ArticleBioinformatics (Oxford, England)2018
MRMAssayDB: an integrated resource for validated targeted proteomics assays.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- The intestinal microbiome potentially affects thrombin generation in human subjects.Journal of thrombosis and haemostasis : JTH · 2020Trial
- Proteomic Evolution from Acute to Post-COVID-19 Conditions.Journal of proteome research · 2024Article
- Proteomics in thrombosis research.Research and practice in thrombosis and haemostasis · 2022Article
- Quantitative Detection of Protein Splice Variants by Selected Reaction Monitoring (SRM) Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A proteomic survival predictor for COVID-19 patients in intensive care.PLOS digital health · 2022Article
- A time-resolved proteomic and prognostic map of COVID-19.Cell systems · 2021Article
- Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling.Cell reports methods · 2021Article
- An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community.Journal of proteome research · 2021Article
- Absolute quantification of transcription factors in human erythropoiesis using selected reaction monitoring mass spectrometry.STAR protocols · 2020Article
- An Exploratory Pilot Study with Plasma Protein Signatures Associated with Response of Patients with Depression to Antidepressant Treatment for 10 Weeks.Biomedicines · 2020Article
- Clinical potential of mass spectrometry-based proteogenomics.Nature reviews. Clinical oncology · 2019Review
- Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards.Journal of proteome research · 2019Article
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3 authors.
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Abstract
Motivation: 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. Results: 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 for a targeted-proteomics assay depending on the user's interests, by using target-protein name or accession number, or using annotations such as subcellular localization, biological pathway, or disease or drug associations. The user can see how many data repositories include a specific peptide assay, and the commonly used transitions for each peptide in all empirical data from the repositories. Availability and implementation: http://mrmassaydb.proteincentre.com. Supplementary information: Supplementary data are available at Bioinformatics online.
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Registered trials
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