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Peptidome Data Submission Form

Types of Files

The Metadata file contains descriptive information about the overall experiment, the biological samples under examination, protocols used to generate the data, and references to associated data files. Metadata is supplied to us by completing the 'Peptidome Metadata Template' spreadsheet in the NCBI_Peptidome_Submission_Template Excel file.

» See full guidelines
The Raw data files contain the MS1 and MS2 information from the instrument. Files should be in one of the standard XML formats (mzData, mzXML, or mzML) or, less desirably, a text format (mgf, pkl, sqt, dta). Proprietary binary data from the manufacturers will not be accepted.

» See full guidelines
The Peptide identification output files are generated by the search engine program that was used to match the MS2 scans to the peptides. We currently accept Mascot DAT files, OMSSA ASN.1 or XML formatted files, or any search engine output that has been converted to PepXML. If no search engine was used, or the format is not yet supported, then your Results table must include references to spectrum files.

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The Results table describes your view of the final, processed results. It lists all proteins, peptides for each protein, and spectra for each peptide. It also lists fixed and variable modifications for each peptide.

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Submissions

FTP Submission

Zip or tar all the files described above into one or more archive files, and transfer to us using one of the FTP methods outlined below. After transferring the file(s), please send an e-mail to peptidome@ncbi.nlm.nih.gov with the following information:

  1. Peptidome account user name
  2. Name(s) of the archive file(s) deposited.
PEPTIDOME FTP INSTRUCTIONS
  1. By FTP client (e.g. FileZilla or Classic FTP for Mac). FileZilla is a good choice for simple and faster transfer if you do not wish to optimize your connection.
  2. Drag-and-drop from your Windows PC:
    1. Double-click 'My Computer' on your Windows Desktop. (or right-click the 'Start' button on your Windows Desktop and select 'Explore').
    2. Paste (DO NOT CLICK)
      into the Address bar of the opened window. Hit Enter on your keyboard to access our private FTP site in the window.
    3. Drag files from your computer into the open window.
Notes:
  • SFTP protocol not supported
  • Where available, optimal buffer size is 32M, e.g.
    sndbuf 33554432