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
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