Algorithms for the de novo sequencing of peptides from tandem mass spectra

peer-reviewed · Expert Review of Proteomics · 2011

peer-reviewed · Expert Review of Proteomics · 2011. Jens Allmer. Proteomics is the study of proteins, their time- and location-dependent expression profiles, as well as their…
Date 2011-10-01
Type peer-reviewed
Venue Expert Review of Proteomics
Publisher Informa UK Limited
Contribution review
DOI 10.1586/epr.11.54
Citations (OpenAlex) 115
Venue 2-year citedness 3.58

Abstract

Proteomics is the study of proteins, their time- and location-dependent expression profiles, as well as their modifications and interactions. Mass spectrometry is useful to investigate many of the questions asked in proteomics. Database search methods are typically employed to identify proteins from complex mixtures. However, databases are not often available or, despite their availability, some sequences are not readily found therein. To overcome this problem, de novo sequencing can be used to directly assign a peptide sequence to a tandem mass spectrometry spectrum. Many algorithms have been proposed for de novo sequencing and a selection of them are detailed in this article. Although a standard accuracy measure has not been agreed upon in the field, relative algorithm performance is discussed. The current state of the de novo sequencing is assessed thereafter and, finally, examples are used to construct possible future perspectives of the field.

Authors

  1. Jens Allmer · Hochschule Ruhr West, Izmir Institute of Technology, Ruhr West University of Applied Sciences, University of Münster, University of Pennsylvania

Methods and tools

Cites (49)

Cited by (33)

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