SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines

peer-reviewed · Journal of Proteome Research · 2018

peer-reviewed · Journal of Proteome Research · 2018. Harald Barsnes et al. Mass-spectrometry-based proteomics has become the standard approach for identifying and quantifying proteins…
Date 2018-05-18
Type peer-reviewed
Venue Journal of Proteome Research
Publisher American Chemical Society
Contribution adjacent
DOI 10.1021/acs.jproteome.8b00175
Citations (OpenAlex) 229
Venue 2-year citedness 3.48

Abstract

Mass-spectrometry-based proteomics has become the standard approach for identifying and quantifying proteins. A vital step consists of analyzing experimentally generated mass spectra to identify the underlying peptide sequences for later mapping to the originating proteins. We here present the latest developments in SearchGUI, a common open-source interface for the most frequently used freely available proteomics search and de novo engines that has evolved into a central component in numerous bioinformatics workflows.

Authors

  1. Harald Barsnes · University of Bergen
  2. Marc Vaudel · Haukeland University Hospital, University of Bergen

Methods and tools

  • SearchGUI: Open-source common interface wrapping a wide set of proteomics database search engines (X!Tandem, MS-GF+, Comet, OMSSA, MS Amanda, MyriMatch, Tide, Andromeda, MetaMorpheus, Sage) plus classical de novo engines (PepNovo+, DirecTag, Novor, pNovo). Sister project to DeNovoGUI from the same CompOmics-aligned Bergen / Ghent group.

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Cited by (3)

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