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Journal of Proteome Research Call for Papers!
2018 HUPO Human Proteome Project Special Issue
Submission Deadline: May 31st, 2018

Journal of Proteome Research will publish its 6th annual Special Issue dedicated to highlight progress on the HUPO Human Proteome Project (HPP). The Special Issue considers papers encompassing both the Chromosome-Centric Human Proteome Project (C-HPP) and the Biology and Disease Human Proteome Project (B/D-HPP).

In addition, we will now consider short definitive reports, submitted in the Letters format, on the discovery of a Missing Protein(s). To be considered for publication, the missing protein(s) must meet the Guidelines v 2.1 and are cast in the context of both the HPP and biological setting in which they were discovered. We anticipate this format will encourage many teams, particularly of the B/D-HPP, to highlight such protein discoveries in a disease and biological context.
I Guest Editors:
Young‐Ki Paik, Yonsei University
Fernando Corrales, Centro Nacional de Biotecnologia (CSIC)
Eric Deutsch, Institute for Systems Biology
Gilbert S. Omenn, University of Michigan
I Associate Editor:
Christopher M. Overall, The University of British Columbia
I Thematic Priorities:
  • 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 2.1 or recent updates
  • Reports 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)
  • Creation of protein lists for the B/D-HPP groups systems for deposition into ProteomeXchange
  • Produce and utilize “popular proteins” lists in B/D-HPP and contribute to the identification of “missing proteins”
  • Generation of post translational modifications (PTM) libraries for chromosome‐based protein sets
  • Proteomic studies of proteoforms produced by proteolytic processing, PTMs, alternative splicing (ASV),
    coding non‐synonymous single nucleotide polymorphisms (cSNPs), or chromosome abnormalities
  • Biological mechanistic analyses inspired from proteomics data in diseases or biological processes
  • Use of targeted proteomics, especially SRM and MS‐SWATH, to extend chromosome‐based protein findings
  • Disease studies utilizing chromosome information, characterizing amplicons, cis‐regulated pathways or networks
  • Integration of genomic, transcriptomic, epigenomic, or metabolomic data with proteomics, using bioinformatics
  • Combined analyses with MS, RNASeq and antibodies for targeted studies of tissue samples
  • Biomarker discoveries based on the identification of novel ASVs, PTMs or cSNPs in proteomic studies
I Submission Procedure:
Manuscripts must be submitted by May 31th, 2017 to be considered for this Special Issue. Manuscripts must be submitted electronically through the ACS Paragon Plus Environment online submission system. Specify in the authors’ cover letter that the manuscript is intended for the HPP Special Issue.
I Review and Publication Process:
Initial editorial review will determine whether manuscripts are appropriate for the HPP Special Issue. Papers must fulfill the HPP checklist to be considered for publication. The completed checklist must be included with the cover letter. The full MS data submission to ProteomeXchange must also be completed prior to initial submission, and the PXD number provided in the abstract. Nonconforming papers will be returned without review. All relevant papers will go through full peer review. As papers are accepted they will post online and be available in time for HUPO-2018 in Orlando. Due to the publication schedule, only papers that are accepted by September 1, 2018 will be published in the December 2018 HPP Special Issue. Those papers requiring more time for revision or falling outside of the scope of the Special Issue will be published at a later date in regular issues of the journal.
I HPP Data Guidelines:
Papers must conform to both Journal of Proteome Research mass spectrometry guidelines and the HPP guidelines v 2.1 (see Deutsch et al.) in order to be sent out for review and for acceptance. Please check for any changes to the HPP guidelines available online before submission. All papers must analyze their data using the Human PeptideAtlas release 2018-01 and neXtProt release 2018-02. Papers not doing so will be returned without review.