ptm: an R package for the study of methionine sulfoxidation and other posttranslational modifications.

Abstract

Methionine sulfoxidation is a posttranslational modification (PTM) playing important roles in cell signaling. Herein, we present ptm, an R package for the study of this modification. However, since many of the analyses applied to methionine modification can be extended to other modifications, the package can be useful to thoroughly analyze PTMs in general. Thus, within a single software environment, ptm can integrate information from up to 11 databases covering nine modifications. Different functions can work coordinately to form pipelines allowing the programmatic analysis of thousands of proteins. Alternatively, the user can simultaneously perform different analyses on the same protein of interest, combining the results into a single output. The flexibility of ptm makes it a suitable tool to address site- and protein-centric hypotheses related to PTMs. Accompanying the package, we maintain a web page containing extended documentation and examples of the tasks that can be performed with ptm. ptm is implemented in R. Release versions are available via CRAN and work on all major operating systems. The development version is maintained at https://bitbucket.org/jcaledo/ptm. Extended documentation can be found at https://metositeptm.com. Supplementary data are available at Bioinformatics online.