PeptideAtlas Software

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

LC-MS/MS spectra identification: SEQUEST (Thermo Finnigan), X!Tandem (the GPM), SpectraST (ISB), and others.

Identification correctness scoring (ISB): Trans-Proteomic Pipeline, including PeptideProphet, InterProphet, 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

Ensembl database queries (EMBL-EBI and Sanger Institute): EnsMart

Nomenclature for Gene Expression Data (SANBI): eVOC