Chromatography Forum

I'm working with a 5890/5972 GC/MS system and am showing an extremely noisy baseline with m/z resembling siloxanes. I have no idea where they are coming from. so far i have changed the column and done full injection port maintenance, cleaned the source and replaced the EM horn. so far nothing has changed. Even running without any injection, just hitting start on the GC, it still shows the same signatures. i am at a total loss on this, does anyone have any advice?

Does the interface have the gold tip with two holes out the sides or one hole in the end?

If it has the hole at the end, could be the column is too far into the source. The one with the holes on the side you just put the column in until it stopped and pulled it back a little, but the one with the hole on the end you had to be sure the column only protruded about 1mm.

Also make sure the interface temperature is not above the column max temperature. Other than that it would have to be major contamination of the injection port as far as I can think of.

Are the siloxanes eluting as sharp peaks or a constant signal that gets worse the hotter the oven temp is?

If it is coming across as discrete peaks either your liner has bits of septum in it, your wash vials are contaminated, or your syringe could be contaminated. If it is a continuous signal this is likely column bleed and is coming from either thermal, oxygen, or chemical damage to the column.

You could vent the MS, cap it off with a no hole ferrule and column nut, and then pump it back down with no column. The siloxane peaks will be gone.

If this works, then do inlet maintenance, change your vials, and if you can go ahead and change the column too you'll be in a better spot to re-assemble the system and test first with blank injections (NO syringe), then solvent injections (with syringe.)