MRMAssayDB: an integrated resource for validated targeted proteomics assays

Bioinformatics
Pallab BhowmickChristoph H Borchers

Abstract

Multiple Reaction Monitoring (MRM)-based targeted proteomics is increasingly being used to study the molecular basis of disease. When combined with an internal standard, MRM allows absolute quantification of proteins in virtually any type of sample but the development and validation of an MRM assay for a specific protein is laborious. Therefore, several public repositories now host targeted proteomics MRM assays, including NCI's Clinical Proteomic Tumor Analysis Consortium assay portals, PeptideAtlas SRM Experiment Library, SRMAtlas, PanoramaWeb and PeptideTracker, with all of which contain different levels of information. Here we present MRMAssayDB, a web-based application that integrates these repositories into a single resource. MRMAssayDB maps and links the targeted assays, annotates the proteins with information from UniProtKB, KEGG pathways and Gene Ontologies, and provides several visualization options on the peptide and protein level. Currently MRMAssayDB contains >168K assays covering more than 34K proteins from 63 organisms; >13.5K of these proteins are present in >2.3K KEGG biological pathways corresponding to >300 master pathways, and mapping to >13K GO biological processes. MRMAssayDB allows comprehensive searches ...Continue Reading

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Citations

Jan 11, 2019·Nucleic Acids Research·Daniel J Rigden, Xosé M Fernández
Dec 7, 2019·Journal of Thrombosis and Haemostasis : JTH·Yassene MohammedThijs E van Mens
Nov 30, 2018·Nature Reviews. Clinical Oncology·Bing ZhangAmanda G Paulovich
Mar 9, 2021·Journal of Proteome Research·Pallab BhowmickYassene Mohammed
Jun 18, 2021·Cell Systems·Vadim DemichevFlorian Kurth

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