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Researchers Now Testing PSI s GE MIAPE Module; Other Modules In Varying Stages of Development


SAN FRANCISCO — Proteomics researchers are currently testing preliminary guidelines released by the gel electrophoresis module of the Proteomics Standards Initiative's Minimum Information About a Proteomics Experiment standard, according to PSI officials.

Frank Gibson, the leader of MIAPE's gel electrophoresis module, reported during the PSI's spring workshop here last week that the MIAPE-GE committee had finished gathering a requirements list, and had obtained comments about the list from a panel of experts on gel electrophoresis. Proteomics researchers are now testing the guidelines.

"The external reviewers said in general that the coverage [of the guidelines] is comprehensive and the clarity is excellent," said Gibson. "Overall, they said, 'Keep it at a minimum. Don't add more.'"

Some of the MIAPE-GE reporting requirements include disclosing the date the experiment was performed; the person who performed the experiment; the name of the electrophoresis process used; the sample name; a description of the loading buffer; the number of dimensions of the electrophoresis process; the separation method employed for each dimension; a description of the gel matrix; the physical dimensions of the gel; a description of the protocol used to run the gel; a description of what was done between gel dimensions; a description of the protein/peptide detection process; the name of the image acquisition process; and a description of the gel image, including image name, dimensions, and resolution.

"MIAPE should, in principle, allow recreation of work, and provide an unambiguous description of a proteomics experiment, and the information [sought] should not be too burdensome."

The MIAPE-GE reporting requirements do not cover sample preparation, spot detection, or proteins or peptide analysis, Gibson noted.

Gabriella Armin, a member of the laboratory separations division at Bio-Rad said that she did not know about the MIAPE-GE reporting standards before last week's PSI workshop.

"We had no idea that this was going on," she said. "This is something that we can participate in."

Armin said that Bio-Rad could possibly develop tools to make it easier for researchers to get together all the information listed in MIAPE-GE.

In the first stage of the MIAPE-GE testing, the requirements were simply listed in a Microsoft Word document, Gibson said. However, it would be a goal in later stages to have software programs that can automate the information-gathering process, he said.

The gel electrophoresis module is one of nine MIAPE modules that have been formed so far. The PSI created the MIAPE guidelines in order to enable researchers to reproduce proteomics experiments originally performed by their peers, and to be able to reanalyze data from those experiments to answer different questions.

Other MIAPE modules have been created for study design and sample generation, separations and sample handling, column chromatography, mass spectrometry, proteoinformatics for mass spectrometry, capillary electrophoresis, gel electrophoresis, proteoinformatics for gel electrophoresis, and molecular interactions.

"MIAPE should, in principle, allow recreation of work, and provide an unambiguous description of a proteomics experiment," said Chris Taylor, a leader of the Human Proteome Organization's PSI, who heads the main committee on minimum reporting requirements. "And the information [sought] should not be too burdensome." Taylor said.

In general the MIAPE development process requires that researchers gather a list of "reporting requirements" that comprise essential information that must be included when reporting a proteomics experiment. It also requires that researchers submit the list for committee review; release the reviewed and revised requirements list to proteomics researchers for testing; and distribute the list to journals for enforcement.

In terms of the other MIAPE modules, the mass spec module, or MIAPE-MS, is one of the most mature. Members of the MIAPE-MS committee have mapped publication guidelines put forth by the journal Molecular & Cellular Proteomics (see ProteoMonitor 8/5/2005) to the MIAPE-MS guidelines to see where there is overlap. A select group of mass spec experts reviewed the MIAPE-MS guidelines in October 2005, and the guidelines are now undergoing public review.

"The external reviewers said in general that the coverage [of the guidelines] is comprehensive and the clarity is excellent. Overall, they said, 'Keep it at a minimum. Don't add more.'"

The PSI's mass spec proteoinformatics group is in the process of identifying a set of semantically equivalent parameters across search engines, while the proteoinformatics group for gel electrophoresis is just getting underway. The remainder of the MIAPE modules are mostly in the beginning stages of development.

Since the MIAPE modules are not completed yet, no one has tested out the MIAPE requirements on a complete proteomics experiment, said Gibson.

To encourage adoption of MIAPE standards by the scientific community, PSI plans to rely on journals and funding bodies to "enforce" the requirements.

Veronique Kiermer, the editor of Nature Methods, and Hans-Joachim Kraus, senior publishing editor of life and medical sciences at Wiley-VCH Verlag, which publishes Proteomics, both said that MIAPE guidelines would at first be presented to scientists as "recommended practice." After the guidelines have been in practice for a while, and tools are available to make the requirements easier to follow, then the journals would consider making the reporting requirements mandatory, the editors said. (See accompanying story for further details on the journals' current stance on PSI standards.)

— Tien-Shun Lee ([email protected])