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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 markers.


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 Peptide assay in resources Best Transitions Pathway Protein–protein interaction (PPI) Involvement in disease 3D structure Go Term Name Drug Bank Assays for FDA approved 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 Peptide assay in resources Best Transitions Pathway Protein–protein interaction (PPI) Involvement in disease 3D structure Go Term Name Drug Bank Assays for FDA approved Marker Mean Concentration

Summary of results


The number of peptides entries in MRMAssayDB, sorted by organism
Species Name Number of unique entries
Homo sapiens 5913 peptide assay corresponding to 231 proteins
NA 22 peptide assay corresponding to 2 proteins
Total 5927 peptide assay corresponding to 233 proteins
Uniqueness and presence in isofroms
Database name Peptide uniqueness in proteome(%) Peptide is specific to one protein isoform(%)
PeptideTracker 93.1% 0.0%
PASSEL 93.82% 0.0%
SRMAtlas 87.36% 0.0%
CPTAC 95.2% 0.0%
PanoramaWeb 87.54% 0.0%
The number of peptides entries in MRMAssayDB, sorted by sub cellular location (Top50)
Sub cellular location Number of unique entries(Proteins)
Secreted 108
Membrane 79
Cell membrane 46
Cytoplasm 45
Lysosome 22
Endoplasmic reticulum 19
Endoplasmic reticulum membrane 16
Nucleus 16
Lysosome membrane 14
Endosome 14
Golgi apparatus 13
Endosome membrane 11
Mitochondrion 9
Late endosome membrane 8
Cell projection 7
Cell junction 6
Microsome 4
Cell surface 4
Chromosome 4
Cytoplasmic vesicle 3
Microsome membrane 3
Membrane raft 3
Mitochondrion inner membrane 3
Lysosome lumen 2
Perikaryon 2
Peroxisome 2
Melanosome 2
Apical cell membrane 2
Cytoplasmic granule 2
Mitochondrion matrix 2
Recycling endosome 2
Lateral cell membrane 2
Mitochondrion membrane 1
Basolateral cell membrane 1
Cleavage furrow 1
Lipid droplet 1
Endomembrane system 1
Recycling endosome membrane 1
Early endosome membrane 1
Mitochondrion outer 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)
protein homodimerization activity 22
protease binding 12
nucleoplasm 14
blood microparticle 35
identical protein binding 43
Golgi lumen 11
intracellular membrane-bounded organelle 13
cell surface 52
proteolysis 26
acute-phase response 14
platelet degranulation 29
plasma membrane 105
chaperone binding 7
serine-type endopeptidase activity 29
Golgi apparatus 26
blood coagulation, intrinsic pathway 15
extracellular region 115
external side of plasma membrane 24
endoplasmic reticulum 62
cytosol 63
endopeptidase inhibitor activity 18
regulation of complement activation 11
ATP binding 17
cytoplasm 55
cell adhesion 29
endoplasmic reticulum lumen 28
metal ion binding 24
blood coagulation 36
platelet alpha granule lumen 23
cellular protein metabolic process 32
extracellular matrix organization 12
extracellular space 105
integral component of plasma membrane 31
collagen-containing extracellular matrix 36
membrane 136
vesicle 57
heparin binding 11
nucleus 44
neutrophil degranulation 38
secretory granule lumen 14
fibrinolysis 15
extracellular exosome 119
enzyme binding 16
protein-containing complex 22
signal transduction 32
Golgi membrane 27
signaling receptor binding 29
endoplasmic reticulum to Golgi vesicle-mediated transport 11
post-translational protein modification 18
integral component of membrane 15

Kegg pathway coverage (Top 10)


Distribution of proteins and peptides among different databases.

      Unique Proteins



      Unique Peptides