Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics

peer-reviewed · Advances in Experimental Medicine and Biology · 2016

peer-reviewed · Advances in Experimental Medicine and Biology · 2016. Thilo Muth et al. Protein identification via database searches has become the gold standard in mass spectrometry based shotgun…
Date 2016-12-15
Type peer-reviewed
Venue Advances in Experimental Medicine and Biology
Publisher Springer International Publishing
Contribution review
DOI 10.1007/978-3-319-41448-5_10
Citations (OpenAlex) 2
Venue 2-year citedness 2.31

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

  1. Thilo Muth · Federal Institute for Materials Research and Testing (BAM), Max Planck Institute for Dynamics of Complex Technical Systems, Robert Koch Institute, glyXera GmbH
  2. Erdmann Rapp · Max Planck Institute for Dynamics of Complex Technical Systems, glyXera GmbH
  3. Frode S. Berven · Haukeland University Hospital, University of Bergen
  4. Harald Barsnes · University of Bergen
  5. Marc Vaudel · Haukeland University Hospital, University of Bergen

Methods and tools

  • Tandem mass spectrum sequencing (review): Book chapter presenting de novo sequencing as the alternative to database search engines in shotgun proteomics, covering its pitfalls and challenges and reviewing the main available tools.

Cites (24)

Cited by (1)

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