PT  - JOURNAL ARTICLE
AU  - Marek Gierlinski
AU  - Francesco Gastaldello
AU  - Chris Cole
AU  - Geoffrey J. Barton
TI  - <em>Proteus</em>: an R package for downstream analysis of <em>MaxQuant</em> output
AID  - 10.1101/416511
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 416511
4099  - http://biorxiv.org/content/early/2018/09/20/416511.short
4100  - http://biorxiv.org/content/early/2018/09/20/416511.full
AB  - Proteus is a package for downstream analysis of MaxQuant evidence data in the R environment. It provides tools for peptide and protein aggregation, quality checks, data exploration and visualisation. Interactive analysis is implemented in the Shiny framework, where individual peptides or protein may be examined in the context of a volcano plot. Proteus performs differential expression analysis with the well-established tool limma, which offers robust treatment of missing data, frequently encountered in label-free mass-spectrometry experiments. We demonstrate on real and simulated data that limma results in improved sensitivity over random imputation combined with a t-test as implemented in the popular package Perseus. Embedding Proteus in R provides access to a wide selection of statistical and graphical tools for further analysis and reproducibility by scripting. Availability and implementation: The open-source R package, including example data and tutorials, is available to install from GitHub (https://github.com/bartongroup/proteus).