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Results for FDA Assay|UVic MRMAssayDB

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The proteomics community possesses a large and increasing amount of knowledge on precise and reproducible targeted assays, but these assays are not yet utilized to their full potential, particularly for clinical applications. The US Food and Drug Administration (FDA) has listed 1140 approved clinical tests, 208 of which are associated with 253 proteins. Using MRMAssayDB, an integrative resource on targeted proteomics assays, we have data-mined all of the available MRM assays to determine which ones can be used for these FDA-approved markers. Because MRMAssayDB links all assays to DrugBank and other knowledge bases, and to protein-protein interactions, it enables straight-forward design of multiplexed MRM assays for studying the pathways and interactions that involve these FDA-approved protein biomarkers.


UniProtKB Accession Protein Gene Organism Subcellular localization Stripped Peptide Sequence Modified Peptide Sequence Peptide unique in proteome Peptide present in isoforms PeptideTracker ID PeptideTracker Transitions PASSEL ID PASSEL Transitions SRMAtlas ID SRMAtlas Transitions CPTAC ID CPTAC Transitions PanoramaWeb ID PanoramaWeb Transitions Number of repositories Best Transitions Biological Pathway Protein–protein interaction Disease Association 3D structure GO Terms Drug Association Protein approved as FDA Marker Mean Concentration
UniProtKB Accession Protein Gene Organism Subcellular localization Stripped Peptide Sequence Modified Peptide Sequence Peptide unique in proteome Peptide present in isoforms PeptideTracker ID PeptideTracker Transitions PASSEL ID PASSEL Transitions SRMAtlas ID SRMAtlas Transitions CPTAC ID CPTAC Transitions PanoramaWeb ID PanoramaWeb Transitions Number of repositories Best Transitions Biological Pathway Protein–protein interaction Disease Association 3D structure GO Terms Drug Association Protein approved as FDA Marker Mean Concentration

Summary of results


The number of peptides entries in MRMAssayDB, sorted by organism
Species Name Number of assays Number of covered proteins
Homo sapiens 6968 222
Total 6968 222
Uniqueness and presence in isofroms
Database name Peptide uniqueness in proteome(%) Peptide is specific to one protein isoform(%)
PeptideTracker 93.97% 0.0%
PASSEL 94.48% 0.0%
SRMAtlas 91.04% 0.0%
CPTAC 95.59% 0.0%
PanoramaWeb 91.46% 0.0%
The number of peptides entries in MRMAssayDB, sorted by sub cellular location (Top50)
Sub cellular location Number of unique entries(Proteins)
Secreted 110
Membrane 70
Cytoplasm 50
Cell membrane 46
Lysosome 19
Endoplasmic reticulum 18
Nucleus 18
Endoplasmic reticulum membrane 16
Endosome 12
Lysosome membrane 11
Mitochondrion 10
Endosome membrane 8
Golgi apparatus 7
Cell projection 7
Cell junction 6
Late endosome membrane 5
Chromosome 5
Cytoplasmic vesicle 3
Microsome membrane 3
Membrane raft 3
Cell surface 3
Early endosome 3
Autolysosome membrane 3
Lysosome lumen 2
Perikaryon 2
Peroxisome 2
Melanosome 2
Apical cell membrane 2
Lipid droplet 2
Cytoplasmic granule 2
Early endosome membrane 2
Mitochondrion inner membrane 2
Recycling endosome 2
Lateral cell membrane 2
Mitochondrion membrane 1
Basolateral cell membrane 1
Cleavage furrow 1
Endomembrane system 1
Mitochondrion matrix 1
Recycling endosome membrane 1
Mitochondrion outer membrane 1
Golgi apparatus membrane 1
Nucleus matrix 1
The number of peptides entries in MRMAssayDB, sorted by GO term name (Top50)
GO Term Name Number of unique entries(Proteins)
protease binding 12
nucleoplasm 17
blood microparticle 35
leukocyte migration 11
identical protein binding 45
zinc ion binding 12
Golgi lumen 13
endoplasmic reticulum 55
early endosome 13
intracellular membrane-bounded organelle 17
cell surface 43
platelet degranulation 29
plasma membrane 96
chaperone binding 7
serine-type endopeptidase activity 23
Golgi apparatus 20
negative regulation of apoptotic process 12
collagen-containing extracellular matrix 37
extracellular region 117
DNA binding 11
retina homeostasis 5
copper ion binding 4
cytosol 66
endopeptidase inhibitor activity 18
ATP binding 17
cytoplasm 61
cell adhesion 29
endoplasmic reticulum lumen 30
metal ion binding 23
endoplasmic reticulum membrane 20
platelet alpha granule lumen 23
cellular protein metabolic process 27
extracellular space 109
membrane 127
heparin binding 12