Reproducibility Issues after system maintenance

Please read up on split and splitless along with inlet maintenance in the GC manuals. 

There are many resources on Agilent.com and here on the Agilent Customer Community.

Maintaining Your Agilent Split/Splitless GC Inlet

Maintaining Your Agilent Split/Splitless GC Inlet - same title, different presentation!

Understanding the GC Inlet. Which one is more appropriate for your method? (agilent.com)

(+) Column Installation - Split/Splitless and Multimode inlets =and= SQ and TQ MS transferlines - Files - GC/MS - Agilent Community

There are some easy questions to start with.  What is your column configuration?  Is it set properly in the software?  You have a guard column, then two columns with a PUU and going to vaccum in the Mass Spec, is the software and method configured properly?  Does column 2 have about 0.1 to 0.2 ml/min MORE than column 1?  This is necessary so that there is always positive flow from the PUU supply so that sample can't go up the PUU gas supply line.    What is your splitless  Purge ON time? What is your inlet temperature and initial oven temperature and initial oven hold time?

The cross gold seal is not necessary.  The cross seal is only required if you are running in modes with very high inlet flows, like split over some few hundred ml/min, or have samples with so much residue that collects on the gold seal that it can become clogged  (this would mean that you should do dramatically more inlet maintenance). 

Thank you very much. Will work through this. I am not totally sure about the column installation. Our system is set up in a way that the flow that goes though the sequence of guard column-PUU-analytical column-PUU-MS Transfer Lines is viewed as one column as far as I understand, so there is only one column and I cannot set the gas flow differently for the different parts of it as it goes from the inlet into the guard column which is connected to analytical column (through 1st PUU), which is then connected to the MS transfer line (through 2nd PUU) and then to the MS. All 3 columns have the same dmensions. Guard column and MS transfer line ar deactivated fused silica. Maybe I need to reconfigure that. I'll look into that using the resources you shared.

And yes, we are injecting a polymer that is non volatile and gets stuck on the liner. It is possible that some of that is collecting in the liner as even burn-outs of inlet and column do not fully get rid of residual peaks.

The column has been used for a loooong time and this material has been injected many times over these past few years. We had a PM done by Agilent last year and I'm pretty sure they cleaned the inlet, but since then we did lots of development work which involved the injection of non-volatiles and compounds with very high boiling points of which I also see impurities in the blanks.

I may have more questions once I went through all the material you shared

You would remove the ALS and manually inject through the septum with a handheld syringe.  However, one way to use the autosampler to do this is to squirt air duster into a vial and cap it off quickly. The sampler will pull up enough air duster gas for you to be able to see a peak.  Set your MS method to scan from, oh, 15-125 or something like that and you should see a peak in the chromatogram that you can use for unretained volume calculations and column calibrations.

Thank you Paul. I was able to do all that now. I also did inlet maintenance:

opened the inlet completely, replaced guard column+fittings (ferrules on both ends, column nut to Ultimate union), gold seal+washer, and inlet reducing nut (used a better looking one from back-inlet), septum retainer nut (used a better looking one from back inlet), opened purge lines which looked clean, cleaned inlet with solvent, replaced vent line traps. Put everything back together and performed inlet leak check which is leak-free. Fixed a leak at the Union/Guard column connection, checked for leaks at inlet/guard column connection. seems leak-free

If I test termperature: 70C, Mode splitless, purge flow: 50 ml/min, column flow: 4 mL/min, and click prep run twice the total flow fluctuates around 6 mL/min. Tune fails - does not complete. I looked through everything and cannot find an issue. 

I gues one thing left to do is replace the purge lines. I have the Cu tubes here (G1544-20610), but would like instructions if possible. I could not find this in the manual.

Is it possible that the valve is malfunctioning?

Best, Bettina

Bettina, turn the column flow down to 1.2 ml/min and try to tune.  4ml/min is much higher than the optimal flow for the ion source.

Thank you so much Paul. I did not understand that this is important. Generally, Will I need to tune the instrument for each method settings and use the associated tune to get meaningful data or can I do a general tune that I can use for all methods? 

The tune completed now, still showing N2/O2 at 14.2/5.5%. So, either I need to give it more time after fiddleing with everything or there is still a leak. 

The total flow is around 6ml/min.... do you have the Septum Purge Flow Mode setup for Standard or Switched?

If it is in Standard mode, the Total Flow during the splitless time is equal to the column flow plus the septum purge flow.

If it is in Switched mode, the Total Flow during the splitless time is equal to the column flow.

Please remember that column flow is always calculated from pressure/temperature/restriction of the column.

The copper split vent line is easy to check when you have the inlet apart for cleaning. When the column and liner are out and the gold seal removed, you can squirt solvent from the disconnected split vent trap end and it will drip out of the bottom of the inlet into the oven.  Since it's all back together clean and leak tight, it's more work to do it again.  Replacing the copper tube requires removing the autosampler bracket to get access. Other than that it is typical 1/8" swagelok fittings on the inlet body and the split vent trap body.

Do you have a flowmeter? Measure the flow out of the split vent and compare it with the setting on the GC in Split mode.  If it tracks, the valve is probably fine. Sure the valve could be malfunctioning, but it is not a high failure part.

What liner are you using in the inlet?  There are liners out there that are just a bit big outside diameter. They can restrict the flow and cause this, too. It's certainly worth putting a split liner inside to test just to be careful.

The total flow is around 6ml/min.... do you have the Septum Purge Flow Mode setup for Standard or Switched?

If it is in Standard mode, the Total Flow during the splitless time is equal to the column flow plus the septum purge flow.

If it is in Switched mode, the Total Flow during the splitless time is equal to the column flow.

Please remember that column flow is always calculated from pressure/temperature/restriction of the column.

The copper split vent line is easy to check when you have the inlet apart for cleaning. When the column and liner are out and the gold seal removed, you can squirt solvent from the disconnected split vent trap end and it will drip out of the bottom of the inlet into the oven.  Since it's all back together clean and leak tight, it's more work to do it again.  Replacing the copper tube requires removing the autosampler bracket to get access. Other than that it is typical 1/8" swagelok fittings on the inlet body and the split vent trap body.

Do you have a flowmeter? Measure the flow out of the split vent and compare it with the setting on the GC in Split mode.  If it tracks, the valve is probably fine. Sure the valve could be malfunctioning, but it is not a high failure part.

What liner are you using in the inlet?  There are liners out there that are just a bit big outside diameter. They can restrict the flow and cause this, too. It's certainly worth putting a split liner inside to test just to be careful.

I only saw your answer below. Sorry. And thank you for this one as well. I cannot change the Septum purge flow Mode on our instrument. As far as I know it is 3 mL/min always, so standard mode. I will find a flowmeter and try to measure flow out of the split vent. Currently our software is down due to the autosampler issue and the attempt to fix it (see other chat on vial out of position), but I can try and do it by using the instrument control display. We are using the following liners: 210-4022-5.

I cannot find a flowmeter that measures such small flows

Can you please provide me with a part number for sth. that has appropriate scale/sensitivity?