g1072 Ci PDF

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4
Table of Contents
Chapter 1 General Information

Specifications, 1-4
Mass range, 1-4
Resolution, 1-4
Sensitivity, SCAN, 1-4
Sensitivity, SIM, 1-4
Scan rates, 1-4
Reagent gases, 1-5
Methane (required), 1-5
Ammonia (optional), 1-5
Isobutane (optional), 1-5
Chapter 2 System Overview

Description, 2-2
Ion source, 2-3
GC interface, 2-5
Reagent gas flow controller, 2-6
Tuning macros, 2-9
Theory of operation, 2-10
Proton transfer, 2-12
Hydride abstraction, 2-14
Addition, 2-15
Charge exchange, 2-16
5
Contents
Chapter 3 Installation
Initial mass spectrometer upgrade (overview), 3-3
To install the CI ion source, 3-4
To install the flow controller, 3-12
To modify the GC interface, 3-14
Preparing the system for CI operation (overview), 3-16
To configure your software for CI operation, 3-17
MS ChemStation (DOS series), 3-17
HP-UX ChemSystem, 3-17
To pump down the MSD (methane off), 3-18
To purge the methane lines (methane on), 3-19
To purge the calibration valve, 3-20
MS ChemStation (DOS series), 3-20
HP-UX ChemSystem, 3-20
To bake out the system, 3-21
To convert from CI to EI, 3-22
To convert from EI to CI, 3-25
Initial upgrade checklist, 3-28
Materials needed, 3-28
To install the CI ion source, 3-28
To install the flow controller, 3-29
To modify the GC interface, 3-29
To prepare the system for CI operation, 3-29
Operation, 3-29
CI-to-EI-conversion checklist, 3-30
EI-to-CI-conversion checklist, 3-31
Chapter 4 Operation
To set the methane flow, 4-3
Coarse adjustment, 4-3
Methane pretune, 4-4
Fine adjustment, 4-6
To perform a CI tune, 4-7
To verify system performance, 4-10
GC parameters, 4-10
MSD parameters, 4-10
Evaluating the results, 4-11
To use other reagent gases, 4-15
Isobutane CI, 4-16
Ammonia CI, 4-19
6
Contents
Chapter 5 Troubleshooting
Pressure-related symptoms (overview), 5-3
Foreline pressure > 100 mTorr without reagent gas flow, 5-4
Foreline pressure >130 mTorr with reagent gas flow, 5-5
Foreline pressure does not change when reagent flow is changed, 5-6
Large high-vacuum pressure fluctuations, 5-8
Temperature-related symptom (overview), 5-9
GC interface temperature OK but analyzer temperature too low, 5-10
Signal-related symptoms (overview), 5-11
No or low reagent gas signal, 5-12
No or low PFTBA signal, 5-15
Excessive noise/low signal-to-noise ratio, 5-17
Large peak at m/z 19, 5-18
Peak at m/z 32 , 5-19
Tuning-related symptoms (overview), 5-20
CI ion ratio is difficult to adjust or unstable, 5-21
High electron multiplier voltage, 5-23
Can not complete autotune, 5-24
Peak widths are unstable, 5-26
Peaks 219 and 414 are out of range, 5-27
Split peaks during autotune, 5-28
Incorrect m/z 70 abundance in tune report, 5-29
Error message: No emission current, 5-30
Leaks, 5-31
Chapter 6 Maintenance
Cleaning the ion source, 6-3
Frequency of cleaning, 6-3
Cleaning procedure, 6-3
Ammonia CI, 6-4
Foreline pump oil, 6-4
Foreline trap, 6-4
Flow control valves, 6-5
7
Contents
Chapter 7 Parts
GC interface parts, 7-3
CI ion source parts, 7-4
Flow controller parts, 7-6
Miscellaneous parts, 7-7
Index, I-1
List of Figures Figure 1-1 GC/MSD system with HP G1072B CI Accessory, 1-3
Figure 2-1 CI ion source, 2-3

2-2 CI ion source ---- exploded view, 2-4
2-3 GC interface modified for CI, 2-5
2-5 Flow controller back panel, 2-7
2-4 Flow controller front panel, 2-7
2-6 Reagent gas controller flow diagram, 2-8
2-7 Typical CI spectrum of methyl octanoate, 2-11
Figure 3-1 Removing the GC interface, 3-5

3-2 Top and main board electrical connections, 3-6
3-3 EI ion source ---- installed, 3-7
3-4 Installing the CI ion source, 3-8
3-5 Connecting the ion source leads, 3-9
3-6 Calibration valve connector, 3-11
3-7 Installing the flow controller, 3-13
3-8 Installing the guide tube assembly, 3-14
Figure 4-1 Ions monitored for methane adjustment, 4-5

4-2 Relationship of ion ratio and pressure, 4-6
4-3 Chromatogram of evaluation sample A, 4-12
4-4 Mass spectrum of dodecane, 4-13
4-5 Mass spectrum of biphenyl, 4-13
4-6 Mass spectrum of p-chlorobiphenyl, 4-14
4-7 Mass spectrum of methyl palmitate, 4-14
4-8 Isobutane spectrum, 4-17
4-9 Tuning for isobutane, 4-18
4-10 Ammonia spectrum, 4-20
4-11 Tuning for ammonia, 4-21
8
1
Specifications, 1-4
Reagent gases, 1-5
General Information
General information
This manual contains information pertaining to the installation, operation,

and maintenance of the HP G1072B Chemical Ionization Accessory for the
HP 5972A MSD (Figure 1-1). The CI accessory consists of a chemical
ionization source, components for modifying the GC/MS interface, an
interface socket, a reagent gas flow controller, and associated hardware.
Tuning macros are included with the data system software. These macros
facilitate automatic tuning of the MSD, using PFTBA as a calibrant and
methane as the reagent gas.
Chapter 1 provides a list of the CI accessory performance specifications

and a list of reagent gases.
Chapter 2 describes the CI accessory components and their functions, and

presents some basics of the theory of chemical ionization and the
advantages it offers.
Chapter 3 provides detailed instructions for installing the CI accessory on

the HP 5972A MSD.
Chapter 4 provides instructions for using the CI accessory.
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 accessory.
1-2
Chapter 1 ---- General Information
Figure 1-1. GC/MSD system with HP G1072B CI Accessory
1-3
Specifications
Specifications
This section lists the principal performance specifications for the HP 5972A MSD
equipped with the CI accessory. These specifications are subject to change
without notice.
Mass range
Scans any mass range between 1.6 and 700 amu in 0.1-amu steps.
Resolution
Unit resolution throughout the mass range established automatically under
computer control. Proper resolution is obtained by adjusting the width of a
calibrated peak at m/z 414 to be 0.50 ± 0.06 amu at half height. Resolution can
also be checked by evaluating isotope ratios.
Sensitivity, SCAN
Typical performance for 50 pg of benzophenone gives a spectrum with a
signal-to-noise ratio of at least 10 to 1 at m/z 183.1 ([MH]+ ion) when the mass
spectrometer is scanned from 80 -- 230 amu.
Sensitivity, SIM
Typical performance for 10 pg of benzophenone gives a spectrum with a
signal-to-noise ratio of at least 10 to 1 when monitoring the [MH]+ ion 183.1 for a
dwell time of 50 msec.
Scan rates
Full spectra can be scanned at rates up to 1500 amu/sec with 0.1-amu mass
resolution.
1-4
Reagent gases
Reagent gases
The following reagent gases and hardware may be required for operation of the CI
accessory with the HP 5972A MSD (depending on user choice of reagent). The
hardware items listed below are available from Matheson and Swagelok. They are
representative of products that are appropriate for the purpose.
Methane (required)
Lecture bottle (0.06 m3, 56 liters), UHP 99.97%
Regulator 3320
Stand, model J05
Swagelok female connector, SS-200-7-2
Ammonia (optional)
Lecture bottle (0.17 kg), anhydrous 99.99%
Regulator 3332
Stand, model J05
Swagelok female connector, SS-200-7-4
Isobutane (optional)
Lecture bottle (0.17 kg), instrument, 99.5%
Regulator 3321 or 3320
Stand, model J05
Swagelok female connector SS-200-7-2
1-5
2
Description, 2-2
Theory of operation, 2-10
System Overview
Chapter 2 ---- System Overview
Description
Description
The HP G1072B Chemical Ionization Accessory allows the HP 5972A MSD to

operate in the positive CI mode and produce high-quality, classical CI spectra,
which include molecular adduct ions. A variety of reagent gases ---- including
methane, ammonia, and isobutane ---- can be used.
The HP G1072B CI accessory contains a CI ion source, parts required for

modifying the GC interface, an interface socket, a reagent gas flow controller, and
associated hardware. Tuning macros are included with the data system software;
they facilitate automatic tuning when PFTBA is used as a calibrant with methane
as the reagent gas.
The CI ion source is relatively easy to install and requires little maintenance.
Because it has so few parts, the ion source is readily disassembled, which makes
routine cleaning easy. Installation requires a slight modification to the GC
interface, but once modified the interface can be used with either EI or CI
operation. Switching back and forth between CI and EI takes less than an hour,
although an 8 -- 12 hour wait is required in order to purge the reagent gas lines
and bake-out contaminants.
To achieve the relatively high source pressure required for CI while still
maintaining a high vacuum in the quadrupole, this CI system has been carefully
optimized for the HP 5972A MSD. Small openings in the source, as well as special
seals along the flow path of the reagent gas, ensure proper system performance.
The CI source, GC interface, reagent gas controller, and tuning macros are
described in more detail in the remainder of this section.
2-2
Description
Ion source
The CI ion source is shown in Figure 2-1; an exploded view is shown in
Figure 2-2. It is similar in most respects to the EI source. However, the CI source
contains only a single filament instead of the two used in the EI source, and it
incorporates changes to the mounting plate, source body, drawout plate, and
drawout cylinder. A new interface socket, which has an insulating seal at the tip,
is also included.
By reducing the diameter of the electron-entrance and ion-exit holes on the CI

source (to 0.5 mm), the conductance of the flow from the ionization volume is
reduced. The repeller is replaced by a mounting plate. Both the source body and
the plate are at ‘‘repeller’’ potential, isolated from the radiator. Slots in the
drawout cylinder and ion-source body provide additional pumpout for the ion
source optics. The polyimide seal in the socket tip ensures a leak-tight seal
between the GC interface and interface socket and electrically isolates the
interface tip from the source.
FILAMENT ASSEMBLY
MOUNTING PLATE
Figure 2-1. CI ion source
2-3
Description
LENS INSULATOR
CI DRAWOUT CYLINDER
CI INTERFACE SOCKET CI SOCKET SEAL
WAVY WASHER
M3 SET SCREW ENTRANCE LENS

FILAMENT ASSEMBLY
M2 × 8L SCREW
ION FOCUS LENS
CI SOURCE BODY
CI DRAWOUT PLATE
M2 × 5L SCREW
MOUNTING PLATE ASSEMBLY
Figure 2-2. CI ion source ---- exploded view
2-4
Chapter 2 — System Overview
Description
GC interface
The GC interface assembly mounts onto the side of the vacuum chamber. One
end of the interface extends into the GC; the other end fits into the socket on the
analyzer. The tip of the interface assembly extends into the ion source chamber.
Installation of the CI ion source requires modification of the standard GC

interface. AU parts required to make the modification are included in the CI
accessory kit: a tee connector, interface tip, and guide tube assembly. The tee
connector provides an inlet for the reagent gas. The interface tip is permanently
swaged over the guide tube to prevent leaks. Details of the modified interface
assembly are shown in Figure 2-3.
REAGENT SUPPLY TUBE

RADIATOR (from Cl flow controller)
SOURCE
CHAMBER
\ GC COLUMN
I Cl INTERFACE SOCKET 1/16 INCH

TUBING NUT
DONUT SEAL
COLUMN FERRULE
G U I D E T U B E GUIDE TUBE/ COLUMN NUT

GUIDE TUBE \
SOCKET SEAL
TIP TIP ASSEMBLY TEE CONNECTOR
Figure2-3. GC interface modified for Cl
2-5
Description
Reagent gas flow controller

The CI reagent gas flow controller provides a means of regulating the flow of
reagent gas to the GC interface. The front and back panels of the controller are
shown in Figures 2-4 and 2-5. A gas-flow schematic is shown in Figure 2-6.
The front panel of the controller contains controls for methane flow, auxiliary
reagent gas flow, and a methane-auxiliary selector. PFTBA calibrant enters
through an automated valve on the back panel. The back panel also provides
inlets for methane and one other reagent gas, as well as an outlet for the line to
the MSD.
When the methane control is on, methane flows from a pressure-regulated

(10 psi, 70 kPa) methane source through a flow control valve, sweeps past the
calibrant valve to the three-way reagent select valve, then out to the GC interface
tee. When the calibration valve is open, PFTBA diffuses into the methane gas
stream, and is carried to the MSD.
The flow controller valves and tubing are stainless steel. They are compatible
with ammonia reagent gas.
2-6
Description
Figure 2-4. Flow controller front panel
Figure 2-5. Flow controller back panel
2-7
Description
IN FROM
PRESSURE REGULATED IN FROM
METHANE SUPPLY PRESSURE REGULATED
(10 PSIG) TO GC INTERFACE AUXILIARY REAGENT
CALIBRATION VALVE
(~100 TORR)
3-WAY REAGENT
SELECT VALVE AUXILIARY FLOW
METHANE FLOW
CONTROLLER CONTROLLER
PFTBA CALIBRANT
RESTRICTOR
Figure 2-6. Reagent gas controller flow diagram
2-8
Description
Tuning macros
Tuning macros and menus are included with the data system software. The
tuning macros provide easy-to-follow instructions for setting the reagent gas flow
and for performing automatic tuning using methane as the reagent gas and
PFTBA as the reference calibrant. No software modifications are required to
support CI operation.
2-9
Theory of operation
Theory of operation
Chemical ionization (CI) is a technique for creating ions used in mass

spectrometric analyses. There are significant differences between CI and
electron-impact (EI) ionization, and, for certain applications, CI offers several
advantages.
In EI, relatively high-energy electrons (70 eV) collide with molecules of the
sample that is to be analyzed. Those collisions produce (primarily) positive ions.
Upon ionization, the molecules of a given substance fragment in fairly constant
patterns (under constant operating conditions), making possible their
identification by the mass spectrometer.
Whereas EI is a direct process in which energy is transferred collisionally from

electrons to sample molecules, CI is a chemical phenomenon. In CI, a mixture of
a reagent gas (often methane) and the sample gas is first ionized by an electron
beam. The ions of the sample are then formed by chemical interactions between
reagent-gas ions and sample molecules.
The ratio of reagent gas to sample is very high; on the order of 1000 to 1 or more.
This ensures sufficient ion-molecule reactions and minimizes direct ionization of
the sample by electron impact. The reagent-gas pressure is likewise relatively
high, usually on the order of 1 Torr. Because of the great number of reagent-gas
molecules relative to sample molecules, the overwhelming majority of the ions
formed by the electron beam are reagent-gas ions. These reagent-gas ions react
with each other, in primary and secondary reaction processes that establish an
equilibrium. They also react in various ways with sample molecules to form
sample ions.
An example of a typical CI spectrum of methyl octanoate is shown in Figure 2-7.

The simple fragmentation pattern, large abundance of the [MH]+ ion, and the
presence of the two adduct ions are characteristic.
2-10
Theory of operation
Although methane is the most frequently used reagent gas for chemical
ionization, other reagent gases offer other capabilities for mass spectrometric
detection. Among the most common of these are isobutane and ammonia. The
less commonly used include hydrogen, trimethylsilane, nitrous oxide, and
methylamine. Different ionization reactions occur with each of these reagent
gases.
There are four fundamental ionization processes that take place during
chemical-ionization mass spectrometry at ion source pressures in the 0.5 -- 1.0
Torr range. These are proton transfer, hydride abstraction, addition, and charge
exchange. Depending on the reagent gas used, one or more of these four
processes can be used to explain the ionization products observed in the resulting
mass spectra.
Figure 2-7. Typical CI spectrum of methyl octanoate
2-11
Theory of operation
Proton transfer
Proton transfer can be expressed as
BH+ + M → MH+ + B
where the reagent gas B has undergone ionization resulting in protonation. If the
proton affinity of the analyte M is greater than that of the reagent gas, then the
protonated reagent gas will transfer its proton to the analyte, thus resulting in the
formation of a positively charged analyte ion.
The most frequently used example of proton-transfer chemical ionization is the

proton transfer from CH5+ to the molecular analyte, which results in formation of
the protonated molecular ion MH+.
The rules that govern the transfer of a proton from the protonated reagent ion to
the molecular analyte can be described using a simple comparison of the proton
affinities of the reagent gas and the analyte. If the analyte has the greater proton
affinity, then the chemical ionization reaction is allowed. It is for this reason that
methane chemical ionization is so commonly used. The proton affinity of CH4 is
sufficiently lower than that of most compounds so as to give almost universal
ionization. Proton affinities can be defined according to the reaction
B + H+ → BH+
where the proton affinities are expressed in kcal/mole. For methane, the proton
affinity is 127 kcal/mole. Table 2-1 lists the proton affinities of several possible
reagent gases.
The spectrum that results from this proton-transfer reaction depends on several
criteria. If the difference in proton affinities is large, which is often the case when
methane is used as the reagent gas, then there is a substantial excess energy
present in the protonated molecular ion, which may result in subsequent
fragmentation. For this reason, isobutane, with a proton affinity of 195 kcal/mole,
may be the preferred chemical-ionization reagent. Notice that ammonia has a
proton affinity of 207 kcal/mole, which makes it less likely to protonate most
analytes. Proton-transfer chemical ionization is considered soft ionization, but
the extent of the ‘‘softness’’ is dependent on the proton affinities of both the
analyte and the reagent gas, as well as on other factors.
2-12
Theory of operation
Table 2-1. Reagent gas proton affinities
Species Proton affinity, kcal/mole Reactant ion formed

H2 100 H3+
CH4 127 CH5+
C2H4 160 C2H5+
H2O 165 H3O+
H2S 170 H3S+
CH3OH 182 CH3OH2+
i-C4H10 195 t-C4H9+
NH3 207 NH4+
Table 2-2 lists the proton affinities of several small organic compounds with
various functional groups.
Table 2-2. Proton affinities of selected organic compounds
Molecule Proton affinity, Molecule Proton affinity,

kcal/mole kcal/mole
Acetaldehyde 185 Methyl amine 211
Acetic acid 188 Methyl chloride 165
Acetone 202 Methyl cyanide 186
Benzene 178 Methyl sulfide 185
2-Butanol 197 Methyl cyclopropane 180
Cyclopropane 179 Nitroethane 185
Dimethyl ether 190 Nitromethane 180
Ethane 121 n-Propyl acetate 207
Ethyl formate 198 Propylene 179
Formic acid 175 Toluene 187
Hydrobromic acid 140 trans-2-Butene 180
Hydrochloric acid 141 Trifluoroacetic acid 167
Isopropanol 190 Xylene 187
Methanol 182
2-13
Theory of operation
Hydride abstraction
In the formation of reagent ions, various reactant ions can be formed that have
high hydride ion (H-) affinities. If the hydride-ion affinity of a reactant ion formed
in the chemical ionization process is higher than the hydride-ion affinity of the ion
formed by the loss of H- of the analyte, then the thermodynamics are favorable,
making this chemical ionization process possible. Examples of this type of
chemical ionization include the hydride abstraction of alkanes in methane
chemical ionization. In the chemical ionization reactions involving methane, both
CH5+ and C2H5+ are capable of hydride abstraction. These species have large
proton affinities, which results in the loss of H- for long-chain alkanes, according
to the general reaction:
R+ + M → [M-H]+ + RH
For example, if R+ is CH5+, the reaction proceeds as follows:
CH5+ + M → [M-H]+ + CH4 + H2
The spectra resulting from hydride abstraction will show an M-1 amu peak
resulting from the loss of H-. Because this reaction is exothermic, fragmentation
of the [M-H]+ ion is often observed.
Often, both hydride-abstraction and proton-transfer ionization can be evident in

the sample spectrum. A case in point is the methane chemical ionization
spectrum of long-chain methyl esters, where both hydride abstraction from the
hydrocarbon chain and proton transfer to the ester function are clearly visible.
2-14
Theory of operation
Addition
For many analytes, proton-transfer and hydride-abstraction chemical ionization
reactions are not thermodynamically favorable. When this is the case, reactant
ions formed by the ionization of the reagent gas are often of sufficient reactivity
to add, either by condensation or association. The resulting ions are often
referred to as adduct ions. Adduct ions are observed in methane chemical
ionization by the presence of [M+C2H5]+ and [M+C3H5]+ ions, which result in
M+29 and M+41 amu mass peaks.
Addition reactions are particularly important in ammonia chemical-ionization

mass spectrometry. Because the NHs has such a high proton affinity, only a
fraction of organic compounds will be able to undergo proton transfer using
ammonia as the reagent gas. In ammonia chemical ionization, a series of
ion-molecular reactions takes place, resulting in the formation of NH4+,
[NH4NH3]+, and [NH4(NH3)2]+. In particular, the ammonium ion, NH4+, will give
rise to an intense [M+NH4]+ ion observed at M+18 amu, either through
condensation or association (clustering). If this resulting ion is unstable,
subsequent fragmentation may also be observed. The neutral loss of H2O or NH3,
observed as a subsequent loss of 18 or 17 amu, respectively, is also common.
2-15
Theory of operation
Charge exchange
Charge-exchange ionization can be described by the reaction
X+• + M → M+• + X
where X+• is the ionized reagent gas, and M is the analyte of interest. Examples
of reagent gases that give rise to this type of ionization include the noble gases
(helium, neon, argon, krypton, xenon, and radon), nitrogen, carbon dioxide,
carbon monoxide, hydrogen, and other gases that do not react ‘‘chemically’’ with
the analyte. Each of these reactant gases, once ionized, has a recombination
energy that is expressed as
X+• + e- → X
or simply the recombination of the ionized reagent with an electron to form a

neutral species. If this energy is greater than the energy required to remove an
electron from the analyte, then the first reaction above is exothermic and
thermodynamically allowed.
Although charge-exchange chemical ionization is significant for some studies, it

has not found widespread use for general analytical applications. It can, however,
be observed in some cases when other chemical ionization processes are not
thermodynamically favored.
2-16
3
Initial mass spectrometer upgrade (overview), 3-3

Preparing the system for CI operation (overview), 3-16
To convert from CI to EI, 3-22
To convert from EI to CI, 3-25
Initial upgrade checklist, 3-28
CI-to-EI-conversion checklist, 3-30
EI-to-CI-conversion checklist, 3-31
Installation
Installation
This chapter provides instructions for installing the HP G1072B CI

Accessory on the HP 5972A MSD and for converting from CI to EI
operation and vice versa. Initial modifications ---- updating the GC
interface and installing the flow controller ---- need be done only once.
Thereafter, only the ion sources and interface sockets have to be
exchanged to convert from EI to CI or from CI to EI. Instructions for
performing these one-time procedures, and for converting from one
operation mode to another, are set out in the sections that follow.
3-2
Chapter 3 ---- Installation
Initial mass spectrometer upgrade (overview)
Initial mass spectrometer upgrade (overview)
This procedure gives an overview of the steps for initial installation of the
HP G1072B CI Accessory on an HP 5972A MSD. Subsequent conversions from EI
to CI require only the shorter procedure listed later in this chapter.
The initial upgrade procedure includes the following tasks:
• To install the CI ion source

• To install the flow controller
• To modify the GC interface
A checklist of the major steps in this procedure is provided near the end of this
chapter. It can be used to keep track of the steps you have completed.
Materials needed Installation of the CI accessory requires the following tools and supplies.
Materials that are not included in the CI accessory shipping kit must be supplied
by the user. See Reagent gases in Chapter 1 for details about reagent gases and
associated hardware.
Reagent-gas regulator
Methane reagent gas
Any other desired reagent gases
Standard wrenches and tools for gas fittings
Gas line fittings for regulator to connect 1⁄8-inch tubing
Screwdriver, Pozidriv #2 (8710-0900)
Open-end wrench, 1⁄2 × 7⁄16-inch (8710-0806)*
Open-end wrench, 1⁄4 × 5⁄16-inch (8710-0510)*
Hex ball driver, 1.5-mm (8710-1570)*
*Furnished with the CI accessory shipping kit (G1072-60006)
3-3
To install the CI ion source
This section describes how to install the CI ion source and the CI interface socket.
1 Perform an EI autotune and save the printed report for future reference. Check
the results for signs of air leaks or water. M/z 18 and m/z 28 should be less than
1% of m/z 69. M/z 18 should be greater than m/z 28. Also note the dc polarity of
the quadrupole.
2 Perform the performance verification procedure listed in the HP 5972A Mass

Selective Detector Installation Manual. Save the printed report for future
reference.
3 Vent the MSD as described in Chapter 2 of the HP 5972A MSD Hardware Manual.
Allow about 60 minutes for cooling and venting.
WARNING The GC interface heater and GC oven operate at dangerously high temperatures. Both
must be given time to cool to near room temperature before you can proceed safely.
4 Carefully slide the MSD far enough away from the GC to allow for removal of the
GC interface.
5 Unplug the GC interface heater cable from the GC (see Figure 3-1).
CAUTION The GC should be turned off before the interface heater cable is unplugged.
3-4
Figure 3-1. Removing the GC interface
6 Remove the KF25 clamp that secures the GC interface to the MSD. Carefully slide
the GC interface out of the vacuum manifold. Place the interface on a clean,
lint-free cloth and set it aside. The GC interface will be modified later.
3-5
7 Remove the top cover of the MSD. Then, disconnect the ribbon cable, filament
supply cable, and detector output cable from the top board (see Figure 3-2).
8 Two clamps secure the top analyzer plate during shipment. If they are in place,
remove them (see Figure 3-2).
9 Lift the analyzer assembly out of the vacuum manifold. Invert the assembly (note
the four rubber bumpers provided on the RF-coil safety cover) and place it on a
clean, convenient work surface.
CAUTION To minimize contamination of analyzer parts, wear clean gloves while performing the
following steps.
Figure 3-2. Top and main board electrical connections
3-6
10 Carefully note the electrical connections between the nine-pin feedthrough and the
pins of the EI ion source so that they can later be reconnected in the same
pattern. Disconnect the wires from the pins on the ion source (see Figure 3-3).
11 Unscrew the interface socket by inserting a suitable rod through the holes on the
socket and turning the socket counterclockwise.
12 Use a 1.5-mm hex ball driver to remove the two mounting screws that attach the
ion source to the radiator.
CAUTION Take care to avoid damaging the two ion source filaments when removing the source
from the analyzer.
INTERFACE SOCKET
Figure 3-3. EI ion source ---- installed
3-7
13 Carefully pull the ion source out of the analyzer.
14 Carefully store the EI ion source, mounting screws, and EI interface socket (the
box the CI ion source comes in works well).
15 Unpack the CI ion source and interface socket.
16 Install the CI ion source in the radiator, using the ion source mounting screws
furnished with the CI assembly (see Figure 3-4). Start the source mounting
screws but do not tighten them.
CAUTION The ends of the source mounting plate are covered with polyimide film to electrically
isolate the source body (which is at repeller voltage) from ground. Do not remove the
insulating film. The CI source must be electrically insulated from the radiator.
Figure 3-4. Installing the CI ion source
3-8
17 Reconnect the electrical leads to the ion source elements. Make the connections
as they were noted in step 10. The two unused wires for the second EI filament
(the DN filament) should be tucked under the radiator (see Figure 3-5).
18 Install the CI interface socket and wavy washer and then tighten the source
mounting screws left loose in step 16. This will ensure a positive seal of the CI
ion source.
If the interface socket cannot be screwed in all the way, check for proper
positioning of the CI socket seal in the hole in the side of the ion source.
19 Reinstall the analyzer onto the vacuum chamber. It is not necessary to reinstall
the shipping clamps.
Figure 3-5. Connecting the ion source leads
3-9
20 Reconnect the detector output cable, ribbon cable, and filament cable to the
appropriate connectors on the top board.
21 Disconnect the EI calibration valve cable from the main board (see Figure 3-6).
Connect the CI calibration valve cable from the flow controller to the connector
on the main board. The location of the flow controller does not matter as long as
the cable can reach the connector.
This completes the installation of the CI ion source. Proceed to the next section,
To install the flow controller.
3-10
Figure 3-6. Calibration valve connector
3-11
To install the flow controller
The reagent-gas flow controller regulates the flow of reagent gas to the GC
interface. For convenience, we recommend that the controller be placed on top
of the GC, toward the rear and away from the heated zones.
1 On the controller front panel, turn the methane and auxiliary flow valves fully
clockwise. Set the reagent select valve to the off position.
2 Connect the 1⁄8-inch end of the reagent line (G1072-80003) to the reagent OUT
connector on the back panel of the flow controller.
3 Remove the left side panel of the GC. If your GC is equipped with an automatic
liquid sampler, you will have to remove it before you can remove the GC side
panel.
4 The other end of the reagent line is 1⁄16-inch diameter with a protective cap.
Route this end along the back of the GC, into and through the flow control
compartment, through the notch into the injection port area and down through
any vacant hole into the GC oven (see Figure 3-7).
5 Reinstall the left side panel of the GC.
6 Set the methane supply pressure to 10 psi (70 kPa).
7 Connect the 2-meter supply line (G1072-80002) between the methane supply and
the methane reagent IN connector on the rear panel of the flow controller.
3-12
REAGENT LINE
FLOW CONTROLLER
TO
METHANE SUPPLY TEE CONNECTOR IN OVEN
SIDE PANEL REMOVED
Figure 3-7. Installing the flow controller
8 If necessary, connect another supply line between another reagent gas supply and
the auxiliary reagent IN connector on the rear panel of the flow controller.
9 At the rear of the flow controller, remove the calibration vial and fill it (to no closer
than 1⁄4-inch of the top) with PFTBA. Reinstall the vial.
Installation of the flow controller is now complete. Proceed to the next section,
To modify the GC interface.
3-13
To modify the GC interface
The GC interface must be modified to accommodate the new CI source. Once

modified, the interface can be used for either CI or EI operation.
1 Unscrew the gold-plated interface tip, and remove the guide tube from inside the
GC interface.
2 Insert the new CI guide-tube assembly into the MSD end of the GC interface and
pass it through the 1⁄16-inch hole at the GC end of the interface. The alignment of
the tube and the 1⁄16-inch hole is facilitated by looking through the GC end of the
interface while holding the interface up to a light source (refer to Figure 3-8).
3 Screw the new guide tube into the MSD end of the interface. Tighten the guide
tube using a 5⁄16-inch wrench. The guide tube should extend 3 to 5 mm beyond
the GC end of the interface.
4 Reconnect the GC interface to the vacuum manifold. Make sure the interface is
properly seated in the interface socket. Reinstall the KF25 clamp.
3 -- 5 mm
Figure 3-8. Installing the guide tube assembly
3-14
5 Reconnect the GC interface heater cable to the GC.
CAUTION The GC power must be off before you reconnect the GC interface heater cable.
Otherwise, the GC fuse may blow.
CAUTION In the next step, exercise care to avoid damaging the protruding guide tube on the GC
interface.
6 Carefully slide the MSD back toward the GC so that the end of the GC interface is
inside the GC oven.
7 Slide the graphitized Vespel ferrule over the GC end of the interface guide tube.
CAUTION Do not use 100% graphite ferrules. Fragments from deteriorating all-graphite ferrules
will clog the transfer line and contaminate the ion source.
8 Screw the male/female tee (0100-1421) onto the end of the GC interface.
9 Attach the 1⁄16-in end of the reagent line to the tee; using a short nut (2740-0015)
and sealing ring (0905-0938).
10 Install your GC column in the GC interface. See Chapter 1 in the HP 5972A MSD
Hardware Manual for more information.
11 Reinstall the MSD cover and reconnect the MSD power cord.
The initial MSD upgrade is now completed. Proceed to the next section,
Preparing the system for CI operation (overview).
3-15
Preparing the system for CI operation (overview)
Preparing the system for CI operation (overview)
After the CI accessory is installed, or after the MSD has been converted from EI
to CI operation, there are a number of steps to complete before the instrument is
ready to be operated.
The following tasks must be completed:
• To configure your software for CI operation

• To pump down the MSD (methane off)
• To purge the methane lines (methane on)
• To purge the calibration lines
• To bake out the system
3-16
To configure your software for CI operation
To configure your software for CI operation
Your data system contains menus and macros for CI operation. To activate these,
reconfigure your data system for CI operation. You only need to reconfigure
once. After that, you can operate in either mode.
MS ChemStation (DOS series)

Use the MS Config program to change the configuration. Its icon is in the
MS ChemStation group of Windows Program Manager. See the documentation
supplied with your ChemStation software for more information.
HP-UX ChemSystem
To change the configuration, open the ChemSystem Menu (root sub-menu). Select
Configure Instrument. The Configuration Panel will be displayed.
3-17
To pump down the MSD (methane off)
To pump down the MSD (methane off)
1 On the flow controller, turn the methane flow valve fully clockwise (low) and the
reagent select valve off.
2 Make sure the MSD, GC, and data system are all plugged in and turned on.
3 From your data system’s vacuum control program, select the pumpdown option to
initiate the pumpdown. When the pumpdown is complete, a message to that
affect will appear on your data system screen. This typically takes about 45
minutes.
4 Set the GC interface (GC detector B or auxiliary temperature zone) and GC oven
to the desired temperatures. Typical temperatures are 280°C for the GC interface
and 100°C for the GC oven.
3-18
To purge the methane lines (methane on)
To purge the methane lines (methane on)
The methane lines are purged to help minimize and delay contamination of the CI
ion source. With the system pumped down, proceed as follows to purge the
methane lines.
1 Make sure the reagent select valve is off. From its fully closed position, open the
methane flow control valve 1⁄2 turn.
2 Use your data system to monitor the foreline pressure. Record the displayed value.
3 Turn the reagent select valve to Methane. Monitor the foreline pressure. It may rise
sharply, even temporarily turning off the diffusion pump. This is normal. Make
sure the diffusion pump turns back on and that the foreline vacuum pressure
drops down to about the same value that was displayed before the valve was
opened.
4 Monitoring the foreline pressure, slowly turn the methane flow valve
counterclockwise until the foreline pressure reading rises 100 -- 150 mTorr above
the reading noted in step 2. Allow a few seconds after each increase in flow for
the foreline pressure to stabilize. Do not exceed 200 mTorr total pressure.
Maintain this flow for at least 60 minutes. Purge for several hours if the
methane supply is more than 2 meters from the flow controller.
5 Once the methane lines are purged, reduce the methane flow until foreline
pressure returns to the level recorded in step 2.
3-19
To purge the calibration valve
To purge the calibration valve
This procedure purges the calibration valve and associated lines of air so there is
no air surge when the calibration valve is used for the first time. This procedure
should be repeated after refilling the calibration vial.
MS ChemStation (DOS series)

From the CITUNE window, select AdjParams. Choose Purge Cal Valve.
HP-UX ChemSystem
From the Tune window, select EditParameters. Choose Purge Cal Valve.
3-20
To bake out the system
To bake out the system
Each time you convert from EI to CI operation, it is essential that you purge the
methane lines for 1 hour and bake out the system for at least 8 hours before
you turn on the analyzer. This will minimize ion source contamination.
CAUTION Failure to adequately purge and bake out the system will result in the almost instant
contamination of the ion source when the analyzer is turned on. This will result in few or
no peaks. You will then have to vent the MSD and clean the ion source.
To bake out the system, set the GC interface temperature to 280°C and the GC
oven temperature to 100°C. Keep the system at these temperatures for at least 8
hours.
CAUTION Carrier gas should be flowing to prevent column damage during bakeout.
When bake-out is complete, proceed to the next chapter, Operation, for

information about CI tuning and related procedures.
3-21
To convert from CI to EI
After the initial installation of the CI accessory, conversion between the two
ionization modes (EI and CI) is simpler. It consists primarily of replacing the ion
source.
1 Perform a CI tune and save a printed copy of the results.
2 Turn off the reagent gas at the supply tank and set the reagent select valve on the
flow controller to Off.
WARNING If both of these valves are not closed, methane can leak into the GC oven creating the
potential for an explosion.
3 Initiate the MSD vent cycle. Allow about 60 minutes for venting.
WARNING The GC interface heater and GC oven operate at dangerously high temperatures. Both
must cool to near room temperature before you can proceed safely.
4 The vent program will display a message when it is complete. After the message
appears, turn off the MSD power switch.
5 Remove the GC capillary column from the GC interface. This will bring the MSD up
to atmospheric pressure.
6 Disconnect the reagent supply tube from the tee on the GC interface. Remove the
tee from the end of the GC interface.
3-22
7 Carefully move the MSD far enough away from the GC to allow the removal of the
GC interface.
the interface out of the vacuum manifold. Place the interface on a clean, lint-free
cloth and set it aside.
9 Remove the top cover of the MSD. Disconnect the ribbon cable, filament supply
cable, and detector output cable from the top board.
10 Lift the analyzer assembly out of the vacuum manifold. Invert the assembly and
place it on a clean, convenient work surface.
following steps.
11 Unscrew and remove the CI interface socket and washer.
12 Carefully note the electrical connections between the nine-pin feedthrough and the
pins of the ion source so that they can later be reconnected in the same pattern.
Disconnect the wires from the pins on the ion source.
13 Remove the CI ion source. Be careful to not damage the filament.
14 Carefully store the CI ion source, mounting screws, CI interface socket, and washer.
15 Install the EI ion source, using the EI ion source mounting screws.
16 Reconnect the electrical leads to the ion source elements (refer to step 12). Be
sure to connect the additional pair of filament leads that are not used in CI.
17 Install the EI interface socket and washer (the EI socket is identifiable by the
absence of wrench flats).
3-23
18 Reinstall the analyzer and reconnect the ribbon cable, filament cable, and detector
output cables to the top board.
19 Disconnect the CI calibration valve cable from the main board; connect the EI
calibration valve cable.
20 Use a 5⁄16-inch open-end wrench to retighten the guide tube.
21 Carefully reconnect the GC interface to the MSD. Make sure the interface is seated
properly in the interface socket. Install and tighten the KF25 clamp.
22 Reinstall the MSD top cover.
23 Carefully slide the MSD toward the GC so that the end of the GC interface is inside
the GC oven.
24 Install a new donut ferrule on the guide tube, then install a new tee (supplied) on
the GC interface. Old tees can be reused by first carefully removing the old
ferrule using the 2-56 tap and pin vise included in the shipping kit.
25 Cap the reagent line inlet with a column nut and blank ferrule.
26 Install your GC column as described in Chapter 1 of the HP 5972A MSD Hardware

Manual.
27 Turn on the MSD. Initiate the pumpdown procedure.
28 Set the GC interface temperature to 280°C and set the GC oven temperature to
100°C. Allow the system to bake out for 4 -- 8 hours.
CAUTION Carrier gas should be flowing to prevent column damage during bakeout.
3-24
To convert from EI to CI
After the initial installation of the CI accessory, conversion between the two
ionization modes (EI and CI) is simpler. It consists primarily of replacing the ion
source.
1 Perform an EI autotune and save the printed report.
2 Initiate the MSD vent cycle. Allow about 60 minutes for venting.
WARNING The GC interface heater and the GC oven operate at dangerously high temperatures.
Both must cool to near room temperature before you can proceed safely.
3 The vent program will display a message when it is complete. After the message
appears, turn off the MSD power switch.
4 Remove the capillary column from the GC interface. This will bring the MSD up to
atmospheric pressure.
5 Remove the tee from the GC end of the GC interface.
6 Carefully move the MSD far enough away from the GC to allow the removal of the
GC interface.
the interface out of the vacuum manifold. Place the interface on a clean, lint-free
cloth and set it aside.
8 Remove the top cover of the MSD. Then, disconnect the ribbon cable, filament
supply cable and detector output cable from the top board.
9 Lift the analyzer assembly out of the vacuum manifold. Invert the assembly and
place it on a clean, convenient work surface.
3-25
following steps.
10 Unscrew and remove the EI interface socket and washer.
11 Carefully note the electrical connections between the nine-pin feedthrough and
the pins of the ion source so that they can later be reconnected in the same
pattern. Disconnect the wires from the pins on the ion source.
12 Remove the EI ion source. Be careful to not damage the filaments.
13 Carefully store the EI ion source, mounting screws, EI interface socket, and
washer (the container for the CI source and socket makes a convenient
storage box).
14 Check the alignment of the filament on the CI source. The filament is properly
aligned when it crosses the center of the small electron-inlet hole in the source
body. If necessary, use tweezers to adjust the filament alignment.
15 Install the CI source using the mounting screws furnished with the CI assembly
(the screws are longer than those used with the EI source). Start the source
mounting screws but do not tighten them. The ends of the source mounting plate
are covered with polyamide film to electrically isolate the source body (which is
at repeller voltage) from ground; be sure the insulating film is in place. The CI
source must be electrically insulated from the analyzer.
16 Reconnect the electrical leads to the ion source elements, being careful to make
the connections as they were noted in step 11. The two unused wires for the
second EI filament (the DN filament) should be tucked under the radiator.
17 Install the CI interface socket and wavy washer and then tighten the source
mounting screws left loose in step 15. This will ensure a positive seal of the CI
ion source. If the CI interface socket cannot be screwed in all the way, check for
proper positioning of the CI socket seal in the hole in the side of the source body.
3-26
18 Reinstall the analyzer and reconnect the ribbon cable, filament cable, and detector
output cable to the top board.
19 Disconnect the EI calibration valve cable from the main board; connect the CI
calibration valve cable.
20 Use a 5⁄16-inch open-end wrench to retighten the guide tube.
21 Carefully reconnect the GC interface to the MSD. Make sure the interface is seated
properly in the interface socket. Install and tighten the KF25 clamp.
22 Reinstall the MSD top cover.
23 Carefully slide the MSD back toward the GC so that the end of the GC interface is
inside the GC oven.
24 Install a new donut ferrule on the guide tube, then install a new tee (supplied) on
the GC interface. Old tees can be reused by first carefully removing the old
ferrule using the 2-56 tap and pin vise included in the shipping kit.
25 Connect the reagent supply line to the tee. Make sure that the tubing has not been
deformed or crimped.
26 Install your GC column as described in Chapter 1 of the HP 5972A MSD Hardware

Manual.
27 Make sure the reagent select valve on the flow controller is off, then open the
methane supply regulator. It should be set to 10 psi (70 kPa).
28 Turn on the MSD.
The EI to CI conversion is now complete. Proceed to the section, To prepare the

system for CI operation (overview), earlier in this chapter.
3-27
Initial upgrade checklist
The following checklist provides a convenient summary of the essential steps in

the initial installation of the HP G1072B Chemical Ionization Accessory. This list
is not a substitute for the step-by-step procedures listed previously in this chapter.
Materials needed
Methane (bottle and regulator), 99.97% pure
Fittings and tools for attaching 1⁄8-inch tubing
Other reagent gases, tubing, fittings, and tools
CI accessory shipping kit

Run EI autotune. Save a printout of the results
Run the performance evaluation procedure from the HP 5972A MSD
Installation Manual. Save a printout of the results
Shut down and vent the MSD
Remove the GC column
Slide the MSD away from GC
Remove the GC interface
Remove the analyzer
Remove the EI interface socket
Remove the EI ion source
Install the CI ion source
Install the CI interface socket
Reinstall the analyzer
Disconnect the EI calibration valve cable and connect the CI calibration
valve cable
3-28

Turn all valves off
Connect line to flow controller and route into oven
Set methane supply to 10 psi
Connect line from methane supply to flow controller
Connect other reagent gas to flow controller (optional)
Fill PFTBA vial

Remove the original GC interface guide tube and tip
Install the new GC interface guide tube assembly
Tighten tip
Reinstall the GC interface
Slide the MSD back to its normal position
Install the tee fitting on the end of the GC interface
Connect the reagent gas supply line to the tee
Install the GC column in the GC interface
To prepare the system for CI operation

Configure the data system for CI operation
Pump down the MSD
Purge the reagent gas lines for at least 60 minutes
Purge the calibration valve
Bake out the system for at least 8 hours
Operation (see the Operation chapter)

Set dc polarity of quadrupole to that of the last EI autotune
Coarse-adjust the methane flow
Perform a methane pretune
Fine-adjust the methane flow
Tune for CI
Perform analysis of GC/MS evaulation sample (optional)
3-29
CI-to-EI-conversion checklist
CI-to-EI-conversion checklist

converting an HP 5972A MSD equipped with the HP G1072B CI Accessory from
the CI operation mode to the EI operation mode. This list is not a substitute for
the step-by-step procedures listed previously in this chapter.
Perform a CI tune and save a printout of the result

Turn off all reagent gas valves
Vent the MSD and turn it off
Remove the GC column from the GC interface
Remove the tee connector
Slide the MSD away from the GC
Remove the analyzer
Remove the CI interface socket
Remove the CI ion source
Install the EI ion source
Install the EI interface socket
Disconnect the CI calibration valve cable and connect the EI calibration valve
cable
Tighten the tip on the GC interface
Move the MSD to its normal position
Install the tee connector on the GC interface
Cap the reagent gas inlet on the tee connector
Turn on the MSD
Pump down the MSD
Bake out the system for 4 -- 8 hours
3-30
EI-to-CI-conversion checklist

converting an HP 5972A MSD equipped with the HP G1072B CI Accessory from
the EI operation mode to the CI operation mode. This list is not a substitute for
the step-by-step procedures listed previously in this chapter.
Perform an EI autotune and save a printout of the result

Vent the MSD and turn it off
Remove the GC column from the GC interface
Remove the tee connector
Slide the MSD away from the GC
Remove the analyzer
Remove the EI interface socket
Remove the EI ion source
Check the alignment of the CI ion source filament
Install the CI ion source
Install the CI interface socket
Disconnect the CI calibration valve cable and connect the EI calibration valve
cable
Tighten the tip on the GC interface
Move the MSD to its normal position
Install the tee connector on the GC interface
Connect the reagent gas line to the tee connector
Turn on the MSD
3-31
Preparing the system for CI operation

Pump down the MSD
Purge the methane lines for at least 60 minutes
Purge the calibration valve
Bake out the system for at least 8 hours
3-32
4
To set the methane flow, 4-3

To perform a CI tune, 4-7
To verify system performance, 4-10
To use other reagent gases, 4-15
Operation
Operation
This chapter provides information and instructions about operating an

HP 5972A MSD equipped with the HP G1072B Chemical Ionization
Accessory. Most of the material is related to methane chemical ionization
but one section discusses the use of other reagent gases. The following
topics are covered in this chapter:
• Setting the methane reagent gas flow to optimize the pressure in the
CI source
• CI tuning
• Using the evaluation sample to demonstrate system performance
• Using reagent gases other than methane
Polarity If this is the first time your ChemStation is being used for CI, you must
specify which quadrupole polarity is to be used. In CI Tune, enter the
quadrupole dc polarity used in the last EI autotune report.
4-2
Chapter 4 ---- Operation
To set the methane flow
The methane reagent flow must be set before tuning the CI system. Adjusting the
methane flow is a three-step process. A coarse adjustment is made based on
foreline pressure. The MSD is pre-tuned on methane reagent ions. A fine
adjustment is then made based on the ratio of m/z 27/28.
You data system is equipped with a macro to simplify the methane flow
adjustment. The same results can be achieved by using the following procedures:
CAUTION The calibration valve must be CLOSED during methane pretune and fine adjustment.
Coarse adjustment
Coarse adjustment of the methane flow is accomplished by monitoring the
foreline pressure while adjusting the methane flow.
1 Set the reagent select valve to Off.
2 Record the foreline pressure (allow 1 minute for the pressure to stabilize).
3 Turn the reagent select valve to Methane. Adjust the methane flow until the foreline
pressure is 20 -- 40 mTorr higher than it was with the methane flow off.
4-3
Methane pretune
The methane pretune tunes the instrument for optimum monitoring of the
methane reagent ion 27/28 ratio. That ratio is monitored during the fine
adjustment of the methane flow. Follow these steps:
1 Use the manual tune program to monitor masses 17, 29, and 41 (see Figure 4-1).
CAUTION 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.
The abundance of m/z 19 should be no more than twice the abundance of m/z 17.
M/z 19 is the protonated ion of water.
2 Adjust the mass offset of the peak at m/z 29 until it is 29.0 ± 0.1.
3 Adjust the amu offset until the width of the peak width at m/z 29 is 0.5 ± 0.05.
4 Adjust the electron multiplier voltage for maximum abundance of m/z 29. This
should be around 250,000 counts.
4-4
Figure 4-1. Ions monitored for methane adjustment
4-5
Fine adjustment
Fine adjustment of the methane flow is accomplished by monitoring the methane
reagent 27/28 ion ratio. This ratio is inversely related to the foreline vacuum
pressure (see Figure 4-2). To increase the 27/28 ratio, decrease the methane
flow; to decrease the ratio, increase the methane flow. A 27/28 ratio of about 0.2
to 0.4 verifies that the source pressure is optimum for CI operation.
CAUTION Turn the methane control valve slowly, about an eighth of a turn at a time. After each
change of the valve setting, wait a few seconds to allow time for the flow to stabilize.
CAUTION If you have increased the foreline pressure more than 40 -- 50 mTorr over the starting
pressure, and the ratio is still too high, there is probably a leak in the methane delivery
path. Find and correct the leak and then repeat this procedure.
Figure 4-2. Relationship of ion ratio and pressure
4-6
To perform a CI tune
After the reagent gas flow is adjusted, the lenses and electronics of the mass
spectrometer can be tuned. As with EI operation of the HP 5972A MSD,
perflourotributylamine (PFTBA) is used as the calibrant. However, instead of
flooding the entire vacuum chamber with PFTBA (as in EI operation), the PFTBA
is introduced directly into the ion source chamber through the GC interface by
means of the methane reagent gas flow.
CI tuning is usually accomplished with CI autotune, an automated CI tuning

program. It is initiated by selecting CI Autotune from the Tune menu on a
DOS-series ChemStation or by selecting CI Autotune from the Autotunes menu on an
HP-UX ChemSystem.
CI tuning can also be accomplished with the manual tune program. Use the
following initial settings for manual CI tuning. These are the same values used by
the CI autotune program.
Tune parameter Parameter abbreviation Initial setting

Filament Fil 1
Emission EMI 50
Repeller Rep 4
Ion focus Focus 65
Entrance lens gain Entr 0
Entrance lens offset Entl 20
Dc polarity Dc From last tune
Amu gain Amug From last tune
Amu offset Amuo From last tune
219 width adjustment 219W From last tune
True total ion mode TTI 0 (Off)
Electron multiplier Emv From last tune
X-ray Xray From last tune
Calibration valve ---- Off
Tune masses ---- 69, 219, 414
4-7
Proceed as follows to manually tune for CI operation. These steps are very
similar to those used in the CI autotune programs. The result of this manual
tuning should be similar to the automated tune report on the following page.
1 Check that the methane reagent 27/28 ion ratio is still in range (0.2 to 0.4).
2 Open the calibration valve and allow time for settling (20 - 60 sec). Settling can be
observed by monitoring the abundance of the reagent gas ion at m/z 41.
3 Set the tune (PFTBA) masses to m/z 69, 219, and 414.
4 Locate and obtain a threshold abundance (well-defined mass peaks) for the tune
peaks. Do not use the standard Threshold command.
5 Adjust the EMV for a mass 414 abundance of 25,000 -- 40,000.
6 Adjust the peak widths to 0.5 amu, using masses 69 and 414.
7 Calibrate the mass axis.
8 Set the entrance lens gain to 0 and optimize the entrance lens offset setting for
maximum 414 abundance.
9 Optimize the ion focus setting for maximum 414 abundance.
10 Optimize the entrance lens offset for maximum 414 abundance.
12 Optimize the X-ray setting for maximum 414 abundance.
13 Adjust the 219 width setting for linear peak widths across the tune range.
17 Calibrate the mass axis.
18 Turn off the calibration valve.
19 Save the tune file as citune.u.
The m/z 70 isotope abundance reported during CI tuning is inaccurate because of

reagent ions at approximately the same mass. These additional ions can, in fact,
result in a scan abundance of 0 at m/z 70. This is normal.
4-8
4-9
To verify system performance
The GC/MS evaluation sample A (05970-60045) is provided with each HP G1072B

CI Accessory. The sample can be used to verify that your system is functioning
correctly and will generate chromatograms and CI spectra.
For DOS-series MS ChemStation users, a CI method file (CI.M) has been included
in the software upgrade disk. For users of other data systems, the same
parameters can easily be entered.
GC parameters
Column: HP-5MS 30 m × 0.25 mm × 0.25 µm
Injection port temperature: 250°C
Initial oven temperature: 70°C

Initial isothermal time: 1.5 min
Oven ramp rate: 25°C/min
Final oven temperature: 285°C (hold for 2 min)
GC interface temperature: 280°C
Injection volume: 1 µl of 10-ng/µl GC/MS evaluation sample A
MSD parameters
Scan mode
23 samples
Scan range: 75 -- 320 amu
4-10
Evaluating the results

Once the analysis is complete, you can use the data analysis program to examine
the results. The results shown in this section are typical but there is no
guarantee that your results will be identical. Results depend on the tuning and
condition of the MSD, condition of the GC and related components, and many
other factors.
Chromatogram
A total ion chromatogram should show four widely separated peaks (see
Figure 4-3). Each peak should rise well above the baseline noise but the
abundances of these peaks may differ significantly from the abundances shown in
Figure 4-3. The retention times may also differ from those shown. In order, the
peaks represent dodecane, biphenyl, p-chlorobiphenyl, and methyl palmitate; the
four constituents of the evaluation sample.
Mass spectra
Mass spectra for each of the four chemicals are shown in Figures 4-4 through 4-7.
Your spectra will probably not be identical to these; relative abundances and
retention times may differ and some of the smaller peaks may not be present. If
your results differ radically from those shown, it may be necessary to
troubleshoot the system.
4-11
Figure 4-3. Chromatogram of evaluation sample A
4-12
Figure 4-4. Mass spectrum of dodecane
Figure 4-5. Mass spectrum of biphenyl
4-13
Figure 4-6. Mass spectrum of p-chlorobiphenyl
Figure 4-7. Mass spectrum of methyl palmitate
4-14
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 HP 5972A MSD with methane
reagent gas before attempting to use other reagent gases.
CAUTION 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 were described in general in the
Theory of operation section in Chapter 2. If you are not experienced with
chemical ionization, we suggest reviewing that material before you proceed.
From an operations standpoint, two changes are necessary to perform GC/MS

analyses with an alternative reagent gas. First, the MSD must be properly tuned.
Second, if selected ion monitoring is to be used, appropriate ions must be
selected based on the chemistry of the alternative reagent gas.
Tuning the instrument for an alternative reagent gas is a two-step process. The
instrument must first be tuned using methane and the standard PFTBA calibrant.
This ensures that the ion source lenses are optimized and that the resolution and
mass assignments are correct. With this standard set of tune conditions satisfied,
tuning for an alternative reagent gas generally requires only that the new reagent
gas be adjusted to the optimum pressure.
4-15
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.
To adjust your MSD for isobutane chemical ionization, use the following
procedure:
1 Perform a standard CI tune with methane and PFTBA.
2 Switch the reagent select valve from Methane to Off. Allow several seconds for the
foreline pressure to settle. The new pressure is the base pressure without
chemical ionization reagent gas. If this is the first time you have used an auxiliary
reagent gas, shut off the auxiliary reagent flow valve; otherwise, leave this valve
set to its previously adjusted position.
3 Set the regulator on the isobutane supply to 3 -- 10 psi (20 -- 70 kPa).
4 Record the base foreline pressure and then turn the reagent select valve to
auxiliary. There will probably be a pressure surge due to gas in the supply lines,
but this pressure should quickly equilibrate back into the normal operating range.
5 Adjust the isobutane flow until the foreline pressure is about 30 mTorr higher than
the base pressure.
6 Scan over the 10 -- 60 amu mass range. The principal isobutane ion is at m/z 57
with lesser ions at m/z 39 and m/z 43 (see Figure 4-8). Other peaks may be
present when switching from one reagent gas to another. Peaks at m/z 17, 29,
and 41 indicate residual methane in the system. Allow the isobutane to flow until
the methane has decreased and the spectrum is predominantly isobutane.
4-16
Figure 4-8. Isobutane spectrum
7 Set the tune masses to 57, 43, and 39 (see Figure 4-9). It will probably be
necessary to decrease the electron multiplier voltage by several hundred volts.
8 Adjust the flow of the isobutane until the ion ratios of 39/57 and 43/57 are both at
or below 10%. Fine-adjust the flow until the abundances of m/z 39 and m/z 43
are within a factor of 2 of each other. At that point, the isobutane flow should be
correct and the system ready for use.
When exiting the CI tune program, do not save the tune file. Saving the tune
file will overwrite the parameter settings (such as the electron multiplier voltage)
in the methane/PFTBA tune file. The methane/PFTBA parameter settings are
still required for data acquisition, even though you will be using a reagent gas
other than methane.
4-17
Figure 4-9. Tuning for isobutane
4-18
Ammonia CI
Ammonia is commonly used for chemical ionization when less fragmentation is
desired in the chemical ionization spectrum. This is because the proton affinity of
ammonia is higher than that of methane; hence, less energy is transferred in the
ionization reaction. Because many compounds of interest have insufficient
proton affinities, ammonia chemical-ionization spectra often result from the
addition of NH4+ and then, in some cases, from the subsequent loss of water.
Ammonia reagent ion spectra have principal ions at m/z 18, 35, and 52,
corresponding to NH4+, NH4(NH3)+, and NH4(NH3)2+.
CAUTION The pellets in the foreline trap must be replaced with stainless steel wool before
ammonia is used as a reagent gas. Use of ammonia affects the maintenance
requirements of the MSD. See Ammonia CI in Chapter 6 for more information.
To adjust your MSD for ammonia chemical ionization, use the following procedure:
1 Perform a standard CI tune with methane and PFTBA.
2 Switch the reagent select valve from Methane to Off. Allow several seconds for the
foreline pressure to settle. The new pressure is the base pressure without
chemical ionization reagent gas. If this is the first time you have used an auxiliary
reagent gas, shut off the auxiliary reagent flow valve; otherwise, leave this valve
set to its previously adjusted position.
3 Set the regulator on the ammonia supply to 3 -- 10 psi (20 -- 70 kPa).
4 With the base foreline pressure recorded, turn the reagent select valve to auxiliary.
There will probably be a pressure surge due to gas in the supply lines, but this
pressure should quickly equilibrate back into the normal operating range.
5 Adjust the ammonia flow until the foreline pressure is about 30 mTorr over the
base pressure.
4-19
6 Scan over the 10 -- 60 amu mass range. The principal ammonia ions are at m/z 18,
35, and 52 (see Figure 4-10). Peaks at m/z 17, 29, and 41 indicate residual
methane in the system. Allow the ammonia to flow until the methane has
decreased and the spectrum is predominantly ammonia.
7 Set the tune masses to 18, 35, and 52 (See Figure 4-11). It may be necessary to
decrease the electron multiplier voltage by several hundred volts.
8 Adjust the flow of the ammonia until the ion ratio of 35/18 is 10% or more with
m/z 52 present. At that point, the ammonia flow should be correct and the
system ready for use.
When exiting the CI tune program, do not save the tune file. Saving the tune
file will overwrite the parameter settings (such as the electron multiplier voltage)
in the methane/PFTBA tune file. The methane/PFTBA parameter settings are
still required for data acquisition, even though you will be using a reagent gas
other than methane.
Figure 4-10. Ammonia spectrum
4-20
Figure 4-11. Tuning for ammonia
4-21
5
Pressure-related symptoms (overview), 5-3

Temperature-related symptom (overview), 5-9
Tuning-related symptoms (overview), 5-20
Error message, 5-30
Leaks, 5-31
Troubleshooting
Troubleshooting
This chapter outlines the troubleshooting of HP 5972A MSDs equipped

with the HP G1072B CI Accessory. Most of the troubleshooting
information in the HP 5972A MSD Hardware Manual (05972-90001)
also applies to MSDs equipped with the CI accessory.
5-2
Chapter 5 ---- Troubleshooting
Pressure-related symptoms (overview)
Pressure-related symptoms (overview)
The following symptoms are all related to foreline pressure or high vacuum
pressure. Foreline pressure can be monitored through the data system. High
vacuum pressure can only be monitored if your MSD is equipped with the
optional high vacuum gauge. Each symptom is discussed in more detail in the
following pages.
• Foreline pressure >100 mTorr without reagent gas flow

• Foreline pressure >130 mTorr with reagent gas flow
• Foreline pressure does not change when reagent flow is changed
• Large high vacuum pressure fluctuations
5-3
Foreline pressure > 100 mTorr without reagent gas flow
Foreline pressure > 100 mTorr without reagent gas flow
Possible Cause Excess water in the background.
Action Scan from 10 -- 40 amu. A large peak at m/z 19 indicates water in the
background. If water is present, allow the instrument to bake out more and flow
reagent gas through the lines to purge any accumulated water.
Possible Cause Air leak.
Action Scan from 10 -- 40 amu. A peak at m/z 32 may indicate air in the system. Check
for and correct any leaks. See the Leaks section at the end of this chapter.
Possible Cause GC carrier gas supply (usually helium) is empty, the carrier gas lines are leaking,
or the carrier gas flow rate is too high.
Action Make sure the carrier gas supply is not empty and is set to the correct flow rate.
If the problem continues, check for and repair any leaks in the carrier gas lines.
Possible Cause The trap on the foreline pump is saturated.
Action Replace the trap element as described in the Maintaining the MSD chapter of
the HP 5972A MSD Hardware Manual.
Possible Cause The foreline pump is not working properly.
Action Replace the pump oil. If that does not help, it may be necessary to replace the
pump. Contact your local Hewlett-Packard Customer Engineer.
CAUTION Chemical ionization with ammonia can shorten the life of the foreline pump oil and
possibly of the foreline pump itself. See the Maintenance chapter in this manual.
5-4
Foreline pressure >130 mTorr with reagent gas flow
Foreline pressure >130 mTorr with reagent gas flow
Possible Cause The reagent gas flow rate is too high.
Action On the flow controller, turn down the methane flow control or the auxiliary flow
control as appropriate.
Action Scan from 10 -- 40 amu. A peak at m/z 32 may indicate air in the system. Check
for and repair any leaks. See the Leaks section at the end of this chapter for
more information.
Possible Cause The interface socket in not seated properly.
Action Remove and reinstall the interface socket.
5-5
Foreline pressure does not change when reagent flow is changed
Foreline pressure does not change when reagent flow

is changed
Possible Cause The reagent select valve is set to Off or set to the wrong reagent.
Action Make sure the position of the reagent select valve corresponds to the reagent gas
you are trying to adjust. In other words, make sure the valve is not set to
Auxiliary when you are trying to adjust the methane flow.
Possible Cause You are adjusting the wrong flow control valve.
Action Make sure you are adjusting the flow control valve that corresponds to the
reagent gas you are using.
Possible Cause The reagent gas regulator is closed.
Action Check and, if necessary, open the reagent gas regulator.
Possible Cause The reagent gas regulator is set to the wrong pressure.
Action Set the reagent gas regulator to 10 psi (70 kPa) for methane or to 3 -- 10 psi
(20 -- 70 kPa) for isobutane or ammonia.
Possible Cause The valve on the reagent gas bottle is closed.
Action Check and, if necessary, open the valve on the reagent gas bottle.
Possible Cause The reagent gas supply is empty.
Action Check and if necessary refill or replace the reagent gas supply.
5-6
Foreline pressure does not change when reagent flow is changed
Possible Cause Reagent lines kinked, bent, pinched, or disconnected.
Action Inspect the reagent lines and repair any defects. Check especially to make sure
the reagent line is connected to the tee connector on the end of the GC interface.
Possible Cause Tee connector, guide tube, or inlet tip clogged.
Action Check for flow and repair or replace components as indicated.
5-7
Large high-vacuum pressure fluctuations
Large high-vacuum pressure fluctuations
Large high-vacuum pressure fluctuations can be observed directly if your MSD is

equipped with the optional high vacuum gauge. It is also indicated by a noisy
background signal.
Possible Cause The diffusion pump is overfilled.
Action Check and, if necessary, adjust the diffusion pump oil level. See the chapter
Maintaining the MSD in the HP 5972A MSD Hardware Manual for details.
5-8
Temperature-related symptom (overview)
Temperature-related symptom (overview)
This section describes problems that can be detected through incorrect

temperatures in the heated zones of the MSD. Temperatures can be monitored
through the data system. Refer to the Temperature symptoms section in the
chapter Troubleshooting the MSD of the HP 5972A MSD Hardware Manual for
more information about how the various parts of the MSD are heated and what
normal temperatures can be expected.
The following symptom is covered in this section:
• GC interface temperature OK but analyzer temperature too low
5-9
GC interface temperature OK but analyzer temperature too low
GC interface temperature OK but analyzer temperature

too low
Possible Cause The interface socket is loose or not installed.
Action Inspect the interface socket. If necessary, install a socket or tighten the socket
that is installed.
Possible Cause The guide tube is loose.
Action Inspect the guide tube in the GC interface. If it is loose, tighten it with a 5⁄16-inch
wrench.
5-10
Signal-related symptoms (overview)
Signal-related symptoms (overview)
This section describes symptoms related to the signal. The symptom may be too
much signal, too little signal, a noisy signal, or an incorrect signal. Signal-related
symptoms are generally observed during tuning but may also be observed during
data acquisition.
The following symptoms are covered in more detail in this section:
• No or low reagent gas signal

• No or low PFTBA signal
• Excessive noise/low signal-to-noise ratio
• Large peak at m/z 19
• Peak at m/z 32
5-11
No or low reagent gas signal
Possible Cause The reagent flow is set too low.
Action Increase the reagent flow.
Possible Cause The ion source is dirty.
Action Clean the ion source. See the Maintenance chapter in this manual for more
information.
Possible Cause Clogged tee connector or guide tube.
Action Check the tee connector and guide tube for flow. If necessary, repair or replace
the components.
Possible Cause Reagent gas line blocked, kinked, pinched, or disconnected.
Action Inspect and, if necessary, repair or replace the reagent gas supply line.
Possible Cause Wrong filament wires connected to filament or wrong filament selected.
Action Make sure that the filament 1 wires (also know as filament B or the UP filament)
are connected to the CI ion source filament and that filament 1 is selected in the
data system software.
Possible Cause Carbon has built up on the filament.
Action Inspect the filament. If necessary, replace the filament.
5-12
Possible Cause Too much air or water in the system.
Action Scan from 10 -- 40 amu. Peaks at m/z 32 and 19 frequently indicate air and water,
respectively. Bake out and purge the instrument until the peak at m/z 32
disappears and the peak at m/z 19 is reduced to a very low level. If the peak at
m/z 32 does not decrease, an air leak is indicated. See the Leaks section at the
end of this chapter for more information.
Possible Cause The filament or filament support is shorted to the ion source body or repeller.
Action Inspect the filament. If necessary, realign the filament support arms.
Possible Cause The electron inlet hole is blocked.
Action Inspect the electron inlet hole. If necessary, clean the hole with the supplied
0.016-inch drill bit. If the electron inlet hole is that dirty, the entire ion source
probably needs to be cleaned. See the Maintenance chapter later in this manual
for more information.
Possible Cause The ion focus and entrance lens wires are reversed.
Action Inspect the wires to the ion focus and entrance lenses. If the connections are
reversed, correct the problem.
Possible Cause The repeller lead is not connected.
Action Inspect the repeller. Make sure the repeller lead is firmly attached to the repeller.
Possible Cause The repeller is shorted to the radiator.
Action Inspect the insulating films that isolate repeller the mounting plate from the
radiator. Look for conductive particles or tears in the films. If necessary, replace
the insulating films.
5-13
Possible Cause The signal cable is not connected.
Action Check and, if necessary, reconnect the signal cable.
Possible Cause One of the electron multiplier leads (in the vacuum manifold) is not connected.
Action Check and, if necessary, reconnect the electron multiplier leads.
5-14
No or low PFTBA signal
Possible Cause No PFTBA in the calibration vial.
Action Inspect the calibration vial on the back of the flow controller. If necessary, fill the
vial with PFTBA. Do not fill the vial completely; keep the level at least 1⁄4-inch
from the top of the vial.
Possible Cause The calibration valve was not purged after it was refilled.
Action Purge the calibration valve as described in To prepare the system for CI
operation in the Installation chapter of this manual.
Possible Cause The calibration valve was overfilled. Excess PFTBA can quench the chemical
ionization reactions.
Action Check the level of the PFTBA in the calibration vial; the level should be at least
1⁄4-inch from the top of the vial. If the vial is overfilled, remove some of the
PFTBA. Reinstall the vial and purge the calibration valve as described in
To prepare the system for CI operation in the Installation chapter of this
manual.
Possible Cause The pressure of the methane entering the flow controller is too high.
Action Make sure the regulator on the methane supply is set to 10 psi (70 kPa).
Possible Cause The CI ion source is dirty.
information.
5-15
Possible Cause The cable for the CI calibration valve (on the back of the flow controller) was not
connected to the appropriate connector on the main board.
Action Remove the MSD covers. Make sure the cable from the EI calibration valve was
disconnected from the main board and that the cable from the CI calibration valve
is connected to the back side of the main board below the EI calibration valve.
5-16
Excessive noise/low signal-to-noise ratio
Excessive noise/low signal-to-noise ratio
Possible Cause The diffusion pump is overfilled.
Action Check the diffusion pump oil level. If necessary, drain some of the oil. See the
chapter Maintaining the MSD in the HP 5972A MSD Hardware Manual for
more information.
5-17
Large peak at m/z 19
Large peak at m/z 19
If the abundance of the peak at m/z 19 is more than twice the abundance of the
peak at m/z 17 or of the peak at m/z 29, then there is probably too much water in
the system.
Possible Cause The system was not baked out sufficiently after it was last vented.
Action Bake out the system as described in the Installation chapter of this manual.
Possible Cause Moisture left over in the reagent gas supply lines.
Action Purge the reagent gas supply lines for at least 60 minutes. See the Installation
chapter in this manual for more information.
Possible Cause Contaminated reagent gas supply.
Action Replace the reagent gas supply.
5-18
Peak at m/z 32
Peak at m/z 32
A peak at m/z 32 often indicates air in the system.
Possible Cause Residual air from recent venting.
Action Bake out the system as described in the Installation chapter of this manual.
Possible Cause New or dirty reagent gas supply lines.
Action Purge the reagent gas supply lines for at least 60 minutes as described in the
Installation chapter of this manual.
Action Check for leaks and correct any that you find. See the Leaks section at the end
of this chapter for more information. After all leaks have been corrected, clean
the ion source.
Possible Cause Contaminated reagent gas supply.
Action Replace the reagent gas supply.
Possible Cause The capillary column is broken or disconnected.
Action Inspect the capillary column. Make sure it is not broken and it is installed
correctly.
5-19
Tuning-related symptoms (overview)
Tuning-related symptoms (overview)
This section describes symptoms related to tuning. Most symptoms involve

difficulties with tuning or with the results of tuning. The following symptoms are
covered in this section:
• CI ion ratio is difficult to adjust or unstable

• High electron multiplier voltage
• Can not complete autotune
• Peak widths are unstable
• Peaks 219 and 414 are out of range
• Split peaks during autotune
• Incorrect m/z 70 abundance in tune report
5-20
CI ion ratio is difficult to adjust or unstable
Possible Cause Residual air and water in the MSD or in the reagent gas supply lines.
Action In a scan of masses 10 -- 40, air will appear as a peak at m/z 32 and water as a
peak at m/z 19. If either of these is present, purge the reagent gas supply lines
and bake out the instrument as described in the To prepare the system for CI
operation section in the Installation chapter of this manual. Continued
presence of a large peak at m/z 32 may indicate an air leak. After correcting the
problems, clean the ion source.
Action Scan over the lower masses (roughly 10 -- 40). A peak at m/z 32 indicates the
possibility of an air leak. See the Leaks section at the end of this chapter for
more information. After all leaks have been corrected, clean the ion source.
Possible Cause The reagent gas supply is at the wrong pressure.
Action Check the regulator on the reagent gas supply. It should be adjusted to 10 psi
(70 kPa).
Possible Cause A leak in the reagent gas delivery path. This is especially likely if you have raised
the foreline pressure more than 40 or 50 Torr and the ion ratio is still not correct.
Action Check the reagent gas path. Tighten fittings.
5-21
Possible Cause The analyzer is not at proper operating temperature.
Action Use the data system to check on the analyzer (MS) temperature and the GC
interface (transfer line) temperature. The GC interface temperature should be
about 280°C and the MS temperature should be between 165°C and 185°C. If the
GC interface is at the correct temperature but the analyzer is too cool, there may
be poor contact between the GC interface and the interface socket.
Action Clean the ion source. See the Maintenance chapter of this manual for more
information.
Possible Cause The seal between the interface socket and ion source or between the interface
socket and the GC interface is bad.
Action Inspect the interface socket. If necessary, remove and reinstall it to insure a good
seal with the CI ion source. Make sure the wavy washer is installed between the
interface socket and ion source. Make sure the GC interface is securely seated in
the socket.
Possible Cause The flow control valve on the flow controller is out of adjustment or installed
incorrectly. The flow control valves contain a mechanism to prevent backlash and
hysteresis. If the compression nut is loose, precise adjustment of the reagent gas
flow can be very difficult.
Action Remove and reinstall the flow control valve. See the Ammonia CI section in the
Maintenance chapter of this manual for more information.
5-22
High electron multiplier voltage
High electron multiplier voltage
The electron multiplier voltage can range from a few hundred volts to 3000 V. If
the CI autotune program consistently sets the electron multiplier voltage at or
near 3000 V, it may indicate a problem.
Possible Cause The analyzer is not at the proper operating temperature.
Action Use the data system to check on the analyzer (MS) temperature and the GC
interface (transfer line) temperature. The GC interface temperature should be
about 280°C and the MS temperature should be between 165°C and 185°C. If the
GC interface is at the correct temperature but the analyzer is too cool, there may
be poor contact between the GC interface and the interface socket.
information.
Possible Cause The electron multiplier (detector) is failing.
Action Replace the electron multiplier.
5-23
Can not complete autotune
Possible Cause The methane reagent 27/29 ion ratio is incorrect. The correct ratio should be
between 0.2 and 0.4.
Action If the ion ratio is incorrect, adjust it. See To set the methane flow in the
Operation chapter of this manual for more information.
information.
Possible Cause The wrong dc polarity is being applied to the quadrupole.
Action Check the printout from the most recent EI autotune. Set the dc polarity to the
same polarity selected by the EI autotune.
end of this chapter for more information. After eliminating these problems, clean
the ion source.
5-24
Possible Cause The repeller is set to a typical EI voltage (15 V) instead of a typical CI voltage
(3 -- 4 V).
Action Reduce the repeller voltage to 4 V.
5-25
Peak widths are unstable
Peak widths are unstable
Action Clean the ion source. See the Maintenance chapter of this manual for more
information.
Action Scan from 10 -- 40 amu. A peak at m/z 32 indicates air in the system. Check for
and repair any leaks. See the Leaks section at the end of this chapter for more
information. After eliminating all air leaks, clean the ion source.
5-26
Peaks 219 and 414 are out of range
Peaks 219 and 414 are out of range
Possible Cause The methane reagent 27/29 ion ratio is incorrect. The correct ratio should be
between 0.2 and 0.4.
Action If the ion ratio is incorrect, adjust it. See To set the methane flow in the
Operation chapter of this manual for more information.
information.
end of this chapter for more information. After eliminating these problems, clean
the ion source.
5-27
Split peaks during autotune
Split peaks during autotune
Possible Cause The repeller default voltage is not optimum for your analyzer.
Action Lower the repeller setting by 1 volt and try again to tune the system. Repeat this
process until you find a repeller voltage that produces peaks which are not split.
If your reach 2 volts and the peaks are still split, return to the original voltage.
Increase the repeller voltage by 1 volt and try again to tune the system. Repeat
this process until you find a repeller voltage that produces peaks which are not
split. If you reach 7 volts and the peaks are still split, contact your
Hewlett-Packard Customer Engineer.
5-28
Incorrect m/z 70 abundance in tune report
Incorrect m/z 70 abundance in tune report
Possible Cause Methane reagent ions with m/z of around 70 mix with the PFTBA m/z 70 isotope
ions. As a result, the m/z 70 isotope peak and valley are obscured, giving
erroneous scan abundances at m/z 70.
Action None. This is normal.
5-29
Error message: No emission current
Error message: No emission current
Possible Cause The wrong filament has been specified in the data system.
Action Check the MSD configuration. Filament 1 should be specified as the active
filament.
Possible Cause The filament wires are not connected to the filament or the wrong filament leads
are connected to the filament.
Action Vent the instrument and remove the analyzer. Inspect the CI ion source. The UP
filament leads should be connected to the filament. If no wires, or the wrong
wires, are connected to the filament, correct the problem.
Possible Cause The filament is burned out.
Action Vent the instrument and remove the analyzer. Inspect the filament. If the
filament is burned out, replace it.
5-30
Leaks
Leaks
Checking for leaks in an MSD equipped with the CI accessory is slightly different
from checking for leaks in a standard EI-only MSD.
The pressure in the CI ion source is much higher than the pressure in an EI ion
source. Air that leaks in to the vacuum manifold normally cannot get into the CI
ion source due to the high pressure gradient. Therefore, leaks in the top seal or
KF fittings on the vacuum manifold do not cause a peak at m/z 32. The only way
they can be detected is through unusually high vacuum readings.
Leaks in a CI-equipped system which do cause a peak at m/z 32 usually originate

in either the reagent supply path or the sample inlet path. All of the connections
in the reagent supply path and the sample inlet path should be checked. The
most common leak site is the tee connector in the GC oven.
The leak testing techniques described in the chapter Troubleshooting the MSD
of the HP 5972A MSD Hardware Manual still apply to MSDs equipped with the
CI accessory. Testing should, however, be concentrated on the reagent supply
path and the sample inlet path.
CAUTION Operating the MSD even a short time with an air leak will contaminate the ion source.
After all leaks are located and eliminated, clean the ion source.
5-31
6

Ammonia CI, 6-4
Maintenance
Maintenance
This chapter describes maintenance procedures and requirements that

are unique to HP 5972A MSDs equipped with the HP G1072B Chemical
Ionization Accessory. Maintenance information in the HP 5972A MSD
Hardware Manual still applies to MSD’s equipped with the CI accessory
unless it is superseded by information in this chapter. Be sure to read
Before starting in the chapter Maintaining the MSD of the HP 5972A
MSD Hardware Manual before using any of the procedures or
information in this chapter.
CI increases the need for ion source cleaning

The primary effect of operating the MSD in a positive CI mode is the need
for more frequent ion source cleaning. In CI operation, the ion source
chamber is subject to more rapid contamination than in EI operation
because of the higher source pressures required for CI. The cleaning
procedure for the CI ion source is slightly different from the procedure for
the EI ion source.
Ammonia CI increases the need for foreline pump maintenance

Ammonia, when used as a reagent gas, it will also change the maintenance
requirements slightly. Ammonia causes the foreline pump oil to break
down more quickly. Therefore, the oil in the foreline vacuum pump must
be checked and replaced more frequently.
6-2
Chapter 6 ---- Maintenance
Cleaning the ion source
Cleaning the ion source
The CI ion source has slightly different cleaning requirements than the standard
EI ion source.
Frequency of cleaning
Because the CI ion source operates at much higher pressures than the EI ion
source, it will probably require more frequent cleaning than the EI ion source.
Cleaning of the source is not a scheduled, periodic maintenance procedure. The
source should be clean whenever there are performance anomalies that are
associated with a dirty ion source. See the Troubleshooting chapter for
symptoms that indicate a dirty ion source. Visual appearance is not an
accurate guide to cleanliness of the CI ion source. The CI ion source can
show little or no discoloration yet still need cleaning. Let analytical
performance be your guide.
Cleaning procedure
Cleaning the CI ion source is very similar to cleaning the EI ion source. Use the
cleaning procedure in the chapter Maintaining the MSD of the HP 5972A MSD
Hardware Manual with the following exceptions:
• The CI ion source may not look dirty but deposits left by chemical ionization
are very difficult to remove. Clean the CI ion source thoroughly.
• The insulating films on the mounting plate (repeller) are very delicate.
Abrasively clean only the repeller surface of the mounting plate.
• Do not ultrasonically clean the mounting plate, the solvents will damage the
insulating films. Use a clean cloth dampened with methanol to wipe off the
repeller surface after abrasive cleaning.
• Use the supplied 0.016-inch drill bit and pin vise to clean out the electron
entrance hold in the source body and the ion exit hole in the drawout plate.
See Also Also refer to the source cleaning video tape (05972-90011 for NTSC format or
05972-90012 for PAL format) for information about cleaning ion sources.
6-3
Ammonia CI
Ammonia CI
The HP G1072B CI Accessory is designed to operate with a variety of reagent

gases. However, ammonia is highly reactive and can affect the maintenance
requirements of the MSD. The affects are primarily related to foreline pump oil,
foreline trap, and the seals in the flow control valves in the flow controller.
Foreline pump oil

Ammonia quickly reacts with the foreline vacuum pump oil, causing it to darken
and gradually become more viscous. As a result, we recommend that you check
the foreline pump oil weekly for excessive darkening and breakdown, and that it
be replaced at least once every month when you are using ammonia CI.
Detailed procedures for checking the foreline pump oil and for replacing it are
given in the Maintaining the MSD chapter of the HP 5972A MSD Hardware
Manual
Extensive use of ammonia as a CI reagent gas can also damage the seals in the
foreline pump. If you plan to use ammonia extensively, we suggest you contact
the pump manufacturer about the possibility of replacing the standard pump
seals with Buna-n seals. These seals are more resistant to ammonia.
Foreline trap
Ammonia also quickly breaks down and destroys the adsorbent pellets (molecular
sieve) in the foreline trap. Replace these pellets with stainless steel wool before
you use ammonia as a CI reagent gas.
6-4
Ammonia CI
Flow control valves

The Buna-n O-rings in the flow control valves were chosen because they are
resistant to ammonia. Still, ammonia is hard on them and they can fail, making it
necessary to replace the O-rings or the entire valve. Replacing the O-rings is
basically straightforward but be sure to use the O-ring installation tool
(G1072-60012). This tool prevents the O-rings from being damaged as they are
installed.
Reinstallation of the valve can be done incorrectly, making use of the valve more
difficult than necessary. Refer to the following steps when reinstalling one of the
flow control valves.
1 Insert the stem of the new valve, with one hex nut at the inner surface of the
controller front panel, through the front cover of the controller.
2 Screw on the other hex nut (against the outer surface of the front panel) and the
compression nut. Make sure the compression nut is finger-tight (snug) so that
the knob/shaft has a firm feel (12-18 in-oz in both directions). Reinstall the knob.
The compression nut secures the spring-loaded mechanism and eliminates

backlash and hysteresis. If the torque on the shaft is too low, it will be very
difficult to properly set the flow.
6-5
7
GC interface parts, 7-3

CI ion source parts, 7-4
Flow controller parts, 7-6
Miscellaneous parts, 7-7
Parts
Parts
This chapter lists parts that may be required to maintain the HP G1072B
CI accessory. The parts listed in this chapter are related directly to the
CI accessory; other parts for the MSD can be found in the Parts chapter
of the HP 5972A MSD Hardware Manual.
To order parts
To obtain parts for the HP G1072B Chemical Ionization Accessory,
address the order or inquiry to your local Hewlett-Packard office. Supply
them with the following information:
• Model and serial number of your MSD

• Model and serial number of your CI accessory
• HP part number(s) of the part(s) needed
• Quantity of each part needed
If you cannot find a part you need

If you need a part that is not listed in this chapter, check the
Hewlett-Packard Analytical Supplies Catalog. If you still cannot find it,
contact your Hewlett-Packard Customer Engineer or your
Hewlett-Packard office.
7-2
Chapter 7 ---- Parts
GC interface parts
GC interface parts
Description HP part number
Guide tube and tip assembly G1072-60008

Tee connector, male/female, 1⁄16-inch 0100-1421
Seal, donut (1⁄16-inch tubing-to-tee connector) 0905-0938
Ferrule, 0.3-mm id 0100-0698
Ferrule, 0.5-mm id 0100-0636
Ferrule, column, 0.4-mm id 0100-1295
Vespel blank (for reagent side of tee connector) 0100-0691
Nut, column 05988-20066
Nut, tubing, 1⁄16-inch 2740-0015
CI GC interface socket G1072-20011
CI socket seal G1072-20012
7-3
CI ion source parts
CI ion source parts
CI ion source (untested) G1072-60002

CI source body G1072-20005
CI drawout plate G1072-20007
CI drawout cylinder G1072-20008
CI GC interface socket G1072-20011
CI socket seal G1072-20012
CI mounting plate assembly G1072-60009
Ion focus (one-piece) 05971-20143
Lens insulators (pair) 05971-20130
Entrance lens 05971-20126
Filament assembly 05972-60053
Screw, M2 × 5L (attaches mounting plate to ion source body) 0515-1077
Screw, M2 × 6L (attaches ion source to radiator) 0515-0221
Screw, M2 × 8L (attaches filament to ion source) 0515-1046
Screw, M3 × 3L (attaches lens stack to ion source) 0515-1446
Washer, curved-spring, for GC interface socket 3050-1324
Box for ion source shipping and storage 1540-1201
Bracket for shipping and storage box G1072-00004
7-4
CI ion source parts
LENS INSULATOR
CI DRAWOUT CYLINDER
CI INTERFACE SOCKET CI SOCKET SEAL
WAVY WASHER
M3 SET SCREW ENTRANCE LENS

FILAMENT ASSEMBLY
M2 × 8L SCREW
ION FOCUS LENS
CI SOURCE BODY
CI DRAWOUT PLATE
M2 × 5L SCREW
MOUNTING PLATE ASSEMBLY
7-5
Flow controller parts
Flow controller parts
CI flow controller (complete) G1072-60001

Calibration valve assembly (with restrictor) G1072-60011
Elbow fitting 0100-0061
Cajon fitting, 1⁄8-inch 0100-1003
Sample vial 05980-20018
Calibration valve cable assembly G1072-60007
Case G1072-40001
Ferrule, back, for 1⁄8-inch tubing 0100-0038
Ferrule, front, for 1⁄8-inch tubing 0100-0034
Front panel G1072-00005
Jumper tube (connects reagent gas select valve to G1072-80004
auxiliary valve)
Nut, for 1⁄8-inch tubing 0100-0057
Nut, M8 x 1.25 brass (for inlet & outlet tubes) 0590-0385
Plug, blank for the auxiliary reagent connector 0100-0071
Reagent gas flow control valve 0101-0646
Reagent gas inlet and outlet tubes (connects inlets and outlet G1072-80005
to flow control valves)
Reagent gas select valve 0101-0653
Rear panel G1072-00006
Screw, 8-32 2510-0041
T-tube (flow control valve to calibration valve to reagent G1072-80001
gas select valve)
Tubing, 2-m, 1⁄8-inch both ends (methane supply to G1072-80002
flow controller)
Tubing, 2-m, 1⁄8-inch and 1⁄16-inch ends (flow controller to GC G1072-80003
interface tee)
Washer, lock 2190-0038
7-6
Miscellaneous parts
Miscellaneous parts
Gloves, clean
large 8650-0030
small 8650-0029
PFTBA sample kit 05971-60571
Powder, alumina 8660-0791
Cotton swabs (100) 8520-0023
Wipes, industrial 9310-0039
Tape, teflon 0460-0516
GC/MS evaluation sample A 05970-60045
7-7
Index
A p-Chlorobiphenyl, example mass spectrum of, 4-14

Chromatogram for evaluation sample A, 4-11, 4-12
Addition ionization process, description of, 2-11, CI
2-15 as a chemical phenomenon, 2-10
Adduct ions in methane CI, 2-15 as different from EI ionization, 2-10
Ammonia discussion of, 2-10 to 2-16
as reagent gas, 2-11 in forming sample ions, 2-10
hardware for, 1-5 GC interface modification for, 3-14 to 3-15
Ammonia CI, 4-19 to 4-21 high pressures in, 2-10
addition reactions in, 2-15 ionization processes of, 2-11
effects on foreline pump oil, 6-2, 6-4 source pressure range in, 2-11
effects on foreline pump seals, 6-4 spectrum of methyl octanoate, 2-10, 2-11
principal ions in, 4-19 using ammonia for. See also Ammonia CI, 4-19
Analyzer assembly, removal of, 3-6 to 4-21
Auxiliary reagent gas control, 2-6 using isobutane for. See also Isobutane CI, 4-16
to 4-18
CI accessory
B checklist for initial upgrade, 3-28 to 3-29
Bake-out, after converting from EI to CI operation, mass range with, 1-4
3-21 operation of, 4-1
Biphenyl, example mass spectrum of, 4-13 principal components of, 1-2
reagent gases used with, 2-2
replacement parts for, 7-3 to 7-7
C resolution with, 1-4
scan rates with, 1-4
Calibration valve, purging of, in preparation for CI
SCAN sensitivity with, 1-4
operation, 3-20
SIM sensitivity with, 1-4
Charge-exchange ionization process, 2-11
CI autotune, 4-7
description of, 2-16
in CI-to-EI conversion, 3-22
noble gases in, 2-16
CI ion source, 2-2
reaction, 2-16
components of, 2-3, 2-4
uses for, 2-16
differs from EI source, 2-3
Checklist
installation of, 3-4 to 3-11
CI-to-EI conversion, 3-30
instructions for cleaning of, 6-3
EI-to-CI conversion, 3-31
replacement parts for, 7-4
Initial upgrade, 3-28 to 3-29
subject to contamination, 6-2
Chemical ionization. See CI
I-1
Index
CI operation E
calibration-valve purging for, 3-20
CI tuning for, 4-7 to 4-9 EI as direct energy-transfer process, 2-10
configuration for, 3-16 EI autotune
conversion from, to EI operation, 3-22 to 3-24 in EI-to-CI conversion, 3-25
effects on ion source, 6-2 in installation of CI ion source, 3-4
methane-line purging for, 3-19 EI ion source
setting methane flow for, 4-3 to 4-6 removal of, 3-7 to 3-8
system bake-out for, 3-21 in EI-to-CI conversion, 3-26
system preparation for, 3-16 to 3-21 EI-to-CI conversion, 3-25 to 3-27
system pumpdown prior to, 3-18 checklist for, 3-31
use of regent gases other than methane for, Electron ionization. See EI
4-15 to 4-21 Error message, no emission current, 5-30
verifying system performance for, 4-10 to 4-14 Evaluation sample A
CI-to-EI conversion, 3-22 to 3-24 chromatogram of, 4-12
checklist for, 3-30 components of, 4-11
CI tuning, 4-7 to 4-9
with CI autotune, 4-7
in converting from CI to EI operation, 3-22 F
initial settings used in manual tuning, 4-7 Flow controller. See Reagent gas flow controller
manual tuning, 4-8 to 4-9 Foreline pump oil, ammonia effects on, 6-4
Configuration for CI operation, 3-17
Conversion G
from CI to EI operation, 3-22 to 3-24
GC/MS evaluation sample A, 4-10
from EI to CI operation, 3-25 to 3-27
GC interface
description of, 2-5
D modification of, for CI operation, 2-5, 3-14 to
3-15
Dodecane, example mass spectrum of, 4-13 removal of, 3-4 to 3-5
used for both EI and CI operation, 3-14
GC parameters for verifying proper CI function, 4-10
Guide tube assembly installation in GC interface,
3-14
I-2
Index
H M
HP 5972A MSD Macros, tuning. See Tuning macros
adjustments for ammonia CI, 4-19 to 4-21 Mass range with CI accessory, 1-4
performance of, when equipped with CI Mass spectrum
accessory, 1-4 of biphenyl, 4-13
upgrading of, for CI operation, 3-3 to 3-15 of p-chlorobiphenyl, 4-14
verifying proper CI function, 4-10 to 4-14 of dodecane, 4-13
Hydride-abstraction ionization process, 2-11, 2-14 of methyl palmitate, 4-14
Hydrogen as reagent gas for CI operation, 2-11 Methane
as most frequently used reagent gas, 2-11
flow control, 2-6
I hardware for, 1-5
pretune in monitoring methane-reagent ion
Interface. See GC interface
27/28 ratio, 4-4 to 4-5
Ionization process
Methane flow
addition, 2-15
coarse adjustment of, 4-3
charge exchange, 2-16
fine adjustment of, 4-6
hydride abstraction, 2-14
setting of, for CI operation, 4-3
proton transfer, 2-12 to 2-13
Methane lines, purging, 3-19
Ion ratio
Methylamine as reagent gas, 2-11
determination of, 4-4
Methyl octanoate, typical CI spectrum of, 2-11
relationship of to system pressure, 4-6
Methyl palmitate, example mass spectrum of, 4-14
Ions, adduct. See also Adduct ions, 2-15
Ion source for CI. See also CI ion source, 2-2
Isobutane CI, 2-11, 4-16 to 4-18
addition, as main ionization process in, 4-16
N
adjusting HP 5972A MSD for operation with, Nitrous oxide as reagent gas, 2-11
4-16 to 4-18 Noble gases in charge-exchange ionization, 2-16
hardware for, 1-5 No emission current error message, 5-30
in producing less fragmentation, 4-16
principal ions in, 4-16
I-3
Index
O R
Organic compounds, proton affinity of, 2-13 Reagent gas
changes necessary when using alternative, 4-15
effects of changing, 4-15
P flow path, 2-6, 2-8
hardware, 1-5
Parts, ordering information for, 7-2
instrument tuning for alternative, 4-15
Perflourotributylamine. See PFTBA
ratio of, to sample, 2-10
Performance specifications, 1-4
Reagent gases, 1-5
PFTBA
frequently used, 2-11
as calibrant in CI tuning, 4-7
for operation of CI accessory, 1-5
as calibrant with methane reagent gas, 2-2
other than methane, 4-15 to 4-21
Polyimide insulating film, 3-8
proton affinities of, 2-12
Pressure
Reagent gas flow control, 2-6 to 2-8
symptoms of excessive foreline, 5-4 to 5-5
Reagent gas flow controller
unchanged by reagent gas flow, 5-6 to 5-7
controls on, 2-6, 2-7
vacuum, symptoms of fluctuations in, 5-8
description of, 2-6 to 2-8
Pressure-related symptoms in troubleshooting, 5-3
flow schematic of, 2-8
to 5-8
functions of, 2-6
Proton affinity, 2-12 to 2-13
installation of, 3-12 to 3-13
of organic compounds, 2-13
location of on GC, 3-12
of reagent gases, 2-13
Proton transfer
Replacement parts, 7-3 to 7-7
expression for, 2-12
Resolution with CI accessory, 1-4
proton affinities in, 2-12
from protonated reagent to molecular analyte,
2-12
Pumpdown in preparation for CI operation, 3-18
I-4
Index
S
Scan rates with CI accessory, 1-4
Sensitivity with CI accessory
in SCAN, 1-4
in SIM, 1-4
Signal-related symptoms in troubleshooting, 5-11 to
5-19
Socket, CI interface. See CI interface socket
T
Temperature-related symptoms in troubleshooting,
5-9 to 5-10
Trimethylsilane as reagent gas, 2-11
Troubleshooting
error message in, 5-30
pressure-related symptoms in, 5-3 to 5-8
signal-related symptoms in, 5-11 to 5-19
temperature-related symptoms in, 5-9 to 5-10
tuning-related symptoms in, 5-20 to 5-29
Tune parameters, used in manual CI tuning, 4-7
Tuning macros
purpose of, 1-2
in regulating reagent gas flow, 2-9
Tuning-related symptoms in troubleshooting, 5-20
to 5-29
I-5

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© Copyright 1993 Noise Declaration Manual Conventions

Hewlett-Packard shall not

Chapter 1 General Information

Chapter 2 System Overview

Figure 2-1 CI ion source, 2-3

Figure 3-1 Removing the GC interface, 3-5

Figure 4-1 Ions monitored for methane adjustment, 4-5

This manual contains information pertaining to the installation, operation,

Chapter 1 provides a list of the CI accessory performance specifications

Chapter 2 describes the CI accessory components and their functions, and

Chapter 3 provides detailed instructions for installing the CI accessory on

Chapter 4 provides instructions for using the CI accessory.

Chapter 5 discusses problems most likely to be encountered and their

Chapter 6 discusses routine maintenance procedures.

Chapter 7 provides information about parts that are available for

Figure 1-1. GC/MSD system with HP G1072B CI Accessory

The HP G1072B Chemical Ionization Accessory allows the HP 5972A MSD to

The HP G1072B CI accessory contains a CI ion source, parts required for

By reducing the diameter of the electron-entrance and ion-exit holes on the CI

Figure 2-1. CI ion source

CI INTERFACE SOCKET CI SOCKET SEAL

M3 SET SCREW ENTRANCE LENS

Figure 2-2. CI ion source ---- exploded view

Installation of the CI ion source requires modification of the standard GC

REAGENT SUPPLY TUBE

I Cl INTERFACE SOCKET 1/16 INCH

G U I D E T U B E GUIDE TUBE/ COLUMN NUT

Figure2-3. GC interface modified for Cl

Reagent gas flow controller

When the methane control is on, methane flows from a pressure-regulated

Figure 2-4. Flow controller front panel

Figure 2-5. Flow controller back panel

Figure 2-6. Reagent gas controller flow diagram

Chemical ionization (CI) is a technique for creating ions used in mass

Whereas EI is a direct process in which energy is transferred collisionally from

An example of a typical CI spectrum of methyl octanoate is shown in Figure 2-7.

Figure 2-7. Typical CI spectrum of methyl octanoate

The most frequently used example of proton-transfer chemical ionization is the

Table 2-1. Reagent gas proton affinities

Species Proton affinity, kcal/mole Reactant ion formed

Table 2-2. Proton affinities of selected organic compounds

Molecule Proton affinity, Molecule Proton affinity,

For example, if R+ is CH5+, the reaction proceeds as follows:

CH5+ + M → [M-H]+ + CH4 + H2

Often, both hydride-abstraction and proton-transfer ionization can be evident in

Addition reactions are particularly important in ammonia chemical-ionization

or simply the recombination of the ionized reagent with an electron to form a

Although charge-exchange chemical ionization is significant for some studies, it

Initial mass spectrometer upgrade (overview), 3-3

This chapter provides instructions for installing the HP G1072B CI

Initial mass spectrometer upgrade (overview)

The initial upgrade procedure includes the following tasks:

• To install the CI ion source

*Furnished with the CI accessory shipping kit (G1072-60006)

To install the CI ion source

2 Perform the performance verification procedure listed in the HP 5972A Mass

Figure 3-1. Removing the GC interface

Figure 3-2. Top and main board electrical connections

Figure 3-3. EI ion source ---- installed

13 Carefully pull the ion source out of the analyzer.

15 Unpack the CI ion source and interface socket.

Figure 3-4. Installing the CI ion source

Figure 3-5. Connecting the ion source leads