SUMMARY: Protein identification by mass spectrometry is commonly accomplished using a peptide sequence matching search algorithm, whose sensitivity varies inversely with the size of the sequence database and the number of post-translational modifications considered. We present the Spectrum Identification Machine, a peptide sequence matching tool that capitalizes on the high-intensity b1-fragment ion of tandem mass spectra of peptides coupled in solution with phenylisotiocyanate to confidently sequence the first amino acid and ultimately reduce the search space. We demonstrate that in complex search spaces, a gain of some 120% in sensitivity can be achieved. AVAILABILITY: All data generated and the software are freely available for academic use at http://proteomics.fiocruz.br/software/sim. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A computer program named MSEQ, based on graph theory has been implemented to aid the sequencing of peptides from collision-activated decomposition (CAD) spectra. Input data required by this program are: the molecular weight of the peptide, the list of the masses of the daughter ions and the masses of the N- and C-terminal groups. The output comprises a list of the most likely sequences with their respective scores and the assignments of the daughter ions. A set of probabilities for each fragment ion was computed from hundreds of CAD spectra obtained from our mass spectrometer. To date many peptides have been sequenced in our laboratory with the help of this program, and in most of them the real sequence ranks among the five top sequences. The program is able to differentiate isobaric amino acids such as leucine and isoleucine when the side-chain fragmentation appears in the spectrum. A criterion is used to discard those sequences that match the spectrum poorly from the earliest steps. The program is fast and consumes no memory.