Chapter

Modern Proteomics – Sample Preparation, Analysis and Practical Applications

Volume 919 of the series Advances in Experimental Medicine and Biology pp 217-226

Date:

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

  • Thilo MuthAffiliated withMax Planck Institute for Dynamics of Complex Technical SystemsglyXera GmbH
  • , Erdmann RappAffiliated withMax Planck Institute for Dynamics of Complex Technical SystemsglyXera GmbH
  • , Frode S. BervenAffiliated withProteomics Unit, Department of Biomedicine, University of BergenKG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of BergenNorwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital
  • , Harald BarsnesAffiliated withProteomics Unit, Department of Biomedicine, University of Bergen Email author 
  • , Marc VaudelAffiliated withProteomics Unit, Department of Biomedicine, University of Bergen

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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.

Keywords

de novo identification Mass spectrum sequencing Quality control Visualization