Siloxanes have a number of sources which include:
GC vials and septa
Inlet septa
and columns
Siloxanes from GC vials and septa show an increase in intensity as the samples sit in the gc vial. Solution: use freshly made samples for trace level analysis.
The inlet septum is a source of siloxanes two ways:
1) siloxanes bleed from the septum as a result of heat. The septum purge on a GC is usually sufficient to take care of this. But if this is turned off for some reason, the siloxanes will show up in chromatograms.
2) As the needle passes multiple times through the septum, small crumbs of the septum will break off and fall down into the inlet. These will either fall onto the packing in a packed inlet liner - on in an open liner can fall through the liner and onto the inlet seal. Either way, when heated, these will bleed siloxanes, which can now travel only the path your sample travels - which includes the GC column.
When you have siloxanes in the GC inlet, you may see a greater signal for them in the first run of the day because they slowly cook out of the inlet and condense on the head of the cooler GC column. And, the longer the instrument sits between injections, the greater the siloxane signal in the next injection.
Solution: Inlet maintenance - change the septum before it starts to crumble from many injections. Replace the inlet liner and seal plate sufficiently often to avoid the buildup of crumbs, crud, and other things that adversely affect your injection.
Columns are a big time source of siloxanes. Many stationary phases are sioxane based polymers. Even a new column will bleed siloxanes. This results from things like thermal degradation of the polymer. As the column ages, the thermal degradation increases. At some point you may have to change the column because the bleed of siloxanes becomes too severe.
To avoid degradation of the polymer, avoid the presence of air in the column, particularly when the column is hot. Do not run a column above the stated maximum operating temperature, if you can avoid it -- in fact don't run at the stated maximum for long periods of time if you can avoid it. (For some types of columns the maximum operating temperature is actually limited by the polyimide coating on the outside of the column - and while you may be able to use the column for a good separation at higher temperature, the polyimide will degrade resulting in column breakage.) Baking out a column at maximum temperature overnight is seldom a good idea. (Yes, I used to do that with 1/4" glass columns - but that was years ago, on hand packed columns, diatomaceous earth support, etc. And, thinking back, it might not have been that great an idea back then.) And, avoid injecting highly corrosive mixtures onto the column. While a bit of HCl generated by derivitization with MSTFA/TMCS will have negligible effect on a column (and adding pyridine helps the derivitization, in most cases, so it will be there), an injection from a solution of methanolic HCl is only asking for a shorter column life.
The coelution when you have siloxanes from degradation of the column: Plan A, clip a bit off the front end of the column (hoping the damage is where stuff hits the column). Plan B, change the column. Trying to bake out a column with serious degradation problems only leads to more serious degradation problems.
And, remember that columns, like inlet liners, inlet seals, septa and GC vials are all consumables. You use them with the knowledge that they will be used up and then thrown away.
