Year: 2017
Type: article
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.
Source: Journal of Proteome Research
Institutions: Institute for Systems Biology, European Bioinformatics Institute, Wellcome Trust, Centre Hospitalier Universitaire Vaudois, Hôpital Orthopédique de la Suisse Romande, University of Antwerp, Ruhr University Bochum, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Research Organization of Information and Systems, Database Center for Life Science, Joint Support-Center for Data Science Research, Hong Kong University of Science and Technology, Ghent University, South African Medical Research Council, Stellenbosch University, University Medical Center of the Johannes Gutenberg University Mainz, University of Liverpool
Language: English
Subfield: Spectroscopy
Field: Chemistry
Domain: Physical Sciences
Open Access status: hybrid
Estimated APC paid: $4,500
Funders: National Science Foundation, Wellcome Trust, South African Medical Research Council, Department of Science and Technology, Republic of South Africa, Department of Science and Technology, Ministry of Science and Technology, India, Bundesministerium für Bildung und Forschung, German Network for Bioinformatics Infrastructure, National Institutes of Health, Medical Research Council, Biotechnology and Biological Sciences Research Council, Japan Society for the Promotion of Science, National Institute of General Medical Sciences, National Institute of Biomedical Imaging and Bioengineering, Division of Information and Intelligent Systems, FP7 Research infrastructures, FP7 Health
Awards: G1423456925, G1443135587, G1564535905, China Partnering Award: Proteomics Data Exchange, ProteoGenomics: Dynamic Linkage of Genomes and Proteomes through Ensembl and ProteomeXchange, PROCESS - Proteomics data Collection, Software and Standards to support open access and long term management of data, Establishment of proteomics analysis methods using RNA-seq in the personal genomic era, MICA: UK MEDical BIOinformatics partnership - aggregation, integration, visualisation and analysis of large, complex data (UK MED-BIO)., Big Data for Discovery Science, G2792250446, Advancing data and metadata standards for proteomics mass spectra, BD Spokes: PLANNING: WEST: Collaborative: Increasing collaborations in proteogenomics applications of genetic data, PROCESS - Proteomics data Collection, Software and Standards to support open access and long term management of data, G554605247, Development of Trans Proteomic Pipeline, an Analysis Suite for Mass Spectrometry, G6314708303, MIDAS - Molecular Interaction Data Availability Standards, ProteoGenomics: Dynamic Linkage of Genomes and Proteomes through Ensembl and ProteomeXchange, Japan Partnering Award: Establishment of an Integrative proteomics bioinformatics platform to enable novel analysis approaches, G701045671, de.NBI - Etablierungsphase - Leistungszentrum - BioInfra.Prot - Bioinformatik der Proteomik, G7474912509, Sharing of metabolomics data and their analyses as Galaxy workflows through a UK-China collaboration, Building the PTM map of the human genome through commensal computing, G8294020440, G849737590, G8842930235, G892962579, G975560111
OpenAlex ID: W2751436602