title: Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results.
abstract: Shotgun proteomics is a high throughput technique for protein identification able to identify up to several thousand proteins from a single sample. In order to make sense of this large amount of data, proteomics analysis software is needed, aimed at making the data intuitively accessible to beginners as well as experienced scientists. This chapter provides insight on where to start when analyzing shotgun proteomics data, with a focus on explaining the most common pitfalls in protein identification analysis and how to avoid them. Finally, the move to seeing beyond the list of identified proteins and to putting the results into a bigger biological context is discussed.
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, Bergen, Norway.
authors.forename: Ragnhild R
authors.initials: RR
authors.lastname: Lereim
authors.affiliation: 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, Bergen, Norway.|Department of Clinical Medicine, University of Bergen, Bergen, Norway.
authors.forename: Eystein
authors.initials: E
authors.lastname: Oveland
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, 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.
authors.forename: Marc
authors.initials: M
authors.lastname: Vaudel
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
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*; D015203:Reproducibility of Results; D057386:Search Engine; D012984:Software; D014584:User-Computer Interface; D057188:Workflow
chemical_list: D011506:Proteins; D020543:Proteome
keywords: Protein annotation; Protein identification; Validation; Visualization