Agilent 5977 Series

MSD System

Concepts Guide

Agilent Technologies
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2 Concepts Guide
In This Guide...
The Concepts Guide explains the operation of the Agilent 5977
Series MSD by helping you understand how the hardware and
software work.

1 Overview
Learn how the Agilent 5977 Series MSD helps you do your job.

2 MSD Theory and System Components

Learn the concepts you need to understand how the Agilent
5977 Series MSD works.

3 MassHunter Acquisition Software

Learn how the Agilent MassHunter Data Acquisition Software
controls the Agilent 5977 Series MSD.

4 Chemical Ionization Theory

Learn the theory behind Chemical Ionization in GC/MS.

Concepts Guide 3
4 Concepts Guide
Contents
1 Overview
System Description 8
5977 Series MSD applications 9
Data acquisition 9
Data analysis 10

2 MSD Theory and System Components

Single Quadrupole MSD Operation 14
How a single quadrupole mass selective detector works 14
Mass Spectrometer Components 18
Vacuum system 18
Analyzer 19
Ion source 20
Quadrupole 24
Detector 24
Analyzer heaters and radiators 25

3 MassHunter Acquisition Software

Overview 28
General Tuning Concepts 29
Components adjusted during tuning 30
Tuning the ion source components 33
Tuning the Quadrupole 34
Types of Tuning Available in MassHunter 39
Autotune 39
Manual tune 40
MSD Data Acquisition 42
Scan acquisition type 42
SIM acquisition type 45

Concepts Guide 5
 SIM and scan acquisition type 46
Source temperature guidelines 47

4 Chemical Ionization Theory

Chemical Ionization Overview 50
References on chemical ionization 51
Positive CI Theory 52
Proton transfer 54
Hydride abstraction 57
Addition 57
Charge exchange 58
Negative CI Theory 59
Electron capture 61
Dissociative electron capture 62
Ion pair formation 62
Ion-molecule reactions 63

6 Concepts Guide
Agilent 5977 Series MSD System
Concepts Guide

1
Overview
System Description 8
5977 Series MSD applications 9
Data acquisition 9
Data analysis 10

This chapter provides an overview of the Agilent 5977 Series

MSD system components and how they work together to acquire
data and analyze results.

Agilent Technologies 7
1 Overview
System Description

System Description

The Agilent 5977 Series MSD is a stand-alone capillary GC

detector for use with an Agilent Series Gas Chromatograph. The
Agilent 5977 Series MSD features:
• Local control panel (LCP) for locally monitoring and
operating the MSD
• One of two different high vacuum pumps
• One of four different foreline pumps
• Three different types of independently MSD heated
electron-ionization (EI) sources available:
standard (stainless), inert, and extraction
• Optional chemical ionization (PCI/NCI) modes are available
that add a chemical-ionization (CI) source, reagent gas flow
controller and plumbing, and CI tuning calibration
• Independently MSD heated hyperbolic quadrupole mass
filter
• High-energy dynode (HED) electron multiplier detector
• Independently GC heated GC/MSD interface
This configuration has advantages for many applications. The
data is acquired through the use of the Agilent MassHunter data
acquisition software. MassHunter Qualitative and Quantitative
Analysis Software packages are provided for analyzing the
acquired data.

8 Concepts Guide
 Overview 1
5977 Series MSD applications

5977 Series MSD applications

The Agilent 5977 Series MSD system provides low detection
limits in complex matrices, as well as high temperature, inert
ion source options. This supports many analytical applications
for active compounds and late-eluters, including pesticides,
endocrine disruptors, and hazardous chemicals.

Data acquisition
The MassHunter Data Acquisition software allows you to
perform the following tasks from a single window.

Prepare the instrument

• Start and stop the instruments from the software
• Download settings to the GC and the MSD in real time to
control the instrument
• Optimize MSD parameters automatically or manually
through Agilent tuning programs and print an Autotune
report
• Monitor the actual conditions of the instrument
• View the real-time plot for chromatograms and instrument
parameters (both GC and MSD) and print a real-time plot
report
• View the centroid line spectrum of a peak or the mass range
profile spectrum of a peak in real time

Set up acquisition methods

• Enter and save parameter values for the GC and the MSD to
an acquisition method
• Select and label the total ion chromatograms or extracted ion
chromatograms that you want to appear in the real-time plot
• Set up time segments for each scan type and analysis where
parameters change with the time segment or with the scans
within the time segment

Concepts Guide 9
1 Overview
Data analysis

• Set up SIM/Scan methods using the MassHunter Method

Editor
• Print an acquisition method report

Acquire data
• Enter sample information, pre- or post-programs (scripts),
and run single samples interactively
• Enter and automatically run both individual samples and
samples organized in a sequence
• Set up pre- and post-scripts to run between samples in a
sequence
• Set up and run a sequence to optimize MSD acquisition
parameters
• Print a sequence report
• View system events, including start and stop times, run
events, and errors
• Print an event log report
To learn how to get started with the Agilent 5977 Series MSD,
see the Agilent 5977 Series MSD Quick Start Guide.
To learn more about how to use the Agilent 5977 Series MSD
with real samples and data, see the Agilent 5977 Series MSD
Familiarization Guide.
To learn how to do individual tasks with the MSD, see the online
help.
To learn more about the Agilent 7890 Series GC system, see the
Agilent 7890 Series GC system documentation.

Data analysis
MassHunter quantitative analysis program
Agilent has designed the quantitative analysis program to help
quantify very low amounts of material. The program has the
following unique features:
• Imports information directly from the acquisition method

10 Concepts Guide
 Overview 1
Data analysis

• Provides a curve-fit assistant to test all fits and statistics on

curve quality
• Presents a batch results window to help you review and
operate on an entire batch of data at once
• Automatically detects outliers
• Provides preconfigured templates for basic reporting and
provides the capability to create custom reports in Microsoft
Excel
Please refer to the Agilent MassHunter Software – Quantitative
Analysis Familiarization Guide or the online Help for the
quantitative analysis program.

MassHunter qualitative analysis program

For fast method development, use this software to quickly
review the qualitative aspects of the data.
Agilent designed the qualitative analysis program to present
large amounts of data for review in one central location. With
the program, you can do these operations for any type of mass
spectrometer data that you open:
• Extract chromatograms
• View and extract peak spectra
• Subtract background
• Integrate the chromatogram
• Find compounds
You can also set up methods to automatically do the tasks in the
list, as well as others, when you open the data files.
Refer to the Agilent MassHunter Software – Qualitative
Analysis Familiarization Guide or the online Help for the
qualitative analysis program.

Concepts Guide 11
1 Overview
Data analysis

12 Concepts Guide
Agilent 5977 Series MSD System
Concepts Guide

2
MSD Theory and System Components
Single Quadrupole MSD Operation 14
How a single quadrupole mass selective detector works 14
Mass Spectrometer Components 18
Vacuum system 18
Analyzer 19
Ion source 20
Quadrupole 24
Detector 24
Analyzer heaters and radiators 25

This chapter explains how the MSD filters out all but specified
ions from reaching the detector before examining the
components that make up the Agilent 5977 Series MSD.

Agilent Technologies 13
2 MSD Theory and System Components
Single Quadrupole MSD Operation

Single Quadrupole MSD Operation

This section reviews the theory behind the single quadrupole

mass selective detector (MSD).

How a single quadrupole mass selective detector works

A conceptual model can be used to explain the theory of a single
quadrupole MSD. See Figure 1.

External Ionization Source

Detector

Quadrupole Mass Filter

Figure 1 Conceptual model of a single quadrupole MSD

In the model:
• All of the ions contained in a sample are formed in the
external ionization source and collected in a funnel. The balls
of different colors and sizes represent different ions having
different m/z values.
• The quadrupole mass analyzer is represented by a moving
belt that serves to filter the ions as they pass through
openings of various sizes. The ions pass from the funnel,
through the filter, to the detector.
• The detector is represented by the collecting funnel below
the filtering belt.

14 Concepts Guide
 MSD Theory and System Components 2
How a single quadrupole mass selective detector works

As the belt (the analyzer) moves, or the quadrupole settings are

changed, ions with different m/z values are filtered through the
quadrupole.
As the MSD moves from a acquiring data for a small m/z value
to increasingly larger values, a full scan is created. For a scan
acquisition the scan range (for example, m/z 50 to 550) is
selected by the user. The quadrupole settings are adjusted to
filter a single mass for a user specified sampling rate before
changing the quadrupole settings for the next ion.
If the belt does not move, the detector continues to monitor a
specified m/z value over the entire scan period. This type of
analysis is known as selected ion monitoring (SIM). The user
may set the dwell time in a SIM acquisition for a specific m/z. It
is the most sensitive operating mode for a single quadrupole
mass spectrometer.

SIM acquisition mode

To obtain the best sensitivity for quantitative measurement, the
single quadrupole is operated in SIM acquisition mode (Figure 2).
The duty cycle is the measure of the instrument’s time actually
devoted to acquiring data. In SIM mode, the quadrupole
acquires data for specific ions almost all of the time. This
results in nearly 100 % acquisition during the cycle.

Detector

Quadrupole Mass Analyzer

Figure 2 Quadrupole in SIM acquisition mode

Concepts Guide 15
2 MSD Theory and System Components
How a single quadrupole mass selective detector works

In this example:
1 All of the ions (+, –, and neutrals) are formed in the electron
impact ionization source.
2 Ion optics guide the ions to the quadrupole mass analyzer.
The Agilent electron impact ion source consists of a series of
lenses and a repeller assembly that directs the ion beam into
the analyzer.
3 In the analyzer, only ions of a particular m/z value,
represented by blue balls, are allowed to pass through to the
detector.
4 The detector completes the analysis.
This system has several advantages:
• Provides the best sensitivity for quantitation
• Increases selectivity
• Improves chromatographic specificity

Scan acquisition mode

In scan acquisition mode, the quadrupole serves as a mass filter
over time, and a scan is carried out by stepping through
increasing DC and RF voltages. This provides filtering through
the corresponding m/z values across a mass spectrum. See
Figure 3.

16 Concepts Guide
 MSD Theory and System Components 2
How a single quadrupole mass selective detector works

Detector

Quadrupole Mass Analyzer

Figure 3 Quadrupole in Scan acquisition mode

The scan acquisition mode is less sensitive because the

detection cycle of each m/z value is considerably less than
100 %. The quadrupole mass analyzer scans sequentially,
passing each m/z value in the selected mass range to the
detector.
A full scan MS is still a useful mode of operation because it
shows all of the ions that are being formed in the ion source
giving valuable structural compound information. This
structural information is required for developing highly
sensitive SIM acquisitions for quantitative analysis.

Concepts Guide 17
2 MSD Theory and System Components
Mass Spectrometer Components

Mass Spectrometer Components

The main components of a mass spectrometer are the vacuum

system, the analyzer, and the electronics.

Vacuum system
The vacuum system creates the high vacuum required for an
MSD to operate. Without the vacuum, the molecular mean free
path would be very short, and the ions would collide with air
molecules, causing fragmentation, before they could reach the
detector. In addition, operation at high temperatures would
damage analyzer components.
The Agilent 5977 Series MSD uses two vacuum pumps to obtain
the necessary vacuum levels. A foreline pump creates a low
vacuum, then a high vacuum pump engages to create the type of
high vacuum needed for efficient operation. The Agilent 5977
Series MSD can use four different types of low vacuum pumps,
and two types of high vacuum pumps.
The parts of the vacuum system are:
• Foreline (rough) pump
• High vacuum (diffusion or turbo) pump
• Side plate (analyzer door)
• Front and rear end plates
• Vacuum seals
• Calibration valve and vent valve
• Vacuum control electronics
• Vacuum gauges and gauge control electronics
The analyzer chamber is the area of the MSD where the analyzer
operates. The chamber manifold is extruded from aluminum
alloy. Large openings in the side, front, and rear of the chamber
are covered by plates, sealing the chamber and keeping the
pressure constant. O-rings provide seals between the plates and
the manifold openings.

18 Concepts Guide
 MSD Theory and System Components 2
Analyzer

The foreline pump initially reduces the pressure in the analyzer

chamber so that the high vacuum pump can operate. It also
pumps away the gas load from the high vacuum pump.
The Agilent 5977 Series MSD provides two options for the high
vacuum pump: a diffusion pump or a turbo pump system. The
diffusion pump supports a maximum flow rate into the MSD of
1.5 mL/min. The diffusion pump uses baffling to prevent vapor
from migrating into analyzer chamber. The diffusion pump
foreline pressure is monitored by a vacuum gauge, and the
diffusion pump heater is controlled by the AC board. Turbo
pumps have a screen to keep debris out of the vacuum chamber,
but a baffle is unnecessary. There is no foreline gauge for the
turbo pumps; the vacuum pressure is controlled by the turbo
controller.

Analyzer
The analyzer is the main component of the MSD. In EI mode, the
sample is vaporized in the GC inlet, separated by compound
properties in the GC column, and entered into the MSD through
the ion source chamber, where it is bombarded with a beam of
electrons that have enough energy to ionize and fragment the
compound.
The resulting ions are repelled from the ion source into the
mass filter. The mass filter allows selected ions to pass through
the filter and strike the detector. The detector generates a signal
current proportional to the number of ions striking it.
The analyzer is attached to the vacuum side of the side plate.
The side plate is hinged for easy access. The ion source and
mass filter are heated independently. Each is mounted inside a
radiator for correct heat distribution.
The main components of the analyzer are:
• Ion source
• Mass filter
• Detector
• Heaters and radiators

Concepts Guide 19
2 MSD Theory and System Components
Ion source

The ionization of a sample occurs in the ion source that is

shown, schematically, on the left in Figure 4. In this case, the
source used is an electron ionization (EI) source, which ionizes
the sample with a charged filament.

Lens insulator
Source body Quadrupole HED
EM
Filament

Repeller
Entrance lens
Ion focus lens
Ion source chamber Drawout or optional extractor lens

Figure 4 MSD analyzer components

Ion source
The EI source operates by electron ionization. The sample
enters the ion source from the GC/MSD interface. Electrons
emitted by a filament enter the ionization chamber, guided by a
magnetic field. The high energy electrons interact with the
sample molecules, ionizing and fragmenting them. The positive
voltage on the repeller pushes the positive ions into the lens
stack, where they pass through several electrostatic lenses.
These lenses concentrate the ions into a tight beam, which is
directed into the mass filter.
Figure 5 on page 21 shows an exploded view of an EI source.
There are two types of lens stacks for the EI sources available
for the Agilent 5977 Series MSD. The source type pictured uses
a nonadjustable static drawout plate lens, and adjustable ion

20 Concepts Guide
 MSD Theory and System Components 2
Ion source

focus and entrance lenses. The other type of lens stack available
replaces the static drawout lens with an adjustable voltage
extractor lens for improved sensitivity.

Source body

Filament 1

Repeller

Filament 2
Entrance lens

Ion focus

Drawout plate

Figure 5 EI source with static drawout lens

The ion source body is a cylinder that holds the other parts of
the ion source, including the lens stack. With the repeller and
lens stack making up its front and back walls, the ionization
chamber is the space in the source body where the ions are

Concepts Guide 21
2 MSD Theory and System Components
Ion source

formed. Slots outside the ionization chamber in the source body

help the vacuum system to pump away carrier gas any
unionized sample molecules or fragments.
A CI source is similar to the EI source, but only has one part in
common with the EI source - the entrance lens. A CI source only
has one filament, as opposed to an EI source which has two. The
single CI filament has a straight wire and a reflector. A dummy
filament provides connections for the other wires.
The unsealed holes in the CI source (electron-entrance and
ion-exit) are very small (0.5 mm), making it possible to
pressurize the ionization chamber. Both the source body and
the plate are at repeller potential, electrically isolated from the
radiator and the CI interface tip. The seal for the interface tip
ensures a leak-tight seal and electrical isolation between the CI
interface and the source.

Filaments
The filaments are the key components of the ion source. Two
filaments are located on opposite sides of the outside of an EI
source. One filament is active at a time. The active filament
carries an adjustable AC emission current. The emission
current heats the filament causing it to emit electrons, which
ionize the sample molecules. In addition, both filaments have an
adjustable DC bias voltage. The bias voltage determines the
energy on the electrons, usually -70 eV.
The CI source has only one filament of a different design from
the EI filaments. A “dummy” filament provides connections for
the Filament 2 wires.
When running the instrument in EI mode, you can select which
filament in the ion source is active since sometimes one source
gives better results than the other. In the CI source, it is always
Filament 1.

22 Concepts Guide
 MSD Theory and System Components 2
Ion source

Magnet
The field created by the magnet directs the electrons emitted by
the filament into and across the ionization chamber. The
magnet assembly is a permanent magnet with a charge of
350 gauss in the center of the field.

Repeller
The repeller forms one wall of the ionization chamber. A
positive charge on the repeller pushes positively charged ions
out of the source through a series of lenses. The repeller voltage
is also known as the ion energy, although the ions only receive
about 20% of the repeller energy.

Drawout plate
The drawout plate forms the back wall of the ionization
chamber in the SST and Inert ion sources. The ion beam passes
through a hole in the drawout plate and into the drawout
cylinder. The drawout cylinder is slotted. The slots correspond
to slots in the source body. These slots allow gas and unionized
sample molecules or fragments to be pulled away by the vacuum
system. The drawout plate and drawout cylinder are both at
ground potential.

Extraction lens
The extraction lens forms the back wall of the ionization
chamber in the EXT ion source. The ion beam passes through a
hole in the lens and into a slotted cylinder. The slots correspond
to slots in the source body. These slots allow gas and unionized
sample molecules or fragments to be pulled away by the vacuum
system. The extraction lens and cylinder are both at ground
potential.

Ion focus
Increasing the ion focus voltage improves sensitivity at lower
masses. Decreasing the ion focus voltage improves sensitivity at
higher masses. Incorrect ion focus adjustment results in poor
high mass response.

Concepts Guide 23
2 MSD Theory and System Components
Quadrupole

Entrance lens
The entrance lens is at the entrance to the quadrupole mass
filter. This lens minimizes the fringing fields of the quadrupole,
which discriminate against high-mass ions. There is a
permanent +4.4 V voltage added to the entrance lens. The total
voltage applied to the entrance lens is the sum of the entrance
lens offset, entrance lens gain, and the +4.4 V permanent offset.
Entrance lens voltage = +4.4 VDC + offset + (gain × mass)
Once through the source, the ions are analyzed by a mass
analyzer (mass filter) that controls the motion of the ions as
they travel to the detector to be converted into actual signals.

Quadrupole
The AMU gain and offset are quadrupole parameters that
permit an ion with a specific m/z to travel in a stable path
through the quadrupole mass filter. These values are ideally
adjusted to obtain unit mass tuning ions having a peak width at
half-height of 0.5 AMU.

Detector
The detector in the MSD analyzer is a high energy conversion
dynode (HED) coupled to an electron multiplier (EM). the
detector is located at the exit end of the quadrupole mass filter.
It receives the ions that have passed through the mass filter. The
detector generates an electronic signal proportional to the
number of ions striking it. The detector has three main
components: the detector ion focus, the HED, and the EM horn.

Detector ion focus

The detector ion focus directs the ion beam into the HED, which
is located off axis. The voltage on the detector focus lens is fixed
at -600 V.

24 Concepts Guide
 MSD Theory and System Components 2
Analyzer heaters and radiators

High energy dynode

The HED operates at -10,000 V for EI and PCI, and +10,000 V for
NCI. It is located off-axis from the center of the quadrupole
mass filter to minimize signals due to photons, hot neutrals, and
electrons coming from the ion source. When the ion beam hits
the HED, electrons are emitted. These electrons are attracted to
the more positive EM horn.

EM horn
The EM horn carries a voltage of up to -3000 V at its opening
and 0 V at the other end. The electrons emitted by the HED
strike the EM horn and cascade through the horn, liberating
more electrons as they go. At the far end of the horn, the
current generated by the electrons is carried through a shielded
cable outside the analyzer to the signal amplifier board.
The voltage applied to the EM horn determines the gain. The
voltage is adjustable from 0 to -3000 VDC. As the EM horn ages,
the voltage required increases over time.

Analyzer heaters and radiators

The ion source and mass filter are housed in cylindrical
aluminum tubes called radiators. The radiators control the
distribution of heat in the analyzer. They also provide electrical
shielding for analyzer components. The ion source heater and
temperature sensor are mounted in the ion source heater block.
The mass filter (quad) heater and temperature sensor are
mounted on the mass filter radiator. Analyzer temperatures can
be set and monitored from the MassHunter Data Acquisition
software.
In selecting the temperatures to use, consider the following:
• Higher temperatures help keep the analyzer clean longer
• Higher ion source temperatures result in more fragmentation
and therefore lower high-mass sensitivity
Recommended settings (for EI operation):
• Ion source (“Source temperature guidelines”)
• Quadrupole 150 °C

Concepts Guide 25
2 MSD Theory and System Components
Analyzer heaters and radiators

The GC/MSD interface, ion source, mass filter (quad) heated

zones interact. The analyzer heaters may not be able to
accurately control temperatures if the setpoint for one zone is
much lower than that of an adjacent zone.

26 Concepts Guide
Agilent 5977 Series MSD System
Concepts Guide

3
MassHunter Acquisition Software
Overview 28
General Tuning Concepts 29
Components adjusted during tuning 30
Tuning the ion source components 33
Tuning the Quadrupole 34
Types of Tuning Available in MassHunter 39
Autotune 39
Manual tune 40
MSD Data Acquisition 42
Scan acquisition type 42
SIM acquisition type 45
SIM and scan acquisition type 46
Source temperature guidelines 47

Agilent Technologies 27
3 MassHunter Acquisition Software
Overview

Overview
MassHunter Data Acquisition Software controls the 5977 Series
MSD and 7890 Series GC from the Instrument Control view,
shown in Figure 6. From here you are able to:
• Control and monitor the 5977 instrument settings
• See the instrument at work through real-time plots
• Automate the running of multiple samples through the
sequence table
• Tune (calibrate) the 5977 MSD
• Set up method acquisition parameters for the GC and the
MSD
• Monitor the chromatogram and mass spectra as samples are
analyzed
• Set up sequences of samples
This chapter provides details for tuning your 5977 and for
creating a data acquisition method using MassHunter. Please
refer to your online Help for details on other functions you may
perform here.

Figure 6 Instrument Control view of the MassHunter Data Acquisition program

28 Concepts Guide
 MassHunter Acquisition Software 3
General Tuning Concepts

General Tuning Concepts

Tuning an MSD involves optimizing a number of instrument

parameters such as voltages, currents, and flows. This allows
the MSD to achieve the maximum mass spectral sensitivity and
proper resolution. The way the instrument is tuned affects all
data acquisition. Tuning one parameter often affects the
optimum value of other parameters. Some parameters are
purely electronic and affect only the way the electronics process
the signal. Other parameters affect voltage settings or currents
to parts in the MSD’s ion source, mass filter, and detector.
Tuning an MS is always performed first in electron ionization
(EI) mode, even when preparing to operate in chemical
ionization (CI) mode.
The parameters that determine when a compound of a specified
mass-to-charge ratio (m/z) reaches the detector are optimized
during tuning to give the most accurate m/z readings of
subsequent compounds.
A standard tuning compound located in a vial directly
connected to the analyzer chamber is used for tuning an MSD.
The tuning compound is introduced into the vacuum manifold
when a tune is performed. In the EI mode,
perfluorotributylamine (PFTBA) is used for tuning because it is
a relatively stable compound. Stability of a tuning compound is
important for reproducible tuning. Typically PFTBA lasts one
year or longer before replacement is necessary. However, the
compound must be volatile enough to flood the ion source so
that heating of the tuning vial is unnecessary. The mass
spectrum of PFTBA fragments over a wide mass range and is
easily interpreted since this compound only has C-13 and N-15
isotopes. During autotune, the fragment compounds 69, 219,
and 502 are used for this calibration.

Concepts Guide 29
3 MassHunter Acquisition Software
Components adjusted during tuning

Components adjusted during tuning

During tuning, the ion source element voltages are set to
optimize the abundance and ion ratio of each tuning ion
fragment reaching the electron multiplier (EM). In addition, the
quadrupole AMU gain and offset are set for proper peak width,
and the mass axis are set for correct mass assignment. The EM
voltage is set to an optimum value and adjusted so that the gain
is constant as the EM ages.
To see how this is done in MassHunter, read “Types of Tuning
Available in MassHunter" on page 39.
Figure 7 shows the MSD and its components with parameters
that are adjusted during the tuning process.

Lens insulator
Source body Quadrupole HED
EM
Filament

Repeller
Entrance lens
Ion focus lens
Lens stack
Ion source chamber Drawout plate
or optional extractor lens

Figure 7 MSD showing components with parameters adjusted during tuning

Filament - The EI source contains two filaments, only one of

which is used at any given time. MassHunter allows you to select
a filament and set its emission current. One EI filament will
usually give better performance than the other. To select the
better of the two filaments, run two autotunes, one with each
filament, and use the filament that gives the best results. The
CI source only has a single filament.

30 Concepts Guide
 MassHunter Acquisition Software 3
Components adjusted during tuning

Even though the filament emission current may be set, the

default setting is recommended as optimal.
The electron energy, which is the amount of energy on the
ionizing electrons, may also be set. However, it is recommended
to set the electron energy to 70 eV to produce spectra typically
seen with libraries of organic molecules.
Repeller - The repeller accelerates ions out of the ion source
chamber toward the lens stack. If the repeller voltage is too low,
too few ions leave the source, resulting in poor sensitivity and
poor high mass response. If the repeller voltage is too high, too
many ions leave the ion source at too high a velocity. This
results in fragmentation and the formation of precursor ions,
providing poor low-mass response.
Drawout plate - The drawout plate is grounded (not adjustable)
acting as a “negative potential”. This plate draws cations from
the ion source chamber into the lens stack. The drawout plate is
one element in the standard, inert, and CI source lens stack.
Extractor lens - This lens is found in the EXT ion source lens
stack. It is an adjustable lens with a negative potential that
replaces the static grounded drawout lens found in the standard
and inert ion sources for improved sensitivity.
Ion focus lens - The ion focus lens is an electrode with a
negative potential that works with the other two lenses to
“focus” the stream of ions exiting the ion source. Poor ion focus
adjustment results in poor high mass response.
Entrance lens - The entrance lens is designed to protrude into
the quadrupole entrance to minimize the fringe effects of the
quadrupole. Setting the entrance lens voltage in the high end of
the allowable range increases the abundances at high mass and
decreases the abundance of low mass ions.
Quadrupole - The AMU gain and offset are quadrupole
parameters that permit an ion with a specific m/z to travel in a
stable path through the quadrupole mass filter. These values are
ideally adjusted to obtain unit mass tuning ions having a peak
width at half-height of 0.5 AMU.

Concepts Guide 31
3 MassHunter Acquisition Software
Components adjusted during tuning

Detector - The High Energy Dynode (HED) operates at -10,000 V

and attracts the positively charged ions exiting the quadrupole.
The ion beam leaving the quadrupole must turn 90 degrees to
reach the HED. This prevents X-rays and photons from
influencing the ion count. When the ion beam hits the HED, it
creates electrons that are attracted to the less negatively
charged EM.
The EM amplifies the signal output by about 105. The EM
voltage is set to 0-3000 V, and affects sensitivity by increasing
the signal output.

32 Concepts Guide
 MassHunter Acquisition Software 3
Tuning the ion source components

Tuning the ion source components

During tuning, the voltage applied to an adjustable ion source
component is varied to determine the voltage that gives the
maximum abundance for each of the three tuning ions. An
example of varying the voltage on the repeller is seen in Figure 8.
The voltage selected during an autotune is not usually one of
these three peak values. As seen in Figure 8, 24V is optimal for
the low tuning mass ion and reduces the abundance of the high
tuning mass ion by 50%. Selecting one ions’ optimum voltage
over the other can change the ion ratios dramatically.
Also, adjusting the voltage of the next component changes the
abundance values from the previous component’s optimized
voltage. This process, by nature, is iterative. Fortunately
MassHunter autotune is very good at selecting the component
voltages that work best for the ions in this autotune range (69 to
502).

Figure 8 Ramping the repeller voltage to find the value of maximum abundance for the 3 tuning ions

Concepts Guide 33
3 MassHunter Acquisition Software
Tuning the Quadrupole

To optimize the voltage readings for a different range of ions,

you can start with the autotune results and use manual tuning
to refine these parameter while interactively adjusting voltages
for different abundances and ion ratios. These targeted values
are determined by your application.

Tuning the Quadrupole

The quadrupole mass filter separates ions according to their
mass-to-charge ratio (m/z). At any given time, only ions of a
selected m/z can pass through the filter to the detector. The
mass filter in the Agilent 5977 Series MSD is a quadrupole.
The quadrupole is a fused-silica (quartz) tube coated with a thin
layer of gold. The four hyperbolic surfaces create the complex
electric fields necessary for mass selection.
Segments 180 degrees apart are electrically connected.
Segments 90 degrees apart are electrically isolated from each
other. Radio frequencies of adjoining segments are 180 degrees
out of phase with each other. One connected pair has a positive
DC voltage added to the RF voltage, the other connected pair
has a negative DC voltage added to the RF voltage. The pair with
a positive bias is the high pass filter that filters out all masses
lower than the selected m/z. The pair with a negative bias is the
low pass filter that filters out all masses higher than the
selected m/z.
A varying RF voltage combined with a DC voltage is applied to
the two pairs of segments. The magnitude of the RF voltage
determines the m/z of the ions that pass through the mass filter
and reach the detector. The ratio of DC-to-RF voltages
determines the resolution (widths of the mass peaks). There are
two parameters that control the DC and RF voltages:
• AMU gain
• AMU offset
The quadrupole filters out all ions except those of one or more
m/z values as determined by the different voltages applied to
the pairs of hyperbolic surfaces.

34 Concepts Guide
 MassHunter Acquisition Software 3
Tuning the Quadrupole

As the voltages are increased, ions with increasing m/z values

are allowed to pass through. A full MS scan is obtained by
increasing the opposite polarity but keeping the same
magnitude DC voltage with the same RF voltages applied to the
connected pairs of hyperbolic surfaces over an expanded range
of values.

Concepts Guide 35
3 MassHunter Acquisition Software
Tuning the Quadrupole

AMU mass adjustment

Figure 9 shows a plot of increasing opposite polarity DC voltage
and 180 degree out of phase RF voltage applied to the adjacent
hyperbolic surfaces of a quadrupole mass filer. This plot is
known as a Mathieu Stability Diagram. The shaded area
represents a stable region that allows the 152 m/z ion to pass
through the quadrupole and be counted by the detector. The
region to the left of this stable region filters out all ions with a
lower m/z, the region to the right filters out all ions with a
higher m/z value. The stable region also includes overlapping
stable regions for other ions allowing them to also pass through
the quadrupole. To obtain unit resolution on the 152 m/z ion the
quadrupole must be adjusted so that only ions with an m/z of
150.5 to 151.5 can reach the detector.

152
DC voltage

Mass too low Mass too high

Stable region

RF voltage

Figure 9 Mathieu Stability Diagram for a single ion

36 Concepts Guide
 MassHunter Acquisition Software 3
Tuning the Quadrupole

Figure 10 is an example of a Mathieu Stability Diagram showing

how the detection of 3 ions vary with the DC and RF voltages on
opposing poles of the mass filter. Each DC/RF pair that allows a
certain mass/charge to oscillate with stability through the
quadrupole is indicated by a separate curve. The goal is to
obtain a unit mass resolution and a half height peak width of 0.5
AMU by varying the AMU Gain and AMU Offset. The slope of the
Scan line is the AMU Gain. Its Y-axis intercept is the AMU
Offset. If you examine where the Scan line intersects the
stability curves for these three ions in Figure 10 you will see that
the region above the Scan line has a unit resolution for these
three ions. Increasing the lines offset improves specificity at the
cost of resolution and peak width.

153

152

151
DC voltage

DY DY
AMU Gain =
DX
Scan line

DX

AMU Offset

RF voltage

Figure 10 Diagram showing AMU Gain and Offset for 3 ions

Concepts Guide 37
3 MassHunter Acquisition Software
Tuning the Quadrupole

The slope of the scan line is the AMU gain. Adjusting the AMU
gain affects the ratio of DC voltage to RF frequency on the mass
filter, which controls the mass of the ions filtered by the mass
analyzer and the width of the mass peaks. A higher gain gives
narrower peaks. Changing this parameter has a greater effect
on the high mass peaks than on the low mass peaks.
Similar to AMU gain, AMU offset can also control the widths of
the mass peaks. A higher offset also yields narrower peaks
equally at all masses. Another part of the tuning process is
calibration of the mass axis to within +/- 0.2 AMU.

502 502

Scan lines adjusted by Scan lines adjusted by

AMU Gain only AMU Offset only

219 219
DC voltage
DC voltage

AMU Offset

69 69

RF voltage
RF voltage

Figure 11 Diagram showing effects of AMU Gain and Offset adjustment for 3 ions

38 Concepts Guide
 MassHunter Acquisition Software 3
Types of Tuning Available in MassHunter

Types of Tuning Available in MassHunter

There are four types of tunes that can be performed with

MassHunter:
• Autotune
• Manual tune
• Quick tune
• Target tune
Here we will discuss Autotune and Manual tune. See your online
Help for details on Quick tune and Target tune.

Autotune
During an autotune, MassHunter calibrates the instrument to
maximize sensitivity across the entire scan range where the
three major ion fragments of the tuning compound PFTBA are
found. The ions used for tuning are 69, 219, and 502 m/z.
Autotune is the best choice for those applications that require
maximum sensitivity across this entire scan range. To increase
maximum sensitivity for a narrower range you can manually
tune the instrument.
When the autotune completes, MassHunter generates an
autotune report showing settings that the autotune selected for
the key analyzer hardware parameters. The tune report lists the
optimal settings to use for subsequent analyses, in order to
obtain the best sensitivity from your instrument.
Once the lens settings are optimized in the autotune, the EM
voltage is adjusted to best capture the ion abundances. The EM
voltage amplifies the ion current from the mass filter to meet
the target signal abundances. The degree of amplification
applied to the EM voltage is described by the EM Gain value.
During an autotune a gain curve is used to adjust EM voltage to
maintain the same abundance values for the tuning ions as
previous autotunes. This adjusts for EM degradation over time
requiring higher voltages to keep results between tunes
consistent while prolonging EM life.

Concepts Guide 39
3 MassHunter Acquisition Software
Manual tune

The EM Gain can be adjusted to produce the signal necessary to

analyze very small quantities of compound in the sample, such
as trace analyses.

Manual tune
The Manual Tune feature allows you to interactively set
individual tune parameters. This provides more flexibility in
studying the performance of your instrument than an autotune.
Manual Tune is especially useful for performing diagnostics on
the MSD, especially when there is the need to test the
instrument for leaks.
Figure 12 shows some of the parameters that can be interactively
set during a manual tune.

Figure 12 MassHunter Manual Tune dialog

40 Concepts Guide
 MassHunter Acquisition Software 3
Manual tune

When performing a manual tune, you can alter the lens voltages
and examine the effect of this adjustment by executing a profile
scan or spectrum scan. A profile scan (SIM) can be performed
by entering the required masses for PFTBA (69, 219, 502) in the
Profile tab of the Manual Tune screen.
The results of the scan are plotted as a real time plot in manual
tune. During a manual tune, you can continue adjusting the
parameters until the desired effect is achieved.
Mass peak widths can be optimized by adjusting the AMU Gain
and AMU Offset settings on the analyzer. For high mass
samples, adjusting the AMU Gain has the greatest effect while
AMU Offset has an equal effect across the entire mass range.
Mass axis calibration is adjusted by changing the Mass Gain and
Mass Offset. Again, for high mass samples, the Mass Gain has
the greatest effect on the mass axis, while the Mass Offset
adjustments have an equal effect across the entire mass range.
The EM voltage is used to adjust the absolute abundance for all
masses, especially m/z 69. Adjustments in the Repeller, Ion
Focus, Entrance Lens, and Entrance Lens Offset voltages can
alter the relative abundance of one mass to another mass.
Finally, after the manual tune is complete, the relationship
between EM Gain and EM voltage can be re-established. Once all
parameters have been optimized, the required settings can be
saved in your own user-created tune file.

Concepts Guide 41
3 MassHunter Acquisition Software
MSD Data Acquisition

MSD Data Acquisition

You create an acquisition method using the MS Method Editor

in MassHunter. In addition to GC Run parameters, methods also
include MSD data acquisition specifications. There are three
types of MSD data acquisition methods available in
MassHunter: Scan, Selected Ion Monitoring (SIM), and
SIM/Scan.

Scan acquisition type

Select the Scan Acquisition type to scan all the masses within a
specific m/z range. It is most useful for analyses in which the
chemical composition of the sample is unknown. The m/z range
is specified for the Start Mass and End Mass method
parameters shown in the Scan Time Segments table in Figure 13.
The scan speed parameter for this Time segment is entered in
the Scan Speed drop down menu. The higher the scan speed the
lower the resolution of the sample.

Figure 13 Single Quadrupole MS Method Editor displaying a Scan method

42 Concepts Guide
 MassHunter Acquisition Software 3
Scan acquisition type

The general acquisition parameters under the operators control

are:
• Solvent delay - This is the expected time for the elution of
the solvent peak from the column. This setting designates the
amount of time to wait to turn on the filament voltage.
Sending voltage to the filament during a time when there is
no solvent can burn out the filament.
• EMV Mode - This designates if the electron multiplier voltage
should be specified as a gain factor, an absolute voltage, or a
voltage relative to the tune voltage.
• MS Source temperature - See “Source temperature
guidelines" on page 47.
• MS Quad temperature
The scan acquisition parameters under the operators control
are:
• Time - This is the time at which a Time Segment begins.
When a time segment begins, its acquisition parameters
becomes active, replacing the previous set of time segment
acquisition parameters. The parameters used in a time
segment ends when the next time segment begins or at the
end of the data acquisition run time.
• Start Mass - This is the lowest m/z for which data is
acquired. The mass range below this setting is not scanned.
• End Mass - This is the highest m/z for which data is acquired.
The mass range above this setting is not scanned.
• Threshold -This designates the minimum abundance for a
mass abundance pair to be stored as a value included in the
spectrum. The lower the threshold, the more mass peaks will
be stored.
• Scan speed - This is defined by the cycle time and the Mass
range. The scan speeds available range from a maximum
speed with a sampling rate of 0 to speeds that decline by half
as the sampling rate increases by 1. The higher the sampling
rate the lower the number a data points on a plotted peak
and the higher is the sensitivity.

Concepts Guide 43
3 MassHunter Acquisition Software
Scan acquisition type

• Frequency - This designates the number of scans/second and

is an estimate of the scan speed. A scan speed that gives a
frequency reading of 1 scan/second is considered the
minimum for good quality data.
• Cycle Time- The cycle time is the time required to scan every
0.1 m/z typical step size in the ion scan range. It also includes
the time to reset the quadrupole to begin the next scan. The
time spent to scan each incremental m/z value is 40 us for a
sampling rate of 0. A sampling rate of 1 requires a scan time
of 80, 2 requires 160 us, and so on. The mass range multiplied
by the steps/mz, and sampling time gives us the scan time.
The cycle time includes a reset time for the changes in the
quadrupole settings to the scan time. A data point for a peak
is collected once every cycle.
• Step Size- This is the incremental value between scans. The
typical value for an MSD is 0.1 mz.

44 Concepts Guide
 MassHunter Acquisition Software 3
SIM acquisition type

SIM acquisition type

In SIM data acquisition mode, you set the instrument to acquire
data for one or more specific m/z of interest, as opposed to
acquiring data for every ion in a mass range, as is done in the
scan mode. SIM mode is used to detect specific compounds with
very high sensitivity. This is because in SIM, the instrument is
set to collect data on each m/z of interest for a time that you
specify known as Dwell Time. The MassHunter Dwell Time
parameter is shown on the SIM tab in Figure 14. In the SIM tab is
also where you can enter one or more specific m/z for
acquisition. A typical dwell time for SIM mode is 100 msec,
which is much longer than a scan. Since the filter is spending a
longer time acquiring each specific mass, sensitivity is
improved.

Figure 14 Single Quadrupole MS Method Editor displaying a SIM method

Concepts Guide 45
3 MassHunter Acquisition Software
SIM and scan acquisition type

The general acquisition parameters under the operators control

are:
• Solvent delay - This is the expected time for the elution of
the solvent peak from the column. This setting designates the
amount of time to wait to turn on the filament voltage.
Sending voltage to the filament during a time when there is
no solvent can burn out the filament.
• EMV Mode - This designates if the electron multiplier voltage
should be specified as a gain factor, an absolute voltage, or a
voltage relative to the tune voltage.
• MS Source temperature - See “Source temperature
guidelines" on page 47.
• MS Quad temperature
The SIM acquisition parameters under the operators control
are:
• Time - This is the time at which a Time Segment begins.
When a time segment begins, its acquisition parameters
becomes active, replacing the previous set of time segment
acquisition parameters. The parameters used in a time
segment ends when the next time segment begins or at the
end of the data acquisition run time.
• m/z - The ion to acquire for the selected time segment.
• Dwell Time - The length of time for the detector to count
these ions.

SIM and scan acquisition type

This Acquisition Type lets you specify both Scan Time
Segment(s) to acquire all ions contained within a specified mass
range while simultaneously acquiring ions of a specific m/z
value in SIM Time Segment(s). For each time segment entered in
a SIM time segment, select the SIM tab located on the right side
of the dialog and specify each ion to acquire during that time.

46 Concepts Guide
 MassHunter Acquisition Software 3
Source temperature guidelines

Source temperature guidelines

Below are high level guidelines for setting the source temperate
in your GC/MSD. When determining the source temperature
consider the effects that this temperature has on
chromatographic and chemical stability. Too low a source
temperature may cause excessive tailing of higher boiling
compounds. Too high a source temperature may cause chemical
degradation of fragile compounds.

Suggested source temperatures by application

Do not exceed the maximum temperature limit of the source
specified for your instrument.

Forensic & Toxicology: 250-280 °C. Many components (or their

derivatives) are adversely affected by high temperatures.

Volatile Compounds: ≈280 °C

Semi-Volatile Compounds: ≈300 °C

PAH and similar: 350 °C: Most compounds are stable at high
temperatures and lower temperatures may affect
chromatography.
For more information, Agilent Application Notes provide
complete analytical conditions, including MS source and
Quadrupole temperatures.

Concepts Guide 47
3 MassHunter Acquisition Software
Source temperature guidelines

48 Concepts Guide
Agilent 5977 Series MSD System
Concepts Guide

4
Chemical Ionization Theory
Chemical Ionization Overview 50
References on chemical ionization 51
Positive CI Theory 52
Proton transfer 54
Hydride abstraction 57
Addition 57
Charge exchange 58
Negative CI Theory 59
Electron capture 61
Dissociative electron capture 62
Ion pair formation 62
Ion-molecule reactions 63

Agilent Technologies 49
4 Chemical Ionization Theory
Chemical Ionization Overview

Chemical Ionization Overview

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

mass spectrometric analyses. There are significant differences
between CI and electron ionization (EI). This section describes
the most common chemical ionization mechanisms.
In EI, relatively high-energy electrons (70 eV) collide with
molecules of the sample to be analyzed. These collisions
produce (primarily) positive ions. Upon ionization, the
molecules of a given substance fragment in fairly predictable
patterns. EI is a direct process; energy is transferred by
collision from electrons to the sample molecules.
For CI, in addition to the sample and carrier gas, large amounts
of reagent gas are introduced into the ionization chamber. Since
there is so much more reagent-gas than sample, most of the
emitted electrons collide with reagent gas molecules, forming
reagent 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. CI formation involves much
lower energy and is much more “gentle” than electron
ionization. Since CI results in much less fragmentation, CI
spectra usually show high abundance of the molecular ion. For
this reason, CI is often used to determine the molecular weights
of sample compounds.
Methane is the most common CI reagent gas. It yields certain
characteristic ionization patterns. Other reagent gases yield
different patterns and may result in better sensitivity for some
samples. Common alternative reagent gases are isobutane and
ammonia. Carbon dioxide is often used in negative CI. Less
common reagent gases are carbon dioxide, hydrogen, freon,
trimethylsilane, nitric oxide, and methylamine. Different
ionization reactions occur with each reagent gas.

Ammonia is toxic and corrosive. Use of ammonia requires special

WA RN I N G
maintenance and safety precautions.

50 Concepts Guide
 Chemical Ionization Theory 4
Chemical Ionization Overview

Water contamination in reagent gases decreases CI sensitivity

dramatically. A large peak at m/z 19 (H30+) in positive CI is a
diagnostic symptom of water contamination. In high enough
concentrations, especially when combined with calibrant, water
contamination will result in a heavily contaminated ion source.
Water contamination is most common immediately after new
reagent gas tubing or reagent gas cylinders are connected. This
contamination will often decrease if the reagent gas is allowed
to flow for a few hours, purging the system.

References on chemical ionization

A. G. Harrison, Chemical Ionization Mass Spectrometry, 2nd
Edition, CRC Press, INC. Boca Raton, FL (1992) ISBN
0-8493-4254-6.
W. B. Knighton, L. J. Sears, E. P. Grimsrud, “High Pressure
Electron Capture Mass Spectrometry”, Mass Spectrometry
Reviews (1996), 14, 327-343.
E. A. Stemmler, R. A. Hites, Electron Capture Negative Ion Mass
Spectra of Environmental Contaminants and Related
Compounds, VCH Publishers, New York, NY (1988) ISBN
0-89573-708-6.

Concepts Guide 51
4 Chemical Ionization Theory
Positive CI Theory

Positive CI Theory

Positive CI (PCI) occurs with the same analyzer voltage

polarities as EI. For PCI, the reagent gas is ionized by collision
with emitted electrons. The reagent gas ions react chemically
with sample molecules (as proton donors) to form sample ions.
PCI ion formation is more “gentle” than electron ionization,
producing less fragmentation. This reaction usually yields high
abundance of the molecular ion and is, therefore, often used for
determining molecular weights of samples.
The most common reagent gas is methane. Methane PCI
produces ions with almost any sample molecule. Other reagent
gases, such as isobutane or ammonia, are more selective and
cause even less fragmentation. Because of the high background
from the reagent gas ions, PCI is not especially sensitive and
detection limits are generally high.
There are four fundamental ionization processes that take place
during PCI at ion source pressures in the 0.8 to 2.0 Torr range.
These are:
• Proton transfer
• Hydride abstraction
• Addition
• 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.
EI, methane PCI, and ammonia PCI spectra of methyl stearate
are shown in Figure 15 on page 53. The simple fragmentation
pattern, large abundance of the [MH]+ ion, and the presence of
the two adduct ions are characteristic of positive chemical
ionization using methane as a reagent gas.
The presence of air or water in the system, especially in the
presence of PFDTD calibrant, quickly contaminates the ion
source.

52 Concepts Guide
 Chemical Ionization Theory 4
Positive CI Theory

Figure 15 Methyl stearate (MW = 298): EI, methane PCI, and ammonia PCI

Concepts Guide 53
4 Chemical Ionization Theory
Positive CI Theory

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 (sample) M is
greater than that of the reagent gas, the protonated reagent gas
will transfer its proton to the analyte forming a positive charged
analyte ion.
The most frequently used example is the proton transfer from
CH5+ to the molecular analyte, which results in the protonated
molecular ion MH+.
The relative proton affinities of the reagent gas and the analyte
govern the proton transfer reaction. If the analyte has a greater
proton affinity than the reagent gas, then proton transfer can
take place. Methane (CH4) is the most common reagent gas
because its proton affinity is very low.
Proton affinities can be defined according to the reaction:
B + H+ BH+
where the proton affinities are expressed in kcal/mole.
Methane's proton affinity is 127 kcal/mole. Tables 1 and 2 on
page 55 list the proton affinities of several possible reagent gases
and of several small organic compounds with various functional
groups.
The mass spectrum generated by a proton-transfer reaction
depends on several criteria. If the difference in proton affinities
is large (as with methane), substantial excess energy may be
present in the protonated molecular ion. This can result in
subsequent fragmentation. For this reason, isobutane with a
proton affinity of 195 kcal/mole may be preferred to methane
for some analyses. Ammonia has a proton affinity of
207 kcal/mole, making it less likely to protonate most analytes.
Proton-transfer chemical ionization is usually considered to be
“soft” ionization, but the degree of the softness depends on the
proton affinities of both the analyte and the reagent gas, as well
as on other factors, including ion source temperature.

54 Concepts Guide
 Chemical Ionization Theory 4
Positive CI Theory

Table 1 Reagent gas proton affinities

Proton affinity Reactant ion

Species kcal/mole formed

H2 100 H3+ (m/z 3)

CH4 127 CH5+ (m/z 17)

C2H4 160 C2H5+ (m/z 29)

H2O 165 H O+ (m/z 19)

3

H2S 170 H3S+ (m/z 35)

CH3OH 182 CH3OH2+ (m/z 33)

t-C4H10 195 t-C4H9+ (m/z 57)

NH3 207 NH4+ (m/z 18)

Table 2 Proton affinities of selected organic compounds for PCI

Proton affinity Proton affinity

Molecule (kcal/mole) Molecule (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 180

cyclopropane

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

Concepts Guide 55
4 Chemical Ionization Theory
Positive CI Theory

Table 2 Proton affinities of selected organic compounds for PCI

(continued)

Proton affinity Proton affinity

Molecule (kcal/mole) Molecule (kcal/mole)

Hydrobromic acid 140 trans-2-Butene 180

Hydrochloric acid 141 Trifluoroacetic acid 167

Isopropyl alcohol 190 Xylene 187

Methanol 182

56 Concepts Guide
 Chemical Ionization Theory 4
Positive CI Theory

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 is higher than the
hydride-ion affinity of the ion formed by the analyte's loss of H–,
the thermodynamics are favorable for this chemical ionization
process. Examples include the hydride abstraction of alkanes in
methane chemical ionization. In methane CI, both CH5+ and
C2H5+ are capable of hydride abstraction. These species have
large hydride-ion affinities, which results in the loss of H– for
long-chain alkanes, according to the general reaction
R+ + M 
 [M–H]+ + RH
For methane, R+ is CH5+ and C2H5+, and M is a long-chain
alkane. In the case of CH5+, the reaction proceeds to form
[M–H]+ + CH 4+ H2. The spectra resulting from hydride
abstraction will show an M–1 m/z peak resulting from the loss
of H–. This reaction is exothermic so fragmentation of the
[M–H]+ ion is often observed.
Often, both hydride-abstraction and proton-transfer ionization
can be evident in the sample spectrum. One example is the
methane CI spectrum of long-chain methyl esters, where both
hydride abstraction from the hydrocarbon chain and proton
transfer to the ester function occur. In the methane PCI
spectrum of methyl stearate, for example, the MH+ peak at
m/z 299 is created by proton transfer and the [M–1]+ peak at
m/z 297 is created by hydride abstraction.

Addition
For many analytes, proton-transfer and hydride-abstraction
chemical ionization reactions are not thermodynamically
favorable. In these cases, reagent-gas ions are often reactive
enough to combine with the analyte molecules by condensation
or association (addition reactions). The resulting ions are called
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 m/z mass peaks.

Concepts Guide 57
4 Chemical Ionization Theory
Positive CI Theory

Addition reactions are particularly important in ammonia CI.

Because the NH3 has a high proton affinity, few organic
compounds will undergo proton transfer with ammonia reagent
gas. In ammonia CI, a series of ion-molecule 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 m/z, either
through condensation or association. If this resulting ion is
unstable, subsequent fragmentation may be observed. The
neutral loss of H2O or NH3, observed as a subsequent loss of
18 or 17 m/z, respectively, is also common.

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 used for charge exchange
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 reagent gases, once
ionized, has a recombination energy 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, the
first reaction above is exothermic and thermodynamically
allowed.
Charge-exchange chemical ionization is not widely used for
general analytical applications. It can, however, be used in some
cases when other chemical ionization processes are not
thermodynamically favored.

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Negative CI Theory

Negative chemical ionization (NCI) is performed with analyzer

voltage polarities reversed to select negative ions. There are
several chemical mechanisms for NCI. Not all mechanisms
provide the dramatic increases in sensitivity often associated
with NCI. The four most common mechanisms (reactions) are:
• Electron capture
• Dissociative electron capture
• Ion pair formation
• Ion-molecule reactions
In all of the cases except the ion-molecule reactions, the reagent
gas serves a function different from the function it serves in
PCI. In NCI, the reagent gas is often referred to as the buffer
gas. When the reagent gas is bombarded with high energy
electrons from the filament, the following reaction occurs:
Reagent gas + e– (230 eV)  Reagent ions + e– (thermal)
If the reagent gas is methane (Figure 16 on page 60), the reaction
is:
CH4 + e– (230 eV)  CH4+ + 2e–(thermal)
The thermal electrons have lower energy levels than the
electrons from the filament. It is these thermal electrons that
react with the sample molecules.
There are no negative reagent gas ions formed. This prevents
the kind of background that is seen in PCI mode and is the
reason for the much lower detection limits of NCI. The products
of NCI can only be detected when the MS is operating in
negative ion mode. This operating mode reverses the polarity of
all the analyzer voltages.
Carbon dioxide is often used as a buffer gas in NCI. It has
obvious cost, availability, and safety advantages over other
gases.

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Negative CI Theory

Figure 16 Endosulfan I (MW = 404): EI and methane NCI

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Negative CI Theory

Electron capture
Electron capture is the primary mechanism of interest in NCI.
Electron capture (often referred to as high-pressure electron
capture mass spectrometry or HPECMS) provides the high
sensitivity for which NCI is known. For some samples under
ideal conditions, electron capture can provide sensitivity as
much as 10 to 1,000 times higher than positive ionization.
Note that all the reactions associated with positive CI will also
occur in NCI mode, usually with contaminants. The positive
ions formed do not leave the ion source because of the reversed
lens voltages, and their presence can quench the electron
capture reaction.
The electron capture reaction is described by:
MX + e– (thermal)  MX– ·
where MX is the sample molecule and the electron is a thermal
(slow) electron generated by the interaction between high
energy electrons and the reagent gas.
·
In some cases, the MX– radical anion is not stable. In those
cases, the reverse reaction can occur:
·
MX–  MX + e–
The reverse reaction is sometimes called autodetachment. This
reverse reaction generally occurs very quickly. Thus, there is
little time for the unstable anion to be stabilized through
collisions or other reactions.
Electron capture is most favorable for molecules that have
hetero-atoms. For example: nitrogen, oxygen, phosphorus,
sulfur, silicon, and especially the halogens: fluorine, chlorine,
bromine, and iodine.
The presence of oxygen, water, or almost any other contaminant
interferes with the electron-attachment reaction. Contaminants
cause the negative ion to be formed by the slower ion-molecule
reaction. This generally results in less sensitivity. All potential
contamination sources, especially oxygen (air) and water
sources, must be minimized.

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Negative CI Theory

Dissociative electron capture

Dissociative electron capture is also known as dissociative
resonance capture. It is a process similar to electron capture.
The difference is that during the reaction, the sample molecule
fragments or dissociates. The result is typically an anion and a
neutral radical. Dissociative electron capture is illustrated by
the reaction equation:
MX + e–(thermal)  M ·+X –

This reaction does not yield the same sensitivity as electron

capture, and the mass spectra generated typically have lower
abundance of the molecular ion.
As with electron capture, the products of dissociative electron
capture are not always stable. The reverse reaction sometimes
occurs. This reverse reaction is sometimes called an associative
detachment reaction. The equation for the reverse reaction is:
·
M + X–  MX + e–

Ion pair formation

Ion pair formation is superficially similar to dissociative
electron capture. The ion pair formation reaction is represented
by the equation:
MX + e–(thermal) M+ + X¯ + e–
As with dissociative electron capture, the sample molecule
fragments. Unlike dissociative electron capture, however, the
electron is not captured by the fragments. Instead, the sample
molecule fragments in such a way that the electrons are
distributed unevenly and positive and negative ions are
generated.

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Ion-molecule reactions
Ion-molecule reactions occur when oxygen, water, and other
contaminants are present in the CI source. Ion-molecule
reactions are two to four times slower than electron-attachment
reactions and do not provide the high sensitivity associated
with electron capture reactions. Ion-molecule reactions can be
described by the general equation:
M + X–  MX–
where X– is most often a halogen or hydroxyl group that was
created by ionization of contaminants by electrons from the
filament. Ion-molecule reactions compete with electron capture
reactions. The more ion-molecule reactions that occur, the fewer
electron capture reactions occur.

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Negative CI Theory

64 Concepts Guide
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Agilent Technologies, Inc. 2013

First Edition, February 2013

Agilent Technologies