Draft Guidelines for Submitting Proteomics Data (v1.1)

  1. Provide all relevant information relating to how the peptide/protein matches were undertaken. Include methods used to process and analyze data, for example, software, mass spectrometer, sequence database and version, number of sequences in database, processing methods, mass tolerances used for matching, variable/fixed modifications, allowable missed cleavages, etc.
  2. Provide as supplementary material information used to identify proteins and/or peptides. Include information such as accession numbers, observed mass (m/z), charge, delta mass, matched mass, peptide/protein scores, peptide modification, miscleavages, peptide sequence, match rank, matched species (for cross species matching), number of peptide matches, indicate ambiguous protein/peptide matches, etc.
  3. Provide information on criteria used to justify threshold or cut-off rates for peptide and protein matches and for large-scale studies include false discovery rates (FDR) for data using these same criteria.
  4. For quantitative proteomics analyses provide information to justify the statistical significance including biological replicates, statistical methods, estimates of uncertainty and the methods used for calculating error.
  5. For peptide matches with biologically relevant post-translational modifications and for any protein match that has occurred using a single mass spectrum, include this information as raw data, annotated spectra or submit data to an online repository (recommended option).

Authors are encouraged to submit all raw or matched data and 2-DE images to public proteomics repositories. Submission codes and/or links to data should be provided within the manuscript.
MS: PRIDE, Tranche, The Global Proteome Machine or Peptide Atlas.
2-DE: World-2DPAGE Constellation.
Note: Further information regarding general requirements for publishing proteomics associated data can be found at the following sites: The Minimum Information About a Proteomics Experiment (MIAPE) (HUPO) Molecular and Cellular Proteomics (ASBMB) Proteomics (Wiley-VCH)Journal of Proteome Research (ACS Publications)