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Guidelines for the next 10 years of proteomics
Wilkins, Marc R.,Appel, Ron D.,Van Eyk, Jennifer E.,Chung, Maxey C. M.,Gö,rg, Angelika,Hecker, Michael,Huber, Lukas A.,Langen, Hanno,Link, Andrew J.,Paik, Young-Ki,Patterson, Scott D.,Pennington, WILEY-VCH Verlag 2006 Proteomics Vol.6 No.1
<P>In the last ten years, the field of proteomics has expanded at a rapid rate. A range of exciting new technology has been developed and enthusiastically applied to an enormous variety of biological questions. However, the degree of stringency required in proteomic data generation and analysis appears to have been underestimated. As a result, there are likely to be numerous published findings that are of questionable quality, requiring further confirmation and/or validation. This manuscript outlines a number of key issues in proteomic research, including those associated with experimental design, differential display and biomarker discovery, protein identification and analytical incompleteness. In an effort to set a standard that reflects current thinking on the necessary and desirable characteristics of publishable manuscripts in the field, a minimal set of guidelines for proteomics research is then described. These guidelines will serve as a set of criteria which editors of PROTEOMICS will use for assessment of future submissions to the Journal.</P>
Progress and Future Direction of Chromosome-Centric Human Proteome Project
Paik, Young-Ki,Overall, Christopher M.,Deutsch, Eric W.,Van Eyk, Jennifer E.,Omenn, Gilbert S. AMERICAN CHEMICAL SOCIETY 2017 JOURNAL OF PROTEOME RESEARCH Vol.16 No.12
<P>This special issue of <I>JPR</I> celebrates the fifth anniversary of the Chromosome-Centric Human Proteome Project (C-HPP). We present 27 manuscripts in four categories: (i) Metrics of Progress and Resources, (ii) Missing Protein Detection and Validation, (iii) Analytical Methods and Quality Assessment, and (iv) Protein Functions and Disease. We briefly introduce key messages from each paper, mostly from C-HPP teams and some from the Biology and Disease-driven HPP. From the first few months of the C-HPP NeXt-MP50 Missing Proteins Challenge, authors report 73 missing protein detections that meet the HPP guidelines using several novel approaches. Finally, we discuss future directions.</P>
Omenn, Gilbert S.,Lane, Lydie,Overall, Christopher M.,Corrales, Fernando J.,Schwenk, Jochen M.,Paik, Young-Ki,Van Eyk, Jennifer E.,Liu, Siqi,Snyder, Michael,Baker, Mark S.,Deutsch, Eric W. American Chemical Society 2018 Journal of proteome research Vol.17 No.12
<P>The Human Proteome Project (HPP) annually reports on progress throughout the field in credibly identifying and characterizing the human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2018-01-17, the baseline for this sixth annual HPP special issue of the <I>Journal of Proteome Research</I>, contains 17 470 PE1 proteins, 89% of all neXtProt predicted PE1-4 proteins, up from 17 008 in release 2017-01-23 and 13 975 in release 2012-02-24. Conversely, the number of neXtProt PE2,3,4 missing proteins has been reduced from 2949 to 2579 to 2186 over the past two years. Of the PE1 proteins, 16 092 are based on mass spectrometry results, and 1378 on other kinds of protein studies, notably protein-protein interaction findings. PeptideAtlas has 15 798 canonical proteins, up 625 over the past year, including 269 from SUMOylation studies. The largest reason for missing proteins is low abundance. Meanwhile, the Human Protein Atlas has released its Cell Atlas, Pathology Atlas, and updated Tissue Atlas, and is applying recommendations from the International Working Group on Antibody Validation. Finally, there is progress using the quantitative multiplex organ-specific popular proteins targeted proteomics approach in various disease categories.</P> [FIG OMISSION]</BR>
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0
Deutsch, Eric W.,Lane, Lydie,Overall, Christopher M.,Bandeira, Nuno,Baker, Mark S.,Pineau, Charles,Moritz, Robert L.,Corrales, Fernando,Orchard, Sandra,Van Eyk, Jennifer E.,Paik, Young-Ki,Weintraub, S American Chemical Society 2019 JOURNAL OF PROTEOME RESEARCH Vol.18 No.12
<P>The Human Proteome Organization’s (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on consensus-reaching discussions with the wider HPP community over the past year. The revised 3.0 guidelines address several major and minor identified gaps. We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards Initiative (PSI). In addition, we discuss updates to the standard HPP pipeline for collecting MS evidence for all proteins in the HPP, including refinements to minimum evidence. We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets. The main checklist has been reorganized under headings and subitems, and related guidelines have been grouped. In sum, Version 2.1 of the HPP MS Data Interpretation Guidelines has served well, and this timely update to version 3.0 will aid the HPP as it approaches its goal of collecting and curating MS evidence of translation and expression for all predicted ∼20 000 human proteins encoded by the human genome.</P> [FIG OMISSION]</BR>