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May 15, 2013 (Vol. 33, No. 10)

Improving Proteomics Approaches

  • Proteomics has undergone the same existential choice, and self-examination, as other biological sciences with respect to automation. On the surface, automation helps laboratories cope with very high-throughput workflows.

    Return on investment can be swift and convincing in an era where large testing laboratories seek to do more with less. Even medium-throughput labs can be convinced that the assay accuracy, consistency, and reduced human error (and its consequence—rework) that robotics bring make an even more compelling case for automation.

    What about discovery-stage science labs operating at the lower echelons of throughput? Suparna Mundodi, Ph.D., global product manager at Rainin Instruments, offered a glimpse into what is in store for them at CHI’s “PepTalk” program on protein sciences. There, Dr. Mundodi presented the case for semi-automation, as exemplified by her company’s PureSpeed protein purification system.

    PureSpeed uses a semi-automated pipetting protocol resident on the company’s E4 XLS electronic pipette, which processes up to 12 samples in parallel. But she said the stars of the show are Rainin’s PureSpeed tips, which purify microscale volumes of target protein, at very high concentration, in as little as 15 minutes. The pipette-fitting PureSpeed tips contain small volumes of standard chromatography resins concentrated in the tip region. Protein A, protein G, IMAC, and other formats are possible.

    Rainin’s technologic competitors in ultra-small-scale protein purification are gravity chromatography and spin columns. Gravity entails very long sample prep times and is unsuitable for parallel processing. “You can’t do three or four samples simultaneously because you have to run between columns pouring buffer.”

    The E4 XLS pipette draws and discharges a protein solution through the resin bed, cycling as much as needed to ensure adequate binding of protein to resin. After washing away impurities, the purified protein is eluted into a tiny volume suitable for such concentration-dependent analyses as surface plasmon resonance, electrophoresis gels, and ELISAs.

    The official book on PureSpeed is it bridges the workflow gap between very low and medium-high throughput experiments. Actually, said Dr. Mundodi, the 12-channel system sits within the sweet spot for most early-stage research. “If you look at the protein purification market, 12 samples can be high throughput in many instances.” Her own market research, conducted before PureSpeed was developed, suggested that the average number of samples in PureSpeed’s target market was just under 10.

    That tells only part of the story. The many benefits of automated liquid handling notwithstanding, it is often simpler and less costly to forgo automation, particularly in labs whose workflows are constantly changing. “Many of our customers, who may be doing expression screening on 40 to 50 clones, find the semi-automated system more straightforward, even faster, than fully automated systems.”

    Since it is semi-automated (or semi-manual, depending on one’s perspective), PureSpeed requires no programming or extensive method development. With the inexorable drain of robotics and IT talent from many labs, semi-automation represents a welcome step forward.

    “The best part is it’s a pipette, which makes people comfortable with using it,” said Dr. Mundodi.

  • Full Automation

    Click Image To Enlarge +
    According to PerkinElmer, its Janus liquid-handling workstation facilitates proteomics analysis.

    The theme of accomplishing more with less recurs in most analytical work. One way to achieve this is through automation, but many managers cannot be convinced of the value proposition. From the laboratory’s perspective, ROI is directly related to freeing high-level scientific talent from repetitive tasks. This was the theme of a talk by PerkinElmer on the marriage of the Janus® BioTx Pro automated liquid-handling system with PerkinElmer’s LabChip® microfluidics-based analyzer. LabChip GxII takes classic SDS PAGE and automates it within a microfluidic platform.

    Together, the two instruments provide automated, small-scale protein purification and characterization. The Janus liquid handler prepares samples based on filter plates, tip-based chromatography, or mini-columns. Users can then feed purified samples into the analysis instrument of their choice, for example the PerkinElmer LabChip GXII microfluidic-based analysis system.

    Krystyna Hohenauer, director of biotherapeutics development, life science & technology at PerkinElmer, explained a clear trend toward biotherapeutics and the need for rapid analysis and characterization of putative products. “Related are biotech patent expirations and the development of biosimilars.”

    There is much analytical work to be done, she said, “but companies are not hiring more analysts. The ones who remain need much more efficient ways to characterize and purify proteins. They want to analyze for key characteristics much earlier in the development process.”

    The combination of sample prep and GXII provides scientists with the information to make better, more timely decisions, and free them from bench time to engage in more high-level data analysis.

    The Janus can be integrated into the GXII to fully automate the workflow from sample prep through to analysis and characterization, or the systems can be set up to be completely separate. This allows the researcher to utilize the instruments to best fit their sample throughput and development needs.

  • Life Raft?

    Membrane-bound biomolecules present numerous challenges for analysis and characterization. One family of membrane structures, the lipid raft microdomains, are attracting attention for their possible roles in disease and wellness.

    Although their precise role is still controversial, current thinking holds that lipid rafts organize or compartmentalize glycolipid-protein interactions necessary for normal biological function. “One purpose is to concentrate cell-signaling molecules,” explained Susan Daniel, Ph.D., assistant professor of chemical and biological engineering at Cornell University.

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