title: Shedding light on black boxes in protein identification.
abstract: Performing a well thought-out proteomics data analysis can be a daunting task, especially for newcomers to the field. Even researchers experienced in the proteomics field can find it challenging to follow existing publication guidelines for MS-based protein identification and characterization in detail. One of the primary goals of bioinformatics is to enable any researcher to interpret the vast amounts of data generated in modern biology, by providing user-friendly and robust end-user applications, clear documentation, and corresponding teaching materials. In that spirit, we here present an extensive tutorial for peptide and protein identification, available at http://compomics.com/bioinformatics-for-proteomics. The material is completely based on freely available and open-source tools, and has already been used and refined at numerous international courses over the past 3 years. During this time, it has demonstrated its ability to allow even complete beginners to intuitively conduct advanced bioinformatics workflows, interpret the results, and understand their context. This tutorial is thus aimed at fully empowering users, by removing black boxes in the proteomics informatics pipeline.
authors.affiliation: Proteomics Unit, Department of Biomedicine, University of Bergen, Norway; Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, Germany.
authors.forename: Marc
authors.initials: M
authors.lastname: Vaudel
authors.forename: A Saskia
authors.initials: AS
authors.lastname: Venne
authors.forename: Frode S
authors.initials: FS
authors.lastname: Berven
authors.forename: René P
authors.initials: RP
authors.lastname: Zahedi
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.forename: Harald
authors.initials: H
authors.lastname: Barsnes
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D030562:Databases, Protein; D011506:Proteins / Q000032:analysis / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins
keywords: Bioinformatics; Open Source; Protein Identification; Publication Guidelines; Tutorial