The Journal of Proteome Research is preparing to publish its 10th annual special issue dedicated to highlighting the progress made on the HUPO Human Proteome Project (HPP). Since 2013, this series of special issues has documented incredibly important discoveries in the field through more than 250 articles that have collectively received more than 5,000 citations.
The editorial team organizing this year’s addition to the series invites you to submit a manuscript for consideration by October 15, 2022.
HPP Special Issue Editorial Team
Journal of Proteome Research Associate Editor Christopher M. Overall of The University of British Columbia will work on this year’s special issue with a team of guest editors:
- Gilbert S. Omenn, University of Michigan
- Robert Moritz, Institute for Systems Biology
- Eric Deutsch, Institute for Systems Biology
- Lydie Lane, Swiss Institute of Bioinformatics
- Fernando Corrales, CSIC, Madrid
- Haojie Lou, Fudan University
For this special issue, the editorial team will consider research papers encompassing both the Chromosome-Centric Human Proteome Project (C-HPP) and the Biology and Disease Human Proteome Project (B/D-HPP), as well from the HPP Resource Pillars (Antibody, MS, Pathology, and Knowledgebase), and short definitive reports, submitted in the Letters format, on the discovery of a missing protein(s).
To be considered, the missing protein(s) must meet the HPP Data Interpretation Guidelines Version 3.0 and be cast in the context of the HPP and biological setting in which they were discovered.
The editorial team is particularly interested in receiving manuscripts that relate to one of these themes:
- Completing the high-resolution draft of the human proteome with new strategies and results leading to confident identifications of neXtProt missing proteins (PE2 – 4) according to the C-HPP Guidelines v 3.0 or recent updates
- Progress on the protein list of individual chromosomes and groups of chromosomes, annotating known proteins and their isoforms/proteoforms and/or credibly identifying missing proteins (PE2 – 4)
- Annotating proteins and their isoforms/proteoforms and/or identifying missing proteins found in rare or under explored cells and tissues, and protein lists of human cell types as a step in creating a human cell proteome atlas
- Produce and use “popular proteins” lists in B/D-HPP and contribute to the identification of missing proteins
- Proteomic studies of proteoforms produced by proteolytic processing, PTMs, alternative splicing (ASV),
coding non‐synonymous single nucleotide polymorphisms (cSNPs), or chromosome abnormalities
- Use of targeted proteomics, especially SRM and MS‐SWATH, to extend chromosome‐based protein findings
- New bioinformatic tools and approaches for annotating the human proteome
- Biological mechanistic analyses inspired from proteomics data in diseases or biological processes
- Biomarker discoveries based on the identification of novel ASVs, PTMs or cSNPs in proteomic studies
- Studies using the Human Protein Atlas to identify missing proteins
Manuscript Requirements & Submission Deadline
Manuscripts must be submitted electronically through the ACS Paragon Plus Environment online submission system by October 15, 2022, to be considered for inclusion in this 10th special issue on the HUPO HPP.
Manuscripts that don’t meet these requirements will be returned without review:
- Papers must conform to both the Journal of Proteome Research Mass Spectrometry Guidelines and the HPP Data Interpretation Guidelines Version 3.0 as judged by the HPP Data Interpretation Guidelines Version 3.0 checklist (see Deutsch et al. J Proteome Res 18, 4,108 – 4,116. DOI: 10.1021/acs.jproteome.9b00542).
- For all papers, authors must analyze their data using the Human Peptide Atlas release 2022-04-06 (http://www.peptideatlas.org/builds/human/), and include protein evidence based on the neXtprot release neXtport release 2022-02-25, (https://www.nextprot.org/about/protein-existence)
- Authors must complete the full MS data submission to ProteomeXchange prior to initial submission and provide the PXD number in the abstract.
- In their cover letter, authors must specify that the manuscript is intended for the HPP Special Issue and include the completed HPP Data Interpretation Guidelines Version 3.0 checklist
HPP Special Issue Review and Publication Process
Editorial triage will determine whether manuscripts are appropriate for the HPP Special Issue and meet all of the above requirements. Nonconforming papers will be returned unreviewed. All relevant papers will go through full peer review.
As papers are accepted, they will be published online and available in time for HUPO 2022. Due to the publication schedule, only papers accepted by September 31, 2022, will be published in the December 2022 HPP Special Issue. Papers requiring more time for revision or falling outside of the scope of the special issue will be published in regular issues of the journal.