AUTOMATED INTERPRETATION OF HIGH-ENERGY COLLISION-INDUCED DISSOCIATION SPECTRA OF SINGLY PROTONATED PEPTIDES BY SEQMS, A SOFTWARE AID FOR DE-NOVO SEQUENCING BY TANDEM MASS-SPECTROMETRY

SeqMS, a software program designed for the automated interpretation of high-energy collision-induced dissociation (CID) mass spectra of sing ly protonated peptides ionized by fast atom bombardment, has been deve loped. The software is capable of probing the sequence of an unknown p eptide, and even of certain modified peptides, The program, compiled f or WINDOWS95 or NT, also permits the retrieval of raw data and the rec onstruction of the spectra on a user-friendly graphical interface with the aid of several tools for processing the spectra, which include se tting multiple threshold levels and automatic peak detection. SeqMS is capable of generating candidate sequences, based on the detected peak s, and of displaying the resulting assignments for each candidate in a spectrum or in tabular form. The software has the following capabilit ies: 1) the ions derived from backbone and side-chain fragmentations, internal and immonium ions, and side-chain loss ions can be used for c alculation; 2) O-18-labeling of a peptide at the C terminus, a methodo logy which was developed to differentiate N-terminal from C-terminal i ons, is applicable as an optional setting; 3) modified amino acids and N- or C-terminal blocking groups are taken into account for calculati on according to the user's setting in a library; 4) amino acid composi tion and partial or complete amino acid sequence of a peptide can be u sed as input for calculation; 5) the assignments of signal output in a spectrum can be graphically edited, and then re-calculated based on t he edited peaks. The efficacy of the program is demonstrated by testin g 74 high-energy CID spectra, obtained using a four-sector instrument, of synthetic, proteolytic, and biologically active peptides, some of which contain modified groups. (C) 1998 John Wiley & Sons, Ltd.