InSilicoSpectro: an open-source proteomics library

Journal of Proteome Research
Jacques ColingeRon D Appel

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.

References

Nov 1, 1984·Biomedical Mass Spectrometry·P Roepstorff, J Fohlman
Oct 30, 1998·Journal of the American Society for Mass Spectrometry·J P DeGnore, J Qin
Oct 9, 2002·Genome Research·Jason E StajichEwan Birney
Jun 26, 2003·Nucleic Acids Research·Elisabeth GasteigerAmos Bairoch
Jul 16, 2004·Journal of Proteome Research·Samir Julka, Fred Regnier
Oct 12, 2004·Journal of Proteome Research·Lewis Y GeerStephen H Bryant
Dec 15, 2004·Journal of Proteome Research·Robertson CraigRonald C Beavis

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Citations

Feb 5, 2013·Amino Acids·Harald Barsnes, Lennart Martens
Sep 24, 2009·Journal of the American Society for Mass Spectrometry·Yihsuan S TsaiDavid R Goodlett
Oct 22, 2008·Bioinformatics·John T Prince, Edward M Marcotte
Oct 31, 2009·BMC Bioinformatics·Jignesh R ParikhJarrod A Marto
Mar 10, 2011·BMC Bioinformatics·Harald BarsnesLennart Martens
Aug 7, 2007·PLoS Computational Biology·Jacques Colinge, Keiryn L Bennett
Oct 3, 2012·PloS One·Timo H J Niedermeyer, Martin Strohalm
Jun 11, 2011·Journal of Proteomics·Yasset Perez-RiverolVladimir Besada
Nov 26, 2014·Proteomics·Harald BarsnesLennart Martens
Oct 17, 2009·Proteomics·Luisa Montecchi-PalazziHenning Hermjakob
May 4, 2011·Electrophoresis·Yassel RamosVladimir Besada
Mar 8, 2013·Biochimica Et Biophysica Acta·Yasset Perez-RiverolJuan Antonio Vizcaíno
Mar 23, 2011·Journal of Proteome Research·Amit Kumar YadavDebasis Dash
Jul 31, 2018·Bioinformatics·Magnus PalmbladVeit Schwämmle
May 16, 2019·Molecular & Cellular Proteomics : MCP·Dain R BrademanJoshua J Coon
Mar 3, 2020·Briefings in Bioinformatics·Jiancheng ZhongJianxin Wang
Aug 9, 2019·Molecular & Cellular Proteomics : MCP·Dain R BrademanJoshua J Coon
Apr 22, 2008·Journal of Proteome Research·Yassel RamosVladimir Besada
Aug 24, 2007·Analytical Chemistry·Jacques Colinge

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