Varian Norman Low
4000 GC/MS
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April 12, 2006
Varian GC/MS
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Page 1 April 12, 2006
Objectives
• Explain the Varian GC/MS product line
• Respond to major claims
• Explain the weaknesses of ion trap technology
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Topics
• History
• Technology review
• GC/MS product line
• Features of Varian 4000
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Recent History of Varian GC/MS
• Acquire rights from Finnigan
– Introduces INTERNAL ionization ion trap for GC
– Finnigan introduces EXTERNAL ionization
• Varian develops ion trap technology
– Becomes sales leader
– Develops INTERNAL, EXTERNAL, and Hybrid ionization
• Varian acquires Bear for GC and LC/MS/MS
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Technology Review: Quads vs Ion Traps
Quadrupoles Internal Ionization Traps
• Ionization in source • Ionization and selection in trap
• Ion selection in quad • Problem with ion-molecule reactions
• Classical spectra • EI, PCI
• EI, PCI, NCI • MS or MSn
• MS or MS/MS capabilities
External Ionization Traps
• Ionization in source
• Ion selection in trap
• Loss of sensitivity
• EI, PCI, NCI
• MS or MSn Varian GC/MS
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Ion Trap Spectra
“Q: What other MS techniques can the NIST02 EI spectra be used with?
A: Most data come from quadropole mass spectromteters.
1) Spectra measured on magnetic sector and TOF instruments can be searched against NIST02 with
good results.
2) Searching with ion trap spectra can be productive but the results need to be considered
thoughtfully.
...
Ion trap spectra of small molecules with oxygen, nitrogen, etc., require attention. Small heteratom
molecules are known to produce mass spectra that differ between quadropole and ion trap
instruments. The differences relate to ion intensities and product ions.
Library searching is difficult when the ion trap spectrum is not unique or the molecular ion is small
or nonexistent..
Ion trap spectra of small molecules (MW 50-225) more often than not were found in NIST98.”
FDM NIST02 FAQ : http://www.fdmspectra.com/fdm_ms_nist_FAQ.htm
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Varian GC/MS Product Line
Model GC Ionization EI Mass Scan Linear Pump Optional
1 pg OFN Range Rate Dyn
Range
2100 3900 Internal EI (PCI) 20 (TP) Diff or SIS, MSn,
20 /5 pg (DP) turbo PCI, inert
source
2200 3800 Internal EI (PCI) 50 10- 6,500 103-104 Turbo SIS, MSn,
650 (fixed) PCI, inert
source
4000 3800 Internal – EI PCI 20 /0.2 ng Int 10- 5,000- 103-104 Turbo
External – EI PCI 30 /0.5 ng Ext 1,000 10,000
NCI
Hybrid – PCI NCI
1200 3800 External – EI PCI 20 10- 500 – 105 Turbo Interface
1200L NCI 800 or 6,000 for LC/MS
MS/MS 1,500
(L)
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Key Features of the Varian 4000
• Most capable ion trap available
• Internal/External ionization
• Ionization capabilities
– Internal EI, PCI
– External EI, PCI, NCI
– Hybrid PCI, NCI
• MS and MSn
• Selective Ion Storage
• Solid phase microextraction
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Internal Ionization on the Varian 4000
• Limited to EI and PCI
• More sensitive than external ionization
• Ion-molecule reaction problems
Transferline - inside ion trap
Filament
Trap
+
e-
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External Ionization on the Varian 4000
• EI, PCI, NCI
• Column does not go into ion volume
• Less sensitive than internal ionziation
• Ion-molecule reactions still possible
Transferline - inside ion trap
Ion
Source Filter
Trap
+ +
CI plunger
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Hybrid CI on the Varian 4000
• CI reagent ions formed in external ion source
• Selected adduct ions ejected to react with sample
Transferline - inside ion trap
Ion Source Filter
Trap
CI plunger
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MSn
• Key selling point for ion traps
• Complex to set up
• Hard to maintain for complex methods
• Requires MS interpretation skills
– Most chemists do not have good interpretation skills
– MSn requires more expertise than most laboratories have
• Most ion trap owners do most of their work in MS1
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MSn Setup
1. Inject standard in EI mode
2. Locate most abundant ion
3. Determine resonance mode
4. Determine proper CID voltage with Automatic Method
Development software (tests 10 voltages / run)
5. Review data to select best voltage
6. Repeat AMD experiment if necessary
7. Repeat entire process for the next analyte
8. Produce method with proper RT windows
9. If column maintenance is done, reset all RT windows
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Selected Ion Storage (SIS)
• Capabilities
– Selected ion storage – single ion or range
– Selected ion ejection (removal of background ions)
• Claimed advantages
– Offer SIM-like capabilities
– Offer library searchable spectra
• Problems
– Limited ion storage capacity of trap
– Matrix ions can also fill trap capacity – less sensitivity
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Solid Phase Micro-Extraction (SPME)
• Syringe with a coated fused silica fiber for extraction
• Claims
– Simple, inexpensive, solvent-free
– Provides low-cost headspace
– Sensitive -- ppt detection limits for some compounds
– May be tailored selectively for specific applications
• Alternatives
– Gerstel Twister
– Ambient headspace
– Micro-extraction
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Review
Give a response for the following features:
1. Ion trap sensitivity
2. MSn
3. Hybrid CI
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Responding to Varian
Feature Response
Sensitivity Ion traps are not any more sensitive than quads.
External ionization Still have problems with non-classical spectra. Must
move to another transfer line to use.
Hybrid CI, MSn Difficult to set up. Requires expert.
SPME Alternative technologies available. Gerstel offers Twister
with better performance.
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Conclusion
• Very focused on MS for both GC and LC
• Has unique features to push
• Most customers do not use many features
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Extra Slides
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Finnigan Technical Note
“External Ionization on GCQ Mass Spectrometers,”
Technical Report #621, 1995
Finnigan Corp.
This note was issued when Finnigan went from internal to
external ion traps
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Quotes – Self CI
“While this architecture [internal ionization] is acceptable for the analysis
of many compounds, the design sometimes contributes to undesirable
ion-molecule reactions inside the trap…Sometimes called “self CI”…the
ensuing reactions can produce by-products that contribute to the
appearance of unwanted additional ions in the mass spectrum or skew
the relative ratio of significant ions.”
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Quotes – Susceptible Classes
“With external ionization…the spectrum is virtually unaffected, producing
the “classical” spectrum seen on traditional quadrupole filter mass
spectrometers…The complete removal of this”self-protonation” effect
has been demonstrated for many other susceptible compound classes
such as amines and esters.”
“Standard hydrocarbon spectra with molecular ions cannot be obtained
with internal ionization ion traps.”
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Quotes – Thermal Decomposition
“Cholesterol has traditionally been used to indicate spectral integrity in
GC/MS. A good cholesterol EI spectrum will contain a molecular ion at
m/z 386 at least twice as abundant as the dehydration ion at m/z 368…
In the traditional ion trap spectrum, the m/z 386 ion is ofsimilar
abundance to them/z 368 ion, indicating that additional thermal
decomposition is occurring.”
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Quotes – Dynamic Range
“Also, by eliminating unwanted interferences, especially at higher
analyte concentrations, the dynamic range is substantially increased, so
detection and quantitation of compounds over a wider range of sample
concentrations is possible.”
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Quotes – Source Temperature
“Since the external ion source is independently heated from the ion trap,
the source temperature can be operated beyond the capability of the
internal ionization system. Higher temperatures eliminate the negative
effects (e.g. peak tailing) caused by sample adsorption seen particularly
with high boiling andhigh polarity analytes.”
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Quotes – Flow Rate
“This new design asures stable mass resolution, independent of the
chromatographic gas flow rates.”
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Quotes – Conclusion
“In summary, the data presented here demonstrate how external
ionization yields classical spectra, with increased dynamic range,
reduced thermal decomposition and superior chromatographic integrity.”
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