How to upgrade MS source to Extractor 350?


I have a 5977 MS with SST source. I'm thinking of upgrading to Xtr 350. The MS can support it (There's an extra jack on the board to connect the extractor lens), but I was wondering if I need to make changes to the software or run the Parts Finder after installing the source. Any help would be greatly appreciated!

Thank you!


  •   What is the model number listed along with the serial number label on your system?  For example, this one is a G7077C, a 5977C system with a turbomolecular high vaccum pump and an extractor ion source.

  • Hi  ,

    Thank you for your attention! The model numberd is G7080B with a diffusion oil pump.

  • I couldn't upload the file, so I copied the whole text here:


    Mon Mar 20 09:53:06 2023

    Control Information
    ------- -----------

    Sample Inlet : GC
    Injection Source : GC ALS
    Injection Location: Front
    Mass Spectrometer : Enabled

    No Sample Prep method has been assigned to this method.

    GC Summary
    Run Time 36.357 min
    Post Run Time 1 min

    Setpoint On
    (Initial) 45 °C
    Hold Time 1 min
    Post Run 45 °C
    #1 Rate 7 °C/min
    #1 Value 240 °C
    #1 Hold Time 1 min
    #2 Rate 20 °C/min
    #2 Value 270 °C
    #2 Hold Time 5 min

    Equilibration Time 0.5 min
    Max Temperature 325 °C
    Maximum Temperature Override Disabled
    Slow Fan Disabled

    Front Injector
    Syringe Size 10 μL
    Injection Volume 2 μL
    Solvent A Washes (PreInj) 2
    Solvent A Washes (PostInj) 2
    Solvent A Volume 8 μL
    Solvent B Washes (PreInj) 2
    Solvent B Washes (PostInj) 2
    Solvent B Volume 8 μL
    Sample Washes 0
    Sample Wash Volume 2 μL
    Sample Pumps 3
    Dwell Time (PreInj) 0 min
    Dwell Time (PostInj) 0 min
    Solvent Wash Draw Speed 300 μL/min
    Solvent Wash Dispense Speed 6000 μL/min
    Sample Wash Draw Speed 300 μL/min
    Sample Wash Dispense Speed 6000 μL/min
    Injection Dispense Speed 6000 μL/min
    Viscosity Delay 0 sec
    Sample Depth Disabled
    Injection Type Standard
    L1 Airgap 0.2 μL
    Solvent Wash Mode A, B

    Front SSZ Inlet He
    Mode Splitless
    Heater On 260 °C
    Pressure On 7.2892 psi
    Gas Saver Off
    Purge Flow to Split Vent 3 mL/min at 0.75 min

    Thermal Aux 1 (MSD Transfer Line)
    Setpoint On
    (Initial) 280 °C
    Post Run 0 °C

    Column #1
    Setpoint On
    (Initial) 1 mL/min
    Post Run 1 mL/min

    Agilent 19091S-433UI
    HP-5ms Ultra Inert
    -60 °C—325 °C (325 °C): 30 m x 250 μm x 0.25 μm
    In Front SSZ Inlet He
    Out MSD
    (Initial) 45 °C
    Pressure 7.2892 psi
    Flow 1 mL/min
    Average Velocity 36.473 cm/sec
    Holdup Time 1.3709 min

    Column Outlet Pressure 0 psi

    Signal #1: Test Plot
    Description Test Plot
    Save Off
    Data Rate 50 Hz
    Dual Injection Assignment Front Sample

    Signal #2: Test Plot
    Description Test Plot
    Save Off
    Data Rate 50 Hz
    Dual Injection Assignment Back Sample

    Signal #3: Test Plot
    Description Test Plot
    Save Off
    Data Rate 50 Hz
    Dual Injection Assignment Back Sample

    Signal #4: Test Plot
    Description Test Plot
    Save Off
    Data Rate 50 Hz
    Dual Injection Assignment Back Sample

    MS Information
    -- -----------

    General Information
    ------- -----------

    Acquisition Mode : Scan
    Solvent Delay (minutes) : 4.3
    Tune file : D:\MassHunter\GCMS\1\5977\ATUNE.U
    EM Setting mode Gain : 1.000000

    Normal or Fast Scanning : Normal Scanning
    Trace Ion Detection : Off
    Run Time (if MS only) : 650 minutes

    [Scan Parameters]
    Start Time : 4.3
    Low Mass : 31
    High Mass : 400
    Threshold : 150
    A/D Samples: : 4


    MS Source : 230 C maximum 250 C
    MS Quad : 150 C maximum 200 C

    Timed Events
    ----- ------
    Number Events= 0


    TUNE PARAMETERS for SN: US1638P001

    Trace Ion Detection is OFF.

    34.593 : EMISSION
    70.007 : ENERGY
    32.907 : REPELLER
    90.331 : IONFOCUS
    17.627 : ENTRANCE_LENS
    1271.928 : EMVOLTS
    1394.3 : Actual EMV
    1.00 : GAIN FACTOR
    2834.000 : AMUGAIN
    138.500 : AMUOFFSET
    1.000 : FILAMENT
    0.000 : DCPOLARITY
    15.482 : ENTLENSOFFSET
    0.000 : Ion_Body
    0.000 : EXTLENS
    323.000 : MASSGAIN
    -25.000 : MASSOFFSET



  • First recommendations and some questions:

    Equilibration Time 0.5 min Please increase to 1 min or more. Cooling to 45 from 270, the oven sheetmetal needs more time for the entire oven to equilibrate. This will improve run to run reproducibility.
    Injection Volume 2 μL 2 µL of what solvent ??  The vapor volume can be calculated to find out if the vapor will even fit into the injection port liner.  Also the initial oven temperature should be 10 to 25 degrees lower than the solvent boiling point for good cold trapping of your sample at the head of the column.
    Viscosity Delay 0 sec Please increase to 2 or 3 seconds. This has been proven to improve reproducibility. 
    Mode Splitless You may want to consider doing a pulsed splitless injection.   What liner is installed in the injection port?
    Heater On 260 °C The typical choice would be to have the inlet the same as your final oven temperature… so 270° C.
    Purge Flow to Split Vent 3 mL/min at 0.75 min This is wrong.  The purge flow to split vent must have the flow set high enough to sweep the liner quickly. I would recommend making this 50 ml/min at 0.75 minutes and then turn on Gas Saver to 30 ml/min at 2 minutes.
    Low Mass : 31 Why are you scanning starting at 31?  Do you need to see m/z 32 for some reason in your run data?
  • Thank you for your valuable recommendations!

    • I will increase the equilibrium time.
    • My solvent is Chloroform and from Vapor Volume Calculator I realized it will occupy ~82% of liner volume (~900ul) at 260C/7psi. So, I thought its feasible to inject 2ul. Chloroform boiling point is 61C, but I wasn't aware of this. Thank you!
    • I will increase the delay to 1-2 sec.
    • Liner is single taper.
    • Thank you for the pulsed splitless injection recommendation. I will use it. What would be the optimum injection pressure and time in that case?
    • I thought keeping inlet cooler than oven by ~10C prevents compound buildup and carry-over. That was the reason I keep it cooler. That's also the reason I put TL 10C higher than column.
    • Purge flow: I thought it might be problematic. I try to save gas since it's grade 5 (9.9999) and expensive. I will change the split vent flow. Is it possible to put the split vent on 3ml/min in standby mode and then increase it to 50ml/min a couple of hours before the start of analysis?
    • Most of the compounds of interest have very low mass (as low as 100). Even for some of them mass 27 is among the main mass peaks. I was even thinking to reduce it to 25m/z. What problem would this make? I usually put the maximum mass as my molecular weight+30Da in case they are methylated during derivatization.
    • Since I keep my split vent low, sometimes I see m/z 32, especially during my blank run before the batch.
  • The lower the injection port pressure, the less realistic is the vapor volume calculator. It's not perfection in there and 82% is too much.  With Chloroform you'd want the initial oven temperature to be 40° C or even lower. You say your compounds are very light, so reducing it to even 35° C might help chromatographic peak shapes.

    Pulsed splitless.30×250×.25 at 1 ml/min is your normal column flow with the inlet at 7.2892 psi at 45°C.  The diffusion pump in your system has a maximum allowable flow of 2 ml/min and the gas calculator says 16.497 psi to get that, so a pulse of 16 psi until 0.5 minutes and then purge flow 50 to split vent at 1.00 minutes would be a good starting point.  Then have gas saver on 25 ml/min at 2.00 minutes. 2 µL of chloroform at 16 psi and 260° C inlet gives 52% expansion, much better, much more realistic/safe/usable.

    The split splitless and multimode inlets require a minimum of at least 15 ml/min of total flow to function properly.  That 15 ml/min is not really enough to eliminate the possibility of air diffusion into the system, so I recommend 25 ml/min at all times.    If you need to save helium, Agilent sells a Helium Conservation Module that will let you switch to nitrogen whenever the system is not being used.

    You can scan from 10 m/z if you'd like as long as you understand that the TIC baseline will include 18, 28, and 32. 

    ANY 32 - oxygen -- in your system degrades the column and oxidizes the ion source requiring more cleaning. 

  • Thank you for your time and valuable information Paul! I really appreciate it! I am aware of water (18), N2 (28), and O2(32) and constantly check their presence.



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