Group Descriptions

Quality Control Workgroup

HUPO Proteomics Standards Initiative
Quality Control Working Group (PSI-QC)

Contents

  1. Quality Control Group Charter
  2. Group Structure (2017)
  3. Formats, Definitions, and Metrics
  4. Getting Involved

 

The PSI Quality Control workgroup is one of the working groups of the Proteomics Standards Initiative.

 

Quality Control Group Charter

Focus and Purpose

The PSI-QC working group is composed of academic, government, and industry researchers, software developers, journal representatives, and instrument manufacturers. The main goal of the PSI-QC working group is to define a community data format and associated controlled vocabulary terms, facilitating data exchange and archiving of mass spectrometry derived quality control metrics.

Current projects of the PSI-QC working group are:

  • The qcML format, which has been developed as a standardized format for the exchange, transmission, and archiving of quality control metrics derived from mass spectrometry.
  • Controlled Vocabulary development: controlled vocabulary terms are developed in common with the PSI-MS and PSI-PI groups.

Goals/Milestones 

  1. submit a perspective manuscript to a journal in the field to announce the PSI-QC WG  (PubMed link)

  2. analyze and revise the already published qcML format for submission to the PSI document process √ 

  3. re-evaluate the CV terms used for qcML, and consolidate the location for these terms in light of the existing PSI-MS CV

  4. adapt the already published jqcML library to handle the updates to qcML and the CV terms; implement validation

  5. implement qcML output from several freely available quality metric tools (e.g., QuaMeter, OpenMS)

  6. establish the revised qcML format and associated CV terms as a HUPO-PSI standard, by submitting the standard to the PSI Document Process

 


 

Group Structure (2017)

Role
Current Encumbent
ChairDavid L. Tabb
Co-chairMathias Walzer, Stefan Tenzer
MIAPE Co-ordinatorWeimin Zhu, Reza Salek
Ontology Co-ordinatorMartin Eisenacher
EditorStefan Tenzer
SecretaryWout Bittremieux
Website MaintainerMathias Walzer

 


Formats, Definitions, and Metrics

You can find the ongoing work and older versions of the qcML format, term definitions, and metric designs on our HUPO-PSI GitHub page.


Getting Involved

If you would like to contribute to the work of the Quality Control workgroup, or just to receive the occasional email when a new version of a format becomes available, please contact us on psidev-qc-dev [at] lists.sourceforge.net or our GitHub page.


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The Minimum Information About a Proteomics Experiment (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 of data sets, and obstructs non-standard searching (e.g. by the order that different liquid chromatography columns were coupled). The requirements of the various journals also differ, so important detail may be lacking in some cases, or presented in an esoteric fashion.

There is then a need for public repositories that contain information from whole proteomics experiments; making explicit both where samples came from, and how analyses of them were performed. It is therefore appropriate to attempt to define the minimum set of information about a proteomics experiment that would be required by such a repository.

Up-to-date released documents and working drafts

Acronym        TopicVersion  StatusComment
MIAPE MIAPE Principles document1.0release 
MIAPE-MSMass Spectrometry2.98releasereplaces v2.24
MIAPE-MSIMass Spectrometry Informatics1.1release 
MIAPE-QuantMass Spectrometry Quantification  1.0release 
MIAPE-GEGel Electrophoresis1.4release 
MIAPE-GIGel Informatics1release 
MIAPE-CCColumn Chromatography1.1release 
MIAPE-CECapillary Electrophoresis0.9.3release 
MIMIxMolecular Interactions1-1-2release 
     
More details and history of the documents are available from the MIAPE-docs page. 
 

Published components of MIAPE:

The 'MIAPE Principles' document:
The minimum information about a proteomics experiment (MIAPE), Nature Biotechnology 25, 887-893 (2007)
-- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Reporting guidelines for Molecular Interactions experiments:
The minimum information required for reporting a molecular interaction experiment (MIMIx)
, Nature Biotechnology 25, 894-898 (2007) -- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Reporting guidelines for Mass Spectrometry experiments:
Guidelines for reporting the use of mass spectrometry in proteomics, Nature Biotechnology 26, 860-861 (2008) -- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Reporting guidelines for Mass Spectrometry Informatics experiments:
Guidelines for reporting the use of mass spectrometry informatics in proteomics, Nature Biotechnology 26, 862 (2008) -- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Reporting guidelines for Gel Electrophoresis experiments:
Guidelines for reporting the use of gel electrophoresis in proteomics, Nature Biotechnology 26, 863 (2008) -- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Reporting guidelines for Gel Informatics experiments:
Guidelines for reporting the use of gel image informatics in proteomics, Nature Biotechnology 28, 655-656 (2010) -- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Reporting guidelines for Column Chromatography experiments:
Guidelines for reporting the use of column chromatography in proteomics, Nature Biotechnology 28, 654 (2010) -- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Reporting guidelines for Capillary Electrophoresis experiments:
Guidelines for reporting the use of capillary electrophoresis in proteomics, Nature Biotechnology 28, 654-655 (2010) -- DOI -- PubMed.
(Free PDF/HTML download direct from Nature Biotechnology.)

Guidelines for reporting quantitative mass spectrometry based experiments in proteomics. Journal of Proteomics 2013 Mar 14-- DOI -- PubMed.

Up-to-date released documents and working drafts available from this site here

MIAPE is now registered with the MIBBI Project (Minimum Information for Biological and Biomedical Investigations), which promotes and coordinates the development and management of Minimum Information (MI) specifications from across the biological and biomedical sciences.

Implementers

ProteoRed: see bioinformatics team wiki page.

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Controlled Vocabularies


Proteomics Standards Initiative

Controlled Vocabularies

Released October, 2006

Last maintenance update, October 2015

Table of Contents

  1. Introduction
  2. OBO PSI CVs by working groups
  3. Recommendation for PSI CVs
  4. Common PSI CVs
  5. Mapping between exchange schema and CVs
  6. Maintenance procedure
  7. Further information and relevant links
  8. References

 

Introduction

The Controlled Vocabularies (CV's) of the Proteomic Standard Initiative (PSI) provide a consensus annotation system to standardize the meaning, syntax and formalism of terms used across proteomics, as required by the PSI Working Groups. Each PSI working group develops the CV's required by the technology or data type it aims to standardize, following common recommendations for devoplement and maintenance. At the PSI meeting in Washington (Science 296, 827), it was decided that all PSI working groups should adopt the same CV's standardizing some overlapping concepts (units and resources). Finally, we propose a common mapping schema to describe for each data file schema the associations between its specific elements and the PSI CV's or other external ontology resources. Such mappings support the validation of XML files.

 

OBO PSI CVs by working groups

 

Recommendation for PSI CV's

The recommendations for creation and maintenance of PSI CVs are defined in the Guidelines for the development of Controlled Vocabularies. Please send any comment to psidev-onto-dev@lists.sourceforge.net

 

Common PSI CV's

Developing CV's is a process of collecting, and if necessary defining terms. Every effort must be made to adopt and re-use existing ontologies or CV's where they exist, to avoid “re-inventing the wheel”. As stated by OBO Foundry “we would strive for community acceptance of a single ontology for one domain, rather than encouraging rivalry between ontologies”. Therefore it is recommended to represent the following concepts as described.

Units It is RECOMMENDED to use, and to contribute to the Unit ontology by requesting required terms via their mailing list .

Chemical Entities For the representation of Chemical entities it is RECOMMENDED to use terms from Chemical Entities of Biological Interest ChEBI. ChEBI is also available from the OBO Foundry website.

Phenotypic quality For the representation of Phenotypic quality (e.g. age, color, shape etc.) it is RECOMMENDED to use terms from the quality ontology and request any missing term via the dedicated mailing list.

As common reference system for databases, the MIRIAM Registry is recommended.

 

Mapping between exchange schema and CV's

The mapping of the exchange schema elements supported by CV's with a common mechanism would greatly increase the cross-compatibility of the PSI resources and facilitate joint development of data validation tools. Therefore we propose a simple XML schema , providing a pattern to write a mapping file (see also the documentation and an example file for MI WG). A validation tool based on this mapping documentation is being developed for both MI and MS WGs.

 

Maintenance procedure

The PSI-MS CV evolved over time by important contributions of a wide community, including hardware and software vendors, which contributed much to the high-quality definition for many terms. The further development of the PSI-MS CV is an ongoing process. For this the HUPO-PSI working groups defined some guidelines for the development of controlled vocabularies. In addition the detailed maintenance process advanced over the time and some informal best practices evolved for it. Previously, requests for new terms were done by filling in a form on the PSI-PI website and by discussing the new term proposals or terms in dispute via an issue tracker. Now everyone in the proteomics community is free to subscribe to the ‘psidev-ms-vocab’ mailing list and to make proposals for new terms or improvements of the already existing ‘psi-ms.obo’ terms. Also requests to restructure parts of the ontology are possible, for instance when it emerges that the current hierarchical structuring of terms is sub-optimal or needs a reorganization because of new technological developments, but in all these cases it is warranted that already existing terms are never deleted from the ontology because of the obsoletion mechnism. Often there are also proposals discussed in the telephone conferences of the various PSI subgroups, so that the update can be done within about 5 working days after such a request, provided that there are no objections and there is consensus about the requested terms. The current maintenance procedure is now described as it has been applied to the ‘psi-ms.obo’ ontology file since January 2012 (see Figure).


This maintenance work is coordinated by the PSI ontology coordinator. He is a member of the proteomics scientific community and is normally elected at the annual HUPO-PSI spring meeting or appointed by the steering committee in the case that an emerged vacancy for this position must be assigned between these meetings. After receiving a request for a new CV term the PSI ontology coordinator checks if the term and its description, data type, parent terms and relations are sensible. If necessary any inconsistencies are clarified by consulting the proposer of the term. The ontology coordinator then checks, whether a term with the same meaning is already present in the ontology or if the term is necessary at all. The coordinator also checks, if the naming of the terms and synonyms are in accordance with the IUPAC (International Union of Pure and Applied Chemistry) nomenclature for mass spectrometry terms. If an attribute with the same meaning is already present in the schema of the corresponding data format, then typically the CV term will not be added to avoid duplication of information.


An additional rule is used if a term is related to MALDI (Matrix Assisted Laser Desorption Ionization)-checking: if the term is already present in the MALDI imaging obo and whether the term would be more suitable in that ontology. If there are proposals about chemical substances, used e.g. for matrix solutions, then it is checked if the substance is already defined in the ChEBI ontology. In that case the request is denied and the proposer is given notice that they should consider to use a CV term referencing the corresponding ChEBI entry instead. If not then the CV coordinator can request the ChEBI team to incorporate the substance into their ontology if it fulfills the criteria for inclusion into ChEBI. If not, it is checked if the substance is defined in the PubChem database, and a new term in the PSI-MS CV is created, which references this PubChem entry by specifying the corresponding ‘dbxref’ term at the end of the def: tag line.


A term which passes all these checks then is included in the next release candidate of the obo file. This release candidate is then sent to the three mailing lists psidev-ms-vocab, psidev-pi-dev,  and psidev-ms-dev for public discussion. In order to allow a prompt update of the CV after requests for new or changed terms, there is no regular schedule for the update process, so that if there is no objection, the new terms of the release candidate become part of the next official release of the obo file, which is made public about 5 working days after the release candidate. Otherwise the term under question is further discussed by the subscribers of the mailing lists, either by email correspondence or, if necessary, in a telephone conference call, until everything gets clarified and the community comes to a consensus about the exact definition of the discussed term, whereat the consensus should be reached by the strength of the arguments. As far as possible the term names should be general and non-proprietary. In case that vendor-specific terms are inevitable, for instance because they describe a proprietary software or product, the term name can be assembled by a leading identification for the proprietary product, followed by a colon and the actually CV term name. This naming mechanism can also help to prevent possible blockades resulting from conflicts of interest between rivaling companies. Then the date and version are updated and the new obo file is officially released by the ontology coordinator by first checking its syntactical correctness using the ‘Verification Manager’ of OBO-Edit and then transferring it to the GitHub website. The release of the new obo version is then announced to the three mailing lists stated above together with a small summary of the new and / or changed terms. The version number of the PSI-MS CV has the format ‘x.y.z’. An increase in x means the release of a major build, i.e. that a change in a root level term took place, whereas an increase of y indicates the addition of new terms or the obsoletion of terms and an increase of z means that only minor changes like the editing of names or definitions was done.


In cases where a merging, splitting, replacement or deprecation of an ontology term is necessary, e.g. due to upcoming new technologies or instruments or changes in standard formats, the old terms must be set obsolete by assigning the ‘is_obsolete’ relation to them, but they must stay inside the ontology to ensure backwards compatibility of instance data files already making use of these now obsoleted terms.

 

Further information and relevant links

 

References


Gerhard Mayer,  mayerg97 :at: rub.de, April 2016

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PSI Editors

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)
Martin Eisenacher, Ruhr-Univ. Bochum (martin.eisenacher :at: rub.de)

Former PSI editors:
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: manchester.ac.uk)

The definition of the PSI document process: here

The history of DocProc submissions: here


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Sample Processing Workgroup

The Sample Processing Working Group has been merged with
the gel group into a Protein Separation working group 

 


Statement of purpose

The remit of the Sample Processing Working Group is to produce reporting guidelines, data exchange formats and controlled vocabulary covering all separation techniques not considered to be 'classical' one- or two-dimensional gel electrophoresis (cf. the Gel WG home page), along with other kinds of sample handling and processing (for example, 'tagging' proteins or peptides, splitting, combining and storing samples). Where possible we seek to develop our products in collaboration with all proteomics stakeholders and, where relevant, developers from other standards communities, most notably metabolomics.
  • Minimum reporting requirements
    The evolving Minimum Information About a Proteomics Experiment (MIAPE) documents offer guidelines on how to adequately report a proteomics experiment. It is expected that these documents will be published, and that the requirements within will be enforced by journals, compliant repositories and funders (cf. MIAME).
  • XML formats for data exchange
    Derived from the FuGE general object model, the formats developed by this workgroup are designed to function both as standalone files and as part of a 'parent' FuGE-ML document. These formats will facilitate data exchange between researchers, and submission to repositories or journals.
  • Controlled vocabularies (CVs) and ontology
    Lists of clearly defined terms are crucial for the construction of unambiguously worded data files. In addition to providing supporting CVs for the individual data capture formats as part of the integrated PSI CV, the Sample Processing WG will contribute terms to the Functional Genomics Ontology (FuGO).



The MIAPE minimum reporting requirements

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 of data sets, and obstructs non-standard searching (e.g. by the order that different liquid chromatography columns were coupled). The requirements of the various journals also differ, so important detail may be lacking in some cases, or presented in an esoteric fashion.

There is then a need for public repositories that contain information from whole proteomics experiments; making explicit both where samples came from, and how analyses of them were performed. It is therefore appropriate to attempt to define the minimum set of information about a proteomics experiment that would be required by such a repository.

Working drafts (see also the MIAPE home page):

The MIAPE 'Parent Document' (gives basic principles and context)
MIAPE: CC v1.1.0 (Column Chromatography)
MIAPE: CE v0.7.0 (Capillary Electrophoresis)
MIAPE: SP v0.1 (Sample preparation and handling)




Exchange format development

Data and metadata produced in different places may be in different formats, making comparison and exchange difficult. We therefore seek to develop consensus interchange formats (XML Schema based) to facilitate the development of effective search and analysis tools, simplifying both the dissemination and exchange of data. These XML Schemata are derived from application-specific object models (themselves subclassed from the generic FuGE object model). The development process will draw on the wisdom and experience of a wide range of concerned people, both in academia and industry.

FormatScopeStatus
spMLLiquid and gas chromatography, centrifugation, rotofors, capillary electrophoresis, general sample handling and chemical modificationsMilestone 1 release
spMLLiquid and gas chromatography, capillary electrophoresis, general sample handling and chemical modificationsMilestone 2 release
The FuGE object model provides the set of 'superclasses' from which all objects in spML will be subclassed.

spML will also have a dedicated controlled vocabulary file to accompany it, the terms from which will be integrated into the overall PSI CV and contributed to the FuGO project.




Controlled vocabulary development

Update to follow soon.




Meeting reports

Update to follow soon.




Moderated email discussion list

This list caters to the activities of the Gel and Sample Processing WGs, providing a central organising point for announcements and discussion.




Contact details (organisers)

Any queries or grumbles should be emailed to Chris Taylor, chris.taylor[@]ebi.ac.uk.

 


Chris Taylor, chris.taylor[@]ebi.ac.uk, August 8th, 2006. - Salvador Martínez de Bartolomé, smartinez@proteored.org, June 16th, 2009



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Protein Separation Workgroup

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 academia, industrial partners and software vendors. The group aims to develop reporting requirements that supplement the MIAPE parent document, describing the minimum information that should be reported about gel-based, and non-gel based separation technologies employed for proteins and peptides in proteomics. The group will also develop data formats for capturing MIAPE-compliant data about these technologies and supporting controlled vocabularies.

  1. MIAPE documents
  2. Data formats
  3. Ontology: sepCV
  4. Meetings and Logistics
  5. Mailing Lists
  6. Group Structure

1. MIAPE documents

  • MIAPE GE
The MIAPE module for Gel Electrophoresis (GE) has been published in Nature biotechology entitled Guidelines for reporting the use of gel electrophoresis in proteomics (Nature Biotechnology 26, 863 - 864 (2008), doi:10.1038/nbt0808-863).
The MIAPE GE module identifies the guidelines for the minimum information to report about the use of n-dimensional gel electrophoresis in a proteomics experiment, in a manner compliant with the aims as laid out in the MIAPE principles document.
The most recent version of the MIAPE GE specification can be found here.
MIAPEGelDB, a web-based tool to edit and store MIAPE Gel electrophoresis document (http://miapegeldb.expasy.org/)
ProteoRed has developed a MIAPE Generator tool accessible by via the ProteoRed portal:
  • MIAPE GI (Gel Informatics)
The MIAPE module for Gel Informatics (GI) has been published in Nature biotechology entitled Guidelines for reporting the use of gel image informatics in proteomics (Nature Biotechnology 28, 655-656 (2010), doi:10.1038/nbt0710-655).
MIAPE: Gel Informatics v1.0 

The MIAPE module for Column Chromatography (CC) has been published in Nature biotechology entitled Guidelines for reporting the use of column chromatography in proteomics (Nature Biotechnology 28, 654 (2010), doi:10.1038/nbt0710-654a). 

MIAPE: CC v1.1

  • MIAPE CE (Capillary Electrophoresis)

The MIAPE module for Capillary Electrophoresis (CE) has been published in Nature biotechology entitled Guidelines for reporting the use of capillary electrophoresis in proteomics (Nature Biotechnology 28, 654-655 (2010), doi:10.1038/nbt0710-654b).  

MIAPE: CE v0.7

  • MIAPE SPPE (Sample Preparation for a Phosphoproteomics Experiment)

This document will be presented as a Recommendation document. It is under preparation before to start the PSI document review process.

MIASPPE v0.91

2. Data formats

  • GelML

GelML is a data exchange format for describing the results of gel electrophoresis experiments.

In September 2010, GelML was published in Proteomics journal:
The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.
Gibson F, Hoogland C, Martinez-Bartolomé S, Medina-Aunon JA, Albar JP, Babnigg G, Wipat A, Hermjakob H, Almeida JS, Stanislaus R, Paton NW, Jones AR
Proteomics 10, 3073-3081 (2010).

 

FormatStatusDownload
GelML

Version 1.1 release

See: http://code.google.com/p/gelml/

Direct link to the XSD schema

 

  • spML

Data and metadata produced in different places may be in different formats, making comparison and exchange difficult. We therefore seek to develop consensus interchange formats (XML Schema based) to facilitate the development of effective search and analysis tools, simplifying both the dissemination and exchange of data. These XML Schemata are derived from application-specific object models (themselves subclassed from the generic FuGE object model). The development process will draw on the wisdom and experience of a wide range of concerned people, both in academia and industry.

 
FormatScopeStatus
spMLLiquid and gas chromatography, centrifugation, rotofors, capillary electrophoresis, general sample handling and chemical modificationsMilestone 1 release
spMLLiquid and gas chromatography, capillary electrophoresis, general sample handling and chemical modificationsMilestone 2 release

3. Ontology

  • sepCV

The sepCV is an ontlogy for sample preparation and processing and covers terminology required for gel electrophoresis and gel informatic investigations. More details on sepCV can be found on the sepCV page

4. Meetings and Logistics

On-going communication between all participants will be achieved via the mailing list (currently mailto:psidev-gps-dev@lists.sourceforge.net).

Every few weeks a telephone conference will be organised to allow discussion of the progress and direction of the working group. Details of the next meeting will be posted here as soon as they are available.

The group will meet face to face each year at the Spring PSI conference and other meetings will be arranged as necessary.

Next Meeting / Teleconference

  • To be arranged

Meeting Minutes

  

5. Mailing lists

In the spirit of the HUPO Proteomics Standards Initiative, this working group is not exclusive and all interested parties are encouraged to join. For further details, please email the current mailing list (mailto:psidev-gps-dev@lists.sourceforge.net) to which you can subscribe.

Details of the teleconferences will be posted to the mailing list. You are encouraged to join these discussions should you wish to contribute.

  

6. Group Structure

Role
 
ChairJuan-Pablo Albar
Co-chairAndy Jones
MIAPE Co-ordinatorMontserrat Carrascal
Ontology Co-ordinatorAlberto Medina
EditorSalvador Martínez de Bartolomé
Secretary 

Last update by: Salvador Martínez de Bartolomé, 22-Apr-2013

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Proteomics Informatics Workgroup

 



HUPO Proteomics Standards Initiative
Proteomics Informatics Working Group (PSI-PI)

Contents

  1. Group Charter
  2. Group Structure
  3. Obtaining the current Documents and Getting Involved
  4. mzIdentML
  5. mzQuantML
  6. Request new CV terms to the PSI-MS Controlled Vocabulary
  7. Meetings and Logistics
  8. Mailing List and Issue Discussion

 

 

The PSI Proteomics Informatics standards group is one of the working groups of the Proteomics Standards Initiative.

 

Proteomics Informatics Group Charter

Please see here.


 

Group Structure (2013)

Role
Current Encumbent
ChairAndy Jones
Co-chairMartin Eisenacher/Juan Antonio Vizcaino
MIAPE Co-ordinatorPierre-Alain Binz
Ontology Co-ordinatorGerhard Mayer
EditorGerhard Mayer
SecretaryJuan Antonio Vizcaino

 

 


 

Obtaining the Current Documents and Getting Involved

The deliverables (XML schema, example documents, specification document etc.) of the standards released by the PSI-PI working group can be found on different pages linked below.

All of the ongoing work, e.g. deliverables and issue list of the versions being under development are managed in GitHub (see URLs on pages linked above!).

GitHub makes use of Git to allow versions of documents to be managed. You can get read-only access all of the files in subversion anonymously, or if you are a member of the group you can check out the contents of the repository, commit changes to the files and add new ones. There are many different clients that you can use to access and write to the Git repository. If you are using Windows, the SourceTree client comes highly recommended.

 


mzIdentML

The main current deliverable of the Proteomics Informatics working group is the mzIdentML data exchange standard (previously known as analysisXML). Please see use cases for mzIdentML to get a flavour of its scope and purpose (mainly storing parameters and results of a spectrum identification search).

Version 1.0.0 of mzIdentML was formally released on 20th August 2009.
Work on an update to version 1.1.0 of mzIdentML was finished in August 2011.
A very minor update to version 1.1.1 was done in July 2015.

More information about mzIdentML is available HERE.

Current status of tools that write and import mzIdentML are on this page.

 


 

mzQuantML

The other current deliverable of the Proteomics Informatics working group is the mzQuantML data exchange standard. It is intended to store parameters and results of quantification workflows.

Version 1.0.0 of mzQuantML was released in Feb 2013. More information about mzQuantML is available HERE.

 


 

Request new CV terms to the PSI-MS Controlled Vocabulary

To request new CV terms to be added to the PSI-MS Controlled Vocabulary, please use the psidev-vocab mailing list.

 


 

Meetings and Logistics

On-going communication between all participants will be achieved via the mailing list psidev-pi-dev@lists.sourceforge.net.

Regularly weekly telephone conferences are organised to allow discussion of the progress and direction of the working group when appropriate. Details of the next meeting will be posted here as soon as they are available.

The group meets face to face at least once a year at the Spring PSI conference.

 


 


Mailing list and Issue Discussion

This is the discussion list for proteomics informatics (mzIdentML and mzQuantML) development.

You can subscribe to the psidev-pi-dev list.

You can view the existing posts to the psidev-pi-dev list.

To post a message to the list, send an email to psidev-pi-dev@lists.sourceforge.net

 


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Protein Modifications Workgroup

 

 

Proteomics Standards Initiative

 

Protein Modifications

 
 
 
 

 

Table of Contents

  1. Introduction
  2. How to comment
  3. Available data
  4. Tools
  5. 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 developing a concensus nomenclature and provide an ontology reconciling in a hierarchical representation the complementary descriptions of residue modifications.

How to comment

If you would like to comment on the PSI-MOD document or , please send a mail to:
psidev-mod-vocab@lists.sourceforge.net


The latest list of features to discuss/include in the future can be found here:
https://sourceforge.net/tracker/?group_id=65472&atid=776607


Available data

The protein modification ontology (PSI-MOD) is available in OBO format or in OBO.xml.
A spreadsheet containing the mapping of the descriptive labels used in various databases and search engines, the concensus list of proposed short name for protein modifications established by collaborative effort of mass spectrometry community, and the proposed rules and recommendations for this nomenclature are available here. These short names are included in the ontology as synonyms of the corresponding terms.
 

Tools

  • PSI-MOD ontology can be searched by mass range: here
  • PSI-MOD ontology can be searched by tree browser: here
  • PSI-MOD ontology can be searched by term search: here

Publications

Further information and relevant links

 

Databases involved:

Companies involved:

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Pages

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