Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Correspondence
  • Published:

NCBI Peptidome: a new public repository for mass spectrometry peptide identifications

Nature Biotechnology volume 27, pages 600–601 (2009)Cite this article

To the Editor:

Great emphasis has been placed on making the deposit procedures as simple as possible, yet still supporting a high level of experimental annotation. Although data from all stages of the experiment are captured, the burden of submission is minimized by accepting standard file formats and using spreadsheet templates for metadata. This method was chosen to allow submissions to be generated either programmatically or by hand, using tools familiar to everyone, without the delay of waiting for the perfect file format and slick graphical user interface to be developed. As the field matures, so will the data submission process. A Peptidome submission includes the following components:

  1. 1

    Biological and methodological metadata. This information gives context to the experimental data and facilitates understanding of the goals of the study, the material under investigation, the instrumentation employed and the protocols used to generate and analyze the data.

  2. 2

    The original raw spectra data, converted to open format. Raw data includes all of the original MS1 and MS2 data before any post-processing, regardless of whether it was identified or not. The availability of raw data is critical for independent verification and validation of the reported study results. Furthermore, collections of raw data greatly benefit the MS community in wider applications, such as preparing custom spectral libraries, conducting large-scale statistical studies of peptide fragmentation and developing new peptide-matching algorithms.

  3. 3

    Peptide identification output files. These files contain matched peptide sequence information derived from the observed spectra using any search algorithm.

  4. 4

    Conclusion-level results. These include the final, filtered list of identified proteins, and the peptides leading to those assignments, as determined by the submitter. This finalized list has much flexibility in that it allows inclusion of identifications from new algorithms or de novo identifications. It also allows the submitter to provide complete results independent of the methodology used, for example, cutoff scores, reverse database searches for false positives or agreement between multiple search engines. Peptidome processing procedures augment these lists with auxiliary information extracted from the peptide identification files, including scores and post-translational modifications. This augmented and enriched list is a convenient mechanism to access the relevant data discussed in an associated manuscript.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1

References

  1. Edgar, R., Domrachev, M. & Lash, A.E. Nucleic Acids Res. 30, 207–210 (2002).

    Article  CAS  Google Scholar 

  2. Barrett, T. et al. Nucleic Acids Res. 37, D885–D890 (2009).

    Article  CAS  Google Scholar 

  3. Jones, P. et al. Nucleic Acids Res. 36, D878–D883 (2008).

    Article  CAS  Google Scholar 

  4. Deutsch, E.W., Lam, H. & Aebersold, R. EMBO Rep. 9, 429–434 (2008).

    Article  CAS  Google Scholar 

  5. Andrews, P.C. in 56th ASMS Conference on Mass Spectrometry and Allied Topics, American Society for Mass Spectrometry, Denver, CO (2008).

    Google Scholar 

  6. Mathivanan, S. et al. Nat. Biotechnol. 26, 164–167 (2008).

    Article  CAS  Google Scholar 

  7. Anonymous. Nat. Biotechnol. 25, 262 (2007).

Download references

Acknowledgements

The authors would like to thank D. Rudnev, D. Troup, R. Muertter, A. Soboleva, M. Tomashevsky and O. Ayanbule for their aid in the development of this project. Advice and support was provided by L. Geer, S. Sechi, S. Markey and the rest of the NIMH Laboratory of Neurotoxicology. This research was supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine.

Author information

Authors and Affiliations

  1. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA

    Douglas J Slotta, Tanya Barrett & Ron Edgar

Authors
  1. Douglas J Slotta
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tanya Barrett
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ron Edgar
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Slotta, D., Barrett, T. & Edgar, R. NCBI Peptidome: a new public repository for mass spectrometry peptide identifications. Nat Biotechnol 27, 600–601 (2009). https://doi.org/10.1038/nbt0709-600

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt0709-600

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing