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Scientific article
English

SwissPIT: An workflow-based platform for analyzing tandem-MS spectra using the Grid

Contributors

Quandt, Andreas; Masselot, Alexandre; Hernandez, Patricia; Hernandez, Céline; Maffioletti, Sergio; Appel, Ron David; Lisacek, Frédérique

Published in

Proteomics, vol. 9, no. 10, p. 2648-2655

Publication date

2009

Abstract

The identification and characterization of peptides from MS/MS data represents a critical aspect of proteomics. It has been the subject of extensive research in bioinformatics resulting in the generation of a fair number of identification software tools. Most often, only one program with a specific and unvarying set of parameters is selected for identifying proteins. Hence, a significant proportion of the experimental spectra do not match the peptide sequences in the screened database due to inappropriate parameters or scoring schemes. The Swiss protein identification toolbox (swissPIT) project provides the scientific community with an expandable multitool platform for automated in-depth analysis of MS data also able to handle data from high-throughput experiments. With swissPIT many problems have been solved: The missing standards for input and output formats (A), creation of analysis workflows (B), unified result visualization (C), and simplicity of the user interface (D). Currently, swissPIT supports four different programs implementing two different search strategies to identify MS/MS spectra. Conceived to handle the calculation-intensive needs of each of the programs, swissPIT uses the distributed resources of a Swiss-wide computer Grid (http://www.swing-grid.ch).

Keywords

  • Computer Communication Networks
  • Protein Processing, Post-Translational
  • Proteins/analysis
  • Proteomics/methods
  • Sequence Analysis, Protein
  • Software
  • Tandem Mass Spectrometry

UNIGE affiliation entities

UNIGE research groups

Citation (ISO format)

QUANDT, Andreas et al. SwissPIT: An workflow-based platform for analyzing tandem-MS spectra using the Grid. In: Proteomics, 2009, vol. 9, n° 10, p. 2648–2655. doi: 10.1002/pmic.200800207

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Identifiers

Journal ISSN

1615-9853
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Technical informations

Creation

25/03/2010 15:18:00

First validation

25/03/2010 15:18:00

Update

26/03/2026 10:50:41

Status update

26/03/2026 10:50:41

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