ProMETAdb

We are currently in the golden era of proteomics, where mass spectrometry (MS) based proteomics datasets are publically available in many repositories. Meta-analysis of existing proteomics through proteogenomics approach shows great potential towards identifying novel proteins and peptides. In 2011, ProteomeXchange(PX) consortium has adopted a unified framework to enable rapid dissemination of proteomics datasets existing in different repositories (PRIDE, MassIVE, PeptideAtlas, jPOST and iProX). PX follows the Minimum Information About a Proteomics Experiment (MIAPE) guidelines for the metadata; it provides only minimal information such as the title, description, species, modification, instrument, keywords and links to the repository etc. Here, we present Proteomics Metadata DataBase (ProMetaDB), which contains additionally curated meta information (phenotypes, conditions/concentrations and their associated raw/processed files) for all existing proteomics studies. We have retrieved all the existing metadata from PRIDE, MassIVE and PeptideAtlas, jPOST and iProx through our custom R-packages. We have re-annotated 195 MassIVE projects out of 2000 projects. Also, we have re-annotated human specific proteomics project based on our enriched metadata of PRIDE. We believe ProMetaDB will enable researchers to perform easy and rapid acquisition of existing datasets for discovering novel proteins/peptides in this golden era of proteomics.