Gas Control area to control reagent gas
flow.
CI Reagent - Selects the reagent gas from the dropdown menu.
CI Gas Flow - Enter percent of maximum volumetric flow for the selected
reagent gas. The actual % transmitted by the flow controller is shown next
to this entry. 20% is a good value for PCI and 40% is a good value for NCI.
Set button - Opens the selected reagent gas supply valve and controls the
reagent gas flow to the entered setpoint.
Off button - Turns off the reagent gas flow.
Purge button - Opens the selected reagent gas valve for 6 minutes to clear
the system of unwanted compounds.
Pumpout button - Closes the reagent gas valve for 4 minutes and evacuates
the system of reagent gases. At the end of the pumpout time the selected
reagent gas valve opens.

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 Operating in Chemical Ionization (CI) Mode 4

To Set a Reagent Gas Flow

After the system has been switched from EI to CI mode, or vented for any other reason,
CAUTION
the MS must be baked out for at least 2 hours before tuning.

Continuing with CI autotune if the MS has an air leak or large amounts of water will
CAUTION
result in severe ion source contamination. If this happens, you will need to vent the
MS and clean the ion source.

Procedure
1 In Instrument Control panel, select the MS Tune icon to display the GC/Q-TOF
Tune dialog box. Select the Manual Tune tab then select the Ion Source tab to
display the ion source parameters.
2 In the CI Reagent Gas Control area, select the CI reagent gas you are using.
3 Enter the reagent gas flow setpoint in the CI Gas Flow field. This value is
entered as a percentage of maximum flow rate. The recommended flow is
20% for a PCI source and 40% for an NCI source.
4 Click the Set button. The Flow Set indication is displayed.
The reagent gas is flowing into the ion source at the rate displayed next to
the setpoint.
5 Click the Files and Reports tab, then click the Save button to save your
changes to the currently loaded tune file.

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4 Operating in Chemical Ionization (CI) Mode

To Perform a CI Autotune

Always verify MS performance in EI before switching to CI operation.

CAUTION

Avoid tuning more often than is absolutely necessary; this will minimize PFDTD
CAUTION
background noise and help prevent ion source contamination.

Procedure
1 Verify that the MS performs correctly in EI mode first.
2 Click the MS Tune icon in the Instrument Control panel to display the
GC/Q-TOF Tune dialog box.
3 If necessary, load a new tune file by clicking on the Files and Report tab then
click the Load button in the Tune File area. Select a tune file and click the OK
button.

The tune file must match the type of ion source in the analyzer. For a CI
ion source select a tune file created for a positive or negative CI source.
4 Click the Autotune tab and select PCI source for a positive CI source or
NCI source for a negative CI source.
5 Select the reagent gas you are using from the dropdown menu in the
CI Reagent Gas area.
6 If a log file and associated data files of the tune are required, click the Files
and Reports tab and in the Log Files section, click on the Browse button to
create a directory and files for the logs. Click on the required log and data
files check boxes.
7 Click on the Manual Tune tab and select the Ion source tab. In the CI Reagent
Gas section, select the reagent gas and then enter a CI Gas Flow rate of 20%
for a PCI source or 40% for an NCI source. Click on the Autotune tab to
return to Autotune.
8 Select the Tune from default settings check box if you are restarting the
system after a system vent, major servicing, or a power outage. If you clear

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 Operating in Chemical Ionization (CI) Mode 4

the Tune from default settings box, the Autotune process starts using
previous tune values.
9 Select Save tune file when done check box to save the new tune parameters
generated by the autotune. Do not select this item if you want to review
the autotune report before saving the newly generated tune parameters.
10 Select the Print autotune report check box to automatically print a tune
report.
11 Click the Autotune button to start the autotune. The Status line displays the
current step in the autotune process and the plot of the tuned parameter
for that step is shown in the top graph. If specified above, at the
completion of the autotune a Tune Report is printed.
To stop the autotune before it completes the autotune parameter selection,
click the Abort Autotune button. The parameters from the last successful
autotune are used.
12 Review the Tune Report. If the results are acceptable and you did not
select the Save tune file when done check box, save the autotune by clicking
the Files and Report tab, then click the Save button.

7200 Accurate-Mass QTOF Operation Manual 73

4 Operating in Chemical Ionization (CI) Mode

74 7200 Accurate-Mass QTOF Operation Manual

 Agilent 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual

5
Using the Removable Ion Source
The Removable Ion Source 76
To Change the Ion Source 78
To Install the RIS Probe Extraction Tool 80
To Remove the Source from the Analyzer Chamber 82
To Change the Ion Source on the RIS Probe Extraction Tool 84
To Install the Ion Source in the Analyzer Chamber 86
To Remove the RIS Probe Extraction Tool from the Instrument 87

This chapter will explain how to use the features of the removable ion source.

Agilent Technologies 75
5 Using the Removable Ion Source

The Removable Ion Source

The removable ion source (RIS) is a feature of the Agilent 7200 Q-TOF GC/MS
that allows changing of the ion source without venting the instrument through
the use of the RIS probe extractor tool. The source must be removed from the
MS periodically for routine cleaning and maintenance, or for changing
ionization modes, and the new RIS minimizes the downtime necessary to
complete these tasks. This process is guided by the MassHunter Workstation
software, which performs the purging, valve operation, and pump down steps
automatically.
The RIS probe extraction tool consists of a RIS bayonet that attaches to the
source, a handle for moving the source in and out of the instrument, and a
cooling chamber for cooling the source prior to removal (Figure 18). The entire
process is guided by the MassHunter Workstation Software.
The RIS cooling chamber is attached to the instrument to provide a place to
vent and purge the source with nitrogen during source changing. An automatic
gate valve closes off the cooling chamber from the instrument to eliminate the
need for venting the instrument during this process. Only the small RIS
cooling chamber is vented.

The software and firmware are revised periodically. If the steps in these procedures do
CAUTION
not match your MassHunter Workstation software, refer to the manuals and online
help supplied with the software for more information.

76 7200 Accurate-Mass QTOF Operation Manual

 Using the Removable Ion Source 5

RIS handle

RIS cooling chamber

RIS bayonet

Figure 18 RIS probe extraction tool

7200 Accurate-Mass QTOF Operation Manual 77

5 Using the Removable Ion Source

To Change the Ion Source

The steps necessary for changing the ion source are provided here and also
interactively in the MassHunter Workstation software. The process is mostly
automated, with the exception of the use of the RIS probe extraction tool to
remove and install the ion source. Purging the chamber, cooling the source,
and pumping down are all performed with the use of the Workstation
software.

 Procedure
1 From MassHunter Data Acquisition software control view, click the MS
Tune icon to display the GC/Q-TOF Tune dialog box.
2 Click the Removable Ion Source tab in the GC/Q-TOF Tune screen. (Figure 19)

Figure 19 GC/Q-TOF Tune dialog box

78 7200 Accurate-Mass QTOF Operation Manual

 Using the Removable Ion Source 5

3 Click the Begin button to purge the instrument.

4 When prompted, remove the RIS chamber door and attach the RIS probe
extraction tool. See “To Install the RIS Probe Extraction Tool” on page 80.
5 Click Next to purge the chamber and pump down.
6 When the system is ready for source removal, click Next to retract the
transfer line and open the gate valve.
The RIS status area will note when the Gate Valve is Open and the Transfer
Line is Full Out.
7 When prompted, remove the source. See “To Remove the Source from the
Analyzer Chamber” on page 82.
8 Once the source is retracted fully into the chamber, click Next to close the
gate valve and purge the cooling chamber. The purge takes approximately
10 minutes.
9 When prompted, open the cooling chamber and change the ion source. See
“To Change the Ion Source on the RIS Probe Extraction Tool” on page 84.
10 After replacing the source and securing the cooling chamber door, click
Next to purge and pump down.
11 When prompted that the system is ready for source installation, click Next
to retract the transfer line and open the gate valve.
12 When prompted, install the ion source in the analyzer chamber. See “To
Install the Ion Source in the Analyzer Chamber” on page 86.
13 Verify in the RIS Status that the ion source temperature readback shows a
source temperature. This ensures that the source is fully inserted into its
socket.

If the ion source is not fully installed, it may interfere with the gate valve as it closes.
CAUTION
Damage to the RIS, the valve, or the transfer line may occur.

14 Click Next to close the gate valve and vent the RIS cooling chamber.
15 Remove the RIS probe extraction tool and replace the RIS chamber cover.
See “To Remove the RIS Probe Extraction Tool from the Instrument” on
page 87.
16 Click Next to pump down the chamber behind the RIS chamber cover.
17 When prompted, click Finish.

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5 Using the Removable Ion Source

To Install the RIS Probe Extraction Tool

 This procedure is part of an automated series of steps controlled by

MassHunter. Do not attempt this procedure unless prompted by MassHunter
to remove the RIS cover door.

Procedure
1 When prompted by MassHunter, remove the upper RIS cover (see “To
Remove the Upper RIS Cover” on page 52).
2 Open the latch on the right side of the RIS cover door.
3 Swing the door open.
4 Lift the RIS cover door straight up to free it from the hinges, and remove.

Do not leave the instrument with the RIS cover off. If you remove the cover, you must
CAUTION
install the RIS probe as soon as possible to minimize contamination in the instrument.

5 Holding the RIS probe extraction tool by the handle, position the RIS
cooling chamber up against the instrument RIS chamber. Hold the handle
perpendicular to the front of the instrument so that the outside edge of the
cooling chamber is flush with the RIS chamber opening on the front
instrument.
6 Line up the pins on the probe hinge with the slots on the instrument
hinge.
7 Lower the pins into the hinge.
8 Close the cooling chamber door, and secure the door with the latch on the
right side.
9 Return to step 5 in the “To Change the Ion Source” on page 78.

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 Using the Removable Ion Source 5

Figure 20 RIS cover door

Figure 21 RIS probe installed

7200 Accurate-Mass QTOF Operation Manual 81

5 Using the Removable Ion Source

To Remove the Source from the Analyzer Chamber

This procedure is part of an automated series of steps controlled by
MassHunter. Do not attempt this procedure unless prompted by MassHunter.
The RIS Status area on the GC/Q-TOF Tune tab must show the Gate Valve is Open
and the Transfer Line is Full Out.

Procedure

 1 Holding the RIS handle, turn the alignment guide, which is the white line
on the RIS handle, to the 2 o’clock position from the top of the handle.
This ensures that the RIS bayonet is aligned properly to attach to the
source.

RIS
Alignment
guide
(white line on
RIS handle)

Figure 22 RIS Alignment guide

While the RIS handle is fully extended, do not bump or push it from the side. Doing so
CAUTION
will break the seal and allow air into the cooling chamber.

Do not try to guide the ion source in manually. Push the RIS handle gently and allow
CAUTION
the RIS bayonet to slide on its own. The RIS bayonet will slide in straight if it is allowed
to move naturally.

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 Using the Removable Ion Source 5

2 Keeping the RIS handle in position, push the RIS handle gently and allow
the RIS bayonet to extend into the analyzer chamber. Ensure the RIS
handle extends fully, to ensure that the RIS bayonet seats in the holes on
the ion source body properly.
3 When the ion source is properly seated, turn the RIS handle counter
clockwise until the alignment guide is in the 12 o’clock position, to lock
the ion source in place.
4 Pull the RIS handle toward you, keeping the alignment guide at the
12 o’clock position, to retract the ion source into the RIS cooling chamber.
5 Return to step 8 in the “To Change the Ion Source” on page 78.

7200 Accurate-Mass QTOF Operation Manual 83

5 Using the Removable Ion Source

To Change the Ion Source on the RIS Probe Extraction Tool

This procedure is part of an automated series of steps controlled by
MassHunter. Do not attempt this procedure unless prompted by MassHunter.
The RIS Status area on the GC/Q-TOF Tune tab must show the Gate Valve is Open
and the RIS vacuum as 0.000 Torr.

If not done correctly, source maintenance can introduce contaminants into the MS.
CAUTION
Always wear clean rubber gloves when handling the source.

 1
2
Undo the latch on the right edge of the RIS cooling chamber.
Swing open the RIS cooling chamber until the RIS handle is parallel with
the front of the instrument.
3 Lock the RIS cooling chamber in the open position by opening it enough to
engage the locking pin on the hinge.

The 7200 Q-TOF GC/MS operates at high temperatures. Ensure the source is cooled
WA R N I N G
to a safe temperature before attempting to remove it from the RIS cooling chamber.

4 Grasp the RIS handle with one hand, and the ion source body with the
other hand.
5 While holding the ion source steady, turn the RIS handle counter
clockwise so that the alignment guide is in the 2 o’clock position. This
guides the pin on the RIS bayonet out of the track on the ion source body.
6 Gently pull the ion source free from the RIS bayonet and set aside.
7 Remove the new ion source from its storage container. The ion source
remains connected to the lid. Twist the lid clockwise to separate the ion
source from the lid.
8 Turn the RIS handle so that the alignment guide is in the 2 o’clock
position.
9 Guide the pin on the RIS bayonet into the tracks on the end of the ion
source body.

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 Using the Removable Ion Source 5

10 While holding the ion source securely, turn the RIS handle counter
clockwise so that the alignment guide is in the 12 o’clock position, to lock
the ion source securely on the bayonet.
11 Retract the RIS handle fully so that the ion source is located completely in
the cooling chamber.
12 Raise the locking pin on the RIS cooling chamber hinge and swing it shut.
13 Secure the RIS cooling chamber to the instrument with the latch on the
right side of the door.
14 Return to step 10 in the “To Change the Ion Source” on page 78.

7200 Accurate-Mass QTOF Operation Manual 85

5 Using the Removable Ion Source

To Install the Ion Source in the Analyzer Chamber

This procedure is part of an automated series of steps controlled by
MassHunter. Do not attempt this procedure unless prompted by MassHunter.
The RIS Status area on the GC/Q-TOF Tune tab must show the Gate Valve is Open
and the Transfer Line is Full Out.

Take care when walking past the front of the instrument when the RIS handle is fully
CAUTION
extended, to avoid damage to the instrument. When closed, the RIS handle extends 48
cm (19 inches) out from the front of the instrument.

Do not try to guide the ion source in manually. Push the RIS handle gently and allow
CAUTION
the RIS bayonet to slide on its own. The RIS bayonet will slide in straight if it is allowed
to move naturally.

Procedure

 1 Ensure the alignment guide on the RIS handle is in the 12 o’clock position.
Push the RIS handle gently towards the analyzer chamber and allow it to
extend into the analyzer chamber. This will seat the ion source securely
into its socket.
2 Once the RIS handle is fully extended, turn the RIS handle clockwise until
the alignment guide is in the 2 o’clock position to release the ion source
body from the RIS bayonet.
3 Pull the RIS handle toward you until it is fully retracted into the RIS
cooling chamber.
4 Return to step 13 in the “To Change the Ion Source” on page 78.

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 Using the Removable Ion Source 5

To Remove the RIS Probe Extraction Tool from the Instrument

This procedure is part of an automated series of steps controlled by
MassHunter. Do not attempt this procedure unless prompted by MassHunter.
The RIS Status area on the GC/Q-TOF Tune tab must show the Gate Valve is Open
and the RIS vacuum as 0.000 Torr.

The 7200 Q-TOF GC/MS operates at high temperatures. Ensure the RIS cooling
WA R N I N G
chamber is at a safe temperature before attempting to remove it from the
instrument.

 1

2
Undo the latch on the right side of the RIS probe extraction tool and open
the door.
Lift the RIS probe extraction tool up to release it from its hinges.
3 Replace the RIS probe extraction tool with the RIS chamber door.
4 Line up the hinge pins on the RIS chamber door with the slots on the
instrument hinge, and lower the pins into the hinge.
5 Swing the RIS chamber door closed and secure the door with the latch on
the right side.
6 Return to step 16 in the “To Change the Ion Source” on page 78.

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5 Using the Removable Ion Source

88 7200 Accurate-Mass QTOF Operation Manual

Agilent 7200 Accurate-Mass Quadrupole Time-of-Flight GC/MS System
Operation Manual

6
General Maintenance
Before Starting 90
Maintaining the Vacuum System 94
Maintaining the Analyzer 95
To Disassemble the EI Ion Source 97
To Assemble the EI Ion Source 99
To Disassemble the CI Ion Source 101
To Assemble the CI Ion Source 103
To Clean the Ion Source 105
To Remove a Filament 109
To Install a Filament 111

Agilent Technologies 89
6 General Maintenance

Before Starting
You can perform much of the maintenance required by your MS. For your
safety, read all of the information in this introduction before performing any
maintenance tasks.

Scheduled maintenance
Common maintenance tasks are listed in Table 9. Performing these tasks
when scheduled can reduce operating problems, prolong system life, and
reduce overall operating costs.
Keep a record of system performance (tune reports) and maintenance
operations performed. This makes it easier to identify variations from normal
operation and to take corrective action.

Table 9 Maintenance schedule

Task Every week Every 6 months Every year As needed

Tune the MS X

Check the foreline pump oil level X

Check the calibration vial(s) X

Replace the foreline pump oil* X

Clean the ion source X

Check the carrier gas trap(s) on the GC and MS X

Replace the worn out parts X

Replace gasket on RIS probe X X

Check the IRM vial X

Replace GC gas supplies X

* Or as needed.

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 General Maintenance 6

Tools, spare parts, and supplies

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

High voltage precautions

Whenever the MS is plugged in, even if the power switch is off, potentially
dangerous voltage (200/240 VAC) exists on the wiring and fuses between
where the power cord enters the instrument and the power switch.
When the power switch is on, potentially dangerous voltages exist on:
• Electronic circuit boards
• Toroidal transformer
• Wires and cables between the boards
• Wires and cables between the boards and the connectors on the back panel
of the MS
• Some connectors on the back panel (for example, the foreline power
receptacle)
Normally, all of these parts are shielded by safety covers. As long as the safety
covers are in place, it should be difficult to accidentally make contact with
dangerous voltages.
Perform no maintenance with the MS turned on or plugged into its power source
WA R N I N G
unless you are instructed to do so by one of the procedures in this chapter.

Some procedures in this chapter require access to the inside of the MS while
the power switch is on. Do not remove any of the electronics safety covers in
any of these procedures. To reduce the risk of electric shock, follow the
procedures carefully.

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6 General Maintenance

Dangerous temperatures
Many parts in the MS operate at, or reach, temperatures high enough to cause
serious burns. These parts include, but are not limited to:
• GC/MS interface
• Analyzer parts
• Vacuum pumps
The foreline pump can cause burns if touched when operating.
WA R N I N G

Never touch these parts while your MS is on. After the MS is turned off, give these
WA R N I N G
parts enough time to cool before handling them.

The GC/MS interface heater is powered by a thermal zone on the GC. The interface
WA R N I N G
heater can be on, and at a dangerously high temperature, even though the MS is off.
The GC/MS interface is well insulated. Even after it is turned off, it cools very
slowly.

The GC inlets and GC oven also operate at very high temperatures. Use the
same caution around these parts. See the documentation supplied with your
GC for more information.

Chemical residue
Only a small portion of your sample is ionized by the ion source. The majority
of any sample passes through the ion source without being ionized. It is
pumped away by the vacuum system. As a result, the exhaust from the foreline
pump will contain traces of the carrier gas and your samples. Exhaust from
the standard foreline pump also contains tiny droplets of foreline pump oil.
An oil mist filter is supplied with the standard foreline pump. This filter stops
only pump oil droplets. It does not trap any other chemicals. If you are using
toxic solvents or analyzing toxic chemicals, install a hose from the mist filter
outlet to the outdoors or into a fume hood vented to the outdoors. Be sure to
comply with your local air quality regulations.

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 General Maintenance 6

The oil trap supplied with the standard foreline pump stops only foreline pump oil. It
WA R N I N G
does not trap or filter out toxic chemicals. If you are using toxic solvents or
analyzing toxic chemicals, use a hose to vent to a safe location.

The fluids in the foreline pump also collect traces of the samples being
analyzed. All used pump fluid should be considered hazardous and handled
accordingly. Dispose of used fluid as specified by your local regulations.

When replacing pump fluid, use appropriate chemical-resistant gloves and safety
WA R N I N G
glasses. Avoid all contact with the fluid.

Ion source cleaning

The main effect of operating the MS in CI mode is the need for more frequent
ion source cleaning. In CI operation, the ion source chamber is subject to more
rapid contamination than in EI operation because of the higher source
pressures required for CI.

Always perform any maintenance procedures using hazardous solvents under a

WA R N I N G
fume hood. Be sure to operate the MS in a well-ventilated room.

Ammonia
Ammonia, used as a reagent gas, increases the need for foreline pump
maintenance. Ammonia causes foreline pump oil to break down more quickly.
Therefore, the oil in the standard foreline vacuum pump must be checked and
replaced more frequently.
Always purge the MS with methane after using ammonia.
Be sure to install the ammonia so the tank is in an upright position. This will
help prevent liquid ammonia from getting into the flow module.

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6 General Maintenance

Maintaining the Vacuum System

Periodic maintenance
As listed in Table 9, some maintenance tasks for the vacuum system must be
performed periodically. These include:
• Checking the foreline pump fluid color and level (every week)
• Checking the calibration vial(s) (every 6 months)
• Replacing the foreline pump oil and oil mist filter (every 6 months or as
needed)
• Replacing the RIS probe seals (yearly or as needed)
Failure to perform these tasks as scheduled can result in decreased
instrument performance. It can also result in damage to your instrument.

Other procedures
Tasks such as replacing an ion vacuum gauge should be performed only when
needed by a certified Agilent service personnel. See the Agilent 7200
Accurate-Mass Q-TOF GC/MS Troubleshooting and Maintenance Manual and
see the online help in the MassHunter WorkStation software for symptoms
that indicate this type of maintenance is required.

More information is available

If you need more information about the locations or functions of vacuum
system components, see the Agilent 7200 Accurate-Mass Q-TOF GC/MS
Troubleshooting and Maintenance Manual.
Most of the procedures in this chapter are illustrated with video clips on the
Agilent GC/MS Hardware User Information & Instrument Utilities and 7200
Q-TOF GC/MS User Information disks.

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 General Maintenance 6

Maintaining the Analyzer

Scheduling
None of the analyzer components requires periodic maintenance. Some tasks,
however, must be performed when MS behavior indicates they are necessary.
These tasks include:
• Cleaning the ion sources
• Replacing filaments
The Agilent 7200 Accurate-Mass Q-TOF GC/MS Troubleshooting and
Maintenance Manual provides information about symptoms that indicate the
need for analyzer maintenance. The troubleshooting material in the online
help in the MassHunter Workstation software provides more extensive
information.

Precautions
Keep components clean during analyzer maintenance. Never open the analyzer
chamber. There are no customer serviceable parts accessible from this door.

If not done correctly, analyzer maintenance can introduce contaminants into the MS.
CAUTION

The analyzers operate at high temperatures. Do not touch any part until you are sure
WA R N I N G
it is cool.

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6 General Maintenance

Electrostatic discharge
The wires, contacts, and cables connected to the analyzer components can
carry electrostatic discharges (ESDs) to the electronics boards to which they
are connected. This is especially true of the mass filter (quadrupole) and
collision cell contact wires which can conduct ESD to sensitive components on
the quad driver board. ESD damage may not cause immediate failure but will
gradually degrade performance and stability.

Electrostatic discharges to analyzer components are conducted to the quad driver

CAUTION
board where they can damage sensitive components. Wear a grounded antistatic wrist
strap and take other antistatic precautions when working on the analyzer.

Analyzer parts that should not be disturbed

The mass filter (quadrupole) and the collision cell require no periodic
maintenance. In general, the mass filter should never be disturbed. In the
event of extreme contamination, it can be cleaned, but such cleaning should
only be done by a trained Agilent Technologies service representative.

Incorrect handling or cleaning of the mass filter can damage it and have a serious,
CAUTION
negative effect on instrument performance. Never open the analyzer door.

More information is available

If you need more information about the locations or functions of analyzer
components, refer to the Agilent 7200 Accurate-Mass Q-TOF GC/MS Concepts
Guide.

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 General Maintenance 6

To Disassemble the EI Ion Source

 Materials needed
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• Hex ball driver, 1.5 mm (8710-1570)
• Hex ball driver, 2.0 mm (8710-1804)
• Wrench, open-end, 10 mm (8710-2353)
• Nut driver, 5.5 mm (8710-1220)
• Tweezers (8710-2460)

Procedure
1 Remove the ion source. See “To Change the Ion Source” on page 78.
2 Remove the filaments. See “To Remove a Filament” on page 109.
3 Separate the ion focus and insulator assembly from the source body. (See
Figure 23.)
4 Remove the two screws from the ion focus insulator and separate it from
the ion focus lens.
5 Remove the extractor lens and its insulator from the source body.
6 Remove the two screws from the RIS bayonet mount on the bottom of the
source body, and remove the RIS bayonet mount.
7 Remove the repeller assembly from the source body.
8 Disassemble the repeller assembly by separating the repeller, the repeller
cap, ring heater and sensor assembly. (See Figure 23.)
9 Remove the clocking button from the repeller cap by removing the screw
that holds it in place. (See Figure 23.)

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6 General Maintenance

Screws

Washers

Bayonet mount

Repeller insulator
Clocking button

Repeller cap

Repeller

Ring heater assembly

RIS Extraction source body

Filaments

Extractor lens insulator

RIS Extraction lens

Ion focus insulator

Ion focus

Screws

Figure 23 Disassembling the EI ion source

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 General Maintenance 6

To Assemble the EI Ion Source

 Materials needed
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• Hex ball driver, 1.5 mm (8710-1570)
• Hex ball driver, 2.0 mm (8710-1804)
• Wrench, open-end, 10 mm (8710-2353)

Procedure
Always wear clean gloves when working in the analyzer chamber to avoid
CAUTION
contamination.

1 Assemble the repeller assembly, by attaching the repeller to the repeller

cap and connecting the clocking button with the screw.
2 Align the heater sensor with the source body.
3 Slide the repeller cap onto the heater sensor, and place the ceramic
repeller insulator on top, aligning the screw holes.
4 Place the RIS bayonet mount on top of the ceramic repeller insulator, and
attach with the washers and screws.
5 Attach the extractor lens insulator to the extractor lens, and slide them
onto the other end of the source body (Figure 23).
6 Place the ion focus insulator on the ion focus lens and attach with the two
screws.
7 Set the ion focus assembly on top of the extractor lens assembly on the
source body.
8 Attach the filaments with the two screws.

While installing, do not overtighten the repeller nut or the ceramic repeller insulators
CAUTION
will break when the source heats up. The nut should only be finger-tight.

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6 General Maintenance

Screws

Washers

Bayonet mount

Repeller insulator
Clocking button

Repeller cap

Repeller

Ring heater assembly

RIS Extraction source body

Filaments

Extractor lens insulator

RIS Extraction lens

Ion focus insulator

Ion focus

Screws

Figure 24 Assembling the EI source

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 General Maintenance 6

To Disassemble the CI Ion Source

 Materials needed
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• Hex ball driver, 1.5 mm (8710-1570)
• Hex ball driver, 2.0 mm (8710-1804)
• Wrench, open-end, 10 mm (8710-2353)
• Nut driver, 5.5 mm (8710-1220)
• Tweezers (8710-2460)

Procedure
1 Remove the CI ion source. See “To Change the Ion Source” on page 78.
2 Remove the filament. See “To Remove a Filament” on page 109.
3 Remove the ion focus lens and insulator. (See Figure 25.)
4 Remove the two screws from the ion focus lens insulator and separate it
from the ion focus lens.
5 Remove the two screws from the RIS bayonet mount and remove the
repeller assembly.
6 Disassemble the repeller assembly by removing the ceramic insulator and
heater assembly from the repeller. (See Figure 25.)
7 Take the repeller off the source body.

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6 General Maintenance

Bayonet mount

Clocking button

Ring heater / Sensor assembly

Repeller

RIS CI source body

Filament

Ion focus insulator

Ion focus lens

Figure 25 Disassembling the CI ion source

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 General Maintenance 6

To Assemble the CI Ion Source

 Materials needed
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• Hex ball driver, 1.5 mm (8710-1570)
• Hex ball driver, 2.0 mm (8710-1804)
• Wrench, open-end, 10 mm (8710-2353)

Procedure

Always wear clean gloves when working in the analyzer chamber to avoid
CAUTION
contamination.

1 Place the ceramic heater assembly on top of the repeller, aligning the
grooves on the repeller with the slot on the heater assembly. (Figure 26).
2 Place the repeller on the source body. (Figure 26).
3 Place the assembled parts into the RIS bayonet mount, heater side first.
4 Align the interface socket in the source body with the alignment groove in
the RIS bayonet mount. Attach with the two screws.
5 Place the ion focus and ion focus insulator together and attach with the
two screws.

While installing, do not overtighten the repeller nut or the ceramic repeller insulator
CAUTION
will break when the source heats up. The nut should only be finger-tight.

6 Set the filament in place.

7 Place the ion focus assembly on the source body, with the insulator against
the source body. Ensure all pins are facing in the same direction.
8 Attach with the two screws.

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6 General Maintenance

Bayonet mount

Clocking button

Ring heater / Sensor assembly

Repeller

RIS CI source body

Filament

Ion focus insulator

Ion focus lens

Figure 26 Assembling the CI ion source

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 General Maintenance 6

To Clean the Ion Source

Frequency of cleaning
Because the CI ion source operates at much higher pressures than the EI ion
source, it will probably require more frequent cleaning than the EI ion source.
Cleaning of the source is not a scheduled maintenance procedure. The source
should be cleaned whenever there are performance anomalies that are
associated with a dirty ion source. See the 7200 Q-TOF GC/MS
Troubleshooting and Maintenance Manual for symptoms that indicate a dirty
ion source.
Visual appearance is not an accurate guide to cleanliness of the CI ion
source. The CI ion source can show little or no discoloration yet still need
cleaning. Let analytical performance be your guide.

Materials needed
• Abrasive paper (5061-5896)
• Alumina abrasive powder (8660-0791)
• Aluminum foil, clean
• Cloths, clean (05980-60051)
• Cotton swabs (5080-5400)
• Glass beakers, 500 mL
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• Solvents
• Acetone, reagent grade
• Methanol, reagent grade
• Methylene chloride, reagent grade
• Ultrasonic bath

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6 General Maintenance

 Preparation
1 Disassemble the ion source. See “To Disassemble the EI Ion Source” on
page 97 or “To Disassemble the CI Ion Source” on page 101.
2 Collect the following parts to be cleaned if you are cleaning a high
sensitivity extractor EI ion source: (Figure 27)
• Repeller
• Source body
• Extractor lens
• Ion focus lens
Collect the following parts to be cleaned if you are cleaning a CI source:
• Repeller
• Source body
• Ion focus lens
These are the parts that contact the sample or ion beam. The other parts
normally should not require cleaning.

If insulators are dirty, clean them with a cotton swab dampened with reagent-grade
CAUTION
methanol. If that does not clean the insulators, replace them. Do not abrasively or
ultrasonically clean the insulators.

Cleaning the CI ion source is very similar to cleaning the EI ion source, with
the following exceptions:
• The CI ion source may not look dirty but deposits left by chemical
ionization are very difficult to remove. Clean the CI ion source thoroughly.
• Use a round wooden toothpick to gently clean out the electron entrance
hole in the source body.
• Do not use halogenated solvents. Use hexane for the final rinse.

Do not use halogenated solvents to clean the CI ion source.

CAUTION

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 General Maintenance 6

Ion focus lens Extractor lens Source body Repeller

Figure 27 Extractor EI Source parts to be cleaned

Ion focus lens Source body Repeller

Figure 28 CI Source parts to be cleaned

The filaments, source heater assembly, and insulators cannot be cleaned

CAUTION
ultrasonically. Replace these components if major contamination occurs.

3 If the contamination is serious, such as an oil backflow into the analyzer,

seriously consider replacing the contaminated parts.

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6 General Maintenance

4 Abrasively clean the surfaces that contact the sample or ion beam.
Use an abrasive slurry of alumina powder and reagent-grade methanol on
a cotton swab. Use enough force to remove all discolorations. Polishing the
parts is not necessary; small scratches will not harm performance. Also
abrasively clean the discolorations where electrons from the filaments
enter the source body.
5 Rinse away all abrasive residue with reagent-grade methanol.
Ensure all abrasive residue is rinsed away before ultrasonic cleaning. If
the methanol becomes cloudy or contains visible particles, rinse again.
6 Separate the parts that were abrasively cleaned from the parts that were
not abrasively cleaned.

Always wear clean gloves to prevent contamination when working in the analyzer
CAUTION
chamber.

7 Ultrasonically clean the parts (each group separately) for 15 minutes in

each of the following solvents:
• Methylene chloride (reagent-grade)
• Acetone (reagent-grade)
• Methanol (reagent-grade)

All of these solvents are hazardous. Work in a fume hood and take all appropriate
WA R N I N G
precautions.

8 Place the parts in a clean beaker. Loosely cover the beaker with clean
aluminum foil (dull side down).
9 Dry the cleaned parts in an oven at 100 °C for 5–6 minutes.

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 General Maintenance 6

To Remove a Filament


Materials needed
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• Hex ball driver, 1.5 mm (8710-1570)
• Tweezers (8710-2460)

Procedure

Always wear clean gloves to prevent contamination when working in the analyzer
CAUTION
chamber.

1 Remove the ion source. See “To Change the Ion Source” on page 78.
2 Remove the screw holding the filament to the ion source body. (See
Figure 29.)
3 Slide the filament off the ion source assembly. (See Figure 29.)

The analyzer, GC/MS interface, and other components in the analyzer chamber
WA R N I N G
operate at very high temperatures. Do not touch any part until you are sure it is cool.

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6 General Maintenance

Filaments Filament

EI Source CI Source

Figure 29 Changing the filament

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 General Maintenance 6

To Install a Filament

Materials needed
• Filament assembly, EI (G7005-60061)
• Filament assembly, CI (G7005-60072)
• Gloves, clean, lint-free
• Large (8650-0030)
• Small (8650-0029)
• Tweezers (8710-2460)

Procedure

1 Remove the old filament. (See “To Remove a Filament” on page 109.)
2 Place the new filament into its position on the ion source body. (See
Figure 29.)
3 Secure the filament to the ion source body with the screw.
4 After installing the filament, verify that it is not grounded to source body.
5 Reinstall the ion source. (See “To Change the Ion Source” on page 78.)
6 Autotune the MS.

Do not overtighten the thumbscrew; it can cause air leaks or prevent successful
CAUTION
pumpdown. Do not use a screwdriver to tighten the thumbscrew.

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6 General Maintenance

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Agilent Technologies

© Agilent Technologies, Inc.

Printed in USA, August 2014

*G3850-90008*
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