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Protein Separation

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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


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 (

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 

  • MIAPE CC (Column Chromatography)

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.


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 ARProteomics 10, 3073-3081 (2010).

GelMLVersion 1.1 releaseSee: 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.

spMLLiquid and gas chromatography, centrifugation, rotofors, capillary electrophoresis, general sample handling and chemical modificationsMilestone 1 release
Specification documentUML model (best viewed with the MagicDraw)Demonstration XML Schema (proof of concept only)Example XML instance fileDirectory of sample files
spMLLiquid and gas chromatography, capillary electrophoresis, general sample handling and chemical modificationsMilestone 2 release
Specification documentUML model(best viewed with the MagicDrawSave as spML_milestone2.mdzip, also requires AndroMDA Profiles (Unzip archive and provide location of file when requested by MagicDraw)spML milestone 2 instances and XML Schema (zip archive)

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

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 ( 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

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

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