A falling baseline indicates that some source of contamination is being swept away. Wait until the baseline reaches an acceptable level. Common causes include:
Check the mass spectra for ions related to column or septum bleed.
If the mass spectra indicate column or septum bleed, take the following steps:
Vent the MSD.
Remove the column from the GC/MSD interface.
Condition the column.
Bake out the septum. Increase the injection port temperature until the baseline falls to an acceptable level.
CAUTION! Do not exceed the temperature limits of the column or septum.
See the MSD maintenance documentation for instructions for venting the MSD and conditioning a column.
Water vapor gets into the MSD when it is vented. Solvents can get into the MSD if parts are such as the ion source are cleaned but not dried properly. The water or solvents are gradually pumped away by the vacuum system. Increase the ion source and mass filter (quad) temperatures to speed the removal of water and solvents.
A splitless injection time that is too long can result in the inlet not being completely swept out. Excess solvent winds up on the column creating a slow solvent decay. If you are using splitless injections, try reducing the injection time.