MRMAssayDB: a comprehensive integrated resource for targeted proteomics assays

Targeted quantitative proteomics is vital for accurate protein measurement in biological samples. Techniques like Multiple Reaction Monitoring (MRM or SRM) and Parallel Reaction Monitoring (PRM), often used with isotopically labeled internal standards, provide absolute quantification, and represent the current gold standard. However, developing and validating assays for individual proteins remains labor-intensive. Several repositories, such as CPTAC, SRMAtlas, PanoramaWeb, and PeptideTracker host targeted assay data with varying levels of detail. MRMAssayDB is an integrated platform that hosts and annotates the curated targeted proteomics assays from these resources.

First launched in 2018 and updated in 2021, the latest release of MRMAssayDB includes over 1.1 million assays for 939,000 peptides, enabling quantification of 61,000 proteins from 146 organisms. The database also maps proteins to 19,000 Gene Ontology terms and 4,000 biological pathways. A newly integrated visualization module projects peptide assays onto Alphafold-predicted 3D protein structures, allowing users to examine peptide locations, post-translational modifications, and disease mutations while also supporting mapping to structures in the Protein Data Bank (PDB).

MRMAssayDB significantly improves access to validated proteotypic peptides and transition data, facilitating efficient assay selection and quantitative panel building for researchers in targeted proteomics. Availability: http://mrmassaydb2.proteomicscentre.com.