The long term goal of the PeptideAtlas project is full annotation
of eukaryotic genomes through a thorough validation of expressed proteins.
The PeptideAtlas provides a method and a framework to accommodate
proteome information coming from high-throughput proteomics
technologies. The online database
administers experimental data
in the public domain. We encourage you to
contribute to the database.
Details of the PeptideAtlas construction can be found within the first
Briefly, the general outline of obtaining high quality peptide sequences,
mapping, and storing in a database is shown in the figure below and outlined here.
A protein mixture sample is prepared (perhaps labeled, digested
with trypsin, purified, separated using chromotography).
The sample is run through a mass spectrometer (e.g., ESI MS/MS).
The MS/MS spectra are compared to theoretical spectra
(SEQUEST, X!Tandem) or actual spectra (SpectraST)
to identify possible peptides.
The peptide identifications are scored, formed into false and true
positive distributions, and subsequently filtered to retain
only the highest scoring identifications (PeptideProphet).
The peptide sequences are compared to protein sequence databases
(e.g. for human, we use the Ensembl, IPI, and Swiss-Prot protein
As the peptides are identified in a given protein,
so are their locations relative to the protein start (CDS coordinates).
The peptide locations in chromosomal coordinates are calculated
from the CDS coordinates.
The protein identifications are clustered and annotated
The data are stored in the SBEAMS database and can be accessed
through web pages
(see Browse Peptides). The peptides are assigned a unique identity of the form
PAp[8-digit number], such as PAp0000001 in our database, but can also
be found via their sequences.
The PeptideAtlas is stored using a database
schema which accommodates different builds
of PeptideAtlas, different versions of ENSEMBL, different organisms
(for example, human, fly, mouse), and different reference protein sequence sets
as starting material.