By detailing every step from data loading to results display, the present supplementary material details how the peptides and proteins are inferred from search engine results and how these are scored, displayed and connected with rich resources for protein identification. PeptideShaker is fully documented and comes with contextual help and extended tutorials. Notably, the use of PeptideShaker does not require extensive knowledge in bioinformatics. All results can be exported in various reports, either for further follow up analyses or for submission to PRIDE. For every identified protein, peptide and spectrum, PeptideShaker delivers useful information like identification confidence, modification site(s) and external information via resources like Ensembl12 or PDB13.
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In combination with SearchGUI9, a user-friendly graphical user interface to conduct proteomics searches, it provides a full identification solution for both locally generated datasets and publicly available data in PRIDE10 via ProteomeXchange11. PeptideShaker allows intuitive interpretation of peptide and protein mass spectrometry based identification results. Here, we present PeptideShaker, an interface to assemble and inspect results from tandem mass spectra identification algorithms.
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MaxQuant2, the TransProteomic pipeline3-4, OpenMS5-7, and ID Picker8 are examples of the efforts of the scientific community to provide free solutions for protein identification.
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Introduction The interpretation of protein identification results from identification algorithms can be conducted in several software environments1, freeware or commercial, some delivered with the instrument by the vendor. 41 10.0 - Documentation, Help, Support and Updates. 33 8.0 - Reports, Follow Up Analyses and Submissions to PRIDE.
14 6.0 - Validating Proteins, Peptides and PSMs. 3 1.0 – Installation and Hardware Requirements. The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Dortmund, Germany Vaudel et al.: PeptideShaker - Supplementary Material Note: Version as accepted after peer review. Neurology, Haukeland University Hospital, Bergen, Norway 6ĭepartment of Medical Protein Research, VIB, Ghent, Belgiumĭepartment of Biochemistry, Ghent University, Ghent, Belgiumīiology Unit, University of Bergen, Norway The Norwegian Multiple Sclerosis Competence Centre, Department of KG Jebsen Centre for MS-research, Department of Clinical Medicine, Of Clinical Medicine, University of Bergen, Bergen, Norway Unit, Department of Biomedicine, University of Bergen, Bergen, Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Dortmund, Berven2,4,5, Albert Sickmann1, Lennart Martens6,7,* and Harald Barsnes2,8 PeptideShaker: Completing the proteomics data cycle Marc Vaudel1,2, Julia M. Vaudel et al.: PeptideShaker: Completing the proteomics data cycle.
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