title: InSilicoSpectro: an open-source proteomics library.
abstract: We present a new proteomics open-source project, InSilicoSpectro, aimed at implementing recurrent computations that are necessary for proteomics data analysis. Illustrative examples are mass list file format conversions, protein sequence digestion, theoretical peptide and fragment mass computations, graphical display, matching with experimental data, isoelectric point estimation, and peptide retention time prediction. The project library is written in Perl, a widely used scripting language in bioinformatics, and it offers a unique framework of integrated objects to implement complex proteomics data analyses. For instance, only a few lines of code are required to digest a protein with fixed and variable modifications, label peptides with 18O, compute the fragmentation spectra and display their match with experimental spectra. We believe that InSilicoSpectro will be of great help to bioinformaticians, without detailed knowledge of proteomics specifics, and to mass spectrometrists with computer programming interest as well.
authors.affiliation: Upper Austria University of Applied Sciences at Hagenberg, Bioinformatics Department, Hauptstrasse 117, A-4232 Hagenberg, Austria. jacques.colinge@fh-hagenberg.at
authors.forename: Jacques
authors.initials: J
authors.lastname: Colinge
authors.forename: Alexandre
authors.initials: A
authors.lastname: Masselot
authors.forename: Pablo
authors.initials: P
authors.lastname: Carbonell
authors.forename: Ron D
authors.initials: RD
authors.lastname: Appel
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D008969:Molecular Sequence Data; D019151:Peptide Library; D040901:Proteomics; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D019151:Peptide Library