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 promote ...

. It aims to define data standards for proteomics to facilitate

data comparison In computing, file comparison is the calculation and display of the differences and similarities between data objects, typically text files such as source code. The methods, implementations, and results are typically called a diff, after the Un ...

exchange Exchange may refer to: Physics *Gas exchange is the movement of oxygen and carbon dioxide molecules from a region of higher concentration to a region of lower concentration. Places United States * Exchange, Indiana, an unincorporated community * ...

and

verification Verify or verification may refer to: General * Verification and validation, in engineering or quality management systems, is the act of reviewing, inspecting or testing, in order to establish and document that a product, service or system meets ...

. 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 for encoding the data, and metadata

ontologies In computer science and information science, an ontology encompasses a representation, formal naming, and definition of the categories, properties, and relations between the concepts, data, and entities that substantiate one, many, or all domains ...

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 proteomics: The gel electrophoresis 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 Sample or samples may refer to: Base meaning * Sample (statistics), a subset of a population – complete data set * Sample (signal), a digital discrete sample of a continuous analog signal * Sample (material), a specimen or small quantity of s ...

pre-processing steps that are carried out before gel electrophoresis or mass spectrometry is applied. Two documents concerning

column chromatography Column chromatography in chemistry is a chromatography method used to isolate a single chemical compound from a mixture. Chromatography is able to separate substances based on differential adsorption of compounds to the adsorbent; compounds move th ...

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 elect ...

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 Selected reaction monitoring (SRM), also called Multiple reaction monitoring, (MRM), is a method used in tandem mass spectrometry in which an ion of a particular mass is selected in the first stage of a tandem mass spectrometer and an ion product ...

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 defined by Merriam-Webster as "reasonable self-esteem" or "confidence and satisfaction in oneself". A healthy amount of pride is good, however, pride sometimes is used interchangeably with "conceit" or "arrogance" (among other words) w ...

(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 genes from a sample (e.g. from a tissue). It is a two-dimensional array on a solid substrate—usually a glass slide or silicon ...

the

MGED Society The Functional GEnomics Data Society (FGED) (formerly known as the MGED Society) was a non-profit, volunteer-run international organization of biologists, computer scientists, and data analysts that aims to facilitate biological and biomedical di ...

defined the

minimum information about a microarray experiment Minimum information about a microarray experiment (MIAME) is a standard created by the FGED Society for reporting microarray experiments. MIAME is intended to specify all the information necessary to interpret the results of the experiment unam ...

(MIAME). The

standards for reporting of diagnostic accuracy Standard may refer to: Symbols * Colours, standards and guidons, kinds of military signs * Standard (emblem), a type of a large symbol or emblem used for identification Norms, conventions or requirements * Standard (metrology), an object th ...

(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 diagnosis with the medical context being implicit. The information r ...

accuracies.

References

{{reflist

External links

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