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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
Author(s) -
FernandezdeCossio Jorge,
Gonzalez Javier,
Betancourt Lazaro,
Besada Vladimir,
Padron Gabriel,
Shimonishi Yasutsugu,
Takao Toshifumi
Publication year - 1998
Publication title -
rapid communications in mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.528
H-Index - 136
eISSN - 1097-0231
pISSN - 0951-4198
DOI - 10.1002/(sici)1097-0231(19981215)12:23<1867::aid-rcm407>3.0.co;2-s
Subject(s) - chemistry , protonation , dissociation (chemistry) , peptide , mass spectrum , collision induced dissociation , ion , tandem mass spectrometry , mass spectrometry , software , amino acid , peptide sequence , analytical chemistry (journal) , side chain , combinatorial chemistry , chromatography , computer science , biochemistry , organic chemistry , operating system , gene , polymer
SeqMS, a software program designed for the automated interpretation of high‐energy collision‐induced dissociation (CID) mass spectra of singly protonated peptides ionized by fast atom bombardment, has been developed. The software is capable of probing the sequence of an unknown peptide, and even of certain modified peptides. The program, compiled for WINDOWS95 or NT, also permits the retrieval of raw data and the reconstruction of the spectra on a user‐friendly graphical interface with the aid of several tools for processing the spectra, which include setting multiple threshold levels and automatic peak detection. SeqMS is capable of generating candidate sequences, based on the detected peaks, and of displaying the resulting assignments for each candidate in a spectrum or in tabular form. The software has the following capabilities: 1) the ions derived from backbone and side‐chain fragmentations, internal and immonium ions, and side‐chain loss ions can be used for calculation; 2) 18 O‐labeling of a peptide at the C terminus, a methodology which was developed to differentiate N ‐terminal from C ‐terminal ions, is applicable as an optional setting; 3) modified amino acids and N ‐ or C ‐terminal blocking groups are taken into account for calculation according to the user's setting in a library; 4) amino acid composition and partial or complete amino acid sequence of a peptide can be used as input for calculation; 5) the assignments of signal output in a spectrum can be graphically edited, and then re‐calculated based on the edited peaks. The efficacy of the program is demonstrated by testing 74 high‐energy CID spectra, obtained using a four‐sector instrument, of synthetic, proteolytic, and biologically active peptides, some of which contain modified groups. Copyright © 1998 John Wiley & Sons, Ltd.