POLARIS GC/MS

POLARIS GC/MS n
Optimized Ion Trap Mass Spectrometry
for real-world sample analysis

POLARIS GC/MS n
Introducing ion trap mass spectrometry
The Finnigan Polaris is the latest ion
trap mass spectrometer for gas
chromatographic detection. It is
especially designed for the benchtop
market requirements among which are
ruggedness, reliability, high sample
throughput, and ease of use and
maintenance. The commercial ion
trap detector was introduced by
Finnigan in the 1980’s and enhanced
in the 1990’s with the addition of
features such as MS/MS and negative
ion chemical ionization. Now with
Polaris, a chromatographer can have
the power of simultaneous full scan EI
and MS/MS available at the click
of a mouse in one versatile, affordable
instrument. The system features:
New TRACE GC
• Electronic flow/pressure control
• Column characterization for
retention time matching
New Xcalibur Software
• Common platform for ThermoQuest
GC/MS, LC and LC/MS systems
• Merlin Report Writer for
customizable, automated reporting
New High Temperature
Ion Source
• Fully customer-tested for
ruggedness and reliability
• Supports EI, MS/MS, CI and
probe analysis in all modes
Benzophenone
10 ng test mix
Xcalibur's Merlin Report Writer gives the analyst complete flexibility and simplicity for
fully automated, customizable reports.
1
2
Polaris, with its new ion source, is designed for high throughput of the most difficult sample matrices.
With a source temperature of 250ºC contamination is minimized. Hundreds of samples can be analyzed
between routine source maintenance.
3
4
1 Removable ionization volume
2 Long-life filament
3 High temperature ion source
4 Ion trap mass analyzer

Full scan EI ANALYSIS key applications: • Industrial
• Environmental
• Residue
Industrial Alcohols
100
100
50
0
0
s s
TIC
1.8 2.0 2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.6 3.8 4.0 4.2 4.4 4.6 4.8 5.0 5.2
Time (min)
100
80
60
40
20
0
Full Scan
EI/MS
41.1
43.1
39.1 45.1
55.1
59.0
73.0
Full scan analysis gives the analyst complete confidence, with NIST library identification
and superior quantitation.
3.43
3.52
3.66
40 50 60 70 80 90 100 110 120 130 140 150
m/z
40 50
55 58
57
50 53 60
60
3.77
69.1 74.1 85.1
84.1 87.1 101.1
Industrial raw materials such as alcohols and ketones can be analyzed without the presence of
ion-molecule reactions which typically cause misidentification by all other ion traps.
Validated compound identification
NIST library
confirmation
36 39
4143
42 45
44
59
67 69 71 74
70
73
80
83
85
87
OH
3.91
3.99
101
90 100
2-methyl-3-pentanol
2-methyl-3-pentanol
110
Ion trap detectors are well known for
their superb sensitivity in the full scan
mode. The analyzer acts similar to an
absorption trap in that the target
analyte concentration builds up over
time (milliseconds) until the
population of ions fills the detector to
capacity. The ions are then expelled
into the electron multiplier for
identification and quantitation.
In this way the ion signal is much
stronger than other types of
mass spectrometers.
In addition to the obvious sensitivity
increase, ion traps also have superb
selectivity for removing unwanted
background interferences. Ion trap
detectors have the ability to select
which ion masses are trapped by the
detector and which ions are allowed to
pass through and not be counted. All
of the storage capacity of the detector
is optimized for the target analytes
and not the matrix. This is especially
useful when measuring PCBs or
dioxins in sludge, drugs in biological
fluids, pesticide residues in fruits and
vegetables, and other difficult
applications.

New Finnigan Polaris GC/MS/MS ultimate selectivity for target analytes
Ion trap GC/MS/MS is the most
powerful chromatography technique a
scientist can utilize. MS/MS is quite
simply this:
A molecule is ionized in the normal
manner and the ions are sent into the
ion trap. The ion trap is tuned to a
single ion mode in which a preselected
(parent) ion is captured and
all other ions are allowed to pass
through the detector. The parent ion
is now energized within the ion trap
to dissociate it into a spectrum of
product ions. These unique product
ions are free from chemical
interference, which allows for extreme
sensitivity and detectivity in
complicated matrices.
High throughput is necessary in
today’s laboratory environment.
Difficult analyses are not exempt
from this requirement. Determination
of pesticides in food, endocrine
disrupters or dioxins in the
environment, drugs in biological fluids
and many others are all applications
that can be performed routinely and
accurately with GC/MS/MS.
Triazolam – Tricyclic Antidepressant
100
0
150
100
203.1
238.1
279.1
316.1
342.0
207.1 239.1 281.1
177.2
240.1 307.1
343.9
176.1
253.1
317.1
163.1
202.1 237.1
267.1
282.2
341.1
344.9
361.1
386.0
0
200 250 300 350 400
m/z
313.1 277.1
100
315.1
100
0
150
313.1
200 250 300 350 400
m/z
16.0 16.5 17.0 17.5 18.0 18.5 19.0 19.5 20.0 20.5 21.0 21.5 22.0
100
80
60
40
20
0
(a)
19.92
20.01
20.23
0
150
174.1
242.2
243.2
278.1
201.2
214.2 251.2 286.2
313.1
313.8
200 250 300 350 400
m/z
The process of MS/MS involves (a) ionization of the compound of interest; (b) isolation of a single ion; and
(c) dissociation of the isolated ion into its product ions. This process increases the selectivity of the analysis by
removing the matrix from the product ions.
Pesticides in Orange Extract – Matrix Removal
Full Scan
EI/MS
MS/MS Chromatogram
MS/MS of Fensulfothion
(parent ion - m/z 293)
156.0
158.1
(b)
Time (min)
21.33
21.35
100 120 140 160 180 200 220 240 260 280
m/ z
Isolation
Ionization Dissociation
The selectivity of MS/MS analysis is far superior to full scan EI or SIM. This allows the chromatographer to
achieve lower detection limits and unambiguous compound identification in the most difficult matrices.
19.91
217.9
236.0
237.0
(c)
263.9
265.0
265.9
293.0
300

100
0
100
0
Full scan
EI/MS
6.7 3
7.57
8.03
6 7 8 9 1 0 1 1
Time (min)
9.30
1 0. 05
1 0.46
6.30 7.1 9 7.7 5
8.4 0
8.9 2
9.86
1 0.54 1 1.06
MS/MS
9.1 4
POLARIS
Collect full scan and MS/MS data simultaneously
9.30
Mevinphos
Mevinphos
(parent ion - m/z 192)
1 0. 06
9 .58 1 0.39
1 1.05
8 0 1 0 0 1 2 0 1 4 0 1 6 0 1 8 0 2 0 0
Simultaneous full scan and MS/MS allows accurate quantitative and qualitative analysis of target compounds
and unknown compounds.
10 0
0
100
0
Full scan
EI/MS
109.1
127.0
m / z
1 6 4 .1
1 9 2.1
78.9 160.1 19 2.8
85. 1 99.0
110.1
149. 1
164.8
194.1
MS/MS
10 2.1
109.1
11 3. 0
127.0
13 5 .1
14 9 .1
1 5 9.9
1 6 4.0
1 6 4.8
key applications:
• Arson
• Pesticide residue
• Sports testing
GC/MS/MS is a target analysis
technique, so you must know what
you are looking for in the sample.
However, full scan EI/MS analysis
allows the chromatographer to
measure any compound that might be
present in the sample provided that
the concentration is sufficient and the
matrix is not too intense in that part
of the chromatogram. As you can well
imagine a combination of full scan and
MS/MS would be very powerful. The
full scan chromatogram can be used to
identify and quantitate compounds
that are not on the target analyte list,
while the MS/MS chromatogram
provides very accurate low level
quantitation for the selected analytes.
Our new Xcalibur software gives the
analyst the ability to collect full scan
and MS/MS data simultaneously. How
is this possible? Polaris combines its
rapid scan speed with the powerful
Xcalibur software which collects and
separates the data appropriately.
Quantitative and qualitative analysis is
both accurate and reliable. This
reduces analysis time, enhances data
quality and maximizes productivity.

Chemical IONIZATION key applications: • Explosives
• MW determination
• Toxicology
Chemical Ionization has always been
an important feature of mass
spectrometry. A significant percent of
the spectra in the standard library
database do not have a molecular ion
present. Clearly this means there is a
strong probability that many of the
compounds tested for in routine or
research laboratories will not show a
molecular ion in the spectrum. By
providing molecular weight
information, positive ion chemical
ionization (PICI) naturally becomes
important in compound identification.
Traditional M+1, M+29, and M+41
adduct ions with methane reagent gas
are invaluable in determining the
molecular weight of a compound.
Negative ion chemical ionization
(NICI) is a very selective and sensitive
tool for determining compounds that
are electronegative such as PCBs,
dioxins, chlorinated pesticides, and
derivatized drugs. Only those
compounds that are electronegative
will respond to any extent and
produce quantities of negative ions.
This makes NICI very selective when
confronted with a difficult matrix.
In combination with MS/MS, highly
halogenated compounds can be
accurately measured at femtogram
levels with consistent library matching
in the most challenging matrices.
PICI Mode – Analgesic/Narcotics
100
9.44
0
8.0 8.2 8.4 8.6 8.8 9.0 9.2 9.4 9.6 9.8 10.0 10.2 10.4 10.6 10.8 11.0
Time (min)
100
80
60
40
20
0
100
174.1
202.1
172.1 218.1
220.1
150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300
m/z
0
8.2 8.4 8.6 8.8 9.0 9.2
Time (min)
9.4 9.6 9.8 10.0 10.2
100
80
60
40
20
0
Methane CI
Positive ion chemical ionization, complete with confirmatory adduct ions, is a powerful complementary
tool for toxicological analysis.
NICI Mode – Explosives
Negative CI
9.10
9.02
197.0
The selectivity and sensitivity of negative ion (electron capture) chemical ionization is useful for testing
compounds such as explosives, derivatized drugs, dioxins, and PCBs.
210.0
181.0 211.0
167.0 198.0
137.1 209.0
Meperidine - MW 247
(Demerol)
232.0
246.0
248.0
Trinitrotoluene - MW 227
(TNT)
249.0
276.0
M+41
288.2
120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300
m/z
226.8
M+1
M+29
CH 3
0 2 N NO 2
NO 2

Direct Probe ANALYSIS key applications: • Research
• Chemical synthesis
• Natural products
Direct Insertion – Antibiotics
100
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
0
98.2
116.1
123.2
132.1
158.2
174.1
(M) Erythromycin - MW 733
176.1
365.1
383.1
179.1 557.3 648.3
715.3
221.1 307.2 334.2
490.2
522.2 660.3
239.1 289.2 384.1
411.0 464.3 574.3
495.2 602.3
644.4 661.4 716.4
100 150 200 250 300 350 400 450 500 550 600 650 700 750
m/z
Direct probe analysis combined with MS/MS can quickly determine the presence of a drug, carcinogen,
endocrine disrupter, or priority pollutant in any matrix without the need for sample preparation or
chromatography.
HO
HO
O
472.2
OH
O O
O
N
OH
558.3
Interchangeable probes for non-GC applications
O
O
O
OH
O
Direct Exposure – DEP
Direct Insertion – DIP
Direct probe mass spectrometry is an
alternative sampling technique when
the sample material cannot pass
through a capillary GC column.
Some examples include sugars, long
chain amino acids, small proteins and
triglycerides. The spectrum of these
compounds can be obtained by placing
the sample onto a probe tip and
inserting the probe directly into the
mass spectrometer.
The direct sample probe can also be
used as a screening tool when
combined with MS/MS. A complex
sample such as soil, blood, hair or
other biological material can be placed
directly onto the probe. By using
MS/MS, the presence or absence of
particular target analytes can be
determined. This efficient technique
eliminates tedious sample preparation
and gas chromatographic analysis,
saving cycle time and money.
Finnigan Polaris offers the
chromatographer a wealth
of fast, powerful and reliable
solutions. Come join us in
the company of scientists –
you’ll see the difference
in your data.

System configuration
Polaris includes the TRACE GC* with Digital
Pressure and Flow Control (DPFC); analyzer with EI
source and full scan EI, SIM, MS/MS and MS n modes.
PC data system † has a minimum of Pentium II 400
MHz processor, 64 MB SDRAM, 6.4 GB hard drive,
32X CD-ROM, 17” SVGA monitor and Xcalibur
software for full instrument control, data acquisition and
fully automated data processing and customized report
generation.
Options/Accessories
Autosampling
AS2000 liquid* or HS2000 headspace* autosampler.
Other sampling accessories available.
Sample introduction
Direct Sample Probe system with interchangeable direct
insertion or direct exposure probes.
TRACE GC
Second detector installed including FID, ECD or NPD.
Programmable Temperature Vaporizer (PTV) for split,
cold split, splitless and large volume injection (LVI) with
digital pressure and flow control (DPFC). Cold
on-column injector with large volume injection and
software optimization.
Polaris MS detector
Open-split or jet separator interface for Megabore
columns.
Vacuum interlock system.
Turbomolecular pump (230 L/sec).
External Ionization CI mode for PICI and
NICI (ECD-MS) applications.
Xcalibur Data System
NIST library
Wiley library
Pfleger-Mauer-Weber library
Finnigan pesticide library
*Comprehensive literature is available or visit our website at www.tmqaustin.com
†Call for current data system specifications.
©1999 ThermoQuest Corporation. Printed in USA. ThermoQuest is a public subsidiary of
Thermo Instrument Systems Inc., a Thermo Electron company.
In the company of scientists – Lockheed
Martin Astronautics, Canada Dept. of
HS2000
Agriculture, Nestle, Headspace New York State Dept. of
Autosampler
Health, US Environmental Protection Agency,
(optional)
Euratom, Federal Bureau of Investigation,
Australia Aeronautical & maritime Residue
Laboratory, Princess Wales Hospital,
University of North Carolina-Charlotte,
Eawag, North Dakota Dept. of Health, N.
Tyneside General Hospital, American Water
Works Service, Dow Agrosciences, Purdue
University, United States Dept. of
Agriculture, Agriculture & Agri-food Canada,
Biochrome GMBH, UCB Chemical Corporation,
Southern Illinois University, Iatsa, NASA
Research Center, CRN Instituto, Clearwater
Fine Foods, Lab Agroalimentario, Kodak,
Centro De Investigation En Alimentacion Y
Desarrollo A.C., IBM, Texas Parks & Wildlife,
University of California, Montana St.
Department of Justice, Alberta Justice
Department, Monsanto, Rockwell Science
Center, Arkansas Crime Lab, University of
Ottawa, Saitama Turbomolecular Food Health, MD Anderson
Cancer
Pump (optional)
Center, Azienda, US Customs,
Commonwealth of Virginia, Dolunay, San
Antonio Water System, University of Almeria,
Charles Stark Draper Lab, Battelle Chemical
and Environmental Technologies, Surface
Science Laboratories, HMT Technology,
University of Colorado Health Sciences
Center, University of Texas, Club Cosmetics,
Polizei Hamburg, Gesellschaft, US Army Dental
Research, Cisesma, Toyoonaka City, Wakayama
Agriculture, University of Dundee, Bracco,
Filtrona, Giotti, GIFU Research Center,
Carbogen, Zeneca Central Toxicology, Denmarks
Tekniske, INTERNATIONAL Lafon, OFFICES University of Stockholm,
AUSTRALIA Tel. (61) 2 9898 9000, Fax. (61) 2 9898 9800
Himeji Institute of Technology, Saga
AUSTRIA Tel. (43) 1 333 50340, Fax. (43) 1 333 503426
Environmental, BELGIUM Tel. (32) 8250670, Medizinische, Fax. (32) 8 8250692 L’oreal, Enscr,
CANADA Tel. (905) 712 2258, Fax. (905) 712 4203 Canada only Tel. (1 800) 721 4260
University FRANCE Tel. (33) 1 of 69 18 88 10, York, Fax. (33) 1 69 29 Suntory 93 82 LTD., Sports
Authority GERMANY Tel. India, (49) 6103 4080, Fax. Unicam, (49) 6103 408222 Beijing University,
ITALY Tel. (39) 02 95059 226, Fax. (39) 02 95059 256
Laborexport JAPAN Tel. (81) 3 3372 KFT, 3001, Fax. American (81) 3 3372 7051 Cyanamid, Kobe Port
NETHERLANDS Tel. (31) 76 587 8722, Fax. (31) 76 571 4171
Quarantine, Hijaz Electronic, Napp
PEOPLE’S REPUBLIC OF CHINA Tel. (86) 10 6221 0839, Fax. (86) 10 6221 0847
Pharmaceuticals, SPAIN Tel. (34) 9 1657 4930, Fax. (34) University 9 1657 4937 of Chicago,
SWEDEN Tel. (46) 8 6800 101, Fax. (46) 8 6800 315
General State Lab Greece, Shandong Medicines
UNITED KINGDOM Tel. (44) 1 442 233555, Fax. (44) 1 442 233667
and UNITED Health, STATES Tel. (01) 800 Pharmacia 876 6711, (01) 512 251 1555, & Fax. (01) Upjohn, 512 251 1597 King
ADDITIONAL REPRESENTATIVES WORLDWIDE
Ultrasonic, Lilly Dev. Centre, Ausimont,
Werthenstein Chemical,
A/POLR/99.07
Equistar Printed Chemicals
on recycled paper
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