PIUS: peptide identification by unbiased search

SUMMARY We present PIUS, a tool that identifies peptides from tandem mass spectrometry data by analyzing the six-frame translation of a complete genome. It differs from earlier studies that have performed such a genomic search in two ways: (i) it considers a larger search space and (ii) it is designed for natural peptide identification rather than proteomics. Differently from other peptidomics tools designed for genome-wide searches, PIUS does not limit the analysis to a set of sequences that match a list of de novo reconstructions. AVAILABILITY Source code, executables and a detailed technical report are freely available at http://dtai.cs.kuleuven.be/ml/systems/pius. CONTACT eduardo.costa@cs.kuleuven.be SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

[1]  Liliane Schoofs,et al.  Comparison of extraction methods for peptidomics analysis of mouse brain tissue , 2011, Journal of Neuroscience Methods.

[2]  P. Pevzner,et al.  Spectral Dictionaries , 2009, Molecular & Cellular Proteomics.

[3]  Ari M Frank,et al.  A ranking-based scoring function for peptide-spectrum matches. , 2009, Journal of proteome research.

[4]  Daniel B. Goodman,et al.  Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. , 2008, Genome research.

[5]  Robertson Craig,et al.  TANDEM: matching proteins with tandem mass spectra. , 2004, Bioinformatics.

[6]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[7]  Nuno Bandeira,et al.  Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra* , 2011, Molecular & Cellular Proteomics.

[8]  J. Sweedler,et al.  A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome. , 2010, Journal of proteome research.

[9]  W. Van Criekinge,et al.  Peptidomics coming of age: a review of contributions from a bioinformatics angle. , 2010, Journal of proteome research.

[10]  Akhilesh Pandey,et al.  Genome annotation of Anopheles gambiae using mass spectrometry-derived data , 2005, BMC Genomics.

[11]  Nuno Bandeira,et al.  Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra* , 2010, Molecular & Cellular Proteomics.