For those proteomics researchers who like to outsource their protein analysis dirty work to core service facilities, the Association of Biomolecular Resource Facilities’ 2004 quality control study, launched last week, could provide important insights. The third annual study, which is intended to evaluate facilities’ abilities to distinguish between the identities of closely related proteins, follows on the heels of a similar study last year that found most facilities lacking.
“For our study last year, we sent out a sample that was phosphorylated, and there were really very few people who got the correct results,” said Kaye Speicher, manager of the proteomics facility at the Philadelphia, Pa.-based Wistar Institute and current chair of ABRF’s proteomics research group. Speicher said that while many facilities were able to identify the protein that was phosphorylated, few could actually locate the exact site of the modification. “This was, to labs that thought, ‘hey, this is a piece of cake,’ a real wake-up call that this is more difficult than [they] thought, and [they] need to take a closer look,” Speicher said. She later added, to clarify, in an email, “The overall feeling was one of surprise that not more labs got the expected results and hence everyone should be taking a closer look at how to do phosphopeptide determinations.”
The samples for the new studies were sent out to about 110 participating labs around the world last week. Results are expected back on Nov. 14, and are slated to be presented at the 2004 ABRF meeting in February in Portland, Ore. Unlike the previous ABRF studies, the samples will consist of intact proteins rather than peptides, so that front-end methods, as well as analysis and back-end methods, can be analyzed. Participants will be expected to identify the proteins and find the differences between them. They must then complete a questionnaire providing descriptions of any methods they used for processes such as protein digestion and peptide analysis, in addition to submitting their results. These descriptions are expected to show a lot of variation because the study is intended, Speicher said, to accommodate many different kinds of labs with different capabilities and methods. “We try to make the samples in such a way that a lab of any capability will be able to get some information,” Speicher said. “Because you have labs that are just starting out and don’t have a whole lot of sophisticated equipment yet, so we want to see how much they can do and what sort of equipment they may decide they need to do the whole thing.”
Perhaps the greatest challenge will be in how ABRF is to make sense of the results. Speicher said she expects to get back “truly astronomical” amounts of data-and she has only a few committee members and a few months to organize and interpret it all.