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HUPO's MIAPE Reports Proteomics Standards


Like many aspects of systems biology, proteomic experiments not only generate a lot of data, but also a lot of metadata. The Human Proteome Organization's Proteomics Standards Initiative announced guidelines governing what information about proteomics experiments should be included in a discussion of the experiment. The guidelines, announced in the August issue of Nature Biotechnology, summarize the minimum information needed for four types of proteomics experiments. The resulting MIAPE, or minimum information about a proteomics experiment, has also teamed up with MIBBI, a program to foster collaborations among biological standards initiatives.

The MIAPE initiative began in 2004 when the combination of academic, pharma, and vendors first decided what to include under the umbrella of standards. "The format shouldn't be telling you what information you should be reporting. It should just be providing you with boxes," says Chris Taylor, a senior software engineer at the European Bioinformatics Institute who has worked on PSI and MIAPE.

Then the group chose which aspects of proteomics to target with standards, beginning with the most popular tools. This first set includes modules on gel electrophoresis, mass spectrometry, mass spec informatics, and molecular interaction experiments. More modules, including capillary electrophoresis and column chromatography, are under way.

To come up with the standards, the MIAPE group drew up a draft list that it then ran by others in the field. "The proper experts then review it and add to it and delete from it," says Taylor. After that first draft was revised, the guidelines were also reviewed by the community prior to being published.

Broadly, the standards ask researchers to provide enough information about an experiment and its context so that others can understand and interpret their data. For example, the gel electrophoresis module asks for a description of the gel matrix and the electrophoresis protocol as well as about how images were acquired; the mass spectrometry informatics guidelines, meanwhile, ask researchers to include input data and parameters as well as the output. "What you are looking for with a lot of these guidelines is not to be too specific," says Taylor, adding that when standards are too specific, they are not as useful to researchers.

Because many tools used in one part of systems biology are used for others, many standards groups, including MIAPE, formed MIBBI in 2006, to support reporting standards in biological research.

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