Release: Devel:

This package aims to bridge R and the peptide database search tool MS-GF+. The main class of the package is msgfPar which handles parsing of parameters to MS-GF+. The msgfPar class has a runMSGF method that starts a peptide search for a given set of MS data files and possibly reimports the results using mzID.

Besides this basic functionality it also supports reading in parameters from mzIdentML files created by MS-GF+ in order to replicate a search setup as well as a very simple gWidgets based GUI to fill out a msgfPar object.

MSGFplus is intended as a pure R wrapper. For a more engaging user experience have a look at MSGFgui which provides a visual interface on top of this package using shiny.


MSGFgui and it's sister package MSGFplus are part of Bioconductor and can be installed through that repository. Instruction are as follows:



Sangtae Kim is the developer behind the MS-GF+ algoritm, without which this package would be rather shallow. Furthermore he has provided fast and helpful feedback during the development process.


  1. MSGFgui (R based GUI for MSGFplus)
  2. MS-GF+ (Original Java program)
  3. mzID (R package)

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MSGFplus documentation built on May 2, 2018, 2:42 a.m.