1
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Deutsch EW, Vizcaíno JA, Jones AR, Binz PA, Lam H, Klein J, Bittremieux W, Perez-Riverol Y, Tabb DL, Walzer M, Ricard-Blum S, Hermjakob H, Neumann S, Mak TD, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Bandeira N, Carver J, Pullman B, Sun Z, Hoffmann N, Shofstahl J, Zhu Y, Licata L, Quaglia F, Tosatto SCE, Orchard SE. Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. J Proteome Res 2023; 22:287-301. [PMID: 36626722 PMCID: PMC9903322 DOI: 10.1021/acs.jproteome.2c00637] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Indexed: 01/11/2023]
Abstract
The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception 20 years ago. Here we describe the general operation of the PSI, including its leadership, working groups, yearly workshops, and the document process by which proposals are thoroughly and publicly reviewed in order to be ratified as PSI standards. We briefly describe the current state of the many existing PSI standards, some of which remain the same as when originally developed, some of which have undergone subsequent revisions, and some of which have become obsolete. Then the set of proposals currently being developed are described, with an open call to the community for participation in the forging of the next generation of standards. Finally, we describe some synergies and collaborations with other organizations and look to the future in how the PSI will continue to promote the open sharing of data and thus accelerate the progress of the field of proteomics.
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Affiliation(s)
- Eric W. Deutsch
- Institute
for Systems Biology, Seattle, Washington 98109, United States
| | - Juan Antonio Vizcaíno
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Andrew R. Jones
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Pierre-Alain Binz
- Clinical
Chemistry Service, Lausanne University Hospital, 1011 976 Lausanne, Switzerland
| | - Henry Lam
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, P. R. China.
| | - Joshua Klein
- Program for
Bioinformatics, Boston University, Boston, Massachusetts 02215, United States
| | - Wout Bittremieux
- Skaggs
School
of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
- Department
of Computer Science, University of Antwerp, 2020 Antwerpen, Belgium
| | - Yasset Perez-Riverol
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - David L. Tabb
- SA MRC
Centre for TB Research, DST/NRF Centre of Excellence for Biomedical
TB Research, Division of Molecular Biology and Human Genetics, Faculty
of Medicine and Health Sciences, Stellenbosch
University, Cape Town 7602, South Africa
| | - Mathias Walzer
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Sylvie Ricard-Blum
- Univ.
Lyon, Université Lyon 1, ICBMS, UMR 5246, 69622 Villeurbanne, France
| | - Henning Hermjakob
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Steffen Neumann
- Bioinformatics
and Scientific Data, Leibniz Institute of
Plant Biochemistry, 06120 Halle, Germany
- German
Centre for Integrative Biodiversity Research (iDiv), 04103 Halle-Jena-Leipzig, Germany
| | - Tytus D. Mak
- Mass Spectrometry
Data Center, National Institute of Standards
and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United
States
| | - Shin Kawano
- Database
Center for Life Science, Joint Support Center for Data Science Research, Research Organization of Information and Systems, Chiba 277-0871, Japan
- Faculty
of Contemporary Society, Toyama University
of International Studies, Toyama 930-1292, Japan
- School
of Frontier Engineering, Kitasato University, Sagamihara 252-0373, Japan
| | - Luis Mendoza
- Institute
for Systems Biology, Seattle, Washington 98109, United States
| | - Tim Van Den Bossche
- VIB-UGent
Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
- Department
of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium
| | - Ralf Gabriels
- VIB-UGent
Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
- Department
of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium
| | - Nuno Bandeira
- Skaggs
School
of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
- Center
for Computational Mass Spectrometry, Department of Computer Science
and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States
| | - Jeremy Carver
- Center
for Computational Mass Spectrometry, Department of Computer Science
and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States
| | - Benjamin Pullman
- Center
for Computational Mass Spectrometry, Department of Computer Science
and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States
| | - Zhi Sun
- Institute
for Systems Biology, Seattle, Washington 98109, United States
| | - Nils Hoffmann
- Institute
for Bio- and Geosciences (IBG-5), Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany
| | - Jim Shofstahl
- Thermo
Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Yunping Zhu
- National
Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, #38, Life Science Park, Changping District, Beijing 102206, China
| | - Luana Licata
- Fondazione
Human Technopole, 20157 Milan, Italy
- Department
of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Federica Quaglia
- Institute
of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR-IBIOM), 70126 Bari, Italy
- Department
of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | | | - Sandra E. Orchard
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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2
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McGowan T, Johnson JE, Kumar P, Sajulga R, Mehta S, Jagtap PD, Griffin TJ. Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration. Gigascience 2020; 9:giaa025. [PMID: 32236523 PMCID: PMC7102281 DOI: 10.1093/gigascience/giaa025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/13/2020] [Accepted: 02/24/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Proteogenomics integrates genomics, transcriptomics, and mass spectrometry (MS)-based proteomics data to identify novel protein sequences arising from gene and transcript sequence variants. Proteogenomic data analysis requires integration of disparate 'omic software tools, as well as customized tools to view and interpret results. The flexible Galaxy platform has proven valuable for proteogenomic data analysis. Here, we describe a novel Multi-omics Visualization Platform (MVP) for organizing, visualizing, and exploring proteogenomic results, adding a critically needed tool for data exploration and interpretation. FINDINGS MVP is built as an HTML Galaxy plug-in, primarily based on JavaScript. Via the Galaxy API, MVP uses SQLite databases as input-a custom data type (mzSQLite) containing MS-based peptide identification information, a variant annotation table, and a coding sequence table. Users can interactively filter identified peptides based on sequence and data quality metrics, view annotated peptide MS data, and visualize protein-level information, along with genomic coordinates. Peptides that pass the user-defined thresholds can be sent back to Galaxy via the API for further analysis; processed data and visualizations can also be saved and shared. MVP leverages the Integrated Genomics Viewer JavaScript framework, enabling interactive visualization of peptides and corresponding transcript and genomic coding information within the MVP interface. CONCLUSIONS MVP provides a powerful, extensible platform for automated, interactive visualization of proteogenomic results within the Galaxy environment, adding a unique and critically needed tool for empowering exploration and interpretation of results. The platform is extensible, providing a basis for further development of new functionalities for proteogenomic data visualization.
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Affiliation(s)
- Thomas McGowan
- Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Praveen Kumar
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
- Bioinformatics and Computational Biology program, University of Minnesota-Rochester, 111 South Broadway, Suite 300, Rochester, MN 55904, USA
| | - Ray Sajulga
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
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3
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Li K, Vaudel M, Zhang B, Ren Y, Wen B. PDV: an integrative proteomics data viewer. Bioinformatics 2020; 35:1249-1251. [PMID: 30169737 DOI: 10.1093/bioinformatics/bty770] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/22/2018] [Accepted: 08/29/2018] [Indexed: 12/20/2022] Open
Abstract
SUMMARY Data visualization plays critical roles in proteomics studies, ranging from quality control of MS/MS data to validation of peptide identification results. Herein, we present PDV, an integrative proteomics data viewer that can be used to visualize a wide range of proteomics data, including database search results, de novo sequencing results, proteogenomics files, MS/MS data in mzML/mzXML format and data from public proteomics repositories. PDV is a lightweight visualization tool that enables intuitive and fast exploration of diverse, large-scale proteomics datasets on standard desktop computers in both graphical user interface and command line modes. AVAILABILITY AND IMPLEMENTATION PDV software and the user manual are freely available at http://pdv.zhang-lab.org. The source code is available at https://github.com/wenbostar/PDV and is released under the GPL-3 license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kai Li
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Marc Vaudel
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yan Ren
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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4
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Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, Hermjakob H, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA. The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. Nucleic Acids Res 2020; 48:D1145-D1152. [PMID: 31686107 PMCID: PMC7145525 DOI: 10.1093/nar/gkz984] [Citation(s) in RCA: 316] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 11/24/2022] Open
Abstract
The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination of mass spectrometry proteomics data worldwide since 2012. In this paper, we describe the main developments since the previous update manuscript was published in Nucleic Acids Research in 2017. Since then, in addition to the four PX existing members at the time (PRIDE, PeptideAtlas including the PASSEL resource, MassIVE and jPOST), two new resources have joined PX: iProX (China) and Panorama Public (USA). We first describe the updated submission guidelines, now expanded to include six members. Next, with current data submission statistics, we demonstrate that the proteomics field is now actively embracing public open data policies. At the end of June 2019, more than 14 100 datasets had been submitted to PX resources since 2012, and from those, more than 9 500 in just the last three years. In parallel, an unprecedented increase of data re-use activities in the field, including 'big data' approaches, is enabling novel research and new data resources. At last, we also outline some of our future plans for the coming years.
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Affiliation(s)
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | | | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jeremy J Carver
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Deepti J Kundu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - David García-Seisdedos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Andrew F Jarnuczak
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Suresh Hewapathirana
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Benjamin S Pullman
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Julie Wertz
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Zhi Sun
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Shin Kawano
- Faculty of Contemporary Society, Toyama University of International Studies, Toyama 930–1292, Japan
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Chiba 277–0871, Japan
| | - Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951–8510, Japan
| | - Yu Watanabe
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951–8510, Japan
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China
| | | | | | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606–8501, Japan
| | - Juan A Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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5
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Guo L, Li L, Zhang Y, Fu S, Zhang J, Wang X, Zhu H, Qiao M, Wu L, Liu Y. Long non-coding RNA profiling in LPS-induced intestinal inflammation model: New insight into pathogenesis. Innate Immun 2019; 25:491-502. [PMID: 31474162 PMCID: PMC6900666 DOI: 10.1177/1753425919872812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
LPS can induce an inflammatory immune response in the intestine, and long
non-coding RNA (lncRNA) is involved in the process of inflammatory disease.
However, the biological role of lncRNA in the intestinal inflammation of piglets
remains unclear. In this study, the lncRNA expression profile of the ileal
mucosa of piglets challenged by LPS was analysed using lncRNA sequencing. In
total, 112 novel lncRNAs were predicted, of which 58 were up-regulated and 54
down-regulated following LPS challenge. Expression of 15 selected lncRNAs was
validated by quantitative PCR. We further investigated the target genes of
lncRNA that were enriched in the signalling pathways involved in the
inflammatory immune response by utilising Gene Ontology and Kyoto Encyclopaedia
of Genes and Genomes analysis, with cell adhesion molecules and mTOR signalling
pathway identified. In addition, the co-expression networks between the
differentially expressed lncRNAs and the target mRNAs were constructed, with
seven core lncRNAs identified, which also demonstrated that the relationship
between lncRNAs and the target genes was highly correlated. Our study offers
important information about the lncRNAs of the mucosal immune system in piglets
and provides new insights into the inflammatory mechanism of LPS challenge,
which might serve as a novel target to control intestinal inflammation.
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Affiliation(s)
- Ling Guo
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan
Polytechnic University, PR China
- Hubei Collaborative Innovation Center for Animal Nutrition and
Feed Safety, PR China
| | - Linna Li
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan
Polytechnic University, PR China
| | - Yang Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan
Polytechnic University, PR China
- Hubei Collaborative Innovation Center for Animal Nutrition and
Feed Safety, PR China
| | - Shulin Fu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan
Polytechnic University, PR China
- Hubei Collaborative Innovation Center for Animal Nutrition and
Feed Safety, PR China
| | - Jing Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan
Polytechnic University, PR China
- Hubei Collaborative Innovation Center for Animal Nutrition and
Feed Safety, PR China
| | - Xiuying Wang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan
Polytechnic University, PR China
- Hubei Collaborative Innovation Center for Animal Nutrition and
Feed Safety, PR China
| | - Huiling Zhu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan
Polytechnic University, PR China
- Hubei Collaborative Innovation Center for Animal Nutrition and
Feed Safety, PR China
| | - Mu Qiao
- Key Laboratory of Animal Embryo Engineering and Molecular
Breeding of Hubei Province, Institute of Animal Husbandry and Veterinary, Hubei
Academy of Agricultural Sciences, PR China
| | - Lingying Wu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan
Polytechnic University, PR China
- Hubei Collaborative Innovation Center for Animal Nutrition and
Feed Safety, PR China
| | - Yulan Liu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan
Polytechnic University, PR China
- Hubei Collaborative Innovation Center for Animal Nutrition and
Feed Safety, PR China
- Yulan Liu, Hubei Key Laboratory of Animal
Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, PR
China.
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6
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Verbruggen S, Ndah E, Van Criekinge W, Gessulat S, Kuster B, Wilhelm M, Van Damme P, Menschaert G. PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms. Mol Cell Proteomics 2019; 18:S126-S140. [PMID: 31040227 PMCID: PMC6692777 DOI: 10.1074/mcp.ra118.001218] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/30/2019] [Indexed: 12/20/2022] Open
Abstract
PROTEOFORMER is a pipeline that enables the automated processing of data derived from ribosome profiling (RIBO-seq, i.e. the sequencing of ribosome-protected mRNA fragments). As such, genome-wide ribosome occupancies lead to the delineation of data-specific translation product candidates and these can improve the mass spectrometry-based identification. Since its first publication, different upgrades, new features and extensions have been added to the PROTEOFORMER pipeline. Some of the most important upgrades include P-site offset calculation during mapping, comprehensive data pre-exploration, the introduction of two alternative proteoform calling strategies and extended pipeline output features. These novelties are illustrated by analyzing ribosome profiling data of human HCT116 and Jurkat data. The different proteoform calling strategies are used alongside one another and in the end combined together with reference sequences from UniProt. Matching mass spectrometry data are searched against this extended search space with MaxQuant. Overall, besides annotated proteoforms, this pipeline leads to the identification and validation of different categories of new proteoforms, including translation products of up- and downstream open reading frames, 5' and 3' extended and truncated proteoforms, single amino acid variants, splice variants and translation products of so-called noncoding regions. Further, proof-of-concept is reported for the improvement of spectrum matching by including Prosit, a deep neural network strategy that adds extra fragmentation spectrum intensity features to the analysis. In the light of ribosome profiling-driven proteogenomics, it is shown that this allows validating the spectrum matches of newly identified proteoforms with elevated stringency. These updates and novel conclusions provide new insights and lessons for the ribosome profiling-based proteogenomic research field. More practical information on the pipeline, raw code, the user manual (README) and explanations on the different modes of availability can be found at the GitHub repository of PROTEOFORMER: https://github.com/Biobix/proteoformer.
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Affiliation(s)
- Steven Verbruggen
- BioBix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Elvis Ndah
- BioBix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Wim Van Criekinge
- BioBix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Siegfried Gessulat
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Munich, Germany; SAP SE, Potsdam, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Munich, Germany
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Munich, Germany
| | - Petra Van Damme
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Gerben Menschaert
- BioBix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
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7
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Wu P, Pu L, Deng B, Li Y, Chen Z, Liu W. PASS: A Proteomics Alternative Splicing Screening Pipeline. Proteomics 2019; 19:e1900041. [PMID: 31095856 DOI: 10.1002/pmic.201900041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/28/2019] [Indexed: 12/11/2022]
Abstract
Alternative splicing (AS) has been well-investigated at the trancriptome level by the application of RNA-seq technology. There is an ongoing debate on the biological importance of AS to proteome complexity. A toolkit for accurately identifying AS from proteome data is urgently needed. Here, a software called PASS is developed to comprehensively detect AS events for the proteomics mass spectrometry (MS) data. Moreover, PASS is well compatible with MS identification by the proteogenomics approach, which provides novel AS candidates for proteome identification. The workflow of PASS mainly contains five core steps: transcripts reconstruction from RNA-Seq data, novel protein sequence generation, MS data searching, proSAM file formatting, and AS detection. Access to the program from either step is supported. PASS is successfully applied to proteome data of mouse hepatocytes and 407 AS events are first identified with proteomics MS evidences. PASS is expected to be widely used to identify AS events on proteome data and provide a deeper understanding of the proteome isoforms. The PASS software is freely available at https://github.com/wupengomics/PASS.
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Affiliation(s)
- Peng Wu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, 300020, China
| | - Lingling Pu
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Bingnan Deng
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Yingying Li
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Zhaoli Chen
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Weili Liu
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
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8
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Binz PA, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp EA, Mendoza L, Baker PR, Collins A, Van Den Bossche T, Deutsch EW. Proteomics Standards Initiative Extended FASTA Format. J Proteome Res 2019; 18:2686-2692. [PMID: 31081335 DOI: 10.1021/acs.jproteome.9b00064] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mass-spectrometry-based proteomics enables the high-throughput identification and quantification of proteins, including sequence variants and post-translational modifications (PTMs) in biological samples. However, most workflows require that such variations be included in the search space used to analyze the data, and doing so remains challenging with most analysis tools. In order to facilitate the search for known sequence variants and PTMs, the Proteomics Standards Initiative (PSI) has designed and implemented the PSI extended FASTA format (PEFF). PEFF is based on the very popular FASTA format but adds a uniform mechanism for encoding substantially more metadata about the sequence collection as well as individual entries, including support for encoding known sequence variants, PTMs, and proteoforms. The format is very nearly backward compatible, and as such, existing FASTA parsers will require little or no changes to be able to read PEFF files as FASTA files, although without supporting any of the extra capabilities of PEFF. PEFF is defined by a full specification document, controlled vocabulary terms, a set of example files, software libraries, and a file validator. Popular software and resources are starting to support PEFF, including the sequence search engine Comet and the knowledge bases neXtProt and UniProtKB. Widespread implementation of PEFF is expected to further enable proteogenomics and top-down proteomics applications by providing a standardized mechanism for encoding protein sequences and their known variations. All the related documentation, including the detailed file format specification and example files, are available at http://www.psidev.info/peff .
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Affiliation(s)
- Pierre-Alain Binz
- CHUV Centre Hospitalier Universitaire Vaudois , CH-1011 Lausanne 14 , Switzerland
| | - Jim Shofstahl
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , United Kingdom
| | - Harald Barsnes
- Proteomics Unit, Department of Biomedicine , University of Bergen , N-5009 Bergen , Norway.,Computational Biology Unit, Department of Informatics , University of Bergen , N-5008 Bergen , Norway
| | - Robert J Chalkley
- University California at San Francisco , San Francisco , California 94143 , United States
| | - Gerben Menschaert
- Biobix, Department of Data Analysis and Mathematical Modelling , Ghent University , 9000 Ghent , Belgium
| | - Emanuele Alpi
- European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , United Kingdom
| | - Karl Clauser
- Broad Institute , Cambridge , Massachusetts 02142 , United States
| | - Jimmy K Eng
- University of Washington , Seattle , Washington 98195 , United States
| | - Lydie Lane
- SIB Swiss Institute of Bioinformatics , CH-1211 Geneva 4 , Switzerland.,Department of Microbiology and Molecular Medicine, Faculty of Medicine , University of Geneva , CH-1211 Geneva 4 , Switzerland
| | - Sean L Seymour
- Seymour Data Science, LLC , San Francisco , California 95000 , United States
| | - Luis Francisco Hernández Sánchez
- K.G. Jebsen Center for Diabetes Research, Department of Clinical Science , University of Bergen , 5021 Bergen , Norway.,Center for Medical Genetics and Molecular Medicine , Haukeland University Hospital , 5021 Bergen , Norway
| | - Gerhard Mayer
- Medical Faculty, Medizinisches Proteom-Center , Ruhr University Bochum , D-44801 Bochum , Germany
| | - Martin Eisenacher
- Medical Faculty, Medizinisches Proteom-Center , Ruhr University Bochum , D-44801 Bochum , Germany
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , United Kingdom
| | - Eugene A Kapp
- Walter & Eliza Hall Institute of Medical Research and the University of Melbourne , Melbourne , VIC 3052 , Australia
| | - Luis Mendoza
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Peter R Baker
- University California at San Francisco , San Francisco , California 94143 , United States
| | - Andrew Collins
- Department of Functional and Comparative Genomics, Institute of Integrated Biology , University of Liverpool , Liverpool L69 7ZB , United Kingdom
| | - Tim Van Den Bossche
- VIB-UGent Center for Medical Biotechnology , Ghent University , 9000 Ghent , Belgium
| | - Eric W Deutsch
- Institute for Systems Biology , Seattle , Washington 98109 , United States
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9
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Levitsky LI, Klein JA, Ivanov MV, Gorshkov MV. Pyteomics 4.0: Five Years of Development of a Python Proteomics Framework. J Proteome Res 2019; 18:709-714. [PMID: 30576148 DOI: 10.1021/acs.jproteome.8b00717] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many of the novel ideas that drive today's proteomic technologies are focused essentially on experimental or data-processing workflows. The latter are implemented and published in a number of ways, from custom scripts and programs, to projects built using general-purpose or specialized workflow engines; a large part of routine data processing is performed manually or with custom scripts that remain unpublished. Facilitating the development of reproducible data-processing workflows becomes essential for increasing the efficiency of proteomic research. To assist in overcoming the bioinformatics challenges in the daily practice of proteomic laboratories, 5 years ago we developed and announced Pyteomics, a freely available open-source library providing Python interfaces to proteomic data. We summarize the new functionality of Pyteomics developed during the time since its introduction.
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Affiliation(s)
- Lev I Levitsky
- Moscow Institute of Physics and Technology , Dolgoprudny, Moscow Region 141701 , Russia.,V.L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Moscow 119334 , Russia
| | - Joshua A Klein
- Bioinformatics Program , Boston University , Boston , Massachusetts 02215 , United States
| | - Mark V Ivanov
- V.L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Moscow 119334 , Russia
| | - Mikhail V Gorshkov
- V.L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Moscow 119334 , Russia
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10
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Ren Z, Qi D, Pugh N, Li K, Wen B, Zhou R, Xu S, Liu S, Jones AR. Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets. Mol Cell Proteomics 2019; 18:86-98. [PMID: 30293062 PMCID: PMC6317475 DOI: 10.1074/mcp.ra118.000832] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/31/2018] [Indexed: 01/22/2023] Open
Abstract
Rice (Oryza sativa) is one of the most important worldwide crops. The genome has been available for over 10 years and has undergone several rounds of annotation. We created a comprehensive database of transcripts from 29 public RNA sequencing data sets, officially predicted genes from Ensembl plants, and common contaminants in which to search for protein-level evidence. We re-analyzed nine publicly accessible rice proteomics data sets. In total, we identified 420K peptide spectrum matches from 47K peptides and 8,187 protein groups. 4168 peptides were initially classed as putative novel peptides (not matching official genes). Following a strict filtration scheme to rule out other possible explanations, we discovered 1,584 high confidence novel peptides. The novel peptides were clustered into 692 genomic loci where our results suggest annotation improvements. 80% of the novel peptides had an ortholog match in the curated protein sequence set from at least one other plant species. For the peptides clustering in intergenic regions (and thus potentially new genes), 101 loci were identified, for which 43 had a high-confidence hit for a protein domain. Our results can be displayed as tracks on the Ensembl genome or other browsers supporting Track Hubs, to support re-annotation of the rice genome.
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Affiliation(s)
- Zhe Ren
- From the ‡BGI-Shenzhen, Shenzhen 518083, China
| | - Da Qi
- From the ‡BGI-Shenzhen, Shenzhen 518083, China
| | - Nina Pugh
- §Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Kai Li
- From the ‡BGI-Shenzhen, Shenzhen 518083, China
| | - Bo Wen
- ‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030;; ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030
| | - Ruo Zhou
- From the ‡BGI-Shenzhen, Shenzhen 518083, China
| | - Shaohang Xu
- From the ‡BGI-Shenzhen, Shenzhen 518083, China
| | - Siqi Liu
- From the ‡BGI-Shenzhen, Shenzhen 518083, China;.
| | - Andrew R Jones
- §Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK;.
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11
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Sajulga R, Mehta S, Kumar P, Johnson JE, Guerrero CR, Ryan MC, Karchin R, Jagtap PD, Griffin TJ. Bridging the Chromosome-centric and Biology/Disease-driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence Variants Detected via Proteogenomics. J Proteome Res 2018; 17:4329-4336. [DOI: 10.1021/acs.jproteome.8b00404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ray Sajulga
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Praveen Kumar
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Bioinformatics and Computational Biology Program, University of Minnesota-Rochester, Rochester, Minnesota 55904, United States
| | - James E. Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Candace R. Guerrero
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Michael C. Ryan
- In-Silico Solutions, Falls Church, Virginia 22043, United States
| | - Rachel Karchin
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland 21218, United States
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21217, United States
| | - Pratik D. Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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12
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Abstract
The recent establishment of cloud computing, high-throughput networking, and more versatile web standards and browsers has led to a renewed interest in web-based applications. While traditionally big data has been the domain of optimized desktop and server applications, it is now possible to store vast amounts of data and perform the necessary calculations offsite in cloud storage and computing providers, with the results visualized in a high-quality cross-platform interface via a web browser. There are number of emerging platforms for cloud-based mass spectrometry data analysis; however, there is limited pre-existing code accessible to web developers, especially for those that are constrained to a shared hosting environment where Java and C applications are often forbidden from use by the hosting provider. To remedy this, we provide an open-source mass spectrometry library for one of the most commonly used web development languages, PHP. Our new library, phpMs, provides objects for storing and manipulating spectra and identification data as well as utilities for file reading, file writing, calculations, peptide fragmentation, and protein digestion as well as a software interface for controlling search engines. We provide a working demonstration of some of the capabilities at http://pgb.liv.ac.uk/phpMs .
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Affiliation(s)
- Andrew Collins
- Department of Functional and Comparative Genomics, Institute of Integrated Biology, University of Liverpool , Liverpool, L69 7ZB, United Kingdom
| | - Andrew R Jones
- Department of Functional and Comparative Genomics, Institute of Integrated Biology, University of Liverpool , Liverpool, L69 7ZB, United Kingdom
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13
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Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR. Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. J Proteome Res 2017; 16:4288-4298. [PMID: 28849660 PMCID: PMC5715286 DOI: 10.1021/acs.jproteome.7b00370] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface). In this work we review the current status of all of these aspects of the PSI, describe synergies with other efforts such as the ProteomeXchange Consortium, the Human Proteome Project, and the metabolomics community, and provide a look at future directions of the PSI.
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Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology , Seattle, Washington 98109, United States
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Pierre-Alain Binz
- CHUV Centre Hospitalier Universitaire Vaudois , 1011 Lausanne, Switzerland
| | - Wout Bittremieux
- Department of Mathematics and Computer Science, University of Antwerp , Middelheimlaan 1, 2020 Antwerp, Belgium
| | - Martin Eisenacher
- Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum , D-44801 Bochum, Germany
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences, Beijing , Beijing 102206, China
| | - Shin Kawano
- Database Center for Life Science, Joint Support Center for Data Science Research, Research Organization of Information and Systems , Kashiwa, Chiba 277-0871, Japan
| | - Henry Lam
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology , Clear Water Bay, Hong Kong, P. R. China.,Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology , Clear Water Bay, Hong Kong, P. R. China
| | - Gerhard Mayer
- Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum , D-44801 Bochum, Germany
| | - Gerben Menschaert
- Lab of Bioinformatics and Computational Genomics (BioBix), Faculty of Bioscience Engineering, Ghent University , 9000 Ghent, Belgium
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Reza M Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - David L Tabb
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town, South Africa
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz , 55131 Mainz, Germany
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Mathias Walzer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Andrew R Jones
- Institute of Integrative Biology, University of Liverpool , South Wirral L64 4AY, United Kingdom
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