title: Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.
abstract: Protein identification via database searches has become the gold standard in mass spectrometry based shotgun proteomics. However, as the quality of tandem mass spectra improves, direct mass spectrum sequencing gains interest as a database-independent alternative. In this chapter, the general principle of this so-called de novo sequencing is introduced along with pitfalls and challenges of the technique. The main tools available are presented with a focus on user friendly open source software which can be directly applied in everyday proteomic workflows.
authors.affiliation: Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.|glyXera GmbH, Magdeburg, Germany.
authors.forename: Thilo
authors.initials: T
authors.lastname: Muth
authors.affiliation: Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.|glyXera GmbH, Magdeburg, Germany.
authors.forename: Erdmann
authors.initials: E
authors.lastname: Rapp
authors.affiliation: Proteomics Unit, Department of Biomedicine, University of Bergen, Jonas Liesvei 91, N-5009, Bergen, Norway.|KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway.|Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway.
authors.forename: Frode S
authors.initials: FS
authors.lastname: Berven
authors.affiliation: Proteomics Unit, Department of Biomedicine, University of Bergen, Jonas Liesvei 91, N-5009, Bergen, Norway. harald.barsnes@biomed.uib.no.
authors.forename: Harald
authors.initials: H
authors.lastname: Barsnes
authors.affiliation: Proteomics Unit, Department of Biomedicine, University of Bergen, Jonas Liesvei 91, N-5009, Bergen, Norway.
authors.forename: Marc
authors.initials: M
authors.lastname: Vaudel
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D057166:High-Throughput Screening Assays; D006801:Humans; D011506:Proteins / Q000032:analysis*; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D057386:Search Engine; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*; D057188:Workflow
chemical_list: D011506:Proteins; D020543:Proteome
keywords: Mass spectrum sequencing; Quality control; Visualization; de novo identification