Giant Peak in Chromatogram

Instrument: 7890B Agilent GC & 7010B TQMS

Hello, our issue started when we noticed a giant peak on a DB-Wax column in the front inlet – it has ions indicative of ethyl ether, which we often use as the solvent in our injections and was injected with the sample that this chromatogram is representing, however, we typically never see the solvent, as it disappears in the solvent delay. Before this front inlet run took place, we ran DHS on our back inlet with the same column, and the chromatogram looked normal with no large peak. There was no solvent in the DHS run, but this proved to us that it likely wasn’t a column or detector issue.

Sample with giant peak (sample was a mix of ~45 flavor standards in diethyl ether solvent), this was a splitless injection on a DB-Wax column and the method has been used previously with no issues:

Mass spectrum of giant peak - looks like ethyl ether:

We ran an air blank (remove solvent from the equation) and the giant peak was still present.

Air blank on DB-Wax (syringe was on and wash station had ethyl ether as it normally does):


We ran a system blank (ran the same method but removed the injection syringe) and the giant peak disappeared, the baseline looked normal.

System blank on DB-Wax (no syringe):


Overlay of the 3 chromatograms:

 At this point, we thought the syringe or wash station bottles could be contributing to the issue, so we changed those out with new parts + solvent (which is ethyl ether) and ran another air blank. We also put in a new liner and septum just in case something was going on with our current ones, though they looked visibly fine. The giant peak was still present.

Air blank with new liner, septum, wash station, and syringe:

At this point, we swapped to a DB-5 column (that we know is in good condition) because we thought maybe something might be wrong with the DB-Wax column. We ran an air blank after installing the new column and there is still an elevated baseline due to the solvent peak…though we are not injecting any solvent into the system (aside from washing the syringe at the wash station). We have run the same method many times before and never have had this type of issue. To note, this issue is reproducible, we ran the air blank twice and the chromatograms overlay almost perfectly.

Air blank on DB-5 column:

After calling Agilent, we checked the gold seal (looks completely fine) and the attempted the clean the channel that leads to the split vent line with solvent- it was clean. We ran an ethyl ether solvent blank, an air blank, and a system blank after performing these actions. The system blank looks normal, while the solvent and air blanks have the giant peak.

Chromatogram overlay (DB-5) of ether solvent blank, air blank, and system blank after cleaning/checking gold seal and solvent vent line (the system blank is the blue line):


The only thing in the front inlet that we have not replaced (that we can think of) is the split vent filter cartridge, but we have just ordered parts to do so. Could this be the issue? Is there something else that we are missing or that might be worth trying?

Note: The only thing that happened in the time span between functioning instrument and giant peak was that various solvent mixtures were run on the front inlet. Testing extraction solvents, someone was running DCM/ether, hexane/ether, DCM/hexane on a DB-Wax column – there may have been some water in the samples (we are not sure), but likely not much.

Tune: The tune looks like previous tunes and nothing is out of the ordinary (normal air/water levels)


Any help you can offer would be greatly appreciated, thanks!

  • All of these peaks are gigantic - they're in the millions to tens of millions when typical peaks should be in the tens to hundreds of thousands.  

    How much sample is injected? What type of sampler? What syringe volume?  What are your splitless parameters?  What injection port temperature? Oven temperature profile? What column dimensions, configuration, flows, carrier gas, short, all of the method parameters as found in the acqmeth.txt file that is located in Windows Explorer underneath your run methods' XXX.M subdirectory?  There is also a flle called qqqacqmethod.xml.  Would you please upload both of those?

    The simplest thing to do is a bit much as once the inlet is cold and apart there are parts to change that might as well all be done together.  Replace the septum, liner, swab the inlet body,  liner O ring, gold seal, column ferrule, the copper split vent line that goes from the inlet to the split vent trap, swab out the side arm of the injection port weldment, the split vent trap cartridge itself.... and reinstall the parts with the column inserted 6 to 8 millimeters above the end of the ferrule - a bit higher is better than too low.

    Diethyl ether should be gone very quickly at higher temperatures.  A seven minute wide peak means that the solvent is going to a dead, unswept volume or a very cold spot or both.

  • Attached below are the two files you mentioned for the most recent DB-5 run:

    1) acqmeth.txt file: 

          Wed Jul 03 14:54:51 2024
    Control Information
    ------- -----------
    Sample Inlet             : GC
    Injection Source         : External Device
    Mass Spectrometer        : Enabled
    Injection Location:  Front
     No Sample Prep method has been assigned to this method.
    GC Summary
    Run Time                                     41 min
    Post Run Time                                0 min
    Setpoint                                     On
    (Initial)                                    40 °C
    Hold Time                                    1 min
    Post Run                                     40 °C
    #1 Rate                                      6 °C/min
    #1 Value                                     250 °C
    #1 Hold Time                                 5 min
    Equilibration Time                           0.5 min
    Max Temperature                              325 °C
    Maximum Temperature Override                 Disabled
    Slow Fan                                     Disabled
    Collision Cell/Backflush
    He Quench Gas                                On    2.25 mL/min
    N2 Collision Gas                             On    1.5 mL/min
    He Backflush EPC                             Supplies Column 2
    Front SS Inlet He
                                                 ***Excluded from Affecting GC's Readiness State***
    Mode                                         Split
    Heater                                       On    250 °C
    Pressure                                     On    27.993 psi
    Total Flow                                   On    10.2 mL/min
    Septum Purge Flow                            On    3 mL/min
    Gas Saver                                    On    20 After 3 min mL/min
    Split Ratio                                  5 :1
    Split Flow                                   6 mL/min
    Liner                                        Agilent 5190-2293: 900 μL (Splitless, single taper, ultra inert )
    Back PTV Inlet He
    Mode                                         Solvent Vent
    Pressure                                     Off
    Total Flow                                   Off
    Septum Purge Flow                            Off
    Purge Flow to Split Vent                     60 mL/min at 2 min
    Vent Flow                                    50 mL/min per min
    Vent Pressure                                23.081 psi Until 0 min
    Thermal Aux 2 (MSD Transfer Line)
    Setpoint                                     On
    (Initial)                                    250 °C
    Post Run                                     0 °C
    Column #1
    Setpoint                                     Off
    (Initial)                                    1.2 mL/min
    Post Run                                     1.2 mL/min
    Agilent 122-5562                             
    -60 °C—325 °C (350 °C): 60 m x 250 μm x 0.25 μm
    Column lock                                  Unlocked
    In                                           Front SS Inlet He
    Out                                          Backflush EPC 
    (Initial)                                    40 °C
    Pressure                                     27.993 psi
    Flow                                         1.2 mL/min
    Average Velocity                             17.992 cm/sec
    Holdup Time                                  5.558 min
    Column #2
    Setpoint                                     Off
    (Initial)                                    1.4 mL/min
    Post Run                                     1.2 mL/min
    Agilent 160-2635-1                           
    -59 °C—449 °C (449 °C): 1 m x 100 μm x 0 μm  
    Column lock                                  Unlocked
    In                                           He Backflush EPC
    Out                                          MSD 
    (Initial)                                    40 °C
    Pressure                                     11.484 psi
    Flow                                         1.4 mL/min
    Average Velocity                             262.74 cm/sec
    Holdup Time                                  0.0063434 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
                                GERSTEL MAESTRO
       Maestro Runtime         : 41.00 min
       GC Cool Down Time       : 6.00 min
       Cryo Timeout            : 25.00 min
                                   GERSTEL CIS
       CIS                     : not used  -  use these parameters if it becomes 'used'
       Cryo Cooling            : used
       Heater Mode             : Standard
       Liner Type              : 013882-010-00 glass liner CIS4, baffled, non deactivated
       Liner Max Temperature   : 400 'C
       Initial Temperature     : -40 'C
       Equilibration Time      : 0.50 min
       Initial Time            : 0.10 min
       Ramp 1                 
           Rate                : 12.00 'C/s
           End Temp            : 250 'C
           Hold Time           : 5.00 min
       Ramp 2                 
           Rate                : 0.0 'C/s
                                   GERSTEL MPS PREP
       Sample Prep             : not used
                            GERSTEL MPS Liquid Injection
       Syringe                 : 10ul
       Sandwich                : not used
       Inj. Volume             : 1.0 uL
       Air Volume below        : 1.0 uL
       Inj. Speed              : 50.00 uL/s
       Fill Volume             : 2.0 uL
       Fill Strokes            : 2
       Fill Speed              : 5.00 uL/s
       Viscositiy Delay        : 1 s
       Eject Speed             : 50.00 uL/s
       Pre Inj. Delay          : 0 s
       Post Inj. Delay         : 0 s
       Inj. Penetration        : 35.00 mm
       Sample Tray Type        : VT98
       Vial Penetration        : 30.00 mm
       Preclean Sample         : 0
       Wash Station 1          : Wash1
       Preclean Solv.1         : 2
       Postclean Solv.1        : 2
       Clean Volume Solv.1     : 70 %
       Fill Speed Solv.1       : 5.00 uL/s
       Viscosity Delay Solv.1  : 0 s
       Eject Speed Solv.1      : 50.00 uL/s
       Wash Station 2          : Wash2
       Preclean Solv.2         : 2
       Postclean Solv.2        : 2
       Clean Volume Solv.2     : 70 %
       Fill Speed Solv.2       : 5.00 uL/s
       Viscosity Delay Solv.2  : 0 s
       Eject Speed Solv.2      : 50.00 uL/s

    2) qqqacqmethod.xml file: 

    <?xml version="1.0"?>
    <MSAcqMethod xmlns:xsi="" xmlns:xsd="">

    We did some of the things you mentioned before posting in the forum (replace the septum, liner, swab the inlet body, liner O ring, gold seal, column ferrule, swab out the side arm of the injection port weldment), but have not swapped out the copper split vent line or split vent cartridge (waiting for some parts).

    Thank you for the reply and helping us figure this out

  • In that acqmeth.txt file...the column flow setpoints for both columns are set to "Off" ?  Please make sure that both are checked ON and save the method.

    They don't say the control type - Constant Flow is typical.  What version of MassHunter Acquisition is running?

    One concern is the very low split ratio of 5:1 with a total flow during injection of only 10.2 ml/min.  That is too low for decent inlet pressure/flow control. If you think you need to go to lower split ratios that result in less than 20 ml/min of total flow try either a more concentrated sample, more injection volume that still fits in the liner, or splitless mode. 

    This could be allowing some expanded vapor to push backwards up the carrier gas supply line and then bleed back into the injection port during the run.  Try a blank run with the split ratio set to 25:1.

    Since you have two columns configured they are probably connected to a Purged Ultimate Union (PUU) in the GC oven.  To get this to work properly, there should be a 1 m × 0.005" i.d. metal tubing bleed restrictor installed in the supply line between the Backflush EPC module and the PUU that would be resting on top of the GC oven underneath the top cover.  This is there to ensure that the Backflush EPC module always has enough forward flow for good control. 

    With some sample/column/flow/pressure combinations if that bleed line is not installed it is possible for stuff to go back up the PUU supply line and then bleed back into the PUU during the run.

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