13 Replies Latest reply on Mar 13, 2019 2:07 AM by s.khatuntsev

    Strange wandering baseline GC-MS


      Hi, guys!

      I have a strange wandering baseline once I run a same calibration sample (orange) after a previous (purple) one immideately.

      It is m/z 181 and 290 C isotermal part of an oven program. Low level of cypermetrin, fenvalerate and deltamethrin are present peaks on a chromatogram.

      If I let an instrument to stand for a while and run sample it runs fine. Previous (lower temperature) SIM parts of a chromatogram are fine. In SCAN it looks the same.

      It's 30m 0.25 0.25 HP-5MS UI column, running 150 kPa constant pressure, 15 kPa (250 kPa CFT and 15 kPa inlet ) postcolumn backflushing on EPC with a CFT device with 1m 0.1mm restrictor to transferline. 7890B+5977B with a turbopump (not a performance one), EI 350 Inert Source.

      If I run it in a constant flow 1.4 ml, it gets much worse.

      What is it?

      Should I run it 120-130 kPa constant pressure or 0.6-0.8 ml/min constant flow? It all helps, but affects efficiency of a column. Why does it happen?


        • Re: Strange wandering baseline GC-MS

          Hi s.khatuntsev,

          In the scan portion of the TIC, any ions like 207 or others that stand out?



          • Re: Strange wandering baseline GC-MS

            If I am on that case, I will change split vent filter first.

            If It is blocked a little bit it can effect peak shape and sensitivity.

            • Re: Strange wandering baseline GC-MS

              Hi! I've never seen a bad split vent trap cartridge so far, all the dirt I've seen gets deposited in a copper tubing g1544-20610 (maybe nuts and ferrules 5080-8750 will be required) before it, as a black oil or gum. Maybe after a long while it will protrude to a vent cartridge. It is quiet expectable, as it is a first cold spot after heated inlet. Did clean it, changed trap anyway. Will keep you informed.

              • Re: Strange wandering baseline GC-MS

                Good Morning,


                It looks like "left overs" or column degradation.


                What temperature is your inlet? What is your injection volume and what solvent? Reason being is we have seen it before that if the liner is over loaded there can be a bit of backflash in the inlet.


                Try rinsing the split vent line with something volatile like DCM and put it back on. Or even easier remove the septum and check for any residual under the septum after the first injection.


                Another area is the CTF union. The length of the columns/restrictors into it maybe too short and have some dead space. To test this you could always disable the Aux EPC in the method and directly plumb the first column into the MS and try again. If the issue is still there then you know it it not a part of the CTF union.

                  • Re: Strange wandering baseline GC-MS

                    Hi, the injection is indeed quiet dirty. It is solvent vent 3 layer sandwich 25ul sample in ACN +2ul APs in ACN:water+2ul top layer solvent ACN. The inlet is 50 C to 290 C in solvent vent and than left for the whole run at 290 C, 350 C when in backflushing.

                    Solvent vent:

                    40 ml/min @ 15kpa for 2.65min (pressure optimized for reduction of DDT and Endrin breakdown, it turned out to be ACN solvatation dependent);

                    Injection speed 11ul/min;

                    50 C inlet for 2.66min;

                    200 C/min to 290 C (speed is optimized for reduction of DDT and Endrin breakdown);

                    split open 60 ml/min @ 4.35 min;

                    Before the end of the run the inlet is heated to 350 C in 0.2 min with 400 C/min, to stay 350 C for the whole backflushing;

                    Gas saver is activated to be 20 ml/min at 5 min. Maybe it is not enough to flush leftovers? It is active in backflush, I guess.

                    The oven is:

                    45 C for 4.36 min;

                    to 155 C with 15 C/min, hold for 2 minutes;

                    to 200 C with 15 C/min, hold for 0 minutes;

                    to 290 C with 5 C/min, hold for 6.4 minutes (number is not round because of optimization for a massive peak eluting in ~1 min after last peak of interest (deltametrin) not to reach the detector);

                    Column (HP-5MSUI 30-0.25-0.25) is at 150kpa constant pressure, 20kpa CFT. When in postcolumn backflushing, it is 15 kpa in the inlet and 250 kpa at CFT.

                    Will try everything you suggested.

                    I don't see any well peaked leftovers, injecting pure ACN, probably it's not backflash. The septum purge (switched or regular) mode doesn't affect anything.

                    The liner is 5190-2296 (2mm dimpled), MMI inlet.


                    But the question persists, why no problem with lower column flow? I kinda have a solution already, but sacrificing plate count.

                      • Re: Strange wandering baseline GC-MS

                        I'm wondering if it was better to have your inlet at a higher temperature to ensure the sample solvent focus on the column. maybe at 280-290 degrees to ensure everything is put onto the column.

                        Also water is a difficult solvent for a GCMS. Would the compounds analysed be better in a volatile solvent that is chlorinated just like DDT and Endrin, like DCM as the matrix solvent. That way they are less likely to break down at higher temperatures in the presence of water.


                        This may seem counter productive but try injecting water in place of the ACN and see if it gets worse? I suspect it may do. But it's worth a try.

                          • Re: Strange wandering baseline GC-MS

                            The solvent is pure ACN for cal samples (there is 25ul ACN plus 2ul sorbit and gulonolactone solution in 70:30 ACN:Water plus 2ul pure ACN top layer on plunger to enhance repeatability of injection.

                            The injection is cold splitless with solvent vent (50 C for venting time) and ramp up to 290 C with a 200 C/min speed.

                            I don't consider a solvent exchange now, it's a quechers emr method with a single quad (don't ask why not triple quad), the solution for GC is ACN, I have a non-coated retention gap attached to the inlet before column with a non-purged ultimate union to eliminate ACN dropleting on HP-5MSUI non-polar phase.

                            I don't care much about focusing solvent, my first peak of interest is eluting at 185 C (a-HCH), cold trapping will work fine. Solvent focusing may even distort peaks, but I can't set the oven higher temp than inlet, as I don't use cryo now. And I don't need it as I have a retention gap.

                      • Re: Strange wandering baseline GC-MS

                        I believe you said you tried a solvent injection after your cal sample and there were no peaks - is this correct ?

                        Have you tried eliminating the backflush from your method, and just extend the run time until all peaks elute ?  This is best done in scan mode, at least for the extended time.  Then run a blank solvent using this same method. If no peaks are present, then it is not inlet related. 

                        I have seen mis-shapen ghost peaks from improper BF setup where the peaks are forced up the Aux line that provides the BF gas.  These typically are not as well defined as your peaks as there is no chromatography when they elute from this line.  Insufficient BF time or flow can cause what you see.  If the BF time and flow allow all peaks to flush from the head of the column, I have not seen them remain in the inlet.  They are swept easily by the purge flow.

                          • Re: Strange wandering baseline GC-MS

                            Thank you, there are some peaks in the begining of the run, but they belong to ACN impurities. Pure ACN causes distortion the same way if I inject it immediately after previous ACN. If I let it stay for 20 min, the problem doesn't appear.

                            Will give a try for your suggestions.

                              • Re: Strange wandering baseline GC-MS

                                I have reread this thread a few times and I have to change my troubleshooting suggestion.

                                1.) Change the method to eliminate the BF portion

                                2.) Add enough extra run time to compensate for no BF.

                                3.) Add an ion to track ACN if in SIM mode

                                4.) Run your standard twice (not standard followed by solvent as I first suggested), just like you did for the purple and orange chromatograms

                                5.)  If the problem of these extra mis-shapen peaks is still present, it probably is not the BF and is most likely inlet


                                LVI-SV with a ACN or ACN/water is tricky and difficult to remove enough solvent to yield good peaks. You said if the system sits for 20 min, the problem is gone.  I wonder if this 20 min is just eliminating excess solvent trapped somewhere.