Discerning matrix-cluster peaks in matrix-assisted laser desorption/ionization time-of-flight mass spectra of dilute peptide mixtures

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry is widely used for the analysis of peptide mixtures such as t hose resulting from protein digestion. Among several useful peptide matrice s, alpha-cyano-4-hydroxycinnamic acid (4-HCCA) appears to be the most popul ar. This matrix does not generally give matrix-cluster peaks at the mass re gion covered by enzyme-digested peptides (i.e., m/z above similar to 500). However, when an analyte mixture is very dilute and/or the sample contains a large amount of salts, ion peaks from matrix clusters can be quite intens e, compared to peptide peaks. This matrix-cluster interference becomes more pronounced as the amount of analyte decreases. In this paper, a simple sch eme for matrix-cluster identification is reported. It is shown that matrix- cluster formation follows a systematic pattern, although the relative inten sities of these cluster ions cannot be predicted. Discerning the matrix-clu ster peaks from the peptide peaks is found to be critical in analyzing dilu te peptide mixtures with both conventional and microspot MALDI-TOF techniqu es. (J Am Soc Mass Spectrom 2000, 11, 88-93) (C) 2000 American Society for Mass Spectrometry.