title: Current methods for global proteome identification.
abstract: In a time frame of a few decades, protein identification went from laborious single protein identification to automated identification of entire proteomes. This shift was enabled by the emergence of peptide-centric, gel-free analyses, in particular the so-called shotgun approaches, which not only rely on extensive experiments, but also on cutting-edge data processing methods. The present review therefore provides an overview of a shotgun proteomics identification workflow, listing the state-of-the-art methods involved and software that implement these. The authors focus on freely available tools where possible. Finally, data analysis in the context of emerging across-omics studies will also be discussed briefly, where proteomics goes beyond merely delivering a list of protein accession numbers.
authors.affiliation: Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany.
authors.forename: Marc
authors.initials: M
authors.lastname: Vaudel
authors.forename: Albert
authors.initials: A
authors.lastname: Sickmann
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
mesh_terms: D019295:Computational Biology / Q000379:methods; D006801:Humans; D010455:Peptides / Q000737:chemistry / Q000302:isolation & purification; D011506:Proteins / Q000737:chemistry / Q000302:isolation & purification; D020543:Proteome / Q000737:chemistry / Q000302:isolation & purification; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides; D011506:Proteins; D020543:Proteome