Frequently Asked Questions

Submitter FAQ

User FAQ

Submitter FAQ

What is Peptidome?

Peptidome is a public repository that archives and freely distributes tandem mass spectrometry peptide and protein identification data generated by the scientific community. The database is administered by the National Center for Biotechnology Information (NCBI) at the National Institutes of Health (NIH).

Mass spectrometry results and conclusion-level information are captured, together with sufficient raw data and descriptive information to enable understanding of the experiment and analysis of the underlying data. Peptidome is not restricted to specific organisms, instruments or experiment types; data from any tandem mass spectrometry experiment from any species are accepted.

In addition to data storage, web-based interfaces are available to help users query, browse and explore individual peptides, proteins, or entire studies, see What kinds of searches are possible in Peptidome?

Why should I submit my data to Peptidome?

The most likely reason is that the journal in which you are publishing your research, or the agency that funds your work, suggests deposit of proteomic data to a public repository. Such open access policy allows the community to review and comprehensively re-examine the data that form the basis of manuscripts. In addition to satisfying possible journal or funding agency requirements, there are other significant benefits to depositing data with Peptidome. Your data receive long term archiving at a centralized repository, and are integrated with other NCBI resources which afford greatly increased usability and visibility.

When do I submit my data to Peptidome?

Some journals require accession numbers for mass spectrometry proteomic data before acceptance of a paper for publication. Thus, ideally, data should be deposited in Peptidome before a manuscript describing the data is sent to a journal for review. Your records may remain private until your data is published. Once your submissions have been approved, you can cite the Peptidome accession number(s) in your manuscript.

Can I keep my data private indefinitely?

No. Peptidome is not intended to become a Laboratory Information Management System (LIMS). While data may be held private until published, the repository is not intended to be used for private data sharing or hosting.

Can I keep my data private while my manuscript is under review?

Yes. Peptidome records may remain private until a manuscript describing the data is published. During the submission process you are prompted to specify a release date for your records. Although the maximum allowable limit is one year, this date may be brought forward or pushed back at any time. This feature allows a submitter to deposit data and receive a Peptidome accession number to quote in a manuscript before the data become public. It is important to inform us as soon as your manuscript is published so that we can release your records and link them with PubMed. If Peptidome accession numbers are quoted in a publication, the records must be released so that the data is accessible to the scientific community.

Reviewers should expect to receive a reviewer URL with the manuscript. This URL allows anonymous, confidential access to the private Peptidome records cited in the paper. To create a reviewer link for a study, click on the 'Create Reviewer Link' button in the Study view. This button is only shown for private, approved studies. This will generate a link that may be copied and pasted to be sent to the appropriate interested parties.

How do I submit my data to Peptidome?

Our goal is to make data submission as simple as possible, while encouraging a high level of experimental annotation. We minimize the burden of data submission by accepting native file formats from which required information is extracted. Data submission involves filling out a spreadsheet with basic descriptive information and packaging it along with original spectrum files and output files from the search engine analysis program(s) you used. Full details are provided in the Submission Guidelines.

When will my data receive Peptidome accession numbers?

Processing time normally takes approximately 5 business days after completion of submission. Thus it is important to make your submission well in advance of when you require the accession numbers for your manuscript. If format or content problems are identified with your submission, a curator will contact you by e-mail explaining how to address the issue. Please address the issues raised by curators; failure to do so may result in processing delays or removal of the records. Once your records pass review, the curator will send you an e-mail confirming your Peptidome accession numbers and their release dates. If you do not receive an e-mail from us within 5 business days of your submission, please first check your spam or junk e-mail folders because some systems recognize Peptidome e-mail correspondence as spam, then e-mail us at peptidome@ncbi.nlm.nih.gov to inquire about your submission. Do not quote Peptidome accession numbers in manuscripts until you have received an approval e-mail notice from a Peptidome curator.

Why do you require the original spectrum files?

A principal reason for Peptidome data deposit is so that the community can access and comprehensively re-examine data that form the basis of scientific reporting. Additionally, your data will remain useful and relevant indefinitely if it can be re-analyzed by newly developing peptide identification methods. For these reasons we require that unfiltered, original MS1 and MS2 spectrum files are provided.

Why should I submit the Results table in addition to the Peptide identification output files?

Peptide match results performed by search engines are probabilistic. Most researchers use a variety of additional criteria (e.g., manual inspection, cutoff scores, machine learning models) to filter these lists to a set of matches deemed most likely correct. Thus, we ask for a Results table of final peptide match results that is consistent with the list you intend to publish.

Why do my Results tables have to list all identified spectra?

In fact, this is not an absolute requirement. If your Results tables contain only proteins and peptides, then all associated spectra will be pulled from the Peptide identification output files. Similarly, if the table contains only proteins, then all associated peptides and spectra will be gleaned from the Peptide identification output files. Note that this might be too permissive, and matches between peptides and spectra that do not pass standard criteria will be unintentionally accepted. We treat your Results table as a filter that describes your view of the final, processed results as discussed in any associated manuscript.

Can you accept identifications that I reached independently of a standard search engine?

Yes. We are happy to accept any identifications that were performed independently and are not included in the Peptide identification output files, and/or you used a new or unsupported identification method. If a given protein-peptide-spectrum set is listed in the Results table, but not found in the Peptide identification output files, then it will be accepted as a de novo result. This may apply to your whole submission.

How is my submission validated?

Your submission is first passed through an automatic validation system that checks for overall submission and file integrity, valid protein identifiers, and valid peptide sequence hits within proteins. A curator then performs a basic review of the descriptive data to check that the records generally contain sufficient information to enable interpretation of the overall experiment. If problems with files or content are found, the curator will work with you until the issues are addressed. It is important to understand that you retain editorial control of your Peptidome records and are responsible for the completeness and accuracy of your submission. If you need any updates to be performed on your Peptidome records, please contact us describing the type of edits required (text, tables and/or files) and we will provide information on how to proceed.

Can I submit data derived from human subjects?

For all studies involving human subjects, it is the submitter's responsibility to ensure that the data and files supplied to Peptidome protect participant privacy in accordance with all applicable laws, regulations and institutional policies. Make sure to remove any direct personal identifiers from your submission. These identifiers are listed in http://privacyruleandresearch.nih.gov/research_repositories.asp, footnote 1.

I have more questions, who do I contact?

If you have any questions or feedback regarding submitting data or navigating the Peptidome site, please e-mail us at peptidome@ncbi.nlm.nih.gov.

User FAQ

Who can use Peptidome data?

Anybody can access and download public Peptidome data. There are no login requirements. For more information, please read the NCBI data disclaimer.

How is the data organized?

A Peptidome Study record provides a focal point and description of the whole experiment. A Study is composed of one or more Sample records. A Sample record contains a description of the biological material being investigated, protocols used to generate the data, the peptides and proteins that were identified, and the original spectra used to make the identifications. Each record is assigned a unique and stable Peptidome accession number that may be cited in a manuscript describing the data. The accession consists of a number and a letter prefix indicating whether the record is a Peptidome Sample (PSM), or Peptidome Study (PSE).

What kinds of searches are possible in Peptidome?

Searches by free text, keyword, accession and other parameters are provided by NCBI Entrez. Studies and samples may be browsed on the Peptidome Browser

To use the Peptidome Browser:

  • Click on a Study title to reveal the Study summary in the lower panel.
  • Use the expand button (+) to list each Sample in the Study.
  • Click on a Sample title to reveal the Sample description in the lower panel.
  • Click on the Sample accession (PSMxxx) to list the proteins and peptides in that Sample - click on either tab at the top of the grid-panel to toggle between proteins and peptides.
  • When tabbed to the Proteins view: Use the expand button (+) to list all the peptides and corresponding spectra used to identify each protein.
  • When tabbed to the Peptides view: Use the expand button (+) to list all the proteins to which each peptide was matched.
  • Follow the Spectra links to view the search engine details and the individual spectrum scans for each peptide.
  • Auxiliary information including protein length and mass, and peptide charge, scores and more are presented where appropriate.
Last modified: Monday, 21-Sep-2009 10:24:16 EDT