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Figure 1
An overview of the build process of PeptideAtlas. Shotgun tandem mass spectrometry (MS/MS) experimental data are contributed by the community to the PeptideAtlas raw data repository, which is linked to other repositories by the ProteomExchange consortium. The raw data are processed through an evolving but consistent analysis and validation pipeline (Trans Proteomic Pipeline (TPP)) and loaded into the PeptideAtlas database, and made available to the community. Tranche, Global Proteome Machine Database (GPMDB), National Institute of Standards and Technology (NIST) and Protein Identifications Database (PRIDE) are currently the main participants in the ProteomExchange consortium.
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Figure 2
An overview of the features provided by PeptideAtlas that allow targeted proteomics workflows. PeptideAtlas and its specialized builds, Unipep (containing N-glycosylation sites) and PhosphoPep (containing phosphorylation sites), allow the community to: select proteotypic peptides for targeting; select SRM transitions for targeting; annotate and view annotations for these peptides and transitions; visualize peptides and proteins with Cytoscape; interface with Targeted Identification for Quantitative Analysis by MRM (TIQAM) for experimental design; obtain approximate protein abundances for spiking in synthetic peptides; obtain spectrum libraries for search and verification; and download PeptideAtlas builds for new projects. MRM, multiple reaction monitoring; SRM, selected reaction monitoring.
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