MRMAssayDB

MRMAssayDB aggregates and maps targeted mass-spectrometry assay information from multiple repositories to support selection and validation of proteotypic peptides for targeted proteomics and quantitative protein measurement.

Key Features:

• Integration and Mapping: Aggregates assay information from NCI's Clinical Proteomic Tumor Analysis Consortium, PeptideAtlas SRM Experiment Library, SRMAtlas, PanoramaWeb, and PeptideTracker and maps these assays to proteins and peptides.
• Comprehensive Annotations: Provides detailed protein and sequence annotations covering over 51,000 proteins from 94 organisms, mapped to more than 2,400 biological pathways and over 21,000 Gene Ontology terms.
• Extensive Assay Collection: Contains over 828,000 assays and exposes proteotypic peptides and commonly used transitions observed in empirical datasets.
• Enhanced Visualization Tools: Supplies peptide- and protein-level visualizations and a module for molecular structural annotations that includes peptide sequences, post-translational modifications (PTMs), disease mutations, and mapping to available 3D protein structures.
• Holistic Proteomics Integration: Integrates diverse targeted-proteomics datasets and annotations to enable identification of suitable peptides for empirical studies and support longitudinal and cohort analyses.

Scientific Applications:

• Targeted protein quantification: Enables precise measurement of proteins using selected reaction monitoring and other targeted MS assays.
• Assay development and validation: Supports design and validation of robust targeted assays using annotated proteotypic peptides and transitions.
• Biological pathway and mechanism studies: Facilitates linking quantified proteins to biological pathways and Gene Ontology terms to study disease mechanisms and therapeutic targets.
• Longitudinal and cohort analyses: Supports reproducible targeted-proteomics studies across time courses and cohorts by providing consolidated assay information and annotations.

Methodology:

Systematic collection and integration of assay data from the listed repositories, mapping of assays to proteins and peptides, and enrichment with sequence, pathway, PTM, mutation, and 3D structural annotations combined with visualization capabilities.