microbiomedata/mepro repository overview

⁠NMDC Meta-proteomics workflow

⁠About

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Meta-proteomics workflow/pipeline is an end-to-end data processing and analyzing pipeline for studying proteomes i.e studying protein identification and characterization using MS/MS data. We identify the active organisms/species in a metagenome corresponding to a wet-lab sample obtained from JGI after gene sequencing. Then the researchers at PNNL culture these samples and make it appropriate to study it as a protein sample. This protein sample may have a single protein or a complex mixture of proteins. Later, this sample is passed through a mass spectrometry instrument to obtain a proprietary data format.RAW file. This file contains MS/MS spectrum i.e mass analysis(mass-to-charge (m/z) ratios) for each peptide sequences identified in the sample.

Additionally, we need sequenced metagenomes for each dataset. Currently, The metagenomes are obtained from NERSC(JGI) in the FASTA(.faa) files.

This workflow kicks in after .raw, .faa, and respective parameter files are available.

FYI, Built it using Dockerfile⁠

Simply pull docker image using docker pull microbiomedata/mepro:2.0.0

To test the workflow, it would be nice to follow project's readme⁠