Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies.
Proteogenomic studies ally the omic fields related to gene expression into a combined approach to improve the characterization of biological samples. Part of this consists in mining proteomics datasets for non-canonical sequences of amino acids. These include intergenic peptides, products of mutations, or of RNA editing events hypothesized from genomic, epigenomic, or transcriptomic data. This approach poses new challenges for standard peptide identification workflows. In this chapter, we present the principles behind the use of peptide identification algorithms and highlight the major pitfalls of their application to proteogenomic studies.
Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway. marc.vaudel@uib.no.|KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway. marc.vaudel@uib.no.|Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway. marc.vaudel@uib.no.
Marc
M
Vaudel
Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway.|KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway.
Harald
H
Barsnes
KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway.|Department of Pediatrics, Haukeland University Hospital, Bergen, Norway.
Helge
H
Ræder
Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway.
Frode S
FS
Berven
D000465:Algorithms; D000595:Amino Acid Sequence; D057225:Data Mining / Q000706:statistics & numerical data*; D030541:Databases, Genetic; D066264:Datasets as Topic; D015894:Genome, Human; D006801:Humans; D058977:Molecular Sequence Annotation; D010455:Peptides / Q000032:analysis* / Q000235:genetics; D000071696:Proteogenomics / Q000295:instrumentation / Q000379:methods*; D012313:RNA / Q000032:analysis* / Q000235:genetics; D017393:RNA Editing; D014584:User-Computer Interface
D010455:Peptides; D012313:RNA
Bioinformatics; Proteogenomics; Proteomics