RefMod is an implementation of the ReCom concept (Laguillo-Gómez et al., 2023) designed to be run as a post-processing step after an open MSFragger search. It is compatible with both DDA and DIA data. When using RefMod, DIA data can be searched in a “pseudo-DDA” workflow, using a curated list of theoretical Δmass values to correct errors caused by the uncertainty in precursor masses contained within the same fragmentation window.
RefMod has been developed at the Cardiovascular Proteomics Lab / Proteomics Unit at CNIC (Spanish National Centre for Cardiovascular Research).
This section provides a brief overview of the basic requirements to run RefMod from the command line. A GUI is also available and can be launched using the RefMod.bat file located in the root directory. If this is your first time using RefMod, or if you’re looking for an in-depth explanation of any step, please refer to the full documentation.
- Download the latest release from the GitHub page.
- Install Python 3.11 and the packages from
requirements.txt. - Prepare your configuration file and run RefMod from the GUI or from the command line:
$ python RefMod.py -i [MSFragger files] -r [MGF or mzML files] -d [Theoretical Δmasses file] -c [Configuration file] - Find the output files in a newly created
refmoddirectory in the same path specified by the -i option.