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2017 HUPO Human Proteome Project Special Issue

Journal of Proteome Research will publish its fifth annual Special Issue dedicated to the HUPO Human Proteome Project (HPP). The scope of the 2017 Special Issue has expanded to highlight progress on the HPP in the broader sense. Thus, starting in 2017, the annual Special Issue will now consider papers encompassing both the Chromosome-Centric Human Proteome Project (C-HPP) and, for the first time, the Biology and Disease Human Proteome Project (B/D-HPP). We warmly invite independent laboratories to submit articles addressing the thematic priorities.
I Guest Editors:
Young‐Ki Paik, Yonsei University
Gilbert S. Omenn, University of Michigan
Eric Deutsch, Institute for Systems Biology
Jennifer Van Eyk, Cedars-Sinai Medical Center

I Associate Editor:
Christopher M. Overall, The University of British Columbia

I Thematic Priorities:
  • Progress on 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 HPP Guidelines v 2.1
  • Reports on the protein list of individual chromosomes and groups of chromosomes, annotating known proteins and their isoforms/proteoforms
  • Generation of “popular proteins” lists supported by SRM analyses by B/D groups for specific organ systems, contributing to the identification of “missing proteins”
  • Generation of post translational modifications (PTM) libraries for chromosome‐based protein sets and organ system-specific popular proteins
  • Proteomic studies of proteoforms produced by proteolytic processing, PTMs, alternative splicing (ASV), coding non‐synonymous single nucleotide polymorphisms (cSNPs), 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 or biology-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 proteogenomic 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 30th, 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. Those falling outside of the scope of the Special Issue may be considered for a regular issue of the journal. Completion and inclusion of the HPP checklist (for more information: and a full MS data submission to ProteomeXchange must be completed prior to initial submission and the PXD number provided in the abstract. Nonconforming papers will be returned without reviews. All relevant papers will go through full peer review. As papers are accepted they will go online and be available in time for HUPO-2017 in Dublin. Only papers accepted by September 1, 2017 will be published in this December 2017 HPP Special Issue. Papers requiring more time for revision will be considered for later regular issues.
I HPP Data Guidelines:
Papers must conform to both the Journal of Proteome Research mass spectrometry guidelines and the HPP guidelines v 2.1 (see Deutsch et al.) in order to be sent to review and for acceptance. Please check for any changes to the HPP guidelines before submission. All papers must analyze their data using the Human PeptideAtlas release 2017-01 and neXtProt release 2017-02, papers not doing so will be returned without review.