sfinx: an R package for the elimination of false positives from affinity purification-mass spectrometry datasets

Kevin Titeca; Pieter Meysman; Kris Laukens; Lennart Martens; Jan Tavernier; Sven Eyckerman

doi:10.1093/bioinformatics/btx076

sfinx: an R package for the elimination of false positives from affinity purification-mass spectrometry datasets

Bioinformatics. 2017 Jun 15;33(12):1902-1904. doi: 10.1093/bioinformatics/btx076.

Authors

Kevin Titeca^{1

2}, Pieter Meysman^{3

4}, Kris Laukens^{3

4}, Lennart Martens^{1

2

5}, Jan Tavernier^{1

2}, Sven Eyckerman^{1

2}

Affiliations

¹ VIB Medical Biotechnology Center, A. Baertsoenkaai 3, Ghent, Belgium.
² Department of Biochemistry, Ghent University, Ghent, Belgium.
³ Advanced Database Research and Modelling (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.
⁴ Biomedical Informatics Research Center Antwerp (biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium.
⁵ Bioinformatics Institute Ghent, Ghent University, Zwijnaarde, Belgium.

PMID: 28186257
DOI: 10.1093/bioinformatics/btx076

Abstract

Summary: We describe sfinx, an R package providing access to the straightforward filtering index (SFINX) for the separation of true positive from false positive protein interactions in affinity purification - mass spectrometry datasets. This package maintains the reliability and user-friendliness of the SFINX web site interface but is faster, unlimited in input size, and can be run locally within R.

Availability and implementation: The sfinx R package is available for download at the comprehensive R archive network (CRAN) https://cran.r-project.org/web/packages/sfinx/ under the Apache License 2.0.

Contact: sven.eyckerman@vib-ugent.be or kevin.titeca@gmail.com.

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Mass Spectrometry / methods*
Proteomics / methods*
Reproducibility of Results
Software*