Scientific workflow optimization for improved peptide and protein identification

BMC Bioinformatics
Sonja HollMagnus Palmblad

Abstract

Peptide-spectrum matching is a common step in most data processing workflows for mass spectrometry-based proteomics. Many algorithms and software packages, both free and commercial, have been developed to address this task. However, these algorithms typically require the user to select instrument- and sample-dependent parameters, such as mass measurement error tolerances and number of missed enzymatic cleavages. In order to select the best algorithm and parameter set for a particular dataset, in-depth knowledge about the data as well as the algorithms themselves is needed. Most researchers therefore tend to use default parameters, which are not necessarily optimal. We have applied a new optimization framework for the Taverna scientific workflow management system (http://ms-utils.org/Taverna_Optimization.pdf) to find the best combination of parameters for a given scientific workflow to perform peptide-spectrum matching. The optimizations themselves are non-trivial, as demonstrated by several phenomena that can be observed when allowing for larger mass measurement errors in sequence database searches. On-the-fly parameter optimization embedded in scientific workflow management systems enables experts and non-experts alike to extr...Continue Reading

References

Feb 21, 2004·Bioinformatics·Robertson Craig, Ronald C Beavis
Jun 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·John E P SykaDonald F Hunt
Mar 18, 2005·Molecular & Cellular Proteomics : MCP·Michael L NielsenRoman A Zubarev
Nov 15, 2005·Mass Spectrometry Reviews·Patricia HernandezRon D Appel
Jan 13, 2006·Methods in Enzymology·J Mitchell Wells, Scott A McLuckey
Aug 8, 2006·Journal of Proteome Research·R CraigR C Beavis
Aug 16, 2006·Analytical Chemistry·Barbara E FrewenMichael J MacCoss
Jan 5, 2008·Journal of Proteome Research·Brian C SearleAlexey I Nesvizhskii
Aug 23, 2008·Current Opinion in Chemical Biology·Xuemei HanJohn R Yates
Dec 3, 2009·Proteomics·Joerg SeidlerWolf D Lehmann
Dec 17, 2009·Methods in Molecular Biology·Henry Lam, Ruedi Aebersold
Sep 11, 2010·Molecular & Cellular Proteomics : MCP·Sangtae KimPavel A Pevzner
Jun 3, 2011·BMC Microbiology·Ekaterina MostovenkoMagnus Palmblad
Jun 7, 2011·Molecular & Cellular Proteomics : MCP·Annette MichalskiStevan Horning
Mar 14, 2012·Molecular & Cellular Proteomics : MCP·Jeroen S de BruinMagnus Palmblad
May 16, 2012·Journal of Proteome Research·Johannes JunkerOliver Kohlbacher
Aug 25, 2012·Journal of Proteome Research·Yassene MohammedMagnus Palmblad
Dec 4, 2012·Nucleic Acids Research·Juan Antonio VizcaínoHenning Hermjakob
Nov 26, 2013·Journal of Proteome Research·Cheryl F LichtiCarol L Nilsson

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Citations

Apr 19, 2017·Briefings in Bioinformatics·Md Rezaul KarimDietrich Rebholz-Schuhmann
Jul 31, 2018·Bioinformatics·Magnus PalmbladVeit Schwämmle
Dec 4, 2021·Mass Spectrometry Reviews·Ágnes RévészLászló Drahos

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Software Mentioned

rt
trapControl
Taverna
SEQUEST
gnuplot
HyStar
PRIDE
PeptideProphet
SSRCalc
Taverna UNICORE

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