HP 5973 MSD User manual

H
Hardware Manual
HP 5973 MSD
PCI /NCI

© Copyright 1998
Hewlett-Packard Company
All Rights Reserved.
Reproduction, adaptation, or
translation without prior
written permission is
prohibited, except as allowed
under the copyright laws.
Document History
Publication number
G1999-90001
First edition, 2/98
Printed in USA
Warranty
The information contained in
this document is subject to
change without notice.
Hewlett-Packard makes no
warranty of any kind with
regard to this material,
including, but not limited to,
the implied warranties of
merchantability and fitness for
a particular purpose.
Hewlett-Packard shall not be
liable for errors contained
herein or for incidental or
consequential damages in
connection with the furnishing,
performance or use of this
material.
Hewlett-Packard assumes no
responsibility for the use or
reliability of its software on
equipment that is not
furnished by Hewlett-Packard.
Noise Declaration
Deutsch
LpA << 70 dB am Arbeitsplatz
normaler Betrieb nach EN
27779:1991
English
LpA << 70 dB operator
position normal operation per
ISO 7779:1988
Instrument
Identification
Each HP 5973 MSD is identi-
fied by a unique 10-character
serial number. This serial
number is located on a label on
the lower left side near the
front of the instrument. On CI
upgrades, a serial number is
located on the flow module.
When corresponding with
Hewlett-Packard about your
instrument, be sure to include
the model number and both
full 10-character serial
numbers.
Write the serial number of your
HP 5973 MSD and flow module
(if applicable) here for
reference:
MSD serial #:
________________________
CI flow module serial #:
________________________
HP 5973 MSD version
HP 5973 MSDs are equipped
with either a diffusion pump or
a turbomolecular (turbo)
pump. Chemical Ionization is
available for the turbo MSD
only. The serial number label
displays a product number that
tells what kind of MSD you
have:
G1098A = Diffusion pump
G1099A = Turbo pump
G1999A = CI (turbo pump)
Manual Conventions
Cautions
Cautions call attention to
procedures which, if not
correctly performed or
adhered to, could result in
damage to the instrument.
Warnings
Warnings call attention to
procedures which, if not
correctly performed or
adhered to, could result in
personal injury.
Part Numbers
In this manual, Hewlett-
Packard part numbers are
generally listed in parentheses
after the name of the part or in
tables in the Parts chapter.
Most Hewlett-Packard part
numbers are either four-digit-
by-four-digit (1234-1234)
numbers or five-digit-by-five-
digit (12345-12345) numbers.
A few tools and supplies listed
have no part numbers and are
not available from Hewlett-
Packard. Most of these can be
obtained from laboratory
supply companies.
Safety Information
Safety Symbols
(on equipment)
Safety class
The HP 5973 Mass Selective
Detector (MSD) is a Safety
Class I instrument and has
been designed and tested in
accordance with IEC
Publication 1010-1 Safety
Requirements for Electrical
Equipment for Measurement,
Control, and Laboratory Use.
WAR NI NG
Connecting an MSD to a power
source which is not equipped
with a protective earth contact
creates a shock hazard for the
operator and can damage the
instrument. Likewise,
interrupting the protective
conductor inside or outside the
MSD or disconnecting the
protective earth terminal
creates a shock hazard for the
operator and can damage the
instrument.
WAR NI NG
Make sure that only fuses with
the required current rating and
of the specified type are used
for replacement. The use of
incorrect or makeshift fuses or
the short-circuiting of fuse
holders creates a shock hazard
for the operator and can
damage the instrument.
WAR NI NG
Any adjustment, maintenance
or repair of the opened
instrument while it is
connected to a power source
should be avoided if possible
and, if required, should be
carried out only by trained
persons who are aware of the
hazards involved.
Safety Information continued
on the inside of the back
cover.
;Refer to operating
instructions
=Indicates hazardous
voltage
+Indicates hot surface
3Indicates earth
(ground) terminal

3
Table of Contents
Chapter 1 General Information
Specifications, 9
Reagent gases and regulators, 10
Chapter 2 Hardware Reference
CI ion source, 14
Reagent gas flow control module, 16
EI/CI GC/MSD interface (CI interface), 20
Chapter 3 Chemical Ionization Theory
Chemical ionization overview, 22
Positive CI theory, 24
Negative CI theory, 30
Chapter 4 CI setup
CI setup, 37
To vent the CI MSD, 38
To remove the CI MSD covers, 39
To pump down the MSD, 40
To install the GC column in the EI/CI GC/MSD interface, 42
To switch from CI to EI operating mode, 44
To switch from EI to CI operating mode, 45
To install the CI ion source, 46
To install the CI interface tip seal, 48

4
Contents
Chapter 5 CI operation
CI operation, 51
To set up the software for CI operation, 52
To set up methane reagent gas flow, 54
To perform CI autotune, 56
To perform a positive CI autotune (methane only), 57
To perform a negative CI autotune (any reagent gas), 58
To verify positive CI performance, 59
To verify negative CI performance, 60
To operate the reagent gas flow control module, 61
To monitor high vacuum pressure, 62
To use other reagent gases, 64
Chapter 6 Troubleshooting
Troubleshooting tips and tricks, 69
Air leaks, 70
Pressure-related symptoms (overview), 74
Poor vacuum without reagent gas flow, 75
High pressure with reagent gas flow, 76
Pressure does not change when reagent flow is changed, 77
Signal-related symptoms (overview), 78
No peaks, 79
No or low reagent gas signal, 81
No or low PFDTD signal, but reagent ions are normal, 83
Excessive noise or low signal-to-noise ratio, 84
Large peak at m/z 19, 85
Peak at m/z 32, 86
Tuning-related symptoms (overview), 87
Reagent gas ion ratio is difficult to adjust or unstable, 88
High electron multiplier voltage, 89
Can not complete autotune, 90
Peak widths are unstable, 91

Contents
5
Chapter 7 Maintenance
To clean the CI ion source, 95
To minimize foreline pump damage from ammonia, 96
To replace the methane/isobutane gas purifier, 97
To refill the CI calibrant vial, 98
To purge the CI calibration valve, 99
To connect the vacuum gauge controller, 100
To clean the reagent gas supply lines (tubing), 102
Chapter 8 Parts
GC/MSD interface parts, 106
CI ion source parts, 108
Flow control module parts, 110
Ferrules, 112
Miscellaneous parts, 113

6

1
General Information
Specifications, 9
Reagent gases and regulators, 10

8
General Information
General information
This manual contains information pertaining to the operation, and
maintenance of the HP 5973 CI MSD. It is intended to be used in
addition to the HP 5973 MSD Hardware Manual. The CI hardware
consists of a chemical ionization source, GC/MSD interface, a reagent
gas mass flow controller, and associated electronics. Setup and tuning
macros are included with the data system software. CI Autotune uses
perfluoro-5,8-dimethyl-3,6,9-trioxidodecane (PFDTD) as a calibrant
and methane as the reagent gas.
Chapter 1 provides a list of the CI performance specifications and a
list of reagent gases.
Chapter 2 presents some basics of the theory of chemical ionization
and the advantages it offers.
Chapter 3 describes the CI hardware components and their functions.
Chapter 4 provides instructions for using CI.
Chapter 5 discusses problems most likely to be encountered and their
probable causes.
Chapter 6 discusses routine maintenance procedures.
Chapter 7 provides information about parts that are available for
maintenance of the CI hardware.

9
Specifications
This section lists the principal performance specifications for the
HP G1999A (HP 5973 MSD with factory-installed CI.) These specifications are
subject to change without notice. These specifications do not apply to CI upgrades;
see the upgrade installation documents.
Sensitivity, Scan
Positive CI: 75:1 RMS for 1 µl of 100 pg/µl Benzophenone (m/z = 183.1)
Negative CI: 500:1 RMS for 1 µl of 1 pg/µl Octafluoronapthalene (m/z = 272.0)
Sensitivity, SIM
Positive CI: 10:1 RMS for 1 µl of 100 fg/µl Benzophenone (m/z = 183.1)
Negative CI: 10:1 RMS for 1 µl of 1 fg/µl Octafluoronapthalene (m/z = 272.0)
NOTE Installation does not include demonstration of SIM sensitivity.

10
General Information
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Reagent gases and regulators
The following reagent gases and hardware may be required for operation of CI with
the HP 5973 MSD (depending on your choice of reagent). Use the highest purity
gases available. Do not use gases of less than the listed purity. The hardware items
listed below are available from Matheson and Swagelok. They are representative of
products that are appropriate for the purpose.
A gas purifier (G1999-80410) is needed for use with methane and isobutane; it
cannot be used with ammonia. A separate purifier is necessary for each gas supply.
Methane (required)
Lecture bottle (0.06 m3, 56 liters), UHP 99.97%
Regulator 3320
Stand, model J05
Swagelok female connector, SS-200-7-2
Isobutane (optional)
Lecture bottle (0.17 kg), instrument, 99.5% purity
Regulator 3321 or 3320
Stand, model J05
Swagelok female connector, SS-200-7-2
Ammonia (optional)
Lecture bottle (0.17 kg), anhydrous, 99.99% purity
Regulator 3332
Stand, model J05
Swagelok female connector, SS-200-7-4

2
Hardware Reference
Description, 12
CI ion source, 14
Reagent gas flow control module, 16
EI/CI GC/MSD interface (CI interface), 20

12
Description
The chemical ionization (CI) hardware allows the HP 5973 MSD to operate in the
positive and negative CI modes (PCI and NCI) and produce high-quality, classical
CI spectra, which include molecular adduct ions. A variety of reagent gases
(including methane, isobutane, and ammonia) can be used.
The HP 5973 CI system adds to the HP 5973 MSD:
• CI ion source
• Redesigned EI/CI GC/MSD interface
• Interface tip seal
• Reagent gas flow control module
• Bipolar HED power supply
• Updated GC/MSD ChemStation software
A triode high vacuum gauge controller (HP 59864B) is not included, but is
required for operation in CI mode.
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 source ensure that all the source gases stay in the source long
enough for the appropriate chemical reactions to occur.
The CI interface has special plumbing for reagent gas. The interface can be used for
both EI and CI operation. A spring-loaded insulating seal fits onto the tip of the
interface to seal the opening to the ion source; this seal must be removed before
installing the EI source.
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.
The CI source, CI interface, and reagent gas control module are described in more
detail in the remainder of this chapter.
To help assure quality of reagent gas entering the system, a methane/isobutane gas
purifier is provided, and is required. It removes oxygen, water, hydrocarbons, and
sulfur compounds.

Hardware Reference
13

14
Hardware Reference
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CI ion source
The CI ion source is similar to the EI source, but only has one part in common with
the EI source — the entrance lens. The single CI filament has a straight wire and a
reflector. There is a “dummy” filament to provide connections for the other wires.
The holes in the ion source (electron-entrance and ion-exit) are very small (0.5
mm), making it possible to pressurize the ionization chamber. Both the source body
and the plate are at repeller potential, electrically isolated from the radiator and the
CI interface tip. The seal for the interface tip ensures a leak-tight seal and electrical
isolation between the CI interface and ion source. Large slots in the drawout
cylinder and ion-source body provide enhanced pumpout for the ion source optics.
CI ion source body
Source heater and
sensor cables
CI interface tip
CI interface tip seal
CI source heater
assembly
Ion focus lens
CI interface cover
CI filament
Entrance lens

Hardware Reference
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15
CI ion focus
lens
CI drawout
cylinder
CI ion source
body
CI lens
insulator
CI drawout
plate
Entrance lens
CI repeller
CI repeller
insulator
CI source
heater
assembly
CI interface tip seal
CI filament
Setscrew
Dummy
filament
CI lens

16
Hardware Reference
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Reagent gas flow control module
The CI reagent gas flow control module regulates the flow of reagent gas into the
EI/CI GC/MSD interface. The flow control module consists of a mass flow controller
(MFC), gas select valves, CI calibration valve, isolation valve, control panel, control
and display electronics, and plumbing. The back panel provides Swagelok inlet
fittings for methane and one other reagent gas. The other fittings in the flow module
are VCR fittings; VCR fittings have a disposable gasket that must be replaced every
time the seal is opened. Operation of the flow module is through the control panel
on the front. Gas A must be plumbed with Methane. Gas B can be plumbed with any
other reagent gas.
Operation of the flow module is through the control panel on the front.
• Each button on the control pane has an LED (light) next to it. When that button
is active, the light is on.
•Gas A or Gas B opens the chosen gas select valve. Only one can be open at a time.
•Gas Off closes the gas select and isolation valves. GasOff also sets the MFC to 0%
flow, unless Purge is on. The Gas Off LED must be off to turn on Gas A or Gas B
• The flow control knob is used to adjust the flow. When no gases are turned on
the Flow Control display will show dashes: ––.
•Purge sets the MFC to 100% of total flow (fully open), regardless of the position
of the flow control knob or the state of the select valves.
Flow controlknob
Flow controldisplay

Hardware Reference
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17
• The flow control display shows the gas flow as a percentage of the total possible
flow (5 ml/min for methane).
• The flow control knob adjusts the gas flow. If the selected flow rate can not be
achieved or maintained, the numbers in the flow control display will flash.
• The CI calibration valve is controlled by the ChemStation software, and opens
automatically during CI autotune or manual tuning, allowing PFDTD to diffuse
into the ion source.
• The isolation valve prevents contamination of the flow control module by
atmosphere while the MSD is vented or by PFTBA during EI operation.
Reagent gas select valve
Mass flow controller
Rear flow module cover
Flow control board (under
Isolation valve
CI calibration valve
Reagent gas inlet lines
Controlpanel
EI/CI GC/MSD interface
&$87,21 Try to avoid tuning any more often than absolutely necessary to minimize PFDTD
background and ion source contamination.

18
Hardware Reference
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Reagent gas flow control module schematic
When you turn off one gas and turn on the other, the system sets a 6-minute delay
with GasOff and Purge both on to pump out the flow control module. The light for the
selected reagent gas will flash, indicating the delay timer is active. Once the delay
is finished, the Purge and GasOff lights will turn off, and the light for the selected gas
will stop flashing and stay on.
When the MSD is turned off, all valves are closed, and all lights are off. At startup,
all valves are closed and all lights are off, except Gas Off.
The flow control board remembers the flow setting for each gas. When either gas is
selected, the control board automatically sets the same flow that was used for that
CI ion
source
Gas A
(Methane)
supply
Gas B
(Other gas)
supply
Mass
Flow
Controller
Gas select
valve A
Gas select
valve B
Restrictor
PFDTD
vial
Calibration
valve
Isolation
valve
EI/CI
GC/MSD
interface
Green
light
Amber
light
GC column

Hardware Reference
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19
gas last time.
Flow controlmodule state diagram:
Result Gas A flows Gas B flows Purge
with Gas A Purge with Gas B Pump out flow module Standby,vented, or EI mode
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 On→setpoint On →setpoint On →100% On →100% On →100% Off (→0%)
Isolation valve Open Open Open Open Open Closed

20
Hardware Reference
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EI/CI GC/MSD interface (CI interface)
The CI interface mounts onto the side of the vacuum manifold, with one end in the
GC oven and the other in the MSD. Reagent gas is plumbed into the interface. The
tip of the interface assembly extends into the ionization chamber. A spring-loaded
seal keeps reagent gases from leaking out around the tip. The reagent gas is
plumbed into the interface body, and mixes with carrier gas and sample in the ion
source. This interface is also used for EI operation in CI MSDs.
Interface tip seal
CI interface weldment
CI interface cover
Vacuum manifold
CI interface insulator
Heater/sensor cable
CI interface heater clamp
Source radiator
CI ionization chamber
GC inlet
Reagent gas inlet