Submissions to PeptideAtlas

Thank you for your interest in contributing to the PeptideAtlas database.

Please submit your MS/MS spectra in either their native format or, preferably, in mzXML or mzML format (both open standard file formats for the representation of MS data). The spectra will then be processed by the PeptideAtlas curators to ensure consistency throughout PeptideAtlas.

When preparing your data for submission, please gather the information listed below as items 1-12, to the extent possible.

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. For additional privacy concerns, please see "What's public about your data?".

To submit your data, email us with the information below using the feedback form. We will then advise you as to how to get the actual data to us. As of this writing, in 2009, we are moving toward having everyone store their data in Tranche via Pride. We will then obtain your data from Pride. However, the Pride submission process is still under development, so it is also possible to get us your data via ftp or even by shipping us a hard drive.

Here is the information you should compile for your submission:

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