DAG papers

Group Publications

2018 (2)

Gierlinski M.; Gastaldello F.; Cole C.; Barton G.J. Proteus: an R package for downstream analysis of MaxQuant output 2018 bioRxiv 416511

\p\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/bartongrouproteus).\\

Ly T.; Endo A.; Brenes A.; Gierlinski M.; Afzal V.; Pawellek A.; Lamond A.I. Proteome-wide analysis of protein abundance and turnover remodelling during oncogenic transformation of human breast epithelial cells 2018 Wellcome Open Research 3:51

2017 (7)

2016 (12)

2015 (13)

2014 (6)

2013 (6)

2012 (6)

2011 (4)

2010 (2)

2009 (2)

2008 (1)