Tandem mass spectrometric analysis of peptides at the femtomole level

In the sequential analysis of peptides by fast atom bombardment (FAB) tandem mass spectrometry (MS/MS), the principal obstacle to decreasing sample quantities was determined to be the signal-to-background ratio of the ionization/desorption process. By decreasing the background ion current, continuous-flow FAB allows complete analysis (both MS and MS/MS) to be performed on 25-75% less sample than required for a conventional FABMS/MS experiment alone. The combination of CF-FAB with array detection permitted sequential analysis of several peptides (900-2000 Da) at the 900 fmol to 5.8 pmol level, without interference from the background. These levels do not produce a molecular ion species easily discernible above the background in conventional FAB.