Call for Papers: 8th Special Issue on the HUPO Human Proteome Project (HPP) - ACS Axial | ACS Publications
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Call for Papers: 8th Special Issue on the HUPO Human Proteome Project (HPP)

The Journal of Proteome Research is preparing to publish its eighth annual special issue dedicated to highlighting the progress made on the HUPO Human Proteome Project (HPP). The journal’s editorial team invites you to submit a manuscript for consideration by July 31, 2020.

Thematic Priorities

For this special issue, the journal 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
  • Disease studies using chromosome information, characterizing amplicons, cis‐regulated pathways or networks
  • 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 July 31, 2020, to be considered for inclusion in this eighth special issue on the HUPO HPP.

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. For all papers, authors must analyze their data using the Human PeptideAtlas release 2020-01-24 and neXtProt release 2020-01-17, and include protein evidence based on the neXtProt release 2020-01-17 protein existence.

Authors must complete the full MS data submission to ProteomeXchange prior to their initial submission and provide the PXD number in the abstract. In their cover letter, they must specify that the manuscript is intended for the HPP Special Issue and include the completed HPP Data Interpretation Guidelines Version 3.0 checklist

Manuscripts that don’t meet these requirements will be returned without review.

HPP Special Issue Review and Publication Process

Manuscripts submitted for this special issue will be handled by Associate Editor Christopher M. Overall of The University of British Columbia and a team of guest editors:

  • Young‐Ki Paik of Yonsei University
  • Eric Deutsch of Institute for Systems Biology
  • Fernando Corrales of CSIC, Madrid
  • Lydie Lane of Swiss Institute of Bioinformatics
  • Gilbert S. Omenn of University of Michigan

Editorial triage will determine whether manuscripts are appropriate for the HPP Special Issue and meet all the requirements. Nonconforming papers will be returned unreviewed. All relevant papers will go through a full peer review.

As papers are accepted, they will be published online and available in time for HUPO-2020. Due to the publication schedule, only papers accepted by September 31, 2020, will be published in the December 2020 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.

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