Submissions to PeptideAtlas

SUBMISSION OF DATA TO THE PEPTIDEATLAS DATABASE

Thank you for your interest in contributing to the PeptideAtlas database. If you are processing the data yourselves, we ask that you use statistical analysis to estimate accurate false positive error rates to help us ensure that only data of consistent quality are added. We have used PeptideProphet and request that it or something comparable be used before submission.

Alternatively, if PeptideProphet or equivalent data products are not available, data contributors can submit the MS/MS spectra in either their native format or in mzXML format (an open standard file format for the representation of MS data). We would prefer the later. The spectra will then be searched by the PeptideAtlas curators using SEQUEST to correlate uninterpretated tandem mass spectra of peptides with amino acid sequences using protein databases such as IPI and the results will be further analyzed with PeptideProphet. This procedure will ensure the highest degree of consistency for the data in PeptideAtlas.

When submitting data, please also include the information listed below as items 1-12. The tissue can best be described via controlled vocabulary such as used in eVOC (eVOC is a system which associates biological samples with a set of hierarchical vocabularies.). Please note a date in item 12 when the raw data may be made available to the public in our repository.

Currently all PeptideAtlas MS/MS spectra are stored in the SBEAMS - Proteomics database, from which PeptideAtlas is derived. While at present it is not possible to access MS/MS spectra starting from the public interface for the database, this possibility could be added in the future. (Access to the raw spectra can be beneficial for many applications not related to the main purpose of PeptideAtlas. Additonally, peptide modifications such as phosphorylation, for example, may become searchable from the web interface.) Currently, outside of the database, the spectra from published datasets are available on our "Download Public Data" page.

Please note item number 12 below if you are concerned about the visibility of your data before you publish it. For additional privacy concerns, please see "What's public about your data?".

We have a web application for data submission, so please write to us using using the feedback form for submission details. In general, the pages will prompt you for:

1: Submitting institution, contact, date
2: URL link for link to www resource
3: Literature reference PubMed identification
4: Experiment description
5: Treatment Description (acid cleavable ICAT? Other cysteine labels? Peptide modifications? Phosphorylation? etc.)
6: Instrument type (LCQ, etc.)
7: Organism NCBI_TaxID (9606 for human)
8: Bio source description (eVOC) anatomical site
9: Developmental stage (eVOC)
10: Pathology (eVOC)
11: Cell-type
12: Date that we may make the raw data available to the public

Example:
1:Institute for Systems Biology, Proteomics Group, 1441 N 34th Street, Seattle, WA 98103, USA, P.D. von Haller, 2003-07-31.
2: http://www.systemsbiology.org
3: PMID: 12832459
4: T Cell Lipid Rafts Lipid rafts were prepared from Jurkat T cells stimulated via T cell receptor/CD28 cross-linking and from control (unstimulated) cells.
5: Acid cleavable ICAT using D0442 and D8450
6: LCQ
7: 9606
8: blood
9: Adult
10: Normal
11: Human Jurkat T cells
12: 2003-07-31