UNIGE document Scientific Article
previous document  unige:5595  next document
add to browser collection
Title

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

Authors
Quandt, Andreas
Hernandez, Céline
Maffioletti, Sergio
Published in Proteomics. 2009, vol. 9, no. 10, p. 2648-55
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 NetworksProtein Processing, Post-TranslationalProteins/analysisProteomics/methodsSequence Analysis, ProteinSoftwareTandem Mass Spectrometry
Identifiers
PMID: 19391179
Full text
Article (Published version) (333 Kb) - document accessible for UNIGE members only Limited access to UNIGE
Supplemental data - I - document accessible for UNIGE members only Limited access to UNIGE
Supplemental data - II - document accessible for UNIGE members only Limited access to UNIGE
Supplemental data - III - document accessible for UNIGE members only Limited access to UNIGE
Supplemental data - VI - document accessible for UNIGE members only Limited access to UNIGE
Other version: http://www3.interscience.wiley.com/journal/122355134/abstract
Structures
Research group Swiss Institute of Bioinformatics
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. 2648-55. https://archive-ouverte.unige.ch/unige:5595

239 hits

10 downloads

Update

Deposited on : 2010-03-25

Export document
Format :
Citation style :