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New MIAPE Modules Cover Four Proteomic Areas, Offer Guidelines for Commercial Reagents

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This story originally ran on July 15.

By Adam Bonislawski

The Proteomics Standards Initiative of the Human Proteome Organization last week released a series of new modules for the Minimum Information About a Proteomics Experiment guidelines, including standards for experiments involving protein affinity reagents, column chromatography, capillary electrophoresis, and gel image informatics.

Published in the current edition of Nature Biotechnology, the modules provide guidelines on what data proteomics researchers should report about their experiments, and, in the case of the protein affinity reagent, or MIAPAR, guidelines, what information affinity reagent manufacturers should provide about their products.

Poor information provided by affinity reagent manufacturers regarding their products has been a problem in proteomics research, Sandra Orchard, senior scientific database curator at the European Bioinformatics Institute and one of the authors of MIAPAR module, told ProteoMonitor.

"People have wasted an awful lot of money over the years buying poor quality [affinity] reagents and coming up with misleading data because of it," she said, citing work by Mathias Uhlen of Stockholm's Royal Institute of Technology that suggests that only a small percentage of antibodies being used by proteomics researchers have the specificity their users assume.

"Whether people are just not bothering to do the appropriate experiments to prove the specificity of their antibodies or whether they know perfectly well they're not as good as they're saying but are still selling them anyway, that's not for me to say," Orchard said. "All we can say is that in many, many cases there has not been enough data made available with the product – be it a commercial product or a donated product – for people to make a full assessment of how valuable a resource it is.

"Our hope is to be able to tackle that head-on and encourage manufacturers to make it clear both what the strengths of the reagents are but also what the limitations are," she said.

To that end, the MIAPAR guidelines stipulate that antibody producers should include details on the particular protein and epitope a reagent is being raised against; how it has been raised; and what its specificity is – how sensitive it is and what indications it should be used for.

The MIAPAR guidelines are somewhat different from the other MIAPE modules in that they are "dealing with a community where the products are largely commercial," Orchard said. The other three modules released are more typical, focusing primarily on what information scientists should include as part of their experimental data and how that data should be presented to make the research as accessible and reproducible as possible.

To what extent antibody manufacturers plan to comply with MIAPAR remains to be seen, Orchard said, noting that antibody vendors like Cambridge, UK-based AbCam – one of the authors on the Nature Biotechnology submission – were involved in the process.

"It's a huge field. There are a lot of people selling antibodies, and there's no way we could contact them all. What the other vendors' responses are will be interesting to see."

Calls to several vendors were not returned in time for publication.

Implementation Phase

The PSI released its first set of MIAPE modules in August 2008, some five years after the program was originally conceived (PM 08/14/2008). Presently there are published guidelines for mass spectrometry, mass spectrometry informatics, gel electrophoresis, gel image informatics, column chromatography, capillary electrophoresis, and sample preparation and handling.

"I would say we've got pretty good coverage of the whole [proteomics] domain. So now we're in the implementation phase, getting people to actually use [the standards] and provide the data in that format," Orchard said.

The exceptions to this are the areas of quantitative mass spectrometry and bioactive entities, where there are still gaps in the MIAPE family, Orchard noted.

With regard to bioactive entities, pharmaceutical companies' increasing willingness to share data on drug target interactions has created the need for standards on what that data should include, she said.

"There's a history of pharmaceutical companies not wanting to give data out, but I'd say that's changing. They're taking what they call pre-competitive information much more seriously and are actually volunteering data," she said. "They're realizing that if they're either paying for this data or acquiring it through the public domain, then they need a certain amount of information for it to be useful data. If that information is missing it’s a valuable resource that's not working to its full potential."

Presently the PSI and EBI are working on a module covering this area, called MIABE, or Minimum Information About a Bioactive Entity.

Work on MIAPE guidelines for quantitative mass spectrometry approaches is also underway, driven, Orchard said, by the growing use of these techniques in proteomics research. The variety of techniques involved and rapid evolution of the field has made devising standardized open source formats for quantitative MS data difficult.

"The quantification field is moving so quickly we need multiple specialists to help us develop these formats. It makes it rather more complex to address," she said, predicting that a format for quantitative MS data will be available around the time of the PSI's April 2011 meeting.

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Data format development is a separate, though complementary, process from establishing reporting guidelines, and one that sometimes proves to be the trickier half of the equation, Andy Jones, a researcher at the University of Liverpool's School of Veterinary Science and a collaborator on the recently released MIAPE modules, told ProteoMonitor.

"Data standard development is quite resource intensive. It's quite a difficult thing to do to get lots of groups to agree to an actual data format that gets sent around between all these different pieces of software," he said.

"In gel image informatics we're still working out what are the best ways to represent this kind of data. We have a data format for gel electrophoresis data, which is going to be published in the next few months, but that doesn't cover all the image informatics to the level of detail that we have in the reporting guidelines. We're working on that format and trying to decide how we get the vendors involved in developing a data standard."

With regard to the established MIAPE modules, the challenge now, Orchard said, is encouraging their adoption. Key to this is bringing the journals onboard.

"For mass spec there are only about half a dozen journals in that field. We're having active dialogue with all of them and most are at least recommending that deposition be made. In other fields it's much harder because the information is scattered over many, many biochemical journals," she said.

According to Jones, some sort of online interface to facilitate reporting of MIAPE information to journals is under consideration.

"We're in discussion with several of the top proteomics journals to have some kind of an online system where people can complete some check boxes saying, 'I've told you this, this, and this, and here is where you can find that information.' So it would formalize this process," he said.

"The large labs, the high-throughput labs are pretty good at submitting [the MIAPE data]," Orchard said. "It's persuading the bench biochemist who's doing one co-IP as part of a series of different experiments to get us the data that's the difficult part. Persuading scientists that it's in their interest to adopt [the MIAPE standards] isn't always trivial, but they always see the general good of it. Some of them object to doing the extra work for their particular dataset, but they're quite in agreement that everyone else should do it."

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