Release: Devel:

This is an R package that functions as a GUI overlay for the MSGFplus package. Besides giving the user a visual way of running MS-GF+, it also present a large and engaging set of functions to evaluate the search results. The GUI is build using shiny and D3.js and thus requires a modern browser (which everyone should use anyway).

Main features


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



After installation the GUI can be launched from R by:


By launching a second R session while the GUI is running, the current identification data in the GUI can be accessed in R by:

data <- currentData()

The communication is one-way one-time though - modifications and deletion in the data from the second R session is not propagated to the GUI and if new data is added in the GUI the currentData() call has to be repeated for this to be visible in R.


Sample overview Sample overview Protein view ![Protein view](/../screenshots/screenshots/protein view.png?raw=true "Protein view") Peptide view ![Peptide view](/../screenshots/screenshots/peptide view.png?raw=true "Peptide view") Scan view ![Scan view](/../screenshots/screenshots/scan view.png?raw=true "Scan view") Filtering Filtering Tooltips Tooltips Settings Settings


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. MSGFplus (R package)
  2. MS-GF+ (Original Java program)

thomasp85/MSGFgui documentation built on May 31, 2019, 11:09 a.m.