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Atlas Data: Data Repository HPPP Data Central PeptideAtlas Builds PeptideAtlas Exports THISP Search Database
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Related: SRMAtlas PASSEL SWATHAtlas
Spectral Libs: Libraries + Info SpectraST Search

Glossary/Terms: Atlas nomenclature Protein ID terms

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PeptideAtlas Software

Several software programs are used in the making of PeptideAtlas. The main packages follow:

LC-MS/MS spectra identification: COMET (UW), MSFragger (U. Michigan), SpectraST (ISB), and others.

Identification correctness scoring (ISB): Trans-Proteomic Pipeline, including PeptideProphet, iProphet, PTMProphet, and ProteinProphet.

Database loading and query (ISB): SBEAMS

Genome Annotation (EMBL-EBI and Sanger Institute): Ensembl

Peptide mapping to Ensembl (NCBI): BioEnsembl and BioPerl

Open-source tools for mass spectrometry (ISB): Sashimi, TPP