Agilent 5973 inert User manual

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5973 inert Mass Selective Detector

Hardware Manual

Agilent Technologies

5973 inert Mass Selective Detector

Hardware Manual

Notices

No part of this manual may be reproduced in any form or by any means (including electronic storage and retrieval or translation into a foreign language) without prior agreement and written consent from Agilent Technologies, Inc. as governed by United States and international copyright laws.

Manual Part Number

G2589-90071

Edition

Second edition, August 2003

Agilent Technologies, Inc. 2850 Centerville Road Wilmington, DE 19808-1610 USA

Acknowledgements

Microsoft® and Windows® are U.S. registered trademarks of Microsoft Corporation.

Warranty

The material contained in this document is provided “as is,” and is subject to being changed, without notice, in future editions. Further, to the maximum extent permitted by applicable law, Agilent disclaims all warranties, either express or implied, with regard to this manual and any information contained herein, including but not limited to the implied warranties of merchantability and fitness for a particular purpose. Agilent shall not be liable for errors or for incidental or consequential damages in connection with the furnishing, use, or performance of this document or of any information contained herein. Should Agilent and the user have a separate written agreement with warranty terms covering the material in this document that conflict with these terms, the warranty terms in the separate agreement shall control.

Safety Notices

CAUTION

A CAUTION notice denotes a hazard. It calls attention to an operating procedure, practice, or the like that, if not correctly performed or adhered to, could result in damage to the product or loss of important data. Do not proceed beyond a CAUTION notice until the indicated conditions are fully understood and met.

WARNING

A WARNING notice denotes a hazard. It calls attention to an operating procedure, practice, or the like that, if not correctly performed or adhered to, could result in personal injury or death. Do not proceed beyond a WARNING notice until the indicated conditions are fully understood and met.

Chapter Introduction

5973 inert MSD Version, 14 About this manual, 15 Other User Information, 16 The 5973 inert MSD, 17 CI MSD hardware description, 19 Important Safety Warnings, 21 Safety and Regulatory Certifications, 24 Cleaning/Recycling the Product, 27

Chapter 1 Installing GC Columns

To prepare a capillary column for installation, 32 To install a capillary column in a split/splitless inlet, 34 To condition a capillary column, 36 To install a capillary column in the GC/MSD interface, 38 To install a capillary column using the installation tool, 40

Chapter 2 Operating the MSD

Verify the tune performance, 61 Verify the sensitivity performance, 61

To remove the MSD covers, 62

Analyzer cover, 62

Lower MSD cover, 62 To vent the MSD, 64 To open the analyzer chamber, 66 To close the analyzer chamber, 68

To pump down the MSD, 70 To pump down the CI MSD, 72 To connect the gauge controller, 73 To move or store the MSD, 75 To set the interface temperature from a 6890 GC, 77

Chapter 3 Operating the CI MSD

To switch from EI to CI operating mode, 82 To set up the software for CI operation, 83 To operate the reagent gas flow control module, 84 To set up methane reagent gas flow, 86 CI autotune, 88 To perform a positive CI autotune (methane only), 90 To perform a negative CI autotune (any reagent gas), 92 To verify positive CI performance, 94 To verify negative CI performance, 95 To monitor high vacuum pressure, 96

Typical pressure readings, 97

To use other reagent gases, 98

Isobutane CI, 99 Ammonia CI, 100 Carbon dioxide NCI, 101

To switch from CI to EI operating mode, 102

Chapter 4 Troubleshooting the MSD

General symptoms, 106

GC does not turn on, 106 MSD does not turn on, 106 Foreline pump is not operating, 106 MSD turns on but then the foreline pump shuts off, 107 Control panel says “No server found”, 107

Chromatographic symptoms, 108

No peaks, 108 Peaks are tailing, 109 Peaks are fronting, 109 Peaks have flat tops, 110 Peaks have split tops, 110 Baseline is rising, 110 Baseline is high, 110

Baseline is falling, 110 Baseline wanders, 111 Retention times for all peaks drift – shorter, 111 Retention times for all peaks drift – longer, 111 Poor sensitivity, 112 Poor Repeatability, 112

Mass spectral symptoms, 113

No peaks, 113 Isotopes are missing or isotope ratios are incorrect, 113 High background, 113 High abundances at m/z 18, 28, 32, and 44 or at m/z 14 and 16, 114 Mass assignments are incorrect, 114 Peaks have precursors, 114 Peak widths are inconsistent, 114 Relative abundance of m/z 502 is less than 3%, 115 Spectra look different from those acquired with other MSDs, 115 High mass sensitivity is poor, 116

Pressure symptoms, 117

Foreline pressure is too high, 117 Analyzer chamber pressure is too high (EI operating mode), 117 Foreline pressure is too low, 118 Analyzer chamber pressure is too low, 118 Gauge controller displays 9.9+9 and then goes blank, 118 Power indicator on the gauge controller does not light, 119

Temperature symptoms, 120

Ion source will not heat up, 120 Mass filter (quad) heater will not heat up, 121 GC/MSD interface will not heat up, 121

Error messages, 122

Difficulty in mass filter electronics, 122 Difficulty with the electron multiplier supply, 122 Difficulty with the fan, 123 Difficulty with the HED supply, 123 Difficulty with the high vacuum pump, 123 High Foreline pressure, 124 Internal MS communication fault, 124 Lens supply fault, 124 Log amplifier ADC error, 124 No peaks found, 124 Temperature control disabled, 125 Temperature control fault, 125 The high vacuum pump is not ready, 126

The system is in standby, 126 The system is in vent state, 127 There is no emission current, 127

There is not enough signal to begin tune, 127 Air leaks, 128 Contamination, 129

Chapter 5 CI Troubleshooting

Troubleshooting tips and tricks, 133 Air leaks, 134

How do I know if I have an air leak?, 134

How do I find the air leak?, 136 Pressure-related symptoms (overview), 138 Poor vacuum without reagent gas flow, 139 High pressure with reagent gas flow, 140 Pressure does not change when reagent flow is changed, 141 Signal-related symptoms (overview), 142 No peaks, 143

No reagent gas peaks in PCI, 143

No PFDTD peaks in PCI, 144

No reagent gas peaks in NCI, 144

No PFDTD calibrant peaks in NCI, 144

No sample peaks in NCI, 144

Large peak at m/z 238 in NCI OFN spectrum, 144 No or low reagent gas signal, 145 No or low PFDTD signal, but reagent ions are normal, 148 Excessive noise or low signal-to-noise ratio, 150 Large peak at m/z 19, 151 Peak at m/z 32, 152 Tuning-related symptoms (overview), 154 Reagent gas ion ratio is difficult to adjust or unstable, 155 High electron multiplier voltage, 157 Can not complete autotune, 158 Peak widths are unstable, 159

Chapter 6 Maintaining the MSD

Before starting, 162

Maintaining the vacuum system 169

To check and add foreline pump oil, 170

To drain the foreline pump, 172 To refill the foreline pump, 174 To replace the turbo pump, 177 To separate the MSD from the GC, 178 To reconnect the MSD to the GC, 180 To remove the EI calibration vial, 182 To refill and reinstall the EI calibration vial, 184 To purge the calibration valves, 186

EI calibration valve, 186

CI calibration valve, 186 To remove the EI calibration valve, 187 To reinstall the EI calibration valve, 189 To replace the fan for the high vacuum pump, 191 To remove the triode gauge tube, 193 To reinstall a triode gauge tube, 195 To lubricate the side plate O-ring, 197 To lubricate the vent valve O-ring, 199

Maintaining the analyzer 201

To remove the ion source, 203 To disassemble the ion source, 205 To clean the ion source, 207 To reassemble the ion source, 212 To reinstall the ion source, 214 To remove a filament, 216 To reinstall a filament, 218 To remove the heater and sensor from the ion source, 220 To reinstall the heater and sensor in the ion source, 222 To remove the heater and sensor from the mass filter, 224 To reinstall the heater and sensor in the mass filter, 226 To replace the electron multiplier horn, 228

Maintaining the GC/MSD interface 230

To remove the GC/MSD interface heater and sensor, 232 To reinstall the GC/MSD interface heater and sensor, 234

Maintaining the electronics 236

To adjust the RF coils, 238 To replace the primary fuses, 240

Chapter 7 CI Maintenance

To set up your MSD for CI operation, 245 To install the CI ion source, 246 To install the CI interface tip seal, 248 To clean the CI ion source, 250

Frequency of cleaning, 250

Cleaning procedure, 250 To minimize foreline pump damage from ammonia, 252 To replace the methane/isobutane gas purifier, 253 To clean the reagent gas supply lines (tubing), 254 To refill the CI calibrant vial, 255

Chapter 8 Vacuum System

Turbo pump MSD vacuum system, 262 Turbo pump analyzer chamber, 263 Side plate, 264 Vacuum seals, 266

Face seals, 266

KF (NW) seals, 266

Compression seals, 266

High voltage feedthrough seal, 267 Foreline pump, 268 Turbomolecular pump and fan, 270 Standard turbo pump, 271 Performance turbo pump, 272 Calibration valves and vent valve, 273

Calibration valves, 273

EI calibration valve, 273

CI calibration valve, 273

Vent valve, 273 Triode gauge tube, 275 Gauge controller, 277

Chapter 9 GC/MSD Interfaces and

CI Flow Control

EI GC/MSD interface, 281 EI/CI GC/MSD interface (CI interface), 282 Reagent gas flow control module, 283

Chapter 10 Analyzer

Ion source, 290

Ion source body, 290 Filaments, 292 Magnet, 293 Repeller, 293 Drawout plate and cylinder, 294 Ion focus, 294 Entrance lens, 294

Source Washer, 295 CI ion source, 297 Quadrupole mass filter, 299

AMU gain, 299

AMU offset, 300

219 width, 300

DC polarity, 301

Mass (axis) gain, 301

Mass (axis) offset, 301

Quadrupole maintenance, 302 Detector, 303

Detector focus lens, 303

High energy dynode, 303

Electron multiplier horn, 303 Analyzer heaters and radiators, 305

Chapter 11 Electronics

Control panel and power switch, 310

Control panel, 310

Power switch, 310 Side board, 312 Electronics module, 313 Main board, 314 Signal amplifier board, 315 AC board, 316 LAN/MSD control card, 318 Power supplies, 319

Low voltage (ac-dc) power supply, 319

High voltage (HED) power supply, 319

Toroid transformer, 319 Back panel and connectors, 320

Interfacing to external devices, 322

Remote control processor, 322 Remote start signals, 322

Chapter 12 Parts

Electronics, 327 Vacuum system, 332 Analyzer, 338 EI GC/MSD interface, 344 Consumables and maintenance supplies, 346 CI Parts, 350

Appendix A Chemical Ionization Theory

Chemical ionization overview, 360

References on chemical ionization, 361

Positive CI theory, 362

Proton transfer, 364 Hydride abstraction, 366 Addition, 366 Charge exchange, 367

Negative CI theory, 368

Electron capture, 370 Dissociative electron capture, 371 Ion pair formation, 371 Ion-molecule reactions, 372

Introduction

This manual describes the operation, troubleshooting, and maintenance of the Agilent Technologies 5973 inert Mass Selective Detector (MSD)

5973 inert MSD Version

5973 inert MSDs are equipped with or one of two turbomolecular (turbo) pumps. Chemical Ionization is available for the turbo pump MSDs only. The serial number label displays a product number that tells what kind of MSD you have. In this manual, the term “CI MSD” applies to the EI/PCI/NCI MSD.

Model number Description

G2578A Standard turbo EI MSD

G2579A Performance turbo EI MSD G2589A Performance turbo EI/PCI/NCI MSD

Introduction

About this manual

• The introduction describes general information about the 5973 inert

MSD.

• Chapter 1 shows you how to prepare and install a capillary column.

• Chapter 2 describes basic tasks such as setting temperatures, monitoring

pressures, tuning, and venting, and pumpdown.

• Chapter 3 describes basic tasks necessary to operate a CI MSD in CI

mode.

• Chapter 4 provides a quick reference for identifying causes of poor

instrument performance or malfunctions.

• Chapter 5 provides a quick reference for identifying problems unique to

CI MSDs.

• Chapter 6 features maintenance procedures.

• Chapter 7 features maintenance procedures unique to CI MSDs.

• Chapter 8 describes operation of the components of the vacuum system.

• Chapter 9 describes the GC/MSD interface, and the CI flow module.

• Chapter 10 describes operation of the analyzer (ion source, mass filter,

and detector).

• Chapter 11 describes the electronics that control the MSD.

• Chapter 12 contains illustrated parts identification and part numbers.

• Appendix A is an overview of chemical ionization theory.

For updated information, check the Agilent Technologies Life Sciences/ Chemical Analysis web site at http://www.agilent.com/chem.

Introduction

Other User Information

Additional information is contained in the following documentation:

• 5973N and 5973 inert Mass Selective Detector Hardware Installation

Manual

• 5973N and 5973 inert Mass Selective Detector Site Preparation Guide

• 6890 Series GC manuals

• GC accessories (autosampler, etc.) manuals

• G1701DA MSD Productivity ChemStations software manuals and online help

• 5973N and 5973 inert Mass Selective Detector Specifications (59889991EN)

• Hydrogen Carrier Gas Safety Guide (5955-5398)

• 5973N and 5973 inert Mass Selective Detector Local Control Panel

(LCP) Quick Reference

• For updated information, see the Agilent Technologies web site at http://www.agilent.com/chem

1. Located on this CD-ROM [5973 and 5973 inert Mass Selective Detector User Information]

Introduction

The 5973 inert MSD

The 5973 inert MSD is a stand-alone capillary GC detector

The 5973 inert Mass Selective Detector (MSD) is designed for use with the 6890 Series Gas Chromatograph. The MSD features:

• Control panel for locally monitoring and operating the MSD

• One of two different high vacuum pumps

• Rotary vane foreline pump

• Independently heated electron-ionization ion source

• Independently heated hyperbolic quadrupole mass filter

• High-energy dynode (HED) electron multiplier detector

• Independently heated GC/MSD interface

• Chemical ionization (EI/PCI/NCI) model available

Physical description

The 5973 inert MSD is a rectangular box, approximately 42 cm high, 26 cm wide, 65 cm deep. The weight is 26 kg for the standard turbo pump mainframe and 29 kg for the performance turbo pump mainframe. The attached rough pump weighs an additional 11 kg.

The basic components of the instrument are: the frame/cover assemblies, the control panel, the vacuum system, the GC interface, the electronics, and the analyzer.

The control panel allows local monitoring and operation of the MSD

The control panel acts as a local user interface to the MSD. You can perform some basic tasks such as running a tune, a method, or a sequence; and monitor MSD status from the control panel.

Introduction

The 5973 inert MSD

An optional gauge controller is available for measuring vacuum

The 5973 inert MSD is equipped with a triode ionization gauge tube. With an 59864B Gauge Controller, the tube can be used to measure pressure (high vacuum) in the vacuum manifold. Installation and operation of the gauge controller is described in this manual.

The gauge controller is

Feature G2578A G2579A G2589A

High vac pump Standard turbo Performance turbo Performance turbo Optimal He column flow mL/min 1 1 to 2 1 to 2

Maximum recommended gas flow, mL/min

Maximum gas flow,

mL/min

Max column id 0.32 mm (30m) 0.53 mm (30 m) 0.53 mm (30 m)

CI capability no no PCI/NCI DIP capability

(3rd Party)

a. Total gas flow into the MSD: column flow plus reagent gas flow (if applicable). b. Expect degradation of spectral performance and sensitivity.

required for chemical ionization (CI) operation.

5973 inert MSD models and features

2.0 4 4

2.4 6.5 6.5

yes yes no

Introduction

CI MSD hardware description

In this manual, the term “CI MSD” applies to the EI/PCI/NCI MSD. The CI hardware allows the 5973 inert MSD to produce high- quality, classical CI spectra, which include molecular adduct ions. A variety of reagent gases can be used.

The 5973 inert CI system adds to the 5973 inert MSD:

• Redesigned EI/CI GC/MSD interface

• CI ion source and interface tip seal

• Reagent gas flow control module

• Bipolar HED power supply (for PCI/NCI MSD

only)

• A methane/isobutane gas purifier is provided, and is required. It removes oxygen, water, hydrocarbons, and sulfur compounds.

A high vacuum gauge controller (59864B) is

required for the CI MSD.

To achieve the relatively high source pressure required for CI while still maintaining high vacuum in the quadrupole and detector, the MSD CI system has been carefully optimized. Special seals along the flow path of the reagent gas and very small openings in the ion source keep the source gases in the ionization volume long enough for the appropriate reactions to occur.

The EI/CI interface has special plumbing for reagent gas. A spring-loaded insulating seal fits onto the tip of the interface.

Switching back and forth between CI and EI takes less than an hour, although a 1– to 2–hour wait is

required in order to purge the reagent gas

lines and bake out water and other contaminants. Switching from PCI to NCI requires about 2 hours for the ion source to cool.

6890 Series

LS tower

6890 Series ALS tray

59864B High Vacuum Gauge Controller

CI gas flow module (EI/PCI/NCI MSD only)

5973 inert Mass Selective Detector

5973 inert MSD control panel

Introduction

CI MSD hardware description

6890 Gas Chromatograph

5973 inert MSD serial number sticker

Introduction

Important Safety Warnings

Before moving on, there are several important safety notices that you should always keep in mind when using the 5973 inert Mass Selective Detector.

Many internal parts of the MSD carry dangerous voltages

If the MSD is connected to a power source, even if the power switch is off, potentially dangerous voltages exist on:

• The wiring between the MSD power cord and the AC power supply, the AC

power supply itself, and 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).

WA R N I N G All these parts are shielded by covers. With the covers in place, it should be difficult to

accidentally make contact with dangerous voltages. Unless specifically instructed to, never remove a cover unless the detector, inlet, or oven are turned off.

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

Agilent service representative.

Electrostatic discharge is a threat to MSD electronics

The printed circuit (PC) boards in the MSD 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. Wear a grounded wrist strap any time you must remove the MSD right side cover.

Introduction

Important Safety Warnings

Many parts are dangerously hot

Many parts of the MSD operate at temperatures high enough to cause serious burns. These parts include but are not limited to:

• The inlets

• The oven and its contents

• The detectors

• The column nuts attaching the column to an inlet or detector

• The valve box

You should always cool these areas of the MSD 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.

WA R N I N G Be careful when working behind the instrument. During cool-down cycles, the MSD emits

hot exhaust which can cause burns.

WA R N I N G The insulation around the inlets, detectors, valve box, and the insulation cups is made of

refractory ceramic fibers. To avoid inhaling fiber particles, we recommend the following safety procedures: ventilate your work area; wear long sleeves, gloves, safety glasses, and a disposable dust/mist respirator; dispose of insulation in a sealed plastic bag; wash your hands with mild soap and cold water after handling the insulation.

Hydrogen

Hydrogen gas may be used as carrier gas, and/or as fuel for the FID. When mixed with air, hydrogen can form explosive mixtures.

Introduction

Important Safety Warnings

W A R N I N G When using hydrogen (H2) as the carrier gas or fuel gas, be aware that hydrogen gas can flow

into the oven and create an explosion hazard. Therefore, be sure that the supply is off until all connections are made, and ensure that the inlet and detector column fittings are either connected to a column or capped at all times when hydrogen gas is supplied to the instrument. Hydrogen is flammable. Leaks, when confined in an enclosed space, may create a fire or explosion hazard. In any application using hydrogen, leak test all connections, lines, and valves before operating the instrument. Always turn off the hydrogen supply at its source before working on the instrument.

WA R N I N G The MSD cannot detect leaks in inlet and/or detector gas streams. For this reason, it is vital

that column fittings should always be either connected to a column, or have a cap or plug installed.

When using hydrogen gas, check the system for leaks to prevent possible fire and explosion hazards based on local Environmental Health and Safety (EHS) requirements. Always check for leaks after changing a tank or servicing the gas lines. Always make sure the vent line is vented into a fume hood.

Introduction

Safety and Regulatory Certifications

The 5973 inert Mass Selective Detector conforms to the following safety standards:

• Canadian Standards Association (CSA): C22.2 No. 1010.1

• CSA/Nationally Recognized Test Laboratory (NRTL): UL 61010A–1

• International Electrotechnical Commission (IEC): 61010–1

• EuroNorm (EN): 61010–1

The 5973 inert Mass Selective Detector 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

•AUS/NZ

This ISM device complies with Canadian ICES-001. Cet appareil ISM est conforme a la norme NMB—001 du Canada.

The 5973 inert Mass Selective Detector is designed and manufactured under a quality system registered to ISO 9001.

Information

The Agilent Technologies 5973 inert Mass Selective Detector meets the following IEC (International Electro-technical Commission) classifications: Safety Class I, Transient Overvoltage Category II, 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 5973 Mass Selective Detector 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.

Introduction

Safety and Regulatory Certifications

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 explosion hazard.

Indicates radioactivity hazard.

Indicates electrostatic discharge hazard.

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:

Introduction

Safety and Regulatory Certifications

1 Relocate the radio or antenna.

2 Move the device away from the radio or television.

3 Plug the device into a different electrical outlet, so that the device and the

radio or television are on separate electrical circuits.

4 Make sure that all peripheral devices are also certified.

5 Make sure that appropriate cables are used to connect the device to

peripheral equipment.

6 Consult your equipment dealer, Agilent Technologies, or an experienced

technician for assistance.

7 Changes or modifications not expressly approved by Agilent Technologies

could void the user’s authority to operate the equipment.

Sound Emission Certification for Federal Republic of Germany

Sound pressure

Sound pressure Lp < 70 dB am according to ISO 7779:1988.

Schalldruckpegel

Schalldruckpegel LP < 70 dB am nach EN 27779:1991.

Introduction

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.

Introduction

Cleaning/Recycling the Product

Installing GC Columns

How to connect GC columns to the 5973 inert MSD

Installing GC columns

Before you can operate your GC/MSD system, you must select, condition, and install a GC column. This chapter will show you how to install and condition a column. For correct column and flow selection, you must know what type of vacuum system your MSD has. The serial number tag on the lower front of the left side panel shows the model number.

Many types of GC columns can be used with the MSD but there are some restrictions

During tuning or data acquisition the rate of column flow into the MSD 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 (unless the GC is set for constant flow). See To measure column flow linear velocity (page 58) for instructions on how to measure actual flow in your column. Use the Flow Calculation software to determine whether a given column will give acceptable flow with realistic head pressure.

Feature G2578A G2579A G2589A

High vac pump Standard turbo Performance turbo Performance turbo, EI/

PCI/NCI

Optimal gas flow, mL/min

Maximum recommended gas flow, mL/min

Maximum gas flow, mL/min

Max column id 0.32mm (30m) 0.53 mm (30m) 0.53mm (30m)

a. Total gas flow into the MSD: column flow plus reagent gas flow (if applicable). b. Expect degradation of spectral performance and sensitivity.

1 1 to 2 1 to 2

2.0 4 4

2.4 6.5 4

1 Installing GC Columns

Conditioning a column before it is installed into the GC/MSD 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 MSD ion source. This decreases MSD 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/MSD interface.

Conditioning ferrules is also beneficial

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

• Note that the column installation procedure for the 5973 MSDs is different from that for another instrument will

all previous MSDs. Using the procedure from

not work, and may damage the column or the

MSD.

• You can remove old ferrules from column nuts with an ordinary push pin.

• Always use carrier gas that is at least 99.999% 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/MSD interface.

WA R N I N G If you are using hydrogen as a carrier gas, do not start carrier gas flow until the column is

installed in the MSD, and the MSD has been pumped down. If the vacuum pumps are off, hydrogen will accumulate in the MSD and an explosion may occur. Read the Hydrogen Carrier Gas Safety Guide (5955-5398) before operating the MSD with hydrogen carrier gas.

WA R N I N G Always wear safety glasses when handling capillary columns. Use care to avoid puncturing

your skin with the end of the column.

1 Installing GC Columns

To prepare a capillary column for installation

Materials needed: Capillary column

Column cutter (5181-8836) Ferrules

0.27-mm id, for 0.10-mm id columns (5062-3518)

0.37-mm id, for 0.20-mm id columns (5062-3516)

0.40-mm id, for 0.25-mm id columns (5181-3323)

0.47-mm id, for 0.32-mm id columns (5062-3514)

0.74-mm id, for 0.53-mm id columns (5062-3512)

Gloves, clean

large (8650-0030)

small (8650-0029) Inlet column nut (5181-8830) Magnifying glass Septum (may be old, used inlet septum)

1 Slide a septum, column nut, and conditioned ferrule onto the free end of

the column.

The tapered end of the ferrule should point away from the column nut.

2 Use the column cutter to score the column 2 cm from the end.

3 Break off the end of the column.

Hold the column against the column cutter with your thumb. Break the column against edge of the column cutter.

4 Inspect the end for jagged edges or burrs.

If the break is not clean and even, repeat steps 2 and 3.

5 Wipe the outside of the free end of the column with a lint-free cloth

moistened with methanol.

Capillary column

Column cutter

Fer rul e

Inlet column nut

1 Installing GC Columns

To prepare a capillary column for installation

Septum

1 Installing GC Columns

To install a capillary column in a split/splitless inlet

Materials needed: Gloves, clean

large (8650-0030)

small (8650-0029) Metric ruler Wrench, open-end, 1/4-inch × 5/16-inch (8710-0510)

To install columns in other types of inlets, refer to your 6890 Series Gas Chromatograph Operating Manual.

1 Prepare the column for installation (page 32).

2 Position the column so it extends 4 to 6 mm past the end of the ferrule.

3 Slide the septum to place the nut and ferrule in the correct position.

4 Insert the column in the inlet.

5 Slide the nut up the column to the inlet base and finger tighten the nut.

6 Adjust the column position so the septum is even with the bottom of the

column nut.

7 Tighten the column nut an additional 1/4 to 1/2 turn.

The column should not slide with a gentle tug.

8 Start carrier gas flow.

9 Verify flow by submerging the free end of the column in isopropanol. Look

for bubbles.

Insulation cup

Reducing nut

1 Installing GC Columns

To install a capillary column in a split/splitless inlet

Capillary column

Ferrule (not visible)

Inlet column nut

Septum

4 to 6 mm

1 Installing GC Columns

To condition a capillary column

Materials needed: Carrier gas, (99.999% pure or better)

Wrench, open-end, 1/4-inch × 5/16-inch (8710-0510)

WA R N I N G Do not condition your capillary column with hydrogen. Hydrogen accumulation in the GC

oven can result in an explosion. If you plan to use hydrogen as your carrier gas, first condition the column with ultrapure (99.999% or better) inert gas such as helium, nitrogen, or argon.

1 Install the column in the GC inlet, page 34.

2 Allow the carrier gas to flow through the column for 5 minutes without

heating GC oven.

3 Ramp the oven temperature at 5°C/minute to 10°C above your highest

analytical temperature.

4 Once the oven temperature exceeds 80°C, inject 5 µL methanol into GC;

repeat two more times at 5-minute intervals.

This will help remove any contamination from the column before it is installed into the GC/MSD interface.

CAUT ION

See Also For more information about installing a capillary column, refer to the

Do not exceed the maximum temperature rating of the column.

5 Hold this temperature. Allow the carrier gas to flow for several hours.

6 Return the GC oven temperature to a low standby temperature.

application note: Optimizing Splitless Injections on Your GC for High Performance MS Analysis, publication number 5988-9944EN.

1 Installing GC Columns

To condition a capillary column

1 Installing GC Columns

To install a capillary column in the GC/MSD interface

Materials needed: Column cutter (5181-8836)

Ferrules

0.3-mm id, for 0.10-mm id columns (5062-3507)

0.4-mm id, for 0.20- and 0.25-mm id columns (5062-3508)

0.5-mm id, for 0.32-mm id columns (5062-3506)

0.8-mm id, for 0.53-mm id columns (5062-3538) Flashlight Hand lens (magnifying glass) Gloves, clean

large (8650-0030)

small (8650-0029) Interface column nut (05988-20066) Safety glasses Wrench, open-end, 1/4-inch × 5/16-inch (8710-0510)

CAUT ION

Note that the column installation procedure for the 5973 MSDs is different from that for all previous MSDs. Using the procedure from another instrument may result in poor sensitivity and possible damage to the MSD.

1 Condition the column (page 36).

2 Vent the MSD (page 64) and open the analyzer chamber (page 66).

Be sure you can see the end of the GC/MSD interface.

3 Slide an 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 Slide the column into the GC/MSD interface until you can pull it out

through the analyzer chamber.

5 Break 1 cm off the end of the column (page 32).

Do not let any column fragments fall into the analyzer chamber. They could damage the turbo pump.

Column



Interface column nut

GC/MSD interface (GC end)

Analyzer chamber

GC/MSD interface (MSD end)

1 Installing GC Columns

To install a capillary column in the GC/MSD interface

1 to 2 mm

MSD

6 Clean the outside of the free end of the column with a lint-free cloth

moistened with methanol.

7 Adjust the column so it projects 1 to 2 mm past the end of the GC/MSD

interface.

Use the flashlight and hand lens if necessary to see the end of the column inside the analyzer chamber. Do not use your finger to feel for the column end.

8 Hand tighten the nut.

Make sure the position of the column does not change as you tighten the nut.

9 Tighten the nut 1/4 to 1/2 turn.

Check the tightness after one or two heat cycles.

GC oven

1 Installing GC Columns

To install a capillary column using the installation tool

Materials needed: Column cutter (5181-8836)

Column installation tool (not supplied with the MSD) (G1099-20030) Ferrules

0.3-mm id, for 0.10-mm id columns (5062-3507)

0.4-mm id, for 0.20- and 0.25-mm id columns (5062-3508)

0.5-mm id, for 0.32-mm id columns (5062-3506)

0.8-mm id, for 0.53-mm id columns (5062-3538)

Gloves, clean

large (8650-0030)

small (8650-0029) Interface column nut (05988-20066) Septum (may be old, used inlet septum) Wrenches, open-end, 1/4-inch × 5/16-inch (8710-0510) – 2 required

Note: The column installation tool is not recommended for applications requiring optimal sensitivity performance. See “To install a capillary column without the installation tool”, page 38.

1 Vent the MSD. See page 64.

2 Slide a septum, interface column nut, and conditioned ferrule onto the

free end of the column.

The tapered end of the ferrule should point toward the nut.

3 Insert the column into the column installation tool.

Slide the column through until the end extends past the end of the tool.

4 Cut 1 cm off the end of the column (page 32).

5 Position the column so that 1 to 2 mm extends past the end of the tool.

Hand tighten the nut.

6 Slide the septum to touch the end of the nut.

The septum will help assure that the position is correct.

7 Use two wrenches to tighten the nut 1/4 to 1/2 turn.

The column should not slide when tugged gently.

Column

Interface column nut

Column installation tool

Interface ferrule

Septum

1 Installing GC Columns

To install a capillary column using the installation tool

1 to 2 mm

CAUT ION

8 Remove the column and nut from the installation tool.

The total length from the septum to the end of the column is 176 mm.

9 Clean the outside of the end of the column with a lint-free cloth moistened

with methanol.

10 Insert the column into the GC/MSD interface.

11 Tighten the nut 1/4 to 1/2 turn.

Check tightness after one or two heat cycles.

12 Pump down the MSD.

The column installation tool must be kept clean to prevent contaminating the column and the ion source. Keep it in its storage tube, and clean it by flushing with methanol after each use.

To view MSD analyzer temperature and vacuum status, 48 To set monitors for MSD temperature and vacuum status, 50 To set the MSD analyzer temperatures, 52 To set the GC/MSD interface temperature from the PC, 54 To monitor high vacuum pressure, 56 To measure column flow linear velocity, 58 To calculate column flow, 59 To tune the MSD, 60 To set the interface temperature from a 6890 GC, 77 To remove the MSD covers, 62 To vent t he MS D, 64 To open the analyzer chamber, 66 To close the analyzer chamber, 68 To pump down the MSD, 70 To connect the gauge controller, 73 To move or store the MSD, 75

Operating the MSD

How to perform some basic operating procedures for the MSD

Operating the MSD

Operation of the MSD from the data system

The software performs tasks such as pumpdown, monitoring pressures, setting temperatures, tuning, and preparing to vent. These tasks are described in this chapter. Data acquisition and data analysis are described in the manuals and online help supplied with the MSD ChemStation software.

Operation of the MSD from the control panel

You can use the 5973 inert MSD control panel to perform many of the same tasks that the ChemStation can perform. See the 5973N and 5973 inert

Mass Selective Detector Local Control Panel (LCP) Quick Reference (G2589-90072) for more information.

Some conditions must be met before you turn on the MSD

Verify the following

before you turn on or attempt to operate the MSD.

• The vent valve must be closed (the knob turned all the way clockwise).

• All other vacuum seals and fittings must be in place and fastened

correctly. (The the front side plate screw should not be tightened, unless

hazardous carrier or reagent gasses are being used.

• The MSD is connected to a grounded power source.

• The GC/MSD interface extends into the GC oven.

• A conditioned capillary column is installed in the GC inlet and in the

GC/MSD interface.

• The GC is on, but the heated zones for the GC/MSD interface, the

injection port, and the oven are off.

• Carrier gas of at least 99.999% purity is plumbed to the GC with the

recommended traps.

• If hydrogen is used as carrier gas, carrier gas flow must be off, and the

front sideplate thumbscrew must be loosely fastened.

• The foreline pump exhaust is properly vented.

2 Operating the MSD

WA R N I N G The exhaust from the foreline pump contains solvents and the chemicals you are analyzing.

It also contains traces of pump oil. The supplied oil trap stops only pump oil. It does not trap or filter out toxic chemicals. If you are using toxic solvents or analyzing toxic chemicals, remove the oil trap. Install a hose (11 mm id) to take the foreline pump exhaust outside or to a fume (exhaust) hood.

WA R N I N G If you are using hydrogen as a carrier gas, do not start carrier gas flow until the MSD has

been pumped down. If the vacuum pumps are off, hydrogen will accumulate in the MSD and an explosion may occur. Read the Hydrogen Carrier Gas Safety Guide (5955-5398) before operating the MSD with hydrogen carrier gas.

The data system or control panel help you pump down the MSD

Pumpdown is mostly automated. Once you close the vent valve and turn on the main power switch (while pressing on the sideplate), the MSD pumps down by itself. The data system software contains a program that monitors and displays system status during pumpdown. When the pressure is low enough, the program turns on the ion source and mass filter heaters. It also prompts you to turn on the GC/MSD interface heater. The 5973 inert MSD will shutdown if it cannot pump down correctly.

Monitoring the pressure in the MSD

The data system displays the turbo pump motor speed for the turbo pump MSDs.

Each MSD is equipped with a triode ionization gauge tube. If your MSD is also equipped with an 59864B Gauge Controller, the triode gauge can measure the pressure in the analyzer chamber. The high vacuum pressure measured by the triode gauge cannot be monitored through the data system. It is displayed on the gauge controller.

2 Operating the MSD

MSD temperatures are controlled through the data system

The MSD has independent heaters and temperature sensors for the ion source and quadrupole mass filter. You can adjust the setpoints and view these temperatures from the data system, or from the control panel.

The GC/MSD interface heater is powered and controlled by the Thermal Aux #2 heated zone of the 6890 Series GC. The GC/MSD interface temperature can be set and monitored from the data system or from the GC keypad.

Column flow is controlled through the data system

Carrier gas flow through the GC column is controlled by head pressure in the GC. For a given head pressure, the column flow will decrease as the GC oven temperature increases. With electronic pneumatic control (EPC) set to

Const Flow (constant flow), the same column flow is be maintained regard-

less of oven temperature.

The MSD 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 MSD. With this time measurement, you can calculate the column flow. See page 58..

The data system aids in venting

A program in the data system guides you through the venting process. It switches off the GC and MSD heaters and the diffusion pump heater or turbo pump at the correct time. It also lets you monitor temperatures in the MSD and indicates when to vent the MSD.

The MSD

will be damaged by incorrect venting. A diffusion pump will

backstream vaporized pump fluid onto the analyzer if the MSD is vented before the diffusion pump has fully cooled. A turbo pump will be damaged if it is vented while spinning at more than 50% of its normal operating speed.

2 Operating the MSD

WA R N I N G Make sure the GC/MSD interface and the analyzer zones are cool (below 100°C) before you

vent the MSD. 100°C is still hot enough to burn skin; always wear cloth gloves when handling analyzer parts.

WA R N I N G If you are using hydrogen as a carrier gas, the carrier gas flow must be off before turning off

the MSD power. If the foreline pump is off, hydrogen will accumulate in the MSD and an explosion may occur. Read the Hydrogen Carrier Gas Safety Guide (5955-5398) before operating the MSD with hydrogen carrier gas.

CAUT ION

Never vent the MSD by allowing air in through either end of the foreline hose. Use the vent valve or

remove the column nut and column.

Do not vent or shut off the power on a diffusion pump MSD while the pump is hot. Do not vent while the turbo pump is still spinning at more than 50%.

Do not exceed the maximum recommended total gas flow. See “5973 inert MSD models and features” on page 18.

Moving or storing the MSD requires special care

The best way to keep your MSD functioning properly is to keep it pumped down and hot, with carrier gas flow. If you plan to move or store your MSD, a few additional precautions are required. The MSD must remain upright at all times; this requires special caution when moving. The MSD should not be left vented to atmosphere for long periods.

2 Operating the MSD

To view MSD analyzer temperature and vacuum status

Software changes The software is revised periodically. If the steps in this procedure do not

match your MSD ChemStation software, refer to the manuals and online help supplied with the software for more information.

See also You can also use the Control Panel to perform this task. See the 5973N and 5973

inert Mass Selective Detector Local Control Panel (LCP) Quick Reference Guide (G2589-90072) for more information.

1 In Instrument Control view, select Edit MS Tune Parameters from the

Instrument menu.

2 Select the tune file you plan to use with your method from the Load MS Tune

File dialog box.

3 Analyzer temperatures and vacuum status are displayed in the Zones field.

Unless you have just begun the pumpdown process, the turbo pump should be running at least 80% speed. MSD heaters remain off as long as the turbo pump is operating at less than 80%. Normally, the turbo pump speed will be at 100%.

The MSD heaters turn off at the beginning of the vent cycle, and turn on at the end of the pumpdown cycle. Note that the reported setpoints will not change during venting or pumpdown, even though both the MSD zones are turned off.

2 Operating the MSD

To view MSD analyzer temperature and vacuum status

2 Operating the MSD

To set monitors for MSD temperature and vacuum status

Monitors display 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 value varies beyond a user-determined limit from the parameter setpoint. This procedure describes how to add monitors to your instrument control view.

Software changes The software is revised periodically. If the steps in this procedure do not

match your MSD ChemStation software, refer to the manuals and online help supplied with the software for more information.

1 Select MS Monitors from the Instrument menu.

2 In the Edit MS Monitors box, under Type, select Zone.

3 Under Parameter, select MS Source and click Add.

4 Under Parameter, select MS Quad and click Add.

5 Under Parameter, select TurboSpd and click Add.

6 Click OK.

The new monitors will be stacked on top of each other in the lower right corner of the Instrument Control window. They must be moved for you to see them all.

7 Click and drag each monitor to the desired position.

See the accompanying illustration for an example of arranging the monitors.

8 To make the new settings part of the method, select Save from the Method

menu.

2 Operating the MSD

To set monitors for MSD temperature and vacuum status

2 Operating the MSD

To set the MSD analyzer temperatures

Setpoints for the MSD ion source and mass filter (quad) temperatures are stored in the current tune (*.u) file. When a method is loaded, the setpoints in the tune file associated with that method are downloaded automatically.

Software changes The software is revised periodically. If the steps in this procedure do not

match your MSD ChemStation software, refer to the manuals and online help supplied with the software for more information.

1 In Instrument Control view, select Edit MS Tune Parameters from the

Instrument menu.

2 Select Temperatures from the MoreParams menu.

3 Type the desired Source and Quad (mass filter) temperatures in the

setpoint fields and click OK.

See Table 1 on page 53 for recommended setpoints

CAUT ION

The GC/MSD interface, ion source, and quadrupole heated zones interact. The analyzer heaters may not be able to accurately control temperatures if the setpoint for one zone is much lower than that of an adjacent zone.

Do not exceed 200°C for the quadrupole or 300°C for the source.

4 Click OK in the Edit Parameters window to apply the new temperature

setpoints.

5 When the Save MS Tune File dialog box appears, either click OK to save your

changes to the same file or type a new file name and click OK.

2 Operating the MSD

To set the MSD analyzer temperatures

Table 1 Recommended temperature settings

EI operation PCI operation NCI operation

MS Source 230 250 150

MS Quad 150 150 150

2 Operating the MSD

To set the GC/MSD interface temperature from the PC

Software changes The software is revised periodically. If the steps in this procedure do not

match your MSD ChemStation software, refer to the manuals and online help supplied with the software for more information.

See also You can also use the Control Panel to perform this task. See the 5973N and 5973

inert Mass Spectrometer Detector Local Control Panel (LCP) Quick Reference (G2589-90072) for more information.

1 Select Instrument Control from the View menu.

2 Click the Aux button to display the Instrument | Edit | Aux: (6890) window.

3 Ve r ify t hat MSD is selected under Type and Thermal Aux #2 is selected under

Aux Channel.

CAUT ION

4 Turn the heater on, and type the setpoint in the Next °C column. Do not set

temperature ramps.

5 The typical setpoint is 280°C.

The limits are 0°C and 350°C. A setpoint below ambient temperature turns off the interface heater.

Never exceed the maximum temperature for your column.

6 Click Apply to download setpoints or click OK to download setpoints and

close the window.

7 To make the new settings part of the method, select Save from the Method

menu.

Make sure that the carrier gas is turned on and the column has been purged of air before heating the GC/MSD interface or the GC oven.

2 Operating the MSD

To set the GC/MSD interface temperature from the PC

2 Operating the MSD

To monitor high vacuum pressure

Materials needed: Gauge controller (59864B)

Triode ionization gauge cable (8120-6573)

WA R N I N G Never connect or disconnect the cable from the triode gauge tube while the MSD is under

vacuum. Risk of implosion and injury due to broken glass exists.

WA R N I N G If you are using hydrogen as a carrier gas, do not turn on the triode gauge tube if there is

any possibility that hydrogen has accumulated in the analyzer chamber. The triode gauge filament can ignite hydrogen. Read the Hydrogen Carrier Gas Safety Guide (5955-5398) before operating the MSD with hydrogen carrier gas.

1 Connect the gauge controller to the ionization gauge tube (page 73).

2 Start up and pump down the MSD (page 70).

3 Switch on the power switch on the back of the gauge controller.

4 Press and release the GAUGE button.

After a few seconds, the pressure should be displayed.

Pressure is displayed in the format X.X – X where – X is the base 10 exponent. Units are Torr.

The gauge controller will not turn on if the pressure in the MSD is above approximately 8 × 10 triode gauge tube can measure pressures between approximately 8 × 10 than 2 × 10

-3

Torr. The gauge controller will display all 9s and then go blank. The

-6

Torr. The gauge controller is calibrated for nitrogen, but all pressures

-3

and less

listed in this manual are for helium. Refer to the manual for the 59864B for information on relative sensitivity to different gases.

The largest influence on operating pressure in EI mode is the carrier gas (column) flow. The following table lists typical pressures for various helium carrier gas flows. These pressures are approximate and will vary from instrument to instrument, by as much as 30%

To monitor high vacuum pressure

Table 2 Typical MSD pressure readings for various helium carrier gas flow rates

Turbo pump MSDs

2 Operating the MSD

Column flow (ml/min) Triode gauge reading (Torr),

Per for m anc e turbo pump

1.0 1.5 × 10

2.0 3.0 × 10

2.4 3.5 × 10

3.0 4.5 × 10

4.0 5.0 × 10

4.0 × 10

8.0× 10

1.0 × 10

Not supported

Triode gauge reading (Torr), Standard turbo pump

(Not recommended)

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

If the pressure rises above approximately 8 × 10 will turn off the triode gauge tube. The gauge tube

-3

Torr, the gauge controller

does not turn back on

automatically.

2 Operating the MSD

To measure column flow linear velocity

Materials needed: Syringe

1 Set Data Acquisition for splitless manual injection and selected ion

monitoring (SIM) of m/z 28.

2 Press the Prep Run button on the GC keypad.

3 Inject 1 µl of air into the injection port and press the Start Run button.

4 Wait until a peak elutes at m/z 28.

Note the retention time.

5 Calculate the average linear velocity.

Average linear velocity (cm/sec) =

100 L

-------------t

where:

L = length of the column in meters t = retention time in seconds

Be sure to account for any pieces of column broken off. A 1-meter section missing from a 25-meter column can yield a 4% error.

6 Use this value to verify the MSD ChemStation flow calculations (page 59).

If the numbers disagree, click the Change button to calibrate the column dimensions.

7 To calculate the volumetric flow rate.

Volumetric flow rate (ml/min) =

0.785 D

-----------------------------

where:

D = internal column diameter in millimeters L = the column length in meters t = the retention time in minutes

To calculate column flow

1 In the Instrument Control view, click the Columns icon.

2 Check that the correct column dimensions are entered.

3 Type the desired value in the pressure field.

2 Operating the MSD

To calculate column flow

4 If the Average Velocity displayed is different from that obtained on

page 58, click the Change button to calibrate the column dimensions.

2 Operating the MSD

To tune the MSD

Software changes The software is revised periodically. If the steps in this procedure do not

match your MS ChemStation software, refer to the manuals and online help supplied with the software for more information.

See also You can also use the Control Panel to run the autotune that is currently loaded in

the PC memory. See the 5973N and 5973 inert Mass Selective Detector Local Control Panel (LCP) Quick Reference (G2589-90072) for more information.

1 In the Instrument Control View, select Perform MS Autotune from the

Instrument menu.

2 Select the tune program you wish to use.

The tune will start immediately. For most applications, Autotune gives the best results. Standard Tune is not recommended, as it may reduce sensitivity. Quick Tune is used to adjust peak width, mass assignment, and abundance, without changing ion ratios. If your system is configured for chemical ionization (CI), you will be able to access the CI Tunepanel from this box. Always tune the MSD with the same GC oven temperature and column flow, and the same analyzer temperatures that will be used for data acquisition.

3 Wait for the tune to complete and to generate the report.

Save your tune reports. To view history of tune results, select View Tunes... under the Qualify menu.

4 To manually tune your MSD or to perform special autotunes, select

Manual Tune from the View menu.

In the Tune and Vacuum Control viewTune and Vacuum Control view, you can manually adjust most tune parameters to suit special needs.

From the Tune menu, in addition to the tunes available from Instrument Control, you can select special autotunes for specific spectral results: DFTPP Tune, BFB Tune, or Target Tune.

See the manuals or online help provided with your MSD ChemStation software for additional information about tuning.

To verify system performance

Materials needed: 1 pg/µl (0.001 ppm) OFN sample (8500-5441)

Verify the tune performance

1 Verify that the system has been pumping down for at least 60 minutes.

2 Set the GC oven temperature to 150°C, and the column flow to 1.0 ml/min.

3 In the Instrument Control view, select Checkout Tune from the Qualify menu.

The software will perform an autotune and print out the report.

4 When the autotune has completed, save the method, and then select Tune

Evaluation from the Qualify menu.

The software will evaluate the last autotune and print a System Verification – Tune report.

2 Operating the MSD

To verify system performance

Verify the sensitivity performance

1 Set up to inject 1 µl of OFN, either with the ALS or manually.

2 In the Instrument Control view, select Sensitivity Check from the Qualify

menu.

3 Click the appropriate icons in the Instrument | Edit window to edit the

method for the type of injection.

4 Click OK to run the method.

When the method is completed, an evaluation report will print out.

Verify that rms signal-to-noise ratio meets the published specification. See the

5973N and 5973 inert Mass Selective Detector Local Control Panel (LCP) Quick Reference (G2589-90072).

2 Operating the MSD

To remove the MSD covers

Materials needed: Screwdriver, TORX T-15 (8710-1622)

The analyzer cover is removed for venting and for many maintenance procedures. The lower MSD cover is removed to check the fluid level in the diffusion pump and for a few maintenance procedures. If you need to remove one of the MSD covers, follow these procedures:

Analyzer cover

1 Grasp the front of the analyzer cover and lift up enough to unlatch the five

front tabs.

2 Reach back and grasp the back edge of the analyzer cover.

3 Pull forward to disengage the rear spring latch.

It may take a firm pull to disengage the latch.

To reinstall the analyzer cover, reverse these steps.

Lower MSD cover

1 Remove the analyzer cover.

2 Remove the 3 screws that hold the lower MSD cover in place.

3 Pull the cover left slightly to disengage the two right side tabs and then

pull it straight forward.

To reinstall the lower MSD cover, reverse these steps.

WA R N I N G Do not remove any covers other than the upper and lower MSD covers. Dangerous voltages

are present under other covers.

Analyzer cover

Latch tabs

Lower cover

2 Operating the MSD

To remove the MSD covers

Slots for tabs

CAUT ION

Do not use excessive force, or the plastic tabs that hold the cover to the mainframe will break off.

2 Operating the MSD

To vent the MSD

Firmware changes The firmware is revised periodically. If the steps in this procedure do not

match your MSD control panel, refer to the manuals and online help supplied with the software, or the 5973N and 5973 inert Mass Selective Detector Local Control Panel (LCP) Quick Reference (G2589-90072) for more information.

1 If your system is equipped with a gauge controller, switch off the triode

gauge controller.

2 Before venting a CI MSD, press the Gas Off button (turns off the reagent

gas flow and closes the isolation valve.)

WAR N ING On a CI MSD, the Gas Off light must be on when the MSD is venting.

3 Select Ve n t from the from the Vacuum menu in the software. Follow the

instructions presented.

4 Set the GC/MSD interface heater and the GC oven temperatures to

ambient (25°C).

WA R N I N G If you are using hydrogen as a carrier gas, the carrier gas flow must be off before turning off

CAUT ION

WAR N ING

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

5 When prompted, turn off the MSD power switch.

6 Unplug the MSD power cord.

When the MSD is vented, do not put the ChemStation into Top view. Doing so will turn on the interface heater.

7 Remove the analyzer cover (page 62).

YES NO

2 Operating the MSD

To vent the MSD

8 Turn the vent valve knob counterclockwise only 3/4 turns or until you hear

the hissing sound of air flowing into the analyzer chamber.

Do not turn the knob too far, or the O-ring may fall out of its groove. Be sure to retighten the knob before pumping down.

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

CAUT ION

WAR N ING

Always wear clean gloves while handling any parts that go inside the analyzer chamber.

When the MSD is vented, do not put the ChemStation into Top view. Doing so will turn on the interface heater.

2 Operating the MSD

To open the analyzer chamber

Materials needed: Gloves, clean, lint-free

large (8650-0030) small (8650-0029)

Wrist strap, anti-static

small (9300-0969) medium (9300-1257) large (9300-0970)

CAUT ION

Electrostatic discharges to analyzer components are conducted to the side board where they can damage sensitive components. Wear a grounded anti-static wrist strap and take other anti-static precautions (see page 168) before you open the analyzer chamber.

1 Ve n t th e MSD (page 64).

2 Disconnect the side board control cable and the source power cable from

the side board.

3 Loosen the side plate thumbscrews, if they are fastened.

The rear side plate thumbscrew should be unfastened during normal use. It is only fastened during shipping. The front side plate thumbscrew should only be fastened for CI operation or if hydrogen or other flammable or toxic substances are used for carrier gas.

4 Gently swing the side plate out.

WA R N I N G The analyzer, GC/MSD interface, and other components in the analyzer chamber operate at

very high temperatures. Do not touch any part until you are sure it is cool.

CAUT ION

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

CAUT ION

If you feel resistance, stop. Do not try to force the side plate open. Verify that MSD is vented. Verify that both the front and rear side plate screws are completely loose.

Front thumbscrew

Rear thumbscrew – do not tighten

Source power cable

Side board control cable

Side plate

2 Operating the MSD

To open the analyzer chamber

2 Operating the MSD

To close the analyzer chamber

Materials needed: Gloves, clean, lint-free

large (8650-0030) small (8650-0029)

1 Make sure all the internal analyzer electrical leads are correctly attached.

2 Check the side plate O-ring.

Make sure the O-ring has a very light coat of Apiezon L high vacuum grease. If the O-ring is very dry, it may not seal well. If the O-ring looks shiny, it has too much grease on it. See page 197 for instructions for lubricating the side plate O-ring.

3 Close the side plate.

4 Reconnect the side board control cable and source power cable to the side

board.

5 Make sure the vent valve is closed.

6 Pump down the MSD (page 70).

7 Gently hand tighten the front side plate thumbscrew.

This is only necessary for CI MSDs, or if hydrogen or other flammable or toxic substance is used for carrier gas.

WA R N I N G This thumbscrew must be fastened for CI operation or if hydrogen (or other hazardous gas)

is being used as the GC carrier gas. In the unlikely event of an explosion, it may prevent the side plate from opening.

CAUT ION

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

8 Once the MSD has pumped down, reinstall the analyzer cover.

Wait until after pumpdown to reinstall the analyzer cover.

Front thumbscrew

Rear thumbscrew – do not tighten

Source power cable

Side board control cable

Side plate

2 Operating the MSD

To close the analyzer chamber

2 Operating the MSD

To pump down the MSD

Software changes The software is revised periodically. If the steps in this procedure do not match

your MSD ChemStation software, refer to the manuals and online help supplied with the software for more information.

See also You can also use the Control Panel to perform this task. See the 5973N and 5973

inert Mass Selective Detector Local Control Panel (LCP) Quick Reference (G2589-90072) for more information.

WA R N I N G Make sure your MSD meets all the conditions listed in the introduction to this chapter (page

44) before starting up and pumping down the MSD. Failure to do so can result in personal injury.

WA R N I N G If you are using hydrogen as a carrier gas, do not start carrier gas flow until the MSD has

1 Plug in the MSD power cord.

2 Select Diagnostics/Vacuum Control from the View menu.

Select Pump Down from the Vacuum menu.

3 When prompted, switch on the MSD

4 Press lightly on the side board to ensure a correct seal.

Press on the metal box on the side board.

The rough pump will make a gurgling noise. This noise should stop within a minute. If the noise continues, there is a plate seal, the interface column nut, or the vent valve.

5 Once communication with the PC has been established, click OK.

large air leak in your system, probably at the side

2 Operating the MSD

To pump down the MSD

CAUT ION

Within 10 to 15 minutes the turbo pump speed should be up to 80%. The turbo pump speed should eventually reach 95%. If these conditions are not met, the MSD electronics will shut off the foreline pump. In order to recover from this condition, you must power cycle the MSD. If the MSD does not pump down correctly, see the manual or online help for information on troubleshooting air leaks and other vacuum problems.

6 When prompted, turn on the GC/MSD interface heater and GC oven. Click

OK when you have done so.

The software will turn on the ion source and mass filter (quad) heaters. The temperature setpoints are stored in the current autotune (*.u) file.

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

7 After the message Okay to run appears, wait two hours for the MSD to reach

thermal equilibrium.

Data acquired before the MSD has reached thermal equilibrium may not be reproducible.

8 Reinstall the MSD top cover.

The top cover was removed during the vent procedure.

2 Operating the MSD

To pump down the CI MSD

Software changes The software is revised periodically. If the steps in this procedure do not match your

MSD ChemStation software, refer to the manuals and online help supplied with the software for more information.

See also You can also use the Control Panel to perform this task. See the 5973N and 5973

inert Mass Selective Detector Local Control Panel (LCP) Quick Reference (G2589-90072) for more information.

1 Follow the instructions in the previous module.

See “To pump down the MSD” on page 70.

After the software prompts you to turn on the interface heater and GC oven, perform the following steps.

2 Check vacuum gauge controller to verify that the pressure is decreasing.

3 Press Gas A and Purge, and verify that the Gas A and Purge lights are on.

4 Ve r ify t hat PCICH4.U is loaded, and accept the temperature setpoints.

Always start up, and verify system performance in PCI mode before switching to NCI.

5 Set the GC/MSD interface to 320°C.

6 Purge for at least one hour.

7 Press the Purge button to turn off Purge.

8 Set Gas A to 20%.

9 Let system bake out and purge for at least two hours. If you will be running

NCI, best sensitivity, bake the MSD out overnight.

2 Operating the MSD

To connect the gauge controller

Materials needed: Gauge controller (59864B)

Power cord Triode gauge cable (8120-6573) The high-vacuum gauge controller is required for operating the MSD in CI mode.

WA R N I N G Never connect or disconnect the cable from the triode gauge tube while the MSD is under

vacuum. Risk of implosion and injury due to broken glass exists.

CAUT ION

Be sure to orient the cable and the gauge tube as illustrated. Excessive force on the pins can break the tube. Do not stress the cable.

1 Connect the triode gauge cable to the triode gauge tube.

2 Connect the other end of the triode gauge cable to the gauge controller.

3 Connect the power cord to the gauge controller.

4 Connect the other end of the power cord to an appropriate electrical

outlet.

If you wish to share one controller among MSDs, obtain one cable for each instrument. Leave a cable connected to the triode gauge tube on each MSD. This will avoid having to vent the MSD before connecting the controller.

5 Pump down the MSD.

Do not use a 59864A (older model) triode gauge controller during data acquisition. This model can be used for diagnostic purposes

only.

Triode gauge tube

Triode gauge cable

2 Operating the MSD

To connect the gauge controller

Gauge controller

Triode gauge cable

Power cord

To move or store the MSD

Materials needed: Ferrule, blank (5181-3308)

Interface column nut (05988-20066) Wrench, open-end, 1/4-inch × 5/16-inch (8710-0510)

1 Ve n t th e MSD (page 64).

2 Remove the column and install a blank ferrule and interface nut.

3 Tighten the vent valve.

4 If the MSD has a gauge controller, disconnect the cable from the triode

gauge tube.

5 Move the MSD away from the GC (page 178).

Unplug the GC/MSD interface heater cable from the GC.

2 Operating the MSD

To move or store the MSD

CAUT ION

6 Install the interface nut with the blank ferrule.

7 Remove the analyzer cover (page 62).

8 Tighten the side plate thumbscrews to “finger tight”.

Do not overtighten the side plate thumbscrews. Overtightening will strip the threads in the analyzer chamber. It will also warp the side plate and cause leaks.

9 Plug the MSD power cord in.

10 Switch the MSD on to establish a rough vacuum.

Verify that the turbo pump speed is greater than 50%.

11 Switch the MSD off.

12 Reinstall the analyzer cover.

13 Disconnect the LAN, remote, and power cables.

Front side plate thumbscrew

Rear side plate thumbscrew

2 Operating the MSD

To move or store the MSD

CAUT ION

The MSD can now be stored or moved. The foreline pump cannot be disconnected. It must be moved with the MSD. Make sure the MSD remains upright and is never tipped on its side or inverted.

The MSD must remain upright at all times. If you need to ship your MSD to another location, contact your Agilent Technologies service representative for advice about packing and shipping.

2 Operating the MSD

To set the interface temperature from a 6890 GC

1 Press the Aux # key on the GC keypad.

2 Press 2.

By default, the GC/MSD interface is powered by heated zone Thermal Aux #2 on the 6890 Series GC. Verify that the display shows THERMAL AUX 2 (MSD).

3 Use the number keys to type in the new temperature setpoint.

The typical setpoint is 280°C. The limits are 0°C and 350°C. A setpoint below ambient temperature turns off the interface heater.

CAUT ION

Never exceed the maximum temperature of your column.

Make sure that the carrier gas is turned on and the column has been purged of air before heating the GC/MSD interface or the GC oven.

4 Press the Enter key to download the new setpoint.

If you want the new setpoint to become part of the current method, click Save under the Method menu. Otherwise, the first time a method is loaded, all the setpoints in the method will overwrite those set from the GC keyboard.

2 Operating the MSD

To set the interface temperature from a 6890 GC

To operate the CI MSD, 80 To switch from EI to CI operating mode, 82 To set up the software for CI operation, 83 To set up methane reagent gas flow, 86 CI autotune, 88 To perform a positive CI autotune (methane only), 90 To perform a negative CI autotune (any reagent gas), 92 To verify positive CI performance, 94 To verify negative CI performance, 95 To operate the reagent gas flow control module, 84 To monitor high vacuum pressure, 96 To use other reagent gases, 98 To switch from CI to EI operating mode, 102

Operating the CI MSD

Operating the MSD in CI mode

This chapter provides information and instructions about operating the 5973 inert CI MSDs in CI mode. Most of the material is related to methane chemical ionization but one section discusses the use of other reagent gases.

NOTE

Sequencing is not appropriate for automating methods that use different reagent gases or gas flows, as these parameters must be set

manually.

The software provides instructions for setting the reagent gas flow and for performing CI autotunes. Autotunes are provided for PCI with methane reagent gas and for NCI with any reagent gas.

General guidelines

• Always use the highest purity methane (and other reagent gases, if applicable.) Methane must be at least 99.99% pure.

• Always verify that the MSD is performing well in EI mode before switching to CI. See “To verify system performance” on page 61.

• Make sure the CI ion source and GC/MSD interface tip seal are installed.

• Make sure the reagent gas plumbing has no air leaks. This is determined in PCI mode, checking for m/z 32 after the methane pre-tune.

To operate the CI MSD

Operating your MSD in the CI mode is slightly more complicated than operating in the EI mode. After tuning, gas flow, source temperature (Table 3 on page 80), and electron energy may need to be optimized for your specific analyte.

Table 3 Temperatures for CI operation

Ion source Quadrupole GC/MSD interface

PCI 250°C 150°C 320°C

NCI 150°C 150°C 280°C

3 Operating the CI MSD

Start the system in PCI mode first.

By bringing the system up in PCI mode first, you will be able to do the following:

• Set up the MSD with methane first, even if you are going to use another reagent gas.

• Check the interface tip seal by looking at the m/z 28 to 27 ratio (in the methane flow adjust panel.).

• Tell if a gross air leak is present by monitoring the ions at m/z 19 (protonated water) and 32.

• Confirm if the MS is generating “real” ions and not just background noise.

It is nearly impossible to perform any diagnostics on the system in NCI. In NCI, there are no reagent gas ions to monitor for any gas. It is difficult to diagnose an air leak and difficult to tell whether a good seal is being created between the interface and the ion volume.

3 Operating the CI MSD

To switch from EI to CI operating mode

CAUT ION

Always verify MSD performance in EI before switching to CI operation. See page 51. Always set up the CI MSD in PCI first, even if you are going to run NCI

1 Vent the MSD. See page 64.

2 Open the analyzer.

3 Remove the EI ion source.

Electrostatic discharges to analyzer components are conducted to the side board where they can damage sensitive components. Wear a grounded anti-static wrist strap See “Electrostatic discharge is a threat to the MSD electronics during maintenance” on page 168. Take anti-static precautions

4 Install the CI ion source. See page 246.

5 Install the interface tip seal. See page 248.

6 Close the analyzer.

7 Pump down the MSD. See page 70.

before you open the analyzer chamber.

3 Operating the CI MSD

To set up the software for CI operation

1 Switch to the Tune and Vacuum Control view.

2 Select Load Tune Values from the File menu.

3 Select the tune file PCICH4.U.

4 If CI autotune has never been run for this tune file, the software will

prompt you through a series of dialog boxes. Accept the default values unless you have a very good reason for changing anything.

The tune values have a dramatic effect on MSD performance. Always start with the default values when first setting up for CI, and then make adjustments for your specific application. See the table below for default values for the Tune Control Limits box.

Default Tune Control Limits, used by CI autotune only. These limits should not be confused with the parameters set in Edit MS Parameters, or with those appearing on the tune report.

Reagent gas Methane Isobutane

1x10

Ion polarity Positive Negative

Abundance targetb,1x10 Peakwidth target

0.6 0.6 N/A

Maximum repeller 4 4 N/A

Maximum emission current

, µA 240 50 N/A

Max electron energy, eV 240 240 N/A

Positive

N/A

Negative

1x10

0.6 N/A

Positive

N/A

Ammonia

4N/Ac4

50 N/A

240 N/A

a. Always set up in PCI with methane first, then switch to your desired ion polarity and reagent gas. b. Adjust higher or lower to get desired signal abundance. Higher signal abundance also gives higher noise

abundance. This is adjusted for data acquisition by setting the EMV in the method.

c. There are no PFDTD ions formed in PCI with any reagent gas but methane, hence, CI autotune is not available with these config-

urations. d. Higher peakwidth values give better sensitivity, lower values give better resolution. e. 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.

Negative

1x10

0.6

240

3 Operating the CI MSD

To operate the reagent gas flow control module

For a video demonstration of the gas flow control module, see the 5973 inert MSD Manual CD-ROM.

Flow control module state diagram:

Result Gas A flows Gas B flows Purge

with Gas A

Control panel lights (LEDs)

Gas A (green) On Off On Off Off Off

Gas B (amber) Off On Off On Off Off

Purge (red) Off Off On On On Off

Gas Off (red) Off Off Off Off On On

Valve state

Valve A Open Closed Open Closed Closed Closed

Valve B Closed Open Closed Open Closed Closed

MFC setting On → setpoint On → setpoint On → 100% On → 100% On → 100% Off (→0%)

Isolation valve Open Open Open Open Open Closed

Purge with Gas B

Pump out flow module

Standby, vented, or EI mode

Flow control knob (mass flow control knob)

Flow control display

3 Operating the CI MSD

To operate the reagent gas flow control module

3 Operating the CI MSD

To set up methane reagent gas flow

To se t up methane reagent gas flow

The reagent gas flow must be adjusted for maximum stability before tuning the CI system. Do the initial setup with methane in positive ion mode (PCI). No flow adjustment procedure is available for NCI, as no negative reagent ions are formed.

Adjusting the methane reagent gas flow is a three-step process: setting the flow control, pre-tuning on the reagent gas ions, and adjusting the flow for stable reagent ion ratios, for methane, m/z 28/27.

Your data system will prompt you through the flow adjustment procedure.

CAUT ION

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

1 Press the Gas A button. Verify that only the Gas A light is on.

2 Adjust the flow to 20% for PCI/NCI MSDs.

3 Check the vacuum gauge controller to verify correct pressure. See page 96.

4 Select Methane Pretune from the Setup menu.

The methane pretune tunes the instrument for optimum monitoring of the ratio of methane reagent ions m/z 28/27.

5 Examine the displayed profile scan of the reagent ions.

• Make sure there is no visible peak at m/z 32. A peak there indicates an air leak.

If such a peak is present, find and repair the leak before proceeding. Operating in the CI mode with an air leak will rapidly contaminate the ion source.

• Make sure that the peak at m/z 19 (protonated water) is less than 50% of the peak at m/z 17.

6 Perform the Methane Flow Adjust.

Adjust the methane flow on the PCI/NCI MSD to get the ratio of between 1.5 and 5.0.

m/z 28/27

3 Operating the CI MSD

To set up methane reagent gas flow

CAUT ION

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

vent the MSD and clean the ion source.

Methane pre-tune after more than a day of baking out. Note the low abundance of m/z 19 and absence of any visible peak at m/z 32. Your MSD will probably show more water at first, but the abundance of m/z 19 should still be less than 50% of m/z 17.

3 Operating the CI MSD

CI autotune

After the reagent gas flow is adjusted, the lenses and electronics of the MSD should be tuned. 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/MSD interface by means of the gas flow control module.

CAUT ION

After the system has been switched from EI to CI mode, or vented for any other reason, the MSD must be purged and baked out for at least 2 hours before tuning. Longer bakeout is recommended before running samples requiring optimal sensitivity.

There is a PCI autotune for methane only, as there are no PFDTD ions produced by other gases in positive mode. PFDTD ions are visible in NCI for any reagent gas. Always tune for methane PCI first regardless of which mode or reagent gas you wish to use for your analysis.

There are no tune performance criteria. If CI autotune completes, it passes. EMVolts (electron multiplier voltage) at or above 2600 V, however, indicates a problem. If your method requires EMVolts set at +400, you may not have adequate sensitivity in your data acquisition.

Always verify MSD performance in EI before switching to CI operation. See page 51. Always set up the CI MSD in PCI first, even if you are going to run NCI

3 Operating the CI MSD

CI autotune

Reagent gas Methane Isobutane Ammonia EI

Ion polarity Positive Negative Positive Negative Positive Negative N/A

Emission 150 µA

Electron energy 150 eV

Filament 1

Repeller 3 V

Ion focus 130 V

Entrance lens offset 20 V

EMVolts 1200

Gas Off Off

Gas select valve A

Suggested flow 20%

Source temp 250°C

Quad temp 150°C

Interface temp 320°C

Autotune Yes

50 µA 150 µA 50 µA 150 µA 50 µA 35 µA

150 eV 150 eV 150 eV 150 eV 150 eV 70 eV

111111 or 2

3 V 3 V 3 V 3 V 3 V 30 V

130 V 130 V 130 V 130 V 130 V 90 V

20 V 20 V 20 V 20 V 20 V 25 V

1200 1200 1200 1200 1200 1200

Off Off Off Off Off On

ABBBBNone

40% 20% 40% 20% 40% N/A

150°C 250°C 150°C 250°C 150°C 230°C

150°C 150°C 150°C 150°C 150°C 150°C

280°C 320°C 280°C 320°C 280°C 280°C

Ye s N o Ye s N o Ye s Ye s

3 Operating the CI MSD

To perform a positive CI autotune (methane only)

CAUT ION

Always verify MSD performance in EI before switching to CI operation. See page 51. Always set up the CI MSD in PCI first, even if you are going to run NCI

1 Verify that the MSD performs correctly in EI mode first. See page 61.

2 Load the PCICH4.U tune file (or an existing tune file for the reagent gas you

are using).

If you use an existing tune file, be sure to save it with a new name if you don’t want to over write the existing values.

3 Accept the default settings.

4 Perform methane setup. See page 86.

5 Under the Tune menu, click CI Autotune.

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

There are no tune performance criteria. If autotune completes, it passes. If the tune sets the electron multiplier voltage (EMVolts) at or above 2600 V, however, you may not be able to acquire data successfully if your method sets EMVolts to “+400” or higher.

The autotune report contains information about air and water in the system.

The 19/29 ratio shows the abundance of water.

The 32/29 ratio shows the abundance of oxygen.

3 Operating the CI MSD

To perform a positive CI autotune (methane only)

3 Operating the CI MSD

To perform a negative CI autotune (any reagent gas)

CAUT ION

Always verify MSD performance in EI before switching to CI operation. See page 51. Always set up the CI MSD in PCI first, with methane as the reagent gas first, even if you are going to be using a different reagent gas or going to run NCI.

1 Load NCICH4.U (or an existing tune file for the reagent gas you are using).

If you use an existing tune file, be sure to save it with a new name if you don’t want to over write the existing values.

2 Accept the default temperature and other settings.

3 If you don’t already have an NCI tune file for your reagent gas, use

Select Reagent Gas under the Setup menu.

4 Under the Tune menu, click CI Autotune.

Avoid tuning unless absolutely necessary; this will minimize PFDTD background noise, and help prevent ion source contamination.

3 Operating the CI MSD

To perform a negative CI autotune (any reagent gas)

3 Operating the CI MSD

To verify positive CI performance

Materials needed: Benzophenone, 100 pg/µL (8500-5440)

CAUT ION

Always verify MSD performance in EI before switching to CI operation. See page 51. Always set up the CI MSD in PCI first, even if you are going to run NCI.

1 Verify that the MSD performs correctly in E1 and PCI mode.

2 Verify that the PCICH4.U tune file is loaded.

3 On the flow control panel, turn Purge off. Set Gas A to 20% flow.

4 In Tune and Vacuum Control view, perform CI setup. See page 88.

5 Run CI Autotune. See page 88.

6 Run the PCI sensitivity method: BENZ_PCI.M, using 1 µL of 100 pg/µL

Benzophenone.

7 Verify that the system conforms to the published sensitivity specification.

See also 5973N and 5973 inert Mass Selective Detector Specifications (5988-9991EN)

To verify negative CI performance

This procedure is for EI/PCI/NCI MSDs only

Materials needed: OFN, 1 pg/µL (8500-5441)

3 Operating the CI MSD

To verify negative CI performance

CAUT ION

Always verify MSD performance in EI before switching to CI operation. See page 51. Always set up the CI MSD in PCI first, even if you are going to run NCI

1 Verify that the MSD performs correctly in EI mode.

2 Load the NCICH4.U tune file, and accept the temperature setpoints.

3 Turn Purge and Gas A on and let the system stabilize for 90 minutes.

4 Turn Purge off, and set Gas A to 40% flow.

5 In Tune and Vacuum Control view, run CI Autotune. See page 95.

Note that there are no criteria for a “passing” Autotune in CI. If the Autotune completes, it passes.

6 Run the NCI sensitivity method: OFN_NCI.M using 1 µL of 1 pg/µL OFN.

7 Verify that the system conforms to the published sensitivity specification.

See also 5973N and 5973 inert Mass Selective Detector Specifications

(5988-9991EN)

3 Operating the CI MSD

To monitor high vacuum pressure

Materials needed: Gauge controller (59864B)

Triode gauge cable (8120-6573)

WA R N I N G Never connect or disconnect the cable from the triode gauge tube while the MSD is under

vacuum. Risk of implosion and injury due to broken glass exists.

WA R N I N G If you are using hydrogen as a carrier gas, do not turn on the triode gauge tube if there is

any possibility that hydrogen has accumulated in the manifold. The triode gauge filament can ignite hydrogen. Read the Hydrogen Carrier Gas Safety Guide (5955-5398) before operating the MSD with hydrogen carrier gas.

1 Connect the gauge controller to the triode gauge tube. See page 73.

2 Start up and pump down the MSD. See page 70.

3 Switch on the power switch on the back of the gauge controller.

4 Press and release the

GAUGE button.

After a few seconds, the pressure should be displayed.

Pressure is displayed in the format X.X – X where – X is the base 10 exponent. Units are Torr.

The gauge controller will not turn on if the pressure in the MSD is above approximately 8 × 10 triode gauge tube can measure pressures between approximately 8 × 10

-6

3 × 10

-3

Torr. The gauge controller will display all 9s and then go blank. The

-3

Torr. The gauge controller is calibrated for nitrogen, but all pressures listed

in this manual are for helium.

The largest influence on operating pressure is the carrier gas (column) flow. The following table lists typical pressures for various helium carrier gas flows. These pressures are approximate and will vary from instrument to instrument.

and

3 Operating the CI MSD

To monitor high vacuum pressure

Typical pressure readings

Use the 59864B high-vacuum gauge controller. Note that the mass flow controller is calibrated for methane, and the high vacuum gauge controller is calibrated for nitrogen, so these measurements are not accurate, but are intended as a guide to typical observed readings. They were taken with the following set of conditions. Note that these are typical PCI temperatures:

Source temperature 250°C

Quad temperature 150°C Interface temperature 320°C

Helium carrier gas flow 1 mL/min

MFC (%) Pressure (Torr)

Methane Ammonia

EI/PCI/NCI MSD (Performance turbo pump)

10 5 . 5 × 10

15 8.0 × 10 20 1.0 × 10

25 1.2 × 10

30 1.5 × 10 35 2.0 × 10

40 2.5 × 10

EI/PCI/NCI MSD (Performance turbo pump)

–5

–4

5.0 × 10

7.0 × 10

8.5 × 10

1.0 × 10

1.2 × 10

1.5 × 10

2.0 × 10

–5

–4

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 MSD and gauge controller to the next.

3 Operating the CI MSD

To use 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 5973 inert MSD with methane reagent gas before attempting to use other reagent gases.

CAUT ION

Do not use nitrous oxide as a reagent gas. It radically shortens the life span of the 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 Appendix A, Chemical Ionization Theory. If you are not experienced with chemical ionization, we suggest reviewing that material before you proceed.

Not all setup operations can be performed in all modes with all reagent gases. See the following table for details.

3 Operating the CI MSD

To use other reagent gases

Reagent gas/ mode Reagent ion

masses

PFDTD Calibrant ions

Flow adj ions: Ratio

EI/PCI/NCI MSD Performance turbo pump Recommended flow: 20%

Methane/ PCI 17, 29, 41

Methane/ NCI 17, 35, 235

41, 267, 599 28/27: 1.5 – 5.0

185, 351, 449 N/A Isobutane/ PCI 39, 43, 57 N/A 57/43: 5.0 – 30.0

Isobutane/ NCI 17, 35, 235 185, 351, 449 N/A

Ammonia/ PCI 18, 35, 52 N/A 35/18: 0.1 – 1.0 Ammonia/ NCI 17, 35, 235 185, 351, 517 N/A

a. There are no PFDTD ions formed with any reagent gas but methane. Tune with methane

and use the same parameters for the other gas.

b. There are no negative reagent gas ions formed. To pretune in negative mode, use back-

ground ions:

17 (OH

), 35 (Cl-), and 235 (ReO

). These ions can not be used for reagent gas flow

adjustment. Set flow to 40% for NCI and adjust as necessary to get acceptable results for your application.

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.

3 Operating the CI MSD

To use other reagent gases

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 NH Ammonia reagent ion spectra have principal ions at m/z 18, 35, and 52, corresponding to NH

To adjust your MSD for isobutane or ammonia chemical ionization, use the following procedure:

1 Perform a standard Positive CI autotune with methane and PFDTD.

2 Under the Setup menu, click Select Reagent Gas and select Isobutane or Ammonia.

This will change the menus to use the selected gas, and select appropriate default tune parameters.

3 Select a new tune file name, or load an existing PCI tune file for the

specific gas.

If you use an existing tune file, be sure to save it with a new name if you don’t want to over write the existing values. Accept the default temperature and other settings.

and then, in some cases, from the subsequent loss of water.

, NH4(NH3)+, and NH4(NH3)

NOTE

4 Turn Gas B on.

After the amber light stops flashing and the Purge light goes off, set the gas flow to 20%.

5 Click Isobutane (or Ammonia) Flow Adjust on the Setup menu.

There is no CI autotune for isobutane or ammonia in PCI.

If you wish to run NCI with isobutane or ammonia, load NCICH4.U, or load an existing NCI tune file for the specific gas.

Be sure to read the following application note: Implementation of Ammonia Reagent Gas For Chemical Ionization On 5973 MSDs (5968-7844).

100

Agilent 5973 inert User manual

Specifications and Main Features

Frequently Asked Questions

User Manual

Table of Contents

Introduction

5973 inert MSD Version

About this manual

Other User Information

The 5973 inert MSD

CI MSD hardware description

Important Safety Warnings

Safety and Regulatory Certifications

Cleaning/Recycling the Product

Installing GC Columns

Installing GC columns

To prepare a capillary column for installation

To install a capillary column in a split/splitless inlet

To condition a capillary column

To install a capillary column in the GC/MSD interface

To install a capillary column using the installation tool

Operating the MSD

Operating the MSD

To view MSD analyzer temperature and vacuum status

To set monitors for MSD temperature and vacuum status

To set the MSD analyzer temperatures

To set the GC/MSD interface temperature from the PC

To monitor high vacuum pressure

To measure column flow linear velocity

To calculate column flow

To tune the MSD

To verify system performance

Verify the tune performance

Verify the sensitivity performance

To remove the MSD covers

Analyzer cover

Lower MSD cover

To vent the MSD

To open the analyzer chamber

To close the analyzer chamber

To pump down the MSD

To pump down the CI MSD

To connect the gauge controller

To move or store the MSD

To set the interface temperature from a 6890 GC

Operating the CI MSD

Operating the MSD in CI mode

To switch from EI to CI operating mode

To set up the software for CI operation

To operate the reagent gas flow control module

To set up methane reagent gas flow

CI autotune

To perform a positive CI autotune (methane only)

To perform a negative CI autotune (any reagent gas)

To verify positive CI performance

To verify negative CI performance

To monitor high vacuum pressure

Typical pressure readings

To use other reagent gases

Isobutane CI

Ammonia CI