hPP dATA iNTERPRETATION gUIDELINEs 

version 3.0

The HPP aims to encourage all participants/authors to uphold rigorous standards for publication and dissemination of results. All data are to be submitted to a ProteomeXchange public data repository, statistical analyses are to be performed to a high standard, and claims of detection of "missing proteins" or novel coding elements require detailed evidence. The first set of HPP datga interpretation guidelines were approved by the HPP in 2012. Version 2.0 of the guidelines was approved in 2015, and a minor substantive update was applied as version 2.1 in July 2016.  A Version 3.0 of the guidelines was released in October 2019. These newest guidelines should be applied to all subsequent manuscripts and data contributions from release.

(Released 2019-10-15)

The current version of HPP Data Interpretation Guidelines is version 3.0.Please apply these guidelines to all new HPP contributions.If errors are detected or slight amendments made, the updated guidelines will be posted here.Therefore, please check back in this location for a final version before submitting your manuscript. A fully completed checklist must be submitted with your manuscript for inspection by editors and reviewers. Any non-adherence to Guidelines v3.0 must be explained in the space provided on the checklist form.


  • HPP Data Interpretation Guidelines version 3.0 [PDF] , [DOCX] - 2019-10-15
  • The article (Deutsch et al. 2019) [PubMed] [JPR] [bioRxiv] that describes many of the details and reasons behind the guidelines is available in the Journal of Proteome Research 2019 HPP Special Issue

IMPORTANT NOTE: If your manuscript is being submitted to JPR for the HPP special issue, the JPR guidelines also apply. In cases where the JPR guidelines and these HPP guidelines conflict, the HPP guidelines are more stringent in all cases and take precedence over the JPR guidelines. See the Current JPR Guidelines.

2016 Guidelines (Deprecated):

  • Obsolete HPP Data Interpretation Guidelines version 2.1 [PDF] - 2016-07-28

  • Changelog: Version 2.1 has been updated in response to the review of the manuscript accompanying these guidelines. Guideline 2 has been altered such that deposition of data in a ProteomeXchange repository must now occur prior to submission of a manuscript rather than prior to review of the manuscript. Guideline 15 was updated to clarify that the two uniquely mapping peptides of length >=9 amino acids may not be fully nested (i.e. one peptide occurring within the other). This was previously intended and implemented in neXtProt and PeptideAtlas, but was not explicit in the checklist.

  • Obsolete HPP Data Interpretation Guidelines version 2.0.4 PDF] - 2016-05-06

  • Changelog: Version 2.0.4 has been updated with new url for the neXtProt unicity checker.
  • Obsolete HPP Data Interpretation Guidelines version 2.0.3 [PDF] - 2016-04-30
  • Changelog: Version 2.0.3 has been updated with minor wording changes as the companion manuscript is being prepared. The requirements of the guidelines themselves are not different from 2.0.0. A URL for the neXtProt unicity checker tool has been added.
  • Obsolete HPP Data Interpretation Guidelines version 2.0.2 [PDF] - 2016-03-22
  • Changelog: Version 2.0.2 has been updated with minor wording changes as the companion manuscript is being prepared. The requirements of the guidelines themselves are not different from 2.0.0.
  • Obsolete HPP Data Interpretation Guidelines version 2.0.1 [PDF] - 2015-12-07
  • Changelog: Version 2.0.1 has been updated with minor wording changes contributed by HPP leaders. The requirements of the guidelines themselves are not different from 2.0.0.
  • Obsolete 2015 HPP Data Interpretation Guidelines version 2.0.0 [PDF] - 2015-11-12

2012 Guidelines (Deprecated):

The 2012 HPP Guidelines were in effect for 3 years and are still mentioned here, but are now considered obsolete. Please apply the current guidelines to efforts for new contributions.





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