Introduction to Mass

Spectrometry
Training course on GC/MS
Nha Trang 13-18/10 2008
Charlotta Rylander
Outline
General principles of mass spectrometry

Ionization techniques

Mass analyzers for GC/MS Detectors

Scan and SIM mode

Tuning

Common problems with GC-MS systems

GC detectors

http://elchem.kaist.ac.kr/jhkwak/analchem/09/03/36.gif
Some useful definitions
Analytes = The compounds we would like to
to analyze.
Isotopes = Atoms with the same number of
electrons and protons, but different number of
neutrons. Isotopes have the same chemical
properties but differ in molecular mass.
5
Analysis by GC-MS
Mixture
Separation Identification
GC
MS
A + B + C B A C
B
A
C
m/z
m/z
m/z
General principles on mass
spectrometry
Sample
introduction
Ionization of
sample in the
ion source
Separation of
ions by mass
analyzer
Detector
Computer
system
Resulting chromatogram
Ionization techniques
The ionization takes place in the ion source.
Samples from GC interface are in gas-phase when introduced into the
MS. The MS is operated in vacuum to make sure analytes are
evaporized and to avoid collisions between analytes and other
compounds.
Two different ionization methods
Electron Impact Ionization (EI)
Chemical Ionization (CI)
Sample
introduction
Ionization of
sample in the
ion source
Separation of
ions by mass
analyzer
Detector
Computer
system
Electron Impact Ionization (EI)
Most widely used method
Analytes are bombared
with high-energy electrons
(usually 70eV)
As a result of collision, an
electron is removed from
the analytes (M),
generating a molecular ion
M+ (radical cation)
M + e
-
M
+
+ 2e
-
Electron Impact Ionization (EI)
Due to excess internal energy, fragmentation
of the molecular ion will occur.
The fragmentation is reproducible and
characteristic of the compund.
It is also possible to predict the fragmentation
on the basis of chemical structures which is
why MS is good tool for structure elucidation
of unknown compounds

Drawbacks with EI
Sometimes the fragmentation is
too great (depending on the
stability of the sample molecules)
and the molecular ion will not
show up in the mass spectra. It is
then possible to reduce the
ionization voltage, but the
disadvantage is that the
fragmentation pattern will change
and the obtained spectra cannot
be compared to standard
litterature spectra.

Another solution is to use
chemical ionization (CI)!

Watson, Introduction to Mass Spectrometry, 4th ed
Chemical Ionization (CI)
Softer ionization technique Less fragmentation Easier to find
molecular ions.

Two different modes: Negative chemical ionization (NCI) and
Positive Chemical Ionization (PCI).

NCI is used for analytes that are able to form stable negative ions,
for example samples containing acidic groups or halogens. NCI is
often used to analyze pesticides (contains Cl or Br).

PCI is used for samples that can form positive ions (most
compounds).


Chemical Ionization (CI)
The principle for NCI and PCI is similar:

Reagent gas (usually methane, isobutane or ammonia) is introduced into the source where
it is ionized:
PCI (simplified): CH
4
+ e
-
CH
4
+
+2e
-
CH
4
+ CH
4
+

CH
3
+ C

H
5
+


NCI: CH
4
+ e
-
CH
4
-



The ionized gas collide with the sample molecules generating a [M+H]
+
or [M+H]
-
ion that is
detected:


PCI:

CH
5
+

+ M [M+H]
+

+ C

H
4


NCI: CH
4
-
+ M [M+H]
-

+ C

H
4




EI spectra/ PCI Spectra
Harris. Quantitative Chemical Analysis, 6th ed.
Mass analyzers
After analytes have been ionized they are separated
according to their mass-to-charge ratio (m/z) in a mass
analyzer (mass filter).
Quadrupoles and ion traps are common mass filters in
GC-MS systems.
Time of flight (TOF) mass filter is very much used
nowadays in LC-MS systems.
Sample
introduction
Ionization of
sample
Separation of
ions by mass
analyzer
Detector
Computer
system
Transport of ions to the mass filter
The ionization takes place in the ion source.
Ions are then transported to the mass filter by
focusing lenses. These have a voltage
running through them and by either attracting
or repelling the ions they guide them into the
mass filter.
High and low resolution MS
Resolution = difference in m/z values of
ions that can be separate from another.
Quadrupoles and ion traps have constant
resolution, meaning that ions that differ
with 1 m/z unit will have the same
separation at m/z 150 an 151 as they do at
m/z 1000 and 1001.
High resolution instruments do not have
constant resolution, but constant resolving
power.


Resolving power (R)
Low resolution MS instruments have a resolving
power of 1000-2000. Quadrupoles and ion traps
has constant resolution (M=1) and R will then
vary with m/z. On the other hand TOF has
contant resolving power, meaning that at lower
m/z the resolution will increase.
2000
1999 2000
2000

low
R
M
n
=2000
M
m
=1999
m n
n
M M
M
R

M
n
=highest mass M
m
=lowest mass
M
n
=250,1807
M
m
=250,1933
19857
1807 , 250 1933 , 250
1933 , 250

high
R
High resolution MS ha a resolving power of
up to 20 000, making it possible to
distinguish between very similar masses.
http://www.ivv.fraunhofer.de/ms/resolve10.gif
Quadrupole mass spectrometers
http://www.bris.ac.uk/nerclsmsf/images/quadrupole.gif
A quadrupole consists of four cylindrical rods, all parallel to each other.
Ions are introduced into the tunnel in between the four rods.
A direct current field is applied to two rods in the quadrupole and a radio
frequency to the others. The rods generate an electric field which ions can travel
through.
For a given DC/RF potential only ions with a specific m/z value are able to pass
through the quadropole and reach the detector.
All other ions will either collide with the rods or travel outside the qudrupole.
Therefore they will never reach the detector.
Quadrupole
http://ael.gsfc.nasa.gov/images/saturn/quadrupole.jpg
The quadrupole instrument
Vacuum
DC and AC Voltage
Ion trap mass spectrometer
The ion trap uses three electrodes to trap ions in small volumes.
Various voltages are applied to the ring electrodes as well as to
the entrance and exit endcap electrodes. A cavity is created were
the ions are trapped.
Depending on different voltage settings, ions at a specific m/z is
ejected and detected.
Time of flight (TOF)
High resolution MS.
Separates ion with the same kinetic energy
but different m/z, because heavier ions
require more time to travel a fixed distance.
Harris. Quantitative Chemical Analysis, 6th ed.
MS detectors
Many different types available
Electron multipliers (EM) are often used
Continuous Dynode Version mainly in GC-MS

Sample
introduction
Ionization of
sample
Separation of
ions by mass
analyzer
Detector
Computer
system
Continious dynode EM

The EM multiplies incident
charges, thereby amplifying the
signal. The current is measured
that is proportional to the amount
of analyte in the sample.
EMs have limited lifetime which is
dependent on the number of ions
that hits the device, i.e., the
amount of samples introduced
and number of samples
analyzed.

+Fast response
+ High sensitivity
Watson, Introduction to Mass Spectrometry, 4th ed
Scan mode
The MS can be operated in scan mode or in
single ion monitoring (SIM).
Scan mode means that the mass filter is set
to pass a range of masses. A spectra is
obtained that is used for interpretation or
mass library search.
Scan mode is less sensitive since most ions
strike the quadropole rods during the scan
and never reaches the detector.
EI Mass spectra
Acetone
Elemental
composition:
C
3
H
6
O
Nominal
mass: 58
Propionaldehyde
Elemental
composition:
C
3
H
6
O
Nominal mass: 58
Harris. Quantitative Chemical Analysis, 6th ed.
Isotope peak pattern
Many POPs contains Cl or Br atoms. Cl has two isotopes;
35
Cl
and
37
Cl. 76% of all chlorine atoms are
35
Cl and 24% are
37
Cl.
The mass spectra we obtain from scan mode show the isotope
composition of fragments.
If we have a molecule containing four Chlorine atoms, there are
five possible combinations of chlorine isotopes:
4 x
35
Cl
3 x
35
Cl + 1 x
37
Cl
2 x
35
Cl + 2 x
37
Cl
1 x
35
Cl + 3 x
37
Cl
4 x
37
Cl

Since every four chlorine atom in nature occur as
37
Cl, most of
the molecules will have the isotope composition 3 x
35
Cl + 1 x
37
Cl. Therefore, the most intensive peak in the mass spectra will
occur at that m/z.
Isotope peak patterns
Single ion monitoring (SIM)
In SIM mode the mass filter is set to pass some specific m/z ratios.
Therefore it is possible to monitor only a few compounds at specific
retention time windows.

In SIM mode, two masses are monitored for each compound. These are
usually the two most intensive isotope peaks within the fragment.


Window 1: Monitor
only PCB 28 & 52
Window 2: Monitor
PCB 99, 101,105
Window 3: Monitor
PCB 138, 153,156
Window 4: Monitor
PCB 170, 180, 194

1
3 4 2
SIM
SIM increases sensitivity and is used for
quantitative analysis.
When using SIM mode one needs to know in
advance which masses that should be
monitored.
When starting to analyze new analytes,
always start by running scan mode to select
appropriate ions for SIM.

Scan and SIM chromatograms
Scan mode
SIM mode
Tuning

Tuning of the MS instrument means optimization of
the technical settings so you will have good
senisitivity when the analysis starts.
Tuning can be performed manually or automatically.
The MS needs to be tuned when it has been
opened.
Frequency of tuning highly instrument dependent.
(Source)

Common problems in GC-MS
systems
PROBLEM SUGGESTED SOLUTION

Poor sensitivity in the MS Tune the MS, if no improvement, the ion
source may be dirty and needs to be
cleaned.
No filament current The filament is broken and needs to be
replaced.
Poor resolution between peaks May depend on a dirty GC-column. Run
the GC-oven isothermal for 3 h at a
temperature close to maximum
temparature for the column (se
specifications from producer). If no
improvement, cut a piece of the column
at the inlet (30-50 cm). If this doesnt
help, one may need to change the
whole column.
GC/MS-MS
MS1
Collision cell
MS2
Taking a Mass spectra of a mass spectra
MS 1 selects an ion cuurent at a specific m/z for entry
into the collision cell.
In the collision cell, the selected ion becomes energized
by collisions.
Some of the selected ions will dissociate in the collision
cell and form fragment ions that are moniored in MS 2.
Use of MS/MS
Quantitative analysis; high specificity and
senistivity.
Structure determination of unknown
compounds.
Mapping fragmentation pathways.