Contamination

Contamination is usually identified by excessive background in the mass spectra. It can come from the GC or from the MSD. The source of the contamination can sometimes be determined by identifying the contaminants. Some contaminants are much more likely to originate in the GC. Others are more likely to originate in the MSD.

Contamination in the GC

Contamination originating in the GC typically comes from one of these sources:

• Column or septum bleed
• Dirty injection port
• Injection port liner
• Contaminated syringe
• Poor quality carrier gas

Contamination in the MSD

Contamination originating in the MSD typically comes from one of the following sources:

• Air leak
• Cleaning solvents
• Diffusion pump fluid
• Foreline pump oil
• Fingerprints

A procedure is available for testing the ion source to see if it is contaminated (dirty):

• Testing for a dirty ion source

Common contaminants

The following table lists some of the more common contaminants, the ions characteristic of those contaminants, and the likely sources of those contaminants.

Ions (m/z)	Compound	Possible source
18, 28, 32, 44 or 14, 16	H20, N2, O2, CO2 or N, O	Residual air and water, air leaks, outgassing from Vespel ferrules
31, 51, 69, 100, 119, 131, 169, 181, 214, 219, 264, 376, 414, 426, 464, 502, 576, 614	PFTBA and related ions	PFTBA (tuning compound)
31	Methanol	Cleaning solvent
43, 58	Acetone	Cleaning solvent
78	Benzene	Cleaning solvent
91, 92	Toluene or xylene	Cleaning solvent
105, 106	Xylene	Cleaning solvent
151, 153	Trichloroethane	Cleaning solvent
69	Foreline pump fluid or PFTBA	Foreline pump vapor or calibration valve leak
73, 147, 207, 221, 281, 295, 355, 429	Dimethylpolysiloxane	Septum bleed or methyl silicone column bleed
77, 94, 115, 141, 168, 170, 262, 354, 446	Diffusion pump fluid and related ions	Diffusion pump fluid
149	Plasticizer (phthalates)	Vacuum seals (O-rings) damaged by high temperatures, vinyl gloves
Peaks spaced 14 m/z apart	Hydrocarbons	Fingerprints, foreline pump oil

The action required to remove contamination in an MSD depends on the type of contamination and the level of contamination. Minor contamination by water or solvents can usually be removed by allowing the system to pump (with a flow of clean carrier gas) overnight. Serious contamination by pump fluid or fingerprints is much more difficult to remove; it may require extensive cleaning.