GC- MS, bakeout/conditioning of GC column - can the MS be scanning?

Baking or conditioning an Agilent column is only needed if your samples have residues with higher boiling points than the highest oven temperature in your run method.  The columns are shipped conditioned and individually tested and do not need conditioning before use. 

It's a two sided problem.  If you bake the column connected to the MS, everything that comes out of the column goes into the ion source and the manifold.  If you remove the column from the MS to bake it, everything that comes out of the column goes into the oven and circulates to contaminate the entire outside of the column - so that when you install the column back into the MS that piece of column in the transferline that is contaminated is now inside the MS and that stuff goes into the ion source and the manifold.   If you feel that baking into the oven is necessary make sure to thoroughly wipe off the part of the column that goes into the MS with a solvent wetted lint free cloth to remove as much of the residue on the outside as possible.

Collecting data while the column is installed into the MS and baking allows you to see what is coming out and when the baking time is sufficient.  Of course anytime the filament is on the lifetime of the filament is reduced.  So, for example, you wouldn't want to bake for eight hours and do an eight hour run as that's eight hours of filament life.   A way around that is to either use timed events in a long run to turn off the MS or to manually bake the oven and do Spectrum Scan in Manual Tune to look at the spectra of what is coming out at that time.

Baking is overrated.  It was useful back in packed column days, but current capillary columns run with the smallest injection volume of the lowest concentrations of the cleanest samples possible reduces the need for baking.  Early inlet maintenance with liner replacement before the liner is fully contaminated reduces column contamination, too. 

Baking or conditioning an Agilent column is only needed if your samples have residues with higher boiling points than the highest oven temperature in your run method.  The columns are shipped conditioned and individually tested and do not need conditioning before use. 

It's a two sided problem.  If you bake the column connected to the MS, everything that comes out of the column goes into the ion source and the manifold.  If you remove the column from the MS to bake it, everything that comes out of the column goes into the oven and circulates to contaminate the entire outside of the column - so that when you install the column back into the MS that piece of column in the transferline that is contaminated is now inside the MS and that stuff goes into the ion source and the manifold.   If you feel that baking into the oven is necessary make sure to thoroughly wipe off the part of the column that goes into the MS with a solvent wetted lint free cloth to remove as much of the residue on the outside as possible.

Collecting data while the column is installed into the MS and baking allows you to see what is coming out and when the baking time is sufficient.  Of course anytime the filament is on the lifetime of the filament is reduced.  So, for example, you wouldn't want to bake for eight hours and do an eight hour run as that's eight hours of filament life.   A way around that is to either use timed events in a long run to turn off the MS or to manually bake the oven and do Spectrum Scan in Manual Tune to look at the spectra of what is coming out at that time.

Baking is overrated.  It was useful back in packed column days, but current capillary columns run with the smallest injection volume of the lowest concentrations of the cleanest samples possible reduces the need for baking.  Early inlet maintenance with liner replacement before the liner is fully contaminated reduces column contamination, too.