Low Abundances on TIC

Lower than normal response - but are the required peaks in your lowest standard still 3x to 5x the baseline noise?  Then it doesn't matter.  Big peaks cause more problems than small peaks do.  You want to run a GCMS system with the smallest amount and concentrations of samples that you can to minimize inlet, column, source, analyzer, and vacuum system maintenance.

You cleaned the MS ion source, which can totally change the response, which is typical and very normal.  Did you replace the filaments?  Insulators?  Do the tune results look at least mostly similar to before the cleaning? Share them both here.   If the tune results are similar but injected chromatographic peaks are smaller, then the issue is not in the MS at all. 

You replaced the column.  Is it exactly the same? Did you calibrate the length in the software?  Are the retention times the same as they were?

Did you do inlet maintenance as well?  S/Sl inlet gold seal, liner, o-ring, septum?  Septum not too tight?  What about the Split Vent trap?  Which liner? Did you set the inlet column insertion distance high enough?  Higher is better than too low - for the S/Sl I like 6mm to 8mm above the ferrule and for the MMI I like 14mm to 15.5mm above the ferrule. 

What about the syringe? Has it been replaced lately?  At least removed and manually pull solvent up and squirt it out to see that it's fine?  Syringes do wear out. 

When you installed the column into the MS - to what distance ?  If the column insertion distance is too long there will be issues. If it's too short it's not bad at all.  I did a test where I pulled the column back into the transferline in stages and got it back 50mm into the transferline before seeing problems with the typical Agilent test samples  - so flush to the tip or even a few millimeters back won't hurt anything, but a few too many millimeters too far will cause problems.

In general Agilent columns do not need to be conditioned or baked as they are done at the factory.  It is necessary to ensure that all the air is removed from the inlet subsystem and column before heating up the inlet or the GC oven, though. This can take five or ten minutes or longer. Don't be in a rush to heat a new column up!   For certain do not condition a column that is going to be installed into a mass spec with its end just hanging in the oven and not in the MS.   This contaminates the outside of the column that will be inserted into the MS and that contamination will go immediately into the ion source after it's installed.

Lower than normal response - but are the required peaks in your lowest standard still 3x to 5x the baseline noise?  Then it doesn't matter.  Big peaks cause more problems than small peaks do.  You want to run a GCMS system with the smallest amount and concentrations of samples that you can to minimize inlet, column, source, analyzer, and vacuum system maintenance.

You cleaned the MS ion source, which can totally change the response, which is typical and very normal.  Did you replace the filaments?  Insulators?  Do the tune results look at least mostly similar to before the cleaning? Share them both here.   If the tune results are similar but injected chromatographic peaks are smaller, then the issue is not in the MS at all. 

You replaced the column.  Is it exactly the same? Did you calibrate the length in the software?  Are the retention times the same as they were?

Did you do inlet maintenance as well?  S/Sl inlet gold seal, liner, o-ring, septum?  Septum not too tight?  What about the Split Vent trap?  Which liner? Did you set the inlet column insertion distance high enough?  Higher is better than too low - for the S/Sl I like 6mm to 8mm above the ferrule and for the MMI I like 14mm to 15.5mm above the ferrule. 

What about the syringe? Has it been replaced lately?  At least removed and manually pull solvent up and squirt it out to see that it's fine?  Syringes do wear out. 

When you installed the column into the MS - to what distance ?  If the column insertion distance is too long there will be issues. If it's too short it's not bad at all.  I did a test where I pulled the column back into the transferline in stages and got it back 50mm into the transferline before seeing problems with the typical Agilent test samples  - so flush to the tip or even a few millimeters back won't hurt anything, but a few too many millimeters too far will cause problems.

In general Agilent columns do not need to be conditioned or baked as they are done at the factory.  It is necessary to ensure that all the air is removed from the inlet subsystem and column before heating up the inlet or the GC oven, though. This can take five or ten minutes or longer. Don't be in a rush to heat a new column up!   For certain do not condition a column that is going to be installed into a mass spec with its end just hanging in the oven and not in the MS.   This contaminates the outside of the column that will be inserted into the MS and that contamination will go immediately into the ion source after it's installed.