Molecular Biology Protein Structure

Proteome Standards Initiative-Molecular Interactions

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The Proteomics Standards Initiative (PSI) is a working group of Human Proteome Organization. It helps in defining data standards for proteomics in order to facilitate data comparison, exchange 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. 

The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, co-chairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion or in early stages of design. 

A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors’ websites or sometimes only in print publications. 

The amount of data currently being generated by proteomics laboratories around the world is increasing exponentially, making it ever more critical that scientists are able to exchange, compare and retrieve datasets when re-evaluation of their original conclusions becomes important. Only a fraction of this data is published in the literature and important information is being lost every day as data formats become obsolete. The Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) was tasked with the creation of data standards and interchange formats to allow both the exchange and storage of such data irrespective of the hardware and software from which it was generated. 

The standard deliverables of each work group are

  • Minimum Information Specification: For the given domain, this specifies the minimum information need for the useful reporting of experimental results in this domain.
  • Formal exchange format for experimental results in the domain. This will usually be an XML format, capable of representing at least the Minimum Information, and normally significant additional detail.
  • Controlled vocabularies.
  • Support for the usage of the standard in publicly available tools.

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