SpecOMS: A Full Open Modification Search Method Performing All-to-All Spectra Comparisons within Minutes
2017
David, Matthieu | Fertin, Guillaume | Rogniaux, Hélène | Tessier, Dominique | Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA) ; Institut National de la Recherche Agronomique (INRA) | Centre National de la Recherche Scientifique (CNRS) | Laboratoire des Sciences du Numérique de Nantes (LS2N) ; Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST) ; Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique) ; Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT) | Combinatoire et Bioinformatique (LS2N - équipe COMBI) ; Laboratoire des Sciences du Numérique de Nantes (LS2N) ; Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST) ; Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique) ; Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST) ; Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique) ; Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT) | Region Pays de la Loire (France) GRIOTE program
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Show more [+] Less [-]English. The analysis of discovery proteomics experiments relies on algorithms that identify peptides from their tandem mass spectra. The almost exhaustive interpretation of these spectra remains an unresolved issue. At present, an important number of missing interpretations is probably due to peptides displaying post-translational modifications and variants that yield spectra that are particularly difficult to interpret. However, the emergence of a new generation of mass spectrometers that provide high fragment ion accuracy has paved the way for more efficient algorithms. We present a new software, SpecOMS, that can handle the computational complexity of pairwise comparisons of spectra in the context of large volumes. SpecOMS can compare a whole set of experimental spectra generated by a discovery proteomics experiment to a whole set of theoretical spectra deduced from a protein database in a few minutes on a standard workstation. SpecOMS can ingeniously exploit those capabilities to improve the peptide identification process, allowing strong competition between all possible peptides for spectrum interpretation. Remarkably, this software resolves the drawbacks (i.e., efficiency problems and decreased sensitivity) that usually accompany open modification searches. We highlight this promising approach using results obtained from the analysis of a public human data set downloaded from the PRIDE (PRoteomics IDEntification) database.
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