Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies

Adv Exp Med Biol. 2016:926:65-75. doi: 10.1007/978-3-319-42316-6_5.

Abstract

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.

Keywords: Bioinformatics; Proteogenomics; Proteomics.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Data Mining / statistics & numerical data*
  • Databases, Genetic
  • Datasets as Topic
  • Genome, Human
  • Humans
  • Molecular Sequence Annotation
  • Peptides / analysis*
  • Peptides / genetics
  • Proteogenomics / instrumentation
  • Proteogenomics / methods*
  • RNA / analysis*
  • RNA / genetics
  • RNA Editing
  • User-Computer Interface

Substances

  • Peptides
  • RNA