1. Conversion of Agilent EI GC/MSD Systems From Helium To Hydrogen Carrier Gas
Bruce D. Quimby, Ph.D.
GPD Solutions Group and
Harry F. Prest, Ph.D.
GC/MS Research and Development
October 9, 2012
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2. Question: Have You Ever Tried Converting Your GC/MS From Helium To Hydrogen Carrier Gas?
Answer 1: “No. Never thought of trying it. Too busy.” Answer 2: “We did that several years ago. It took some effort, but it has been working fine.” Answer 3: “We tried it once. The results were horrible and confusing! We had a very high background, high noise, and very bad peak shapes. After 4 days, we went back to helium.”
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October 9, 2012

3. Introduction: Converting from He to H2 Carrier Gas
Many GC/MS users are considering changing from helium to hydrogen carrier gas due to price/availability problems with helium.
Read Chemical and Engineering News - July 16, 2012 (Page 32-34)
This talk describes the steps recommended for converting EI GC/MS methods.
It is important to recognize the differences with using hydrogen carrier. Time should be allotted for adapting the method, optimization, and resolving potential problems. Areas that will need attention include:
choice of supply of H2
remove/bypass carrier gas filter (may be re-installed later if needed)
GC/MSD hardware changes
choosing new chromatographic conditions
potential reduction in signal-to-noise ratio (2-5x)
changes in spectra and abundance ratios for some compounds
activity and reactivity with some analytes
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4. Introduction: Converting from He to H2 Carrier Gas
Methods that will generally require less optimization include analytes that are:
“durable” compounds
at higher concentrations
analyzed with split injections
derivatized
Methods that will generally require more optimization include analytes that are:
“fragile” compounds
at trace concentrations
Allow time for necessary updates to SOPs and validation
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5. H2 Safety
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6. Letter from Agilent Safety Engineer: Describes H2 Safety Features of Agilent GCs
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7. Designed for Reliability – H2 Safety
Safety Shutdown
When gas pressure set points are not met, the valve and heater are shut off to prevent explosion
Flow Limiting Frit
If valve fails in open position, inlet frit limits the flow
Oven ON/OFF Sequence
Fan purges the oven before turning on heater to remove any collected H2
Explosion Test
GC and MS designed to contain parts in case of explosion
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8. Safety First: Read This Before You Start G3170-90010
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9. Source of H2 Carrier
and
Plumbing
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10. Source of Hydrogen: Use a Hydrogen Generator
Higher initial expense than cylinders, much lower cost over time
Very clean H2, > % available
More consistent purity
Safety considerations
H2 is only generated at needed pressure (like 40 psig)
Flow is limited (like 250 mL/min)
Auto-shutdown if set point pressure cannot be maintained
Minimal stored gas (like 50 mL at 40 psig) of H2 at any one time
Make sure to buy a good one with a low spec for water and oxygen
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11. Hydrogen Generation
This is an example of the type of generator to use for H2 carrier gas.
Look for generators with a > % specification and low individual specs on water and oxygen.
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12. Plumbing the Instrument
Chromatographic quality stainless steel tubing is often recommended for H2 plumbing and is probably the best choice if available. Users may have to follow local codes or internal company guidelines. We have also used new 1/8th copper that has been cleaned for GC use. Dirty tubing will cause huge contamination problems, as H2 appears to carry dirt out of metal more than He does. Don’t use really old copper tubing, as it becomes brittle and can break. Note that MSD leak checks will not always find big outgoing leaks. Leak check when complete with electronic leak detector. When plumbing a H2 generator, start out with no traps. Only add traps if needed. Make sure the water and oxygen levels are low enough.
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13. Split Vent and Septum Purge Vent Should be Connected to Exhaust
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14. MS Components Required for Conversion:
Magnet and Draw
Out Lens
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15. Check the Magnet in the 5975
If the magnet in the does NOT have a serial number along the left edge (as viewed through the source window), it is suitable for use with Helium, but not Hydrogen.
If not, please contact your Agilent service engineer to change it to a Helium and Hydrogen compatible magnet before converting the system to H2 carrier.
Note: All 5973 magnets are compatible with both He and H2
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16. Replace the Standard 3 mm Draw Out Lens With the Optional Hydrogen Draw Out Lens
Hydrogen Draw Out Plate, Inert
Standard 3 mm
Draw Out Plate, Inert
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17. Choosing a Column and Method Conditions
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18. MSD Pumping Capacity for H2 is Less than for He
MSD Pumping Capacity for H2 is Less than for He This Limits Column Choice
These are approximate values for the Maximum flow of H2 to maintain reasonable source pressure:
Performance turbo: 2 mL/min
Standard turbo: 1 mL/min
Diffusion pump: 0.75 mL/min
Pressure pulsing: turbo < 3 mL/min, diffusion < 2.5 mL/min
It is very helpful to have an ion gauge on the MS to monitor the vacuum vs. column flow.
Try to avoid flows that produce pressures higher than 5 x 10-5 torr. You can get useful data above this pressure, but performance may start to degrade
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19. Guidelines for Choosing Column Dimensions and Flows for Method Converted from He to H2
Determine max flow of H2 into MS that will give source pressure of 5 x torr or less source pressure. This is your max column flow.
Choose column dimensions at initial oven temp of method to give:
a flow < max column flow for vacuum pump
a flow > min column flow for efficiency
an inlet pressure of at least 5 psig
Keeping a temperature ramp of the same number of °C/void time will give similar elution order. Use the Agilent method translator for this.
These are only approximate guidelines. Sometimes you may have to deviate from them.
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20. Use 35 cm/sec as minimum for H2
Van Deemter Curves
If the flow of He or H2 is too low, you loose efficiency MUCH FASTER than if it is too high. This is why operating at or above minimum linear velocity is important.
Use 35 cm/sec as minimum for H2
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21. Column Choice When in doubt (or a hurry) use:
Use 20m x 180 um column and set constant flow at mL/min.
Try to get a linear velocity of at least 35 cm/sec
Try to use the same phase and phase ratio to get similar elution order.
Smaller bore columns have lower capacity. You may have overloading on high level calibration standards, or samples
You may need to use pulsed injection to load sample into small bore columns when using a low flow rate.
The flow range for your H2 setup is limited on the low side by the flow to get 35 cm/sec and on the high side by the vacuum pump capacity
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22. Using the Agilent Flow Calculator: Set Linear Velocity to 35 for H2 Carrier
If Inlet Pressure Too Low, Raise Flow
Inlet pressure is too low
Set inlet pressure to 5 psig
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23. Using the Agilent Method Translator: 30m x 0. 25 mm id x 0
Using the Agilent Method Translator: 30m x mm id x 0.25 um Checkout Column with Perf Turbo
Meets flow requirements for pump and column efficiency with 2x speed gain
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24. Using the Agilent Method Translator: With Perf Turbo and Std Turbo
For 20m x 0.18 mm id x 0.18 um Column:
Meets flow requirements for standard turbo pump.
Flow here is chosen to give a 2.5 x speed gain.
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25. Initial Startup with Hydrogen
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26. Initial Problems with Switching GC/MS Methods to from He to H2 Carrier Gas
High background that looks like hydrocarbons 
Reduced signal to noise (worse MDL) 
Significant tailing for many compounds 
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27. Switch to H2 1st Problem: High Background
You will see this throughout work with H2.
It will get much smaller with time and use.
It used to takes days or weeks for background to fall to acceptable levels.
Agilent developed a new conditioning protocol to clean-up the background much faster.
(see later slide)
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28. GC/MS Toxicology Analyzer Checkout Sample1
Amphetamine 2
Phentermine 3
Methamphetamine 4
Nicotine 5
Methylenedioxyamphetamine(MDA) 6
Methylenedioxymethamphetamine(MDMA) 7
Methylenedioxyethylamphetamine 8
Meperidine 9
Phencyclidine 10
Methadone 11
Cocaine 12
SKF-525a (RTL Compound) 13
Oxazepam 14
Tetrahydrocannabinol 15
Codeine 18
Lorazepam 16
Diazepam 17
Hydrocodone 19
Oxycodone 20
Temazepam 22
Diacetylmorphine 23
Nitrazepam 24
Clonazepam 25
Alprazolam 26
Verapamil 27
Strychnine 28
Trazodone 21
Flunitrazepam
5 ng/uL each compound 2 4 6 8 10 12 14 16 18 9 17 16 8 10 12 4 11 7 22 3 15 18 2 21 25 27 6 26 14 20 1 19 24 28 23 5 13
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29. Switch to H2 2nd Problem – Peak Tailing
2.00
3.00
4.00
5.00
6.00
7.00
8.00
9.00
10.00
11.00
12.00
13.00
200000
400000
600000
800000
Time-->
Abundance
20m x 0.18mm id x 0.18 um DB-5MSUI
Hydrogen
4.00
6.00
8.00
10.00
12.00
14.00
16.00
18.00
200000
400000
600000
800000
Time-->
Abundance
Helium
Immediately after conversion to H2, peak shapes on TIC are poor and tailing badly.
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30. Switch to H2 3rd Problem: Spectrum Changes over Peak Profile
There is More Happening Here than Simple Peak Tailing
Cocaine
7.20
7.40
7.60
7.80
8.00
8.20
8.40
8.60
8.80
9.00
Peak Spectrum
Tail Spectrum 40 60 80
100
120
140
160
180
200
220
240
260
280
300
320
340
2000
4000
6000
8000
10000
12000
14000
m/z-->
Abundance
Average of to min.: ToxCKO_H2_4.D\data.ms 91 78 41 64
115
167
128
141
207
191
221
154
281
242
265
341
327
314 40 60 80
100
120
140
160
180
200
220
240
260
280
300
320
340
2000
4000
6000
8000
10000
12000
14000
16000
18000
20000
22000
24000
m/z-->
Abundance
Average of to min.: ToxCKO_H2_4.D\data.ms 82
182 42
105 55 68
303
198
122
167
152
272
135
215
244
230
259
341
288
327
Cocaine
Not Cocaine
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31. Main Ions of Cocaine Do Not Tail. Tail Made Up of Other Ions
Tail is different than peak. May be formed from catalytically shredded main component. This problem is reduced with time
Cocaine
Tail is not cocaine ions
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32. Considerations for Success
H2 Conversion
Considerations for Success
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33. Agilent’s Recipe for H2 Success: Minimizing the Time for Chromatography and Background to Stabilize
Have a good source of clean hydrogen like a > % purity hydrogen generator.
Keep H2 flow limited to value suitable for your pumping system
Use optional Hydrogen draw out lens
After setup, purging and pump down:
Set the source to max temp for your source (check to see what yours is)
Reduce the EMV to 800V
Leave the FILAMENT ON overnight. This cleans up background rapidly.
Peak shape will be much better and background will be much lower in the morning.
Lower the source temp to method value, retune, and run some samples
It is a good idea to have an extra set of filaments on hand in case one burns out. This hasn’t been a problem, but a good idea.
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34. Agilent’s Recipe for H2: Success
Peak Shape Much Better
Background is Lower
Better Signal-to-Noise
2.00
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4.00
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6.00
7.00
8.00
9.00
10.00
11.00
12.00
13.00
14.00
200000
400000
600000
800000
Time-->
Abundance
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October 9, 2012

35. Agilent Toxicology Analyzer
Features:
Configured, tuned and tested for the application
Retention time locked (RTL) with DRS database
Constant flow to MS
Backflush to reduce cycle time and remove matrix artifact
Challenge:
Convert from He to H2 carrier without altering performance criteria
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36. He Constant Flow Toxicology Analyzer
Parameters:
Constant Flow to MS
RTL DRS Method
Liquid
Injector
AUX EPC
Vent
S/S Inlet
~12psi
1m x 0.15 mm id
1.7 mL/min
Column
PUU
5975C
MSD
7890A GC
15 m X 0.25 mm id X 0.25 um DB-5MSUI
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37. H2 Constant Flow Toxicology Analyzer
Parameters:
Constant Flow to MS
RTL DRS Method
Liquid
Injector
No Change in Performance
AUX EPC
Vent
S/S Inlet
~8psi
0.81m x 0.12 mm id
1.7 mL/min
Column
PUU
5975C
MSD
7890A GC
15 m X 0.25 mm id X 0.25 um DB-5MSUI
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38. Converting Toxicology Analyzer from He to H2
3.00
4.00
5.00
6.00
7.00
8.00
9.00
10.00
11.00
12.00
13.00
14.00
200000
400000
600000
800000
Time-->
Abundance
Toxicology Check Out Mix
Helium
Hydrogen
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39. Switching GC/MS Methods to from He to H2 Carrier Gas
Reduced high background that looks like hydrocarbons 
Improved signal-to-noise relative to pre-conditioned state 
Reduced tailing for many compounds 
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40. Performance Expectations
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41. Performance Expectations
Signal-to-noise ratio is often worse by about 2-5 x. This obviously varies from compound to compound While most spectra remain same, there are always exceptions. Users should check the reference spectra for important targets to make sure they have not changed Same comment for target/qualifier ratios Some compounds may disappear at low levels. Examples include: some nitrogen and oxygen containing compounds (alcohols, aldehydes, ketones) like those found in flavor samples
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42. Library Match Factors – Helium and Hydrogen Carrier Gas Comparison
NIST (Forward)
NIST (Reverse)
Helium
Hydrogen
Helium
Hydrogen
Dichlorvos
924
867
929
904
Mevinphos
925
852
973
967
Ethalfluralin
927
897
927
897
Trifluralin
897
856
897
857
Atrazine
914
901
915
908
BHC-gamma (Lindane, gamma HCH)
925
858
931
878
Chlorpyrifos-methyl
922
897
926
908
Heptachlor
926
851
929
856
Malathion
916
836
953
846
Chlorpyrifos
901
890
902
892
DDE, p,p'-
934
903
946
940
Dieldrin
926
903
927
903
Hexazinone
901
832
906
912
Propargite
851
821
857
829
Leptophos
884
847
884
847
Mirex
903
881
914
934
Fenarimol
905
872
908
877
Coumaphos
864
804
870
813
Etofenprox (Ethofenprox)
906
842
916
843
In general, these 20 spectra in hydrogen carrier show lower match factors than in helium carrier gas. They can still be properly identified in library search.
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43. Lindane Observations Ion ratios changed Extra peaks in H2
Helium Carrier Gas
NIST Forward Match = 925
Hydrogen Carrier Gas
NIST Forward Match = 858
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44. Heptachlor Observations Ion ratios changed Helium Carrier Gas
NIST Forward Match = 926
Hydrogen Carrier Gas
NIST Forward Match = 851
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45. Other Considerations:
H2 is not an inert gas, and therefore inertness problems will still exist or be worse.
Use the lowest inlet temp that works (to reduce reactions with H2)
Use pulsed injection, especially with small bore columns
Consider using an MMI in cold splitless mode for fragile compounds
Using a deactivated S/SL weldments might help (but don’t ever scrub it)
Avoid using methylene chloride as a solvent (especially wet).
At higher inlet temps (like >280C), HCl is formed and causes problems.
If must be used, use lowest inlet temp and maybe a deactivated S/SL weldment, or Multimode inlet
Avoid carbon disulfide as a solvent
Use liners with a taper at bottom to minimize sample contact with gold seal
Use Agilent Ultra Inert Liners.
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46. Hydrogen Carrier Summary
Get a GOOD hydrogen generator and plumb it properly
Pick a column that meets the flow needs of method and MSD pump
Do magnet update (if necessary) and install Hydrogen draw out lens
After purging and pump down, set source to max temp and EM to 800V. Leave filaments on all night.
Reset source temp, retune, and run samples. Run practice samples for a few days to make sure system has stabilized
Source cleaning will be needed much less frequently
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47. Thank You for Your Attention
For additional information please visit:
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