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

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.

[1]  Lennart Martens,et al.  Protein complex analysis: From raw protein lists to protein interaction networks. , 2017, Mass spectrometry reviews.

[2]  Mihaela E. Sardiu,et al.  Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics , 2008, Proceedings of the National Academy of Sciences.

[3]  R. Aebersold,et al.  Analysis of protein complexes using mass spectrometry , 2007, Nature Reviews Molecular Cell Biology.

[4]  Hyungwon Choi,et al.  SAINT: Probabilistic Scoring of Affinity Purification - Mass Spectrometry Data , 2010, Nature Methods.

[5]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[6]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[7]  Jan Tavernier,et al.  Trapping mammalian protein complexes in viral particles , 2016, Nature Communications.

[8]  S. Gygi,et al.  Defining the Human Deubiquitinating Enzyme Interaction Landscape , 2009, Cell.

[9]  Gábor Csárdi,et al.  The igraph software package for complex network research , 2006 .

[10]  J. Tavernier,et al.  SFINX: Straightforward Filtering Index for Affinity Purification-Mass Spectrometry Data Analysis. , 2016, Journal of proteome research.

[11]  Marco Y. Hein,et al.  A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances , 2015, Cell.

[12]  B. Séraphin,et al.  A generic protein purification method for protein complex characterization and proteome exploration , 1999, Nature Biotechnology.

[13]  Brian Burke,et al.  A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells , 2012, The Journal of cell biology.

[14]  D. Chan,et al.  Analysis of the Human Endogenous Coregulator Complexome , 2011, Cell.

[15]  A. Emili,et al.  Protein-protein interaction networks: probing disease mechanisms using model systems , 2013, Genome Medicine.