Update on the moFF Algorithm for Label-Free Quantitative Proteomics

Andrea Argentini, An Staes, Björn Grüning, Subina Mehta, Caleb Easterly, Timothy J Griffin, Pratik D Jagtap, Francis Impens, Lennart Martens

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

moFF is a modular and operating-system-independent tool for quantitative analysis of label-free mass-spectrometry-based proteomics data. The moFF workflow, comprising matching-between-runs and apex quantification, can be applied to any upstream search engine's output, along with the corresponding Thermo or mzML raw file. We here present moFF 2.0, with improvements in speed through multithreading, the use of a new raw file access library, and a novel filtering approach in the matching-between-runs module. This filter allows moFF to correctly identify features that are present in one run but not in another, as demonstrated using spiked-in iRT peptides. Moreover, moFF 2.0 also provides a new peptide summary export that can be used in downstream statistical analysis. moFF is open source and freely available and can be downloaded from https://github.com/compomics/moFF

Original languageEnglish (US)
Pages (from-to)728-731
Number of pages4
JournalJournal of Proteome Research
Volume18
Issue number2
DOIs
StatePublished - Feb 1 2019

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Proteomics
Labels
Search Engine
Peptides
Workflow
Search engines
Libraries
Mass spectrometry
Mass Spectrometry
Statistical methods
Chemical analysis

Keywords

  • MS1-peptide intensity
  • bioinformatics tool
  • label-free quantification
  • singleton peptides

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

Cite this

Argentini, A., Staes, A., Grüning, B., Mehta, S., Easterly, C., Griffin, T. J., ... Martens, L. (2019). Update on the moFF Algorithm for Label-Free Quantitative Proteomics. Journal of Proteome Research, 18(2), 728-731. https://doi.org/10.1021/acs.jproteome.8b00708

Update on the moFF Algorithm for Label-Free Quantitative Proteomics. / Argentini, Andrea; Staes, An; Grüning, Björn; Mehta, Subina; Easterly, Caleb; Griffin, Timothy J; Jagtap, Pratik D; Impens, Francis; Martens, Lennart.

In: Journal of Proteome Research, Vol. 18, No. 2, 01.02.2019, p. 728-731.

Research output: Contribution to journalArticle

Argentini, A, Staes, A, Grüning, B, Mehta, S, Easterly, C, Griffin, TJ, Jagtap, PD, Impens, F & Martens, L 2019, 'Update on the moFF Algorithm for Label-Free Quantitative Proteomics', Journal of Proteome Research, vol. 18, no. 2, pp. 728-731. https://doi.org/10.1021/acs.jproteome.8b00708
Argentini, Andrea ; Staes, An ; Grüning, Björn ; Mehta, Subina ; Easterly, Caleb ; Griffin, Timothy J ; Jagtap, Pratik D ; Impens, Francis ; Martens, Lennart. / Update on the moFF Algorithm for Label-Free Quantitative Proteomics. In: Journal of Proteome Research. 2019 ; Vol. 18, No. 2. pp. 728-731.
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