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| Project Overview
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The SRMAtlas is a compendium of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. It results from high-quality measurements of natural and synthetic peptides conducted on a triple quadrupole mass spectrometer, and is intended as a resource for selected/multiple reaction monitoring (SRM/MRM)-based proteomic workflows.
Users can currently query transitions from Yeast, Human, and Mouse. The yeast library is based on both natural samples and synthetic pepides run on a 4000 QTRAP instrument, supplemented with ion-trap observations and predictions, where QQQ spectra are not available.
We provide a web-interface and command-line tools which allow users to query these assays. The optimal coordinates for establishing an SRM assay can be readily exported and uploaded to the SRM/MRM method of a triple quadrupole mass spectrometer. The assays can then be used to detect and quantify at high-throughput deliberately chosen set of target proteins in any biological sample of interest.
Publicly available today
The database contains SRM transitions from a variety of data sources. The table below summarizes the coverage of each target proteome, and shows the number of proteins* covered by QQQ spectra, QTOF spectra, ion trap spectra, or any of these. For each organism, predicted spectra are used to predict likely transitions from peptides and proteins which are not covered by existing experiments.
| Organism | QQQ | QTOF | Ion Trap | Any Instrument | W/ theoretical |
| Yeast | 96.8% | 8.9% | 59.7% | 97.2% | 99.5% |
| Human | - | 11.7% | 62.6% | 62.7% | 99.7% |
| Mouse | - | 7.5% | 45.8% | 46.5% | 98.8% |
Coming Soon!
The database will soon be expanded to include QQQ observations for most proteins in all three organisms, as detailed below.
Human - ~157K peptides, ~20,200 proteins, ~99% proteome coverage*
Mouse - 60K peptides, ~12,000 proteins, ~80% proteome coverage*
Empirical Human Glyco - 7K peptides, ~3,000 proteins
*Proteome coverage calculated based on particluar target proteome:
Yeast, SGD (2009-10)
Human, Uniprot/SwissProt (2010-05)
Mouse, Uniprot/SwissProt (2010-05)
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SRMAtlas |
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