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Jan 1, 2009 (Vol. 29, No. 1)

Exploring the Human Proteome in Depth

Need for Extensive and Reliable Identification of Proteins Is Now Widely Recognized

  • Collaborations: Better Research

    Using well-established techniques in novel ways is PPD’s forte, notes Becker. “Part of the paradigm of the industry involves profiling for the discovery phase and then developing those results,” he says. “You can have any number of samples, from 20 to 500. How do you choose which markers you are going to pursue for validation by a method such as multiple reaction monitoring? And there is much discussion about different methods of quantification. What’s the best way?”

    Regarding quantification, PPD participated, along with other laboratories, in a study done by The Association of Biomolecular Resource Facilities (ABRF), which does yearly blind studies on methods, materials, and standards in its ongoing Quantitative Proteomics Study.

    “They did a blind test in 2007—a study of a matrix of E. coli lysate with spiked unknowns at varying concentrations and 36 labs responded,” says Becker. “When comparing methods, label-free did very well, followed by iTRAQ. But even with these proven methods, many responders failed. That means that a lot of people out there are still in the learning phase.”

    Becker says that the ABRF study fueled several email exchanges; one participant observed that no one has ever done a label-free whole proteome study. “But we have. We were very careful, and did a replicate study before publishing. Not everyone in the proteomics field realizes this has been done. We published this study in the Journal of Clinical Oncology. Sometimes, it’s thought that if a study is not published in a proteomics journal, it doesn’t exist.”

    Proteomics is gaining ground in clinical applications, a little at a time, Becker explains. “The field is making progress after a rough start where some researchers wanted to use signatures of signals without understanding the identification of the underlying proteins. But the field has been maturing, and there is now widespread recognition that results with extensive and reliable protein identifications are essential.”


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