The Proteomics Standards Initiative (PSI) is a working group of the

Human Proteome Organization The Human Proteome Organization (HUPO) is an international consortium of national proteomics research associations, government researchers, academic institutions, and industry partners. The organization was launched in February 2001, and it promotes ...

. It aims to define data standards for

proteomics Proteomics is the large-scale study of proteins. Proteins are vital macromolecules of all living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replicatio ...

to facilitate data comparison,

exchange Exchange or exchanged may refer to: Arts, entertainment and media Film and television * Exchange (film), or ''Deep Trap'', 2015 South Korean psychological thriller * Exchanged (film), 2019 Peruvian fantasy comedy * Exchange (TV program), 2021 Sou ...

and verification. The Proteomics Standards Initiative focuses on the following subjects: minimum information about a proteomics experiment defines the metadata that should be provided along with a proteomics experiment. a data

markup language A markup language is a Encoding, text-encoding system which specifies the structure and formatting of a document and potentially the relationships among its parts. Markup can control the display of a document or enrich its content to facilitate au ...

for encoding the data, and metadata

ontologies In information science, an ontology encompasses a representation, formal naming, and definitions of the categories, properties, and relations between the concepts, data, or entities that pertain to one, many, or all domains of discourse. More ...

for consistent annotation and representation.

Minimum information about a proteomics experiment

Minimum information about a proteomics experiment (MIAPE) is a minimum information standard, created by the Proteomics Standards Initiative of the

, for reporting proteomics experiments. You can't just introduce the results of an analysis, it is intended to specify all the information necessary to interpret the experiment results unambiguously and to potentially reproduce the experiment. While the MIAPE guidelines define the content required for compliant reports, it does not specify the format in which this data should be presented (which is left to the corresponding *ML format, also defined by PSI), nor does it define how to perform experiments.

Working groups

Several working groups work on several documents covering the different areas of

: The

gel electrophoresis Gel electrophoresis is an electrophoresis method for separation and analysis of biomacromolecules (DNA, RNA, proteins, etc.) and their fragments, based on their size and charge through a gel. It is used in clinical chemistry to separate ...

working group defined reporting requirements for gel electrophoresis experiments. The document is at the stage of a recommendation and has been published. The corresponding data exchange format is called ''GelML,'' and a stable version was released in late 2007. The gel electrophoresis working group also focuses on image analysis with the gel image informatics recommendation that is currently in the public review phase while the corresponding exchange format is only a draft (as of April 2009). The sample processing working group defines requirements concerning all the sample pre-processing steps that are carried out before gel electrophoresis or

mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used ...

is applied. Two documents concerning

column chromatography Column chromatography in chemistry is a chromatography method used to isolate a single chemical compounds, chemical compound from a mixture. Chromatography is able to separate substances based on differential absorption of compounds to the adsorbe ...

and

capillary electrophoresis Capillary electrophoresis (CE) is a family of electrokinetic separation methods performed in submillimeter diameter capillaries and in micro- and nanofluidic channels. Very often, CE refers to capillary zone electrophoresis (CZE), but other electr ...

are in the early draft stages and the ''Sample preparation and handling'' is still a project (as of April 2009). The data exchange format (spML) is also under development. Mass spectrometry and mass spectrometry informatics documents have been published as recommendations by the mass spectrometry working group. The working group has released several data exchange format: the mzML, for the capture of data generated by a mass spectrometer, which is a merge of the previous mzData (developed by PSI) and mzXML (developed at the Seattle Proteome Center at the Institute for Systems Biology); mzIdentML, for Mass spectra informatics analysis that capture the results of the identification of proteins and peptides from mass spectrometry data; and TraML, for selected reaction monitoring input file. Finally, they develop ''MS CV'', a controlled vocabulary to use with the previous file formats. The molecular interactions working group of PSI only works on ''PSI MI XML'', a data exchange format, and on its corresponding ontologies. They have published the MIMIx guidelines (minimum information about a molecular interaction experiment) Study design and sample generation and statistical analysis of data MIAPE recommendations are also being planned or drafted.

Standard-compliant proteomics repositories

Several standard-compliant proteomics repositories exist, allowing researchers to publish their data while enforcing MIAPE guidelines. For example: MIAPEGelDB (for gel electrophoresis data),

PRIDE Pride is a human Emotion, secondary emotion characterized by a sense of satisfaction with one's Identity (philosophy), identity, performance, or accomplishments. It is often considered the opposite of shame or of humility and, depending on conte ...

(for mass spectrometry data), an
ProteoRed
MIAPE Generator tool (for gel electrophoresis and mass spectrometry data) It is expected that journal editors will eventually request authors to publish all their data to such repositories before publication.

Similar initiatives

There are similar initiatives that try to define minimal requirements. For

microarrays A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of biological interactions. It is a two-dimensional array on a solid substrate—usually a glass slide or silicon thin-film cell� ...

the MGED Society defined the minimum information about a microarray experiment (MIAME). The standards for reporting of diagnostic accuracy (STARD) is available for studies reporting

medical diagnosis Medical diagnosis (abbreviated Dx, Dx, or Ds) is the process of determining which disease or condition explains a person's symptoms and signs. It is most often referred to as a diagnosis with the medical context being implicit. The information ...

accuracies.

References

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External links

PSI web site (psidev.info)
Bioinformatics software Minimum Information Standards Proteomics