mPE-MMR

The mPE-MMR method is an integrated approach that combines three previously reported methods of treating MS/MS data for precursor mass refinement. It increases sensitivity in peptide identification and provides increased accuracy.

mPE-MMR can be used to create a MGF file with refined parent ion masses and charges, which can lead to more accurate search results from MS/MS spectra. mPE-MMR (Multiplexed Post-Experiment Monoisotopic Mass Refinement) supports multiplexed MS/MS spectra, and consists of the following:

• Multiplexing of precursor masses to assign multiple monoisotopic masses of cofragmented peptides to the corresponding multiplexed MS/MS spectra
• Multiplexing of charge states to assign correct charges to the precursor ions of MS/MS spectra with no charge information
• Mass correction for inaccurate monoisotopic peak picking.

mPEMMR uses two external programs: RAPID and msconvert

RAPID can be downloaded here, (https://github.com/HanyangBISLab/RAPID)

msconvert can be installed from ProteoWizard (https://proteowizard.sourceforge.io/download.html).

After that

1. Modify the paths of RAPID and MSCONVERT in the mPEMMR_param.txt file.
2. Modify PEMMR_HOME to the appropriate path in mPEMMR_3.1.cmd file and execute the command below.

and execute the command below

build docker image

sudo docker load -i pqt_save.tar

make a parquet file

raw2mzparquet {raw file name}

run RAPID

rapid_new ./rapid_ms.txt

run mPE-MMR

mPEMMR_3.1.sh ./mPEMMR_param.txt ./some_raw.raw