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# HUPO Proteomics Standards Initiative

The HUPO Proteomics Standards Initiative (HUPO-PSI) develops and maintains global standards, data formats, and vocabularies for proteomics and mass spectrometry research.

## Sitemaps

- [XML Sitemap](https://www.psidev.info/sitemap.xml): Contains all public & indexable URLs for this website.

## Pages

- [Homepage](https://www.psidev.info/) - HUPO-PSI is a global effort to develop and maintain community-driven standards, data formats, and controlled vocabularies for proteomics and mass spectrometry-based research.
- [History of PSI DocProc submissions](https://www.psidev.info/history-of-psi-docproc-submissions) - (report missings or errors to sylvie.ricard-blum:at:univ-lyon1.fr) mzML [handling editors: Norman Paton / Christian Stephan]final (ver 1.0.0): June 1st, 2008update, begin of public and external review phase: April 17th, 2009update, final (ver 1.1.0): June 1st, 2009without DocProc?: update of index wrapper schema (ver 1.1.1.): June 1st, 2010 MIAPE Column Chromatography [handling editor: Norman Paton] PEFF community practice document [handling
- [mzML](https://www.psidev.info/mzml) - History From 2005-2008 there existed two separate XML formats for encoding raw spectrometer output: mzData developed by the PSI and mzXML developed at the Seattle Proteome Center at the Institute for Systems Biology (ISB). It was recognized that the existence of two separate formats for essentially the same thing generated confusion and required extra programming
- [Metabolomics Workgroup](https://www.psidev.info/metabolomics-workgroup)
- [mzPeak: a next generation MS run file format](https://www.psidev.info/mzpeak) - mzPeak is a new binary file format to represent instrument runs in a compact, fast, and cloud-or-local-friendly manner. It is built on top of Apache Parquet, a featureful, robust and production-tested data format with implementations available in virtually all major programming languages today. You can read it from your hard drive, a object store
- [ProForma](https://www.psidev.info/proforma) - Proforma v2.1 finalised ProForma (Proteoform and Peptidoform Notation) Protein and peptide sequences are usually represented using a string of amino acidsusing a well-known one letter code endorsed by the IUPAC. However, there was still no clear consensus about how torepresent ‘proteoforms’ and ‘peptidoforms’, meaning all possible variations of a protein/peptide sequence, includingprotein modifications, both artefactual
- [HUPO-PSI Meeting 2026](https://www.psidev.info/hupo-psi-meeting-2026) - About The HUPO-PSI Spring Meeting is an annual event organized by the HUPO Proteomics Standards Initiative, aiming to advance data standardization efforts. This meeting brings together scientists from various areas of proteomics to collaborate on the development of standardized data formats, which are crucial for the field’s continued growth. We are pleased to announce that
- [Peak Annotation Format (mzPAF)](https://www.psidev.info/mzpaf) - The mzPAF proposed standard is a specification for a fragment ion peak annotation format for mass spectra, focused on peptides. This provides for a standardized format for describing the origin of fragment ions to be used in spectral libraries, other formats that aim to describe fragment ions, and software tools that annotate fragment ions. Status Updated:
- [Documents in Progress](https://www.psidev.info/documents-in-progress) - FeatureTab The FeatureTab specification has been released on January 8th, 2026. MIAPE-MIDAP (Minimal Information Describing a Proteoform) The MIAPE-MIDAP document has been reviewed by two members of the Steering Group and is in the public and external review phase until March 19th, 2026. ProForma 2.1 (Proteoform and Peptidoform Notation) The ProForma 2.1 specification is under
- [Molecular Interactions](https://www.psidev.info/molecular-interactions) - The Molecular Interactions workgroup is concentrating on: improving the annotation and representation of molecular interaction data wherever it is published, be this in journal articles, authors web-sites or public domain databases improving the accessibility of molecular interaction data to the user community. This we aim to achieve by presenting our data in a common
- [FeatureTab - specification description and link](https://www.psidev.info/featuretab-specification-description-and-link) - The PSI standard, PSI-MI FeatureTab, is an exchange format for molecular interaction features. The PSI-MI FeatureTab format is part of the PSI-MI 2.5 standard. It is related to the tabular format provided by PSI MITAB 2.5 and subsequent updates. However, while the PSI MITAB 2.5 describes binary interactions, one pair of interactors per row, in
- [MIRAGE/Glycosylation Working Group](https://www.psidev.info/groups/mirage-glycosylation-working-group) - 13 August 2026 -
- [PSI-MI TAB FeatureTab: exchange format for molecular interaction features](https://www.psidev.info/psi-mi-tab-featuretab-exchange-format-for-molecular-interaction-features) - PSI draft recommendation
- [GelML 1.1.0 Specification](https://www.psidev.info/gelml) - The GelML 1.1.0 specification was developed by the PSI in 2007-2010 and published in 2010 and available via PubMed. The schema itself is available at https://github.com/HUPO-PSI/gelml The format is currently effectively deprecated since it never achieved widespread use. Other links: Protein Separation Specifications
- [AI-readiness](https://www.psidev.info/ai-readiness) - The AI working group of HUPO-PSI aims to make public proteomics data accessible through collaborative efforts and standards.
- [Roles and Responsibilities](https://www.psidev.info/roles-and-responsibilities)
- [mzSpecLib](https://www.psidev.info/mzspeclib) - mzSpecLib is a formal standard and file format in development at HUPO-PSI to store and distribute spectral libraries. The main target audience for this format is the developers of spectral library search tools and resources. Past file formats have been created to store and disseminate spectral libraries, such as MSP, X!Hunter binary MGF, BiblioSpec SQLite
- [Specifications](https://www.psidev.info/specifications) - FeatureTab mzIdentML mzML mzQC mzSpecLib mzTab PEFF proBAM proBed ProForma PSI-MI XML TraML Universal Spectrum Identifier
- [PSI-MI XML Maker v1.1 User Guide](https://www.psidev.info/psi-mi-xml-maker-v1-1-user-guide) - PSI-MI XML Maker User Guide ⚠️ It is necessary to download Java 11 **JDK** -> https://adoptium.net/en-GB/temurin/archive/?version=11 - Use the installer so it is downloaded directly in the right folder - Access to the demo: https://drive.google.com/drive/folders/1VftTaAUfWdJF_dyFLEH9b-23i-454qDY?usp=sharing 1. Introduction 1.1 What is the PSI-MI XML Maker? The PSI-MI XML Maker is a tool
- [mzIdentML](https://www.psidev.info/mzidentml) - mzIdentML is one of the standards developed by the Proteomics Informatics working group of the PSI. For general information of the activities and the organization of this working group see HERE. Contents 1. mzIdentML 1.3.0 (current release) 2. mzIdentML 1.2.0 3. mzIdentML 1.1.1 4. mzIdentML 1.1.0: XML Schema, Documentation and Ontology 5. mzIdentML Tools and Implementations
- [About the HUPO Proteomics Standards Initiative (HUPO-PSI)](https://www.psidev.info/about-the-hupo-proteomics-standards-initiative-psi) - The Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) is a global collaborative effort aimed at creating and maintaining community-driven standards, data formats, and controlled vocabularies for proteomics and mass spectrometry-based research. Through its working groups and annual workshops, HUPO-PSI encourages collaboration and ensures thorough public review of proposals before their adoption as standards. By advocating
- [PSI Document Process (DocProc) Definition](https://www.psidev.info/psi-document-process-docproc-definition) - Document templates can be found here. Revision 2021: version 1.1.2, current version ("online document editing" systems mentioned for public review / removed the mentioning of the insecure "comment" function on psidev.info website, shortened public and invited review phase from 60 to 45 days; changed license model from Copyright to CC-BY-NC 4.0; pre-final after Steering Group review:
- [PSI documents](https://www.psidev.info/psi-documents) - Proteomics Standards Initiative Document Process and Minimum Document Requirements The PSI Community Practice Document (Version 1.1.2 FINAL 10th May 2021) describes the processes and practices that characterize the document review processes run by the Proteomics Standards Initiative is available here. PSI documents fall into one of the following categories: Community Practice Documents, which inform and
- [Mass Spectrometry Standards Working Group Charter](https://www.psidev.info/mass-spectrometry-standards-working-group-charter) - Submitted: 2025-06-17Template Rev2016b 1.Administrative Section Status (New/Update): Update Group Name: Mass Spectrometry Standards Working Group (PSI-MS WG) Chair (with affiliation and current email address):Eric Deutsch, Institute for Systems Biology (edeutsch@systemsbiology.org) Co-Chairs (1 or 2) (with affiliation and current email address):Pierre-Alain Binz, CHUV Centre Hospitalier Universitaire Vaudois (Pierre-Alain.Binz@chuv.ch)Henry Lam, Hong Kong University of Science and Technology
- [AI-readiness Working Group Charter](https://www.psidev.info/ai-readiness-working-group-charter) - Submitted: 2025-13-06 Administrative Section Status (New/Update): New Group Name: HUPO PSI AI-readiness Working Group (PSI-AI WG) Chair (with affiliation and current email address): Tine Claeys (tineclae.claeys@ugent.be) – Ghent University – VIB, Ghent, Belgium Co-Chairs (1 or 2) (with affiliation and current email address): Samuel Wein, –(samuel.wein@uni-tuebingen.de) University of Tübingen – OpenMS, Tübingen, GermanyRalf Gabriels (ralf.gabriels@ugent.be),
- [Molecular Interaction Working Group Charter](https://www.psidev.info/molecular-interaction-working-group-charter) - Submitted: 2025-04-03Template Rev2016b 1.Administrative Section Status (New/Update): Update Group Name:HUPO PSI Molecular Interaction Working Group (PSI-MI WG) Chair (with affiliation and current email address):Luana Licata (luana.licata@gmail.com) Co-Chairs (1 or 2) (with affiliation and current email address):Sylvie Ricard-Blum (sylvie.ricard-blum@univ-lyon1.fr)Kalpana Panneerselvam (kalpanap@ebi.ac.uk) Secretary: Other officers (optional) (with affiliation and current email address):Editor(s): Sylvie Ricard-Blum (sylvie.ricard-blum@univ-lyon1.fr)Minimal Reporting Requirements
- [Groups](https://www.psidev.info/groups) - AI-readiness Controlled Vocabularies Intrinsically Disordered Proteins workgroup Mass Spectrometry Workgroup Molecular Interactions Protein Modifications Workgroup Protein Separation Workgroup Proteomics Informatics Workgroup PSI Editors Quality Control Workgroup Sample Processing Workgroup
- [HUPO-PSI Meeting 2025](https://www.psidev.info/spring-meeting-2025) - About The HUPO-PSI Spring Meeting is an annual event organized by the HUPO Proteomics Standards Initiative, aiming to advance data standardization efforts. This meeting brings together scientists from various areas of proteomics to collaborate on the development of standardized data formats, which are crucial for the field's continued growth. This year, the HUPO-PSI Spring Meeting
- [PROXI](https://www.psidev.info/proxi) - The Proteomics eXpression Interface is a suite of integrated APIs each targeting a different aspect of exchanging proteomics information between ProteomeXchange data partners and consumers. The specifications and more details can be found on the github repository: https://github.com/HUPO-PSI/proxi-schemas.
- [Controlled Vocabularies](https://www.psidev.info/controlled-vocabularies) - Controlled VocabulariesReleased October, 2006Last maintenance update, October 2017 Table of Contents Introduction OBO PSI CVs by working groups Recommendation for PSI CVs Common PSI CVs Mapping between exchange schema and CVs Maintenance procedure Further information and relevant links References Introduction The Controlled Vocabularies (CV's) of the Proteomic Standard Initiative (PSI) provide a consensus annotation system
- [Quality Control](https://www.psidev.info/quality-control) - PSI-QC: Quality Control Working Group The PSI-QC working group is composed of academic researchers, bioinformatics software developers, and government researchers. The main goal of the PSI-QC working group is to provide a unifying framework for quality control information in biological mass spectrometry, by defining the community-driven standardized mzQC file format and associated controlled vocabulary terms.
- [Quality Control Working Group Charter](https://www.psidev.info/quality-control-working-group-charter) - Submitted: 2018-04-19Revised: 2025-04-03Template Rev2016b 1. Administrative Section Status (New/Update): Update Group Name: HUPO PSI Quality Control Working Group (PSI-QC WG) Chair (with affiliation and current email address): Wout Bittremieux (wout.bittremieux@uantwerpen.be) – University of Antwerp, Antwerp, Belgium Co-Chairs (1 or 2) (with affiliation and current email address): Mathias Walzer (walzer@ebi.ac.uk) – Scientist-at-large Secretary: None. Other officers
- [Universal Spectrum Identifier](https://www.psidev.info/usi) - Status (updated 2024-02-16) The Universal Spectrum Identifier is multi-part key identifier for identifying mass spectra contained in public data repositories, primarily focused on proteomics. A USI such as mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_05_2Feb12_Cougar_11-10-09.mzML:scan:12298:[iTRAQ4plex]-LHFFM[Oxidation]PGFAPLTSR/3 encodes the dataset, the MS Run, the scan number and the proposed peptidoform and charge of the ions responsible for the spectrum. Such an identifier enables communication and
- [mzTab](https://www.psidev.info/mztab-specifications) - mzTab is one of the standards developed by members of the Proteomics Informatics working group of the PSI. mzTab-M is a separate standard for Metabolomics and small molecules developed by members of the Proteomics Informatics working group of the PSI and the Data Standards Task Group of the Metabolomics Society. For general information of the
- [HUPO-PSI meeting 2024](https://www.psidev.info/hupo-psi-meeting-2024) - HUPO PSI meeting 2024 The PSI meeting 2024 took place on March 18-20th 2024 at the Kyoto University, Japan. The meeting was sponsored by JPOST (JST-NBDC) and JPDM (JSPS), but also by BBSRC (UKRI) and HUPO. Organisers: Yasushi Ishihama & Shujiro Okuda. Agenda The agenda of the PSI meeting was made available here and a more detailed
- [SDRF Proteomics - Sample and Data Relationship Format](https://www.psidev.info/sdrf-sample-data-relationship-format) - About The SDRF-Proteomics format is a tab-delimited format that describes the sample characteristics and the relationships between samples and data files included in a dataset. The information in SDRF files is organized to follow the natural flow of a proteomics experiment. SDRF-Proteomics structure. The main requirements to be fulfilled for the SDRF-Proteomics format are: The SDRF
- [Mass Spectrometry Standards Working Group](https://www.psidev.info/mass-spectrometry) - Updated: 2024-02-22 About us The PSI Mass Spectrometry Standards Working Group defines community guidelines, data formats, and controlled vocabularies to facilitate data exchange and archiving in the field of mass spectrometry-based proteomics. Current projects Developing the mzSpecLib format, which will provide a PSI-standardized model and implementation for storing metadata-rich spectral libraries. Developing mzPAF, a fragmentation
- [Mass Spectrometry Workgroup](https://www.psidev.info/mass-spectrometry-workgroup) - This page is deprecated. Please see: https://www.psidev.info/mass-spectrometry PSI-MS: Mass Spectrometry Standards Working Group | About us | The mzML format | The TraML format | The mzData format || Controlled vocabulary development | Email discussion list | Updated: 2024-01-26 About us The PSI-MSS working group defines community data formats and controlled vocabulary terms facilitating data exchange and archiving in the the field of proteomics
- [mzQC](https://www.psidev.info/mzqc) - The mzQC format is a data standard for reporting and exchanging quality-related information in biological mass spectrometry. For general information on the format and the activities and organization of the HUPO-PSI Quality Control working group see HERE. mzQC v1.0.0 (final version) This is the final release of the mzQC format. The format is designed to
- [HUPO-PSI meeting 2022](https://www.psidev.info/hupo-psi-meeting-2022) - HUPO PSI Meeting 2022 The PSI meeting 2022 took place from Wed 11th to Friday 13th May 2022 at EMBL-EBI, Hinxton, Cambridge, UK. Agenda The agenda of the meeting is available HERE. Registration Registration is no longer available. Location EMBL-EBI (European Bioinformatics Institute) Wellcome Trust Genome Campus Hinxton, Cambridge, UK CB10 1SD (Remote participation will be enabled via Zoom) Accommodation Every
- [MIAPE](https://www.psidev.info/miape) - Reporting guidelines for proteomics The context-sensitive nature of transcriptome, metabolome and proteome data necessitates the capture of a richer set of metadata (data about the data) than is required for basic genetic sequence, where usually knowing the organism of origin will suffice. The use of paper citations as proxies for actual metadata hinders the reassessment
- [MIAPE 2 - backup](https://www.psidev.info/miape-2) - View documents for this group Reporting guidelines for proteomics The context-sensitive nature of transcriptome, metabolome and proteome data necessitates the capture of a richer set of metadata (data about the data) than is required for basic genetic sequence, where usually knowing the organism of origin will suffice. The use of paper citations as proxies for actual metadata
- [PEFF](https://www.psidev.info/peff) - The PSI Extended Fasta Format (PEFF) is a ratified PSI standard that provides a unified format for protein and nucleotide sequence databases to be used by sequence search engines and other associated tools (spectra library search tools, sequence alignment software, data repositories, etc). This format enables consistent extraction, display and processing of information such as
- [Protein Separation](https://www.psidev.info/protein-separation) - Group currently inactive – historical documents shown here HUPO Proteomics Standards Initiative HUPO Proteomics Standards Initiative - Protein Separation Workgroup (PSI-PS) The group has been formed following a merger of the PSI-GEL and SP (sample processing and separations) workgroups PS Group Charter The PSI Protein Separation work group is a collaboration of researchers from
- [Protein Modifications](https://www.psidev.info/protein-modifications) - Table of Contents Introduction How to comment Available data Tools Further information and relevant links Introduction The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. For detailed information on all PSI activities, please see the home page. The protein modification workgroup focuses on
- [proBAM](https://www.psidev.info/probam) - proBAM is one of the standards developed by members of the Proteomics Informatics working group of the PSI. For general information of the activities and the organization of this working group see HERE. Contents proBAM (version 1.0.0): Specification documents proBAM Tools and Implementations proBAM (version 1.0.0): Specification documents The proteomics BAM (proBAM) file format is designed
- [proBed](https://www.psidev.info/probed) - proBed is one of the data standards developed by members of the Proteomics Informatics working group of the PSI. For general information of the activities and the organization of this working group see HERE. The original BED format (Browser Extensive Data, https://genome.ucsc.edu/FAQ/FAQformat.html – format1), developed by the UCSC (University of California, Santa Cruz) team, is used to
- [HUPO-PSI meeting 2014](https://www.psidev.info/hupo-psi_meeting2014) - Sun, 04/13/2014 - 12:00 This meeting was sponsored by the BBSRC BBR grant 'PROCESS' [BB/K01997X/1] and by the EU FP7 grants 'ProteomeXchange' [no. 260558] and 'COSMOS' [no. 312941]
- [TraML](https://www.psidev.info/traml) - The HUPO PSI Mass Spectrometry Standards Working Group (MSS WG) has developed a specification for a standardized format for the exchange and transmission of transition lists for selected reaction monitoring (SRM) experiments. This specification has now completed rigorous review with the PSI document process and is complete. Please email the list psidev-ms-dev@lists.sourceforge.net with your questions,
- [Intrinsically Disordered Proteins](https://www.psidev.info/intrinsically-disordered-proteins) - About us The goal of the HUPO PSI-IDP Community is to develop the guidelines, controlled vocabularies and standardised formats to allow the unambiguous annotation of the basic structural and structure-function attributes of an intrinsically disordered region. The main tasks of the PSI-IDP working group are to: Maintain the Minimum Information About Disordered Experiments (MIADE) guidelines to standardise the description of
- [mzQuantML](https://www.psidev.info/mzquantml) - Formal version 1.0 release (Specification 1.0.1) Direct Links to current documents: mzQuantML 1.0 Schema (xsd) Additional semantic validation rules for the different techniques are HERE, under Schema_rules_X PSI-MS Controlled Vocabulary (OBO File) Mapping file is HERE Specification Document (Microsoft Word format) Twenty minute guide to mzQuantML (introductory tutorial) Mapping to MIAPE Quant Mapping to MCP guidelines find
- [Test new page](https://www.psidev.info/test-new-page) - HUPO-PSI defines community standards for data representation in proteomics to facilitate data comparision, exchange and verification. It was founded at the HUPO meeting in Washington, April 28-29, 2002 (see Science 296, 827). Note that we do not address issues of quality.
- [mzIdentML Conformance to MCP Guidelines](https://www.psidev.info/mzidentml-conformance-to-mcp-guidelines) - This table lists each point in the Molecular and Cellular Proteomics Publication guidelines for the analysis and documentation of peptide and protein identifications. It states the xpath/CV available to provide the required information. Do not edit this page directly because the editor on psidev.info is useless for tables. Source for this page is under svn here.
- [mzIdentML Conformance to MIAPE](https://www.psidev.info/mzidentml-conformance-to-miape) - This table lists each point in the MIAPE guidelines and states the xpath/CV available to provide conformance Do not edit this page directly because the editor on psidev.info is useless for tables. Source for this page is under svn here. You should edit the source html and copy/paste to here. The MIAPE document is available here, and
- [HUPO PSI-PAR: standard format for protein affinity reagents](https://www.psidev.info/hupo-psi-par-standard-format-for-protein-affinity-reagents) - List of Contents News Introduction to the PSI-PAR format Purpose of this web page MIAPAR (Minimum Information About a Protein Affinity Reagent) XML schema Controlled Vocabularies User manual Example data in PSI-PAR Software and tools Meetings Release schedule List of planned features Links Contact News The PSI-PAR is available in Pubmed Report: A community standard
- [Molecular Interaction XML Format: schema changes from version 1.0 to 2.5](https://www.psidev.info/molecular-interaction-xml-format-schema-changes-from-version-1-0-to-2-5) - HUPO Proteomics Standards Initiative Protein Interaction Specification Documentation Molecular Interaction XML Format 2.5 Documentation of schema changes from version 1.0 to 2.5 December 2005 Significant changes have been made from MIF 1.0 to 2.5. The overall aims were to increase the expressive power of the format, going from “intersection” to “union” of molecular interaction
- [PSI-MI XML](https://www.psidev.info/psi-mi-xml-specification) - Proteomics Standards Initiative Molecular Interaction XML Format Documentation Version 2.5 Released 2005, Last maintenance update to version 2.5.4 Version 3.0 Available for use now, estimated formal release – Spring 2016 Table of Contents Introduction Purpose of the PSI-MI XML format Purpose of this document Directory structure Release schedule Changes from PSI-MI 1.0 to 2.5 Maintenance
- [mzIdentML Development Timeline](https://www.psidev.info/mzidentml-development-timeline) - Spring 2006, Meeting in San Francisco, USA– start of a UML model for AnalysisXML (universal standard for all types of proteome informatics) Orchard et al. Proteomics 2006, 6, 4439–4443: “PSI-Proteomics Informatics (PSI-PI) working group now has responsibility for the production of the mass spectrometry informatics standards, such as analysisXML, which will cover, among other things, protein identification reporting. The
- [Proteomics Informatics](https://www.psidev.info/proteomics-informatics) - View documents for this group HUPO Proteomics Standards InitiativeProteomics Informatics Working Group (PSI-PI) Contents Group Charter Group Structure Obtaining the current Documents and Getting Involved mzIdentML mzQuantML Request new CV terms to the PSI-MS Controlled Vocabulary Meetings and Logistics Mailing List and Issue Discussion The PSI Proteomics Informatics standards group is one of the working groups
- [Tools implementing mzIdentML](https://www.psidev.info/tools-implementing-mzidentml) - Status of support for mzIdentML in proteome informatics software Tool Type Status / Description URL I/E F/C Byonic (Protein Metrics Inc.) Search Byonic search engine supports mzIdentML 1.1 as an output format http://www.proteinmetrics.com/products/byonic/ E C Crux Search Supports mzIdentML 1.1 as an output format and reads mzIdentML 1.1 to generate spectral count data http://crux.ms/
- [mzIdentML Use Cases](https://www.psidev.info/mzidentml-use-cases) - Use Cases for mzIdentML It should be possible to create a tool that loads an mzIdentML document and enables users to examine results from an MS, MS-MS, MSn or tag searches. (For MSn searches, the assumption is that matches will be of a similar format to those from MS-MS searches and there will be no
- [PSI Structure and Management](https://www.psidev.info/psi-structure-and-management) - The STRUCTURE document should be read / considered BEFORE the MANAGEMENT document. Revision 2016 (current version): version 1.1.0 (correction of minor inconcistencies, clarifications and updates according to 10 years experience) Original 2006: version 1.0.0 (January 2006, no version number given at that time) Find documents here
- [Semantic Validation](https://www.psidev.info/semantic-validation) - The PSI Validator generic framework The PSI semantic validator tackle the issue of automatically checking that experimental data reported using a specific format and various semantic resources are indeed compliant with the MIAPE recommendations. The semantic validator not only check the XML syntax but it enforces many rules as to how controlled vocabulary terms classes
- [PSI Editors](https://www.psidev.info/psi-editors-2) - PSI editors manage the document process and the communication between external reviewers, the public and the steering commitee. Current PSI editors:Sylvie Ricard-Blum, Univ. Lyon (sylvie.ricard-blum :at: univ-lyon1.fr) Former PSI editors:Martin Eisenacher, Ruhr-Univ. Bochum (martin.eisenacher :at: rub.de)Andy Jones, Univ. of Liverpool (andrew.jones :at: liverpool.ac.uk)Christian Stephan, Ruhr-Univ. Bochum (christian.stephan :at: rub.de)Norman Paton, Univ. of Manchester (npaton :at:
- [Test blank page](https://www.psidev.info/test-blank-page) - Hi
- [PSI Document Templates](https://www.psidev.info/psi-document-templates) - The attached document templates may be used for newly created PSI documents. There is one template for recommendation, informational or community practice documents and another template for MIAPE documents (the latter should be also found here). Attachments 20051205_PSI_Document_Template_MIAPE.doc 20070103_PSI_Document_Template_nonMIAPE_original.doc
- [Events](https://www.psidev.info/events) - HUPO-PSI Events HUPO-PSI meeting 2023 Plexus Student Centre, Leiden, The Netherlands HUPO-PSI meeting 2022 EMBL-EBI, Hinxton, Cambridge, UK HUPO-PSI meeting 2021 virtual HUPO-PSI meeting 2020 virtual HUPO-PSI meeting 2019 Capetown, South Africa HUPO-PSI meeting 2018 EMBL Heidelberg, Germany HUPO-PSI meeting 2017 Beijing Proteome Reseach Center, China HUPO-PSI meeting 2016 Het Pand, Ghent, Belgium HUPO-PSI meeting
- [HUPO-PSI meeting 2015](https://www.psidev.info/hupo-psi-meeting-2015) - HUPO-PSI meeting 2015 Mon, 04/13/2015 - 12:00 PSI/COSMOS meeting 13-15th April 2015 Venue Institute for Systems Biology 401 Terry Avenue North, Seattle, WA, 98109, USA The address of the venue is: 401 Terry Avenue North, Seattle, WA, 98109 (Note that the “North” is very important! Without the “North”, it’s a
- [HUPO-PSI meeting 2023](https://www.psidev.info/hupo-psi-meeting-2023) - HUPO PSI meeting 2023 The PSI meeting 2023 took place from April 17-19th 2023 at the Plexus Student Centre, Leiden, The Netherlands. The meeting was sponsored by NWO and BBSRC. Agenda The provisional agenda of the meeting is available here. Registration Registration for attending the meeting is now CLOSED. Location Plexus Student Centre Kaiserstraat 25 2311 GN
- [HUPO-PSI Working groups and Outputs backup](https://www.psidev.info/hupo-psi-working-groups-and-outputs) - The HUPO Proteomics Standards Initiative defines community standards for data representation in proteomics and interactomics to facilitate data comparison, exchange and verification.
- [Mailing lists](https://www.psidev.info/mailing-lists) - psi-announce@ebi.ac.ukGeneral PSI Announcements. psidev-ms-dev@lists.sourceforge.netDiscussion list mass spectrometry standards development. psi-mi@ebi.ac.ukDiscussion list for the molecular interaction standard and related controlled vocabularies. psidev-pi-dev@lists.sourceforge.netDiscussion list for proteomics informatics (mzIdentML and mzQuantML) development. psidev-mod-vocab@lists.sourceforge.netDiscussion list for controlled vocabulary of protein modifications. psidev-ms-vocab@lists.sourceforge.netDiscussion list for controlled vocabulary of mass spectrometry psi-idp@ebi.ac.ukDiscussion list for disordered proteins HUPO-PSI Slack workspace: https://hupo-psi.slack.com Tags General
- [sepCV](https://www.psidev.info/sepcv) - sepCV: Sample processing and separations controlled vocabulary Motivation The sepCV is a controlled vocabulary for teminology associated with sample preparation and sample processing for proteomics. The sepCV was originally designed to provide terminology for the MIAPE GE reporting guidelines and the gelML data transfer format. It has now been expanded to include terminology for gel
- [The Minimum Information About a Bioactive Entity (MIABE)](https://www.psidev.info/the-minimum-information-about-a-bioactive-entity-miabe) - Introduction to MIABE The work on MIABE was initiated as part of the EMBL-EBI Industry Programme and carried out by EMBL-EBI and the PSI-MI work group. The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. For detailed information on all PSI activities, please see PSI Home Page. Drug-target interactions
- [The Minimum Information about a Molecular Interaction eXperiment (MIMIx)](https://www.psidev.info/the-minimum-information-about-a-molecular-interaction-experiment-mimix) - MIMIx is a community guideline advising the user on how to fully describe a molecular interaction experiment and which information it is important to capture. The document is designed as a compromise between the necessary depth of information to describe all relevant aspects of the interaction experiment, and the reporting burden placed on the scientist
- [IDP work group charter](https://www.psidev.info/idp-work-group-charter) - Intrinsically Disordered Proteins Working Group Charter Submitted: 2019-08-20Template Rev2016b 1. Administrative Section Status (New/Update): New Group Name: HUPO PSI Intrinsically Disordered Proteins Working Group (PSI-IDP WG) Chair (with affiliation and current email address):Norman Davey – The Institute of Cancer Research, London, UK (norman.davey@icr.ac.uk) Co-Chairs (1 or 2) (with affiliation and current email address):Silvio C. E.
- [Proteomics Informatics Standards Working Group Charter](https://www.psidev.info/proteomics-informatics-standards-working-group-charter) - Submitted: 2018-11-21 1.Administrative Section Status (New/Update): Update Group Name: A group name should be reasonably descriptive or identifiable. Additionally, the group must define an acronym (maximum of 8 printable ASCII characters) to reference the group in the PSI directories, mailing lists, and general documents. The name and acronym must not conflict with any other PSI
- [Privacy Policy](https://www.psidev.info/privacy-policy) - Who we areSuggested text: Our website address is: https://pgb.liv.ac.uk/~kawinnat.CommentsSuggested text: When visitors leave comments on the site we collect the data shown in the comments form, and also the visitor’s IP address and browser user agent string to help spam detection.An anonymised string created from your email address (also called a hash) may be provided
- [Sample Processing](https://www.psidev.info/sample-processing) - View documents for this group Group currently inactive – historical documents shown here The Sample Processing Working Group has been merged withthe gel group into a Protein Separation working group | Statement of purpose | MIAPE modules | Exchange format development || Controlled vocabulary development | Meeting reports | Email discussion list | Contact details | Statement of purpose The remit of the Sample Processing Working Group is to produce reporting guidelines,
- [HUPO-PSI meeting 2021](https://www.psidev.info/hupo-psi-meeting-2021) - Sun, 01/03/2021 - 12:00 Due to the COVID-19 pandemic the PSI meeting 2021 will also be fully virtual (like it was the case of the 2020 meeting) and it will still take place from Mon 22nd to Friday 26th March 2021. Agenda The agenda is available at: https://docs.google.com/spreadsheets/d/13vBlgsI00AL5Py66uNStY6BACqhiLVgUriZjvjguTco/preview Registration Registration is now closed. Location We will be fully virtual. Our slack workspace "HUPO-PSI" will
- [HUPO-PSI meeting 2020](https://www.psidev.info/hupo-psi-meeting-2020) - Mon, 03/23/2020 - 12:00 Due to the COVID-19 outbreak the PSI meeting 2020 will be fully virtual for the first time and it will still take place from Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the Universal Spectrum Identifier, ProXI (the protein eXpression
- [HUPO-PSI meeting 2019](https://www.psidev.info/hupo-psi-meeting-2019) - Mon, 03/18/2019 - 12:00 Agenda Agenda is available HERE. Registration Registration for the HUPO-PSI meeting 2019 is now CLOSED. Accommodation The meeting will take place at the Breakwater Lodge at the V&A Waterfront. Participants may book rooms at the associated Protea Hotel by Marriott. The Commodore Hotel and Portswood Hotel are just a block away. Budget-conscious participants may want to consider the Atlantic Point Backpackers. HUPO-PSI does
- [HUPO-PSI meeting 2018](https://www.psidev.info/hupo-psi-meeting-2018) - Tue, 07/04/2017 - 12:00
- [HUPO-PSI meeting 2017](https://www.psidev.info/hupo-psi-meeting-2017) - Fri, 04/28/2017 - 12:00 Agenda Please see the preliminary agenda, all suggestions welcome! Topics include New: For the first time, we'll have a poster session. Please see "Practical Information". Quality control: qcML Proteogenomics formats proXI: proteomics eXpression Interface Privacy and Proteomics Data Completing the human interactome Evaluation of network analysis tools IMEx - how can you contribute?
- [HUPO-PSI meeting 2016](https://www.psidev.info/hupo-psi-meeting-2016) - Mon, 04/18/2016 - 12:00 The meeting took place in Het Pand, Ghent, Belgium. This meeting was sponsored by the BBSRC BBR grant 'PROCESS' [BB/K01997X/1] and by FWO Scientific Research Network ‘Novel Knowledge from Public Life Sciences Data’. Many of the presentations of the meeting are available here. PSIWorkshopGent_Agenda_draft_04022016.xls

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