Literature DB >> 27573249

Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016.

Jennifer E Van Eyk1, Fernando J Corrales2, Ruedi Aebersold3, Ferdinando Cerciello3, Eric W Deutsch4, Paola Roncada5, Jean-Charles Sanchez6, Tadashi Yamamoto7, Pengyuan Yang8, Hui Zhang9, Gilbert S Omenn10.   

Abstract

The Biology and Disease-driven Human Proteome Project (B/D-HPP) is aimed at supporting and enhancing the broad use of state-of-the-art proteomic methods to characterize and quantify proteins for in-depth understanding of the molecular mechanisms of biological processes and human disease. Based on a foundation of the pre-existing HUPO initiatives begun in 2002, the B/D-HPP is designed to provide standardized methods and resources for mass spectrometry and specific protein affinity reagents and facilitate accessibility of these resources to the broader life sciences research and clinical communities. Currently there are 22 B/D-HPP initiatives and 3 closely related HPP resource pillars. The B/D-HPP groups are working to define sets of protein targets that are highly relevant to each particular field to deliver relevant assays for the measurement of these selected targets and to disseminate and make publicly accessible the information and tools generated. Major developments are the 2016 publications of the Human SRM Atlas and of "popular protein sets" for six organ systems. Here we present the current activities and plans of the BD-HPP initiatives as highlighted in numerous B/D-HPP workshops at the 14th annual HUPO 2015 World Congress of Proteomics in Vancouver, Canada.

Entities:  

Keywords:  B/D-HPP; Biology and Disease-driven Human Proteome Project; MS; SRM−MS; mass spectrometry; selected reaction monitoring−MS

Mesh:

Substances:

Year:  2016        PMID: 27573249      PMCID: PMC5129618          DOI: 10.1021/acs.jproteome.6b00444

Source DB:  PubMed          Journal:  J Proteome Res        ISSN: 1535-3893            Impact factor:   4.466


  29 in total

Review 1.  A human proteome detection and quantitation project.

Authors:  N Leigh Anderson; Norman G Anderson; Terry W Pearson; Christoph H Borchers; Amanda G Paulovich; Scott D Patterson; Michael Gillette; Ruedi Aebersold; Steven A Carr
Journal:  Mol Cell Proteomics       Date:  2009-01-07       Impact factor: 5.911

2.  Too many roads not taken.

Authors:  Aled M Edwards; Ruth Isserlin; Gary D Bader; Stephen V Frye; Timothy M Willson; Frank H Yu
Journal:  Nature       Date:  2011-02-10       Impact factor: 49.962

3.  Transcriptome and proteome of human hepatocellular carcinoma reveal shared metastatic pathways with significant genes.

Authors:  Huali Shen; Fan Zhong; Yang Zhang; Hongxiu Yu; Yinkun Liu; Lunxiu Qin; Fuchu He; Zhaoyou Tang; Pengyuan Yang
Journal:  Proteomics       Date:  2015-03-18       Impact factor: 3.984

4.  Proteomics. Tissue-based map of the human proteome.

Authors:  Mathias Uhlén; Linn Fagerberg; Björn M Hallström; Cecilia Lindskog; Per Oksvold; Adil Mardinoglu; Åsa Sivertsson; Caroline Kampf; Evelina Sjöstedt; Anna Asplund; IngMarie Olsson; Karolina Edlund; Emma Lundberg; Sanjay Navani; Cristina Al-Khalili Szigyarto; Jacob Odeberg; Dijana Djureinovic; Jenny Ottosson Takanen; Sophia Hober; Tove Alm; Per-Henrik Edqvist; Holger Berling; Hanna Tegel; Jan Mulder; Johan Rockberg; Peter Nilsson; Jochen M Schwenk; Marica Hamsten; Kalle von Feilitzen; Mattias Forsberg; Lukas Persson; Fredric Johansson; Martin Zwahlen; Gunnar von Heijne; Jens Nielsen; Fredrik Pontén
Journal:  Science       Date:  2015-01-23       Impact factor: 47.728

5.  Mass-spectrometry-based draft of the human proteome.

Authors:  Mathias Wilhelm; Judith Schlegl; Hannes Hahne; Amin Moghaddas Gholami; Marcus Lieberenz; Mikhail M Savitski; Emanuel Ziegler; Lars Butzmann; Siegfried Gessulat; Harald Marx; Toby Mathieson; Simone Lemeer; Karsten Schnatbaum; Ulf Reimer; Holger Wenschuh; Martin Mollenhauer; Julia Slotta-Huspenina; Joos-Hendrik Boese; Marcus Bantscheff; Anja Gerstmair; Franz Faerber; Bernhard Kuster
Journal:  Nature       Date:  2014-05-29       Impact factor: 49.962

6.  Priorities and trends in the study of proteins in eye research, 1924-2014.

Authors:  Richard D Semba; Maggie Lam; Kai Sun; Pingbo Zhang; Debra A Schaumberg; Luigi Ferrucci; Peipei Ping; Jennifer E Van Eyk
Journal:  Proteomics Clin Appl       Date:  2015-09-16       Impact factor: 3.494

7.  Proteomics and the eye.

Authors:  Richard D Semba; Jan J Enghild
Journal:  Proteomics Clin Appl       Date:  2014-04       Impact factor: 3.494

Review 8.  Development of data representation standards by the human proteome organization proteomics standards initiative.

Authors:  Eric W Deutsch; Juan Pablo Albar; Pierre-Alain Binz; Martin Eisenacher; Andrew R Jones; Gerhard Mayer; Gilbert S Omenn; Sandra Orchard; Juan Antonio Vizcaíno; Henning Hermjakob
Journal:  J Am Med Inform Assoc       Date:  2015-02-28       Impact factor: 4.497

9.  ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.

Authors:  Yasset Perez-Riverol; Julian Uszkoreit; Aniel Sanchez; Tobias Ternent; Noemi Del Toro; Henning Hermjakob; Juan Antonio Vizcaíno; Rui Wang
Journal:  Bioinformatics       Date:  2015-04-24       Impact factor: 6.937

10.  Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics.

Authors:  Jun Fan; Shyamasree Saha; Gary Barker; Kate J Heesom; Fawaz Ghali; Andrew R Jones; David A Matthews; Conrad Bessant
Journal:  Mol Cell Proteomics       Date:  2015-08-12       Impact factor: 5.911

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  8 in total

Review 1.  Proteomic analysis of the cardiac extracellular matrix: clinical research applications.

Authors:  Merry L Lindsey; Mira Jung; Michael E Hall; Kristine Y DeLeon-Pennell
Journal:  Expert Rev Proteomics       Date:  2018-01-09       Impact factor: 3.940

2.  The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.

Authors:  Jochen M Schwenk; Gilbert S Omenn; Zhi Sun; David S Campbell; Mark S Baker; Christopher M Overall; Ruedi Aebersold; Robert L Moritz; Eric W Deutsch
Journal:  J Proteome Res       Date:  2017-10-10       Impact factor: 4.466

3.  The proteomes of the human eye, a highly compartmentalized organ.

Authors:  Gilbert S Omenn
Journal:  Proteomics       Date:  2016-12-21       Impact factor: 3.984

4.  Progress in the Chromosome-Centric Human Proteome Project as Highlighted in the Annual Special Issue IV.

Authors:  Young-Ki Paik; Christopher M Overall; Eric W Deutsch; William S Hancock; Gilbert S Omenn
Journal:  J Proteome Res       Date:  2016-11-04       Impact factor: 4.466

5.  Advances of the HUPO Human Proteome Project with broad applications for life sciences research.

Authors:  Gilbert S Omenn
Journal:  Expert Rev Proteomics       Date:  2016-12-22       Impact factor: 3.940

Review 6.  Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry.

Authors:  P Boomathi Pandeswari; Varatharajan Sabareesh
Journal:  RSC Adv       Date:  2019-01-02       Impact factor: 4.036

7.  The SysteMHC Atlas project.

Authors:  Wenguang Shao; Patrick G A Pedrioli; Witold Wolski; Cristian Scurtescu; Emanuel Schmid; Juan A Vizcaíno; Mathieu Courcelles; Heiko Schuster; Daniel Kowalewski; Fabio Marino; Cecilia S L Arlehamn; Kerrie Vaughan; Bjoern Peters; Alessandro Sette; Tom H M Ottenhoff; Krista E Meijgaarden; Natalie Nieuwenhuizen; Stefan H E Kaufmann; Ralph Schlapbach; John C Castle; Alexey I Nesvizhskii; Morten Nielsen; Eric W Deutsch; David S Campbell; Robert L Moritz; Roman A Zubarev; Anders Jimmy Ytterberg; Anthony W Purcell; Miguel Marcilla; Alberto Paradela; Qi Wang; Catherine E Costello; Nicola Ternette; Peter A van Veelen; Cécile A C M van Els; Albert J R Heck; Gustavo A de Souza; Ludvig M Sollid; Arie Admon; Stefan Stevanovic; Hans-Georg Rammensee; Pierre Thibault; Claude Perreault; Michal Bassani-Sternberg; Ruedi Aebersold; Etienne Caron
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

8.  Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach.

Authors:  Elizabeth Guruceaga; Alba Garin-Muga; Gorka Prieto; Bartolomé Bejarano; Miguel Marcilla; Consuelo Marín-Vicente; Yasset Perez-Riverol; J Ignacio Casal; Juan Antonio Vizcaíno; Fernando J Corrales; Victor Segura
Journal:  J Proteome Res       Date:  2017-10-11       Impact factor: 4.466

  8 in total

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