Table 1.

Checklist of the HUPO-2015 Human Proteome Project Data Interpretation Guidelines version 2.1.0.

General Guidelines:
√	1. Complete this HPP Data Interpretation Guidelines checklist and submit with your manuscript.
	2. Deposit all MS proteomics data (DDA, DIA, SRM), including analysis reference files (search database, spectral library), to a ProteomeXchange repository as a complete submission. Provide the PXD identifier(s) in the manuscript abstract and reviewer login credentials.
	3. Use the most recent version of the neXtProt reference proteome for all informatics analyses, particularly with respect to potential missing proteins.
	4. Describe in detail the calculation of FDRs at the PSM, peptide, and protein levels.
	5. Report the PSM-, peptide-, and protein-level FDR values along with the total number of expected true positives and false positives at each level.
	6. Present large-scale results thresholded at equal to or lower than 1% protein-level global FDR.
	7. Recognize that the protein-level FDR is an estimate based on several imperfect assumptions, and present the FDR with appropriate precision.
	8. Acknowledge that not all proteins surviving the threshold are “confidently identified”.
	9. If any large-scale datasets are individually thresholded and then combined, calculate the new, higher peptide- and protein-level FDRs for the combined result.
Guidelines for extraordinary detection claims (e.g., missing proteins, novel coding elements)
	10. Present “extraordinary detection claims” based on DDA mass spectrometry with high mass-accuracy, high signal-to-noise ratio (SNR), and clearly annotated spectra.
	11. Consider alternate explanations of PSMs that appear to indicate extraordinary results.
	12. Present high mass-accuracy, high-SNR, clearly annotated spectra of synthetic peptides that match the spectra supporting the extraordinary detection claims.
	13. If SRM verification for extraordinary detection claims is performed, present target traces alongside synthetic heavy-labeled peptide traces, demonstrating co-elution and very closely matching fragment mass intensity patterns.
	14. Even when very high confidence peptide identifications are demonstrated, consider alternate mappings of the peptides to proteins other than the claimed extraordinary result. Consider isobaric sequence/mass modification variants, all known SAAVs, and unreported SAAVs.
	15. Support extraordinary detection claims by two or more distinct uniquely-mapping, non-nested peptide sequences of length ≥9 amino acids. When weaker evidence is offered for a previously unreported protein or a coding element proposed translation product, justify that other peptides cannot be expected.