Click here for MCATSCAN software and users manual.

Click here for Twinpeaks software and users manual.

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Program DescriptionsTwo Perl-based computer programs, MCATSCAN and TWINPEAKS, have been written to facilitate high-throughput spectral processing and de novo sequencing of peptides using the MCAT approach. MCATSCAN extracts common ion peaks (b-ion candidates) and ion peaks offset by 42 m/z (y-ion candidates) from pairs of input tandem mass spectra of sister modified- and unmodified peptides and calculates the most likely peptide sequence based on a maximum path algorithm. TWINPEAKS is a tool that sorts and filters large LC-MS/MS datafiles (specifically, the output file from the EXTRACTMS program (J. Eng; Institute for Systems Biology, Seattle, WA) for pairs of sister (unmodified and MCAT modified) peptide precurser ions that differ by 42, 21 or 14 m/z units (corresponding to +1, +2, or +3 charged ions) and that satisfy chromatographic criteria typical of MCAT-paired peptides. While both programs are in beta development, the current release versions are effective and are freely available from www.utoronto.ca/emililab/links/software. Users are requested to cite these programs and this laboratory in any publication resulting from their use.