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Putting It All Together

By Mark D. Uehling

April 15, 2005 | Where does the instrument end and the data begin? That question was in the air at this year’s Pittcon meeting in Orlando, Florida. Equipment vendors are trying to accommodate customers who want the most direct path possible between a sample and the analysis of a sample — even if that path leads through someone else’s instrument, software or consultant.

A case in point is Agilent. The company previewed the first high-performance liquid chromatography (HPLC)-chip/mass spectrometry (MS) system for protein identification. The chip unites the sample enrichment and separation capability of a nanoflow chromatography system with the intricate connections and spray tips used in electrospray MS. Agilent said its technology eliminates half of the fittings and connections typically required in an LC/MS system, reducing the possibility of leaks and dead volumes.

Agilent also announced a new service for pharmaceutical labs. The company will put Agilent engineers on-site to handle maintenance, repair, compliance, workflow and reporting issues for chromatography and other machines, regardless of who built them.

ABI’s Suite Spot
Applied Biosystems (ABI) meanwhile, announced a new suite of instruments, reagents and software for biomarker quantitation and detection. As proof of its usefulness, the company presented charts showing wide swings in peptide levels of a single patient who had not been treated for anything.
thermoGetting detailed data about hour-by-hour fluctuations of proteins in patients is obviously a game only a small number of companies can play. “We are really looking at a dynamic system,” said Art Sims, ABI’s global marketing manager for proteomics. “How much change will there be in a patient who has been treated?”
In announcing an alliance with Deloitte, ABI said it would work with the consulting firm to help customers design and integrate complex laboratory workflows. ABI confessed to having been inspired by IBM — and to be eager to harvest services-related dollars that customers are willing to spend on intricate projects. “A lot of our customers are asking for end-to-end solutions,” said Ramin Cyrus, ABI’s senior director of services.

Thermo Electron previewed 20 new products in Orlando. Jo Webber, general manager for informatics at the company, introduced a new off-the-shelf laboratory information system (LIMS), Darwin, designed specifically for large, regulated companies in biotech and pharma. Darwin handles samples and data from preclinical through manufacturing.

Webber emphasized the plug-and-play nature of the data and instruments that Darwin will connect. “You can switch out an instrument, you can switch out a robot. We’ve given them the ability to manage the chromatography data with the lab data,” she said.

It was not just behemoths that were worrying about putting it all together. Wyatt Technology, a family-owned chromatography company in Santa Barbara, uses more than a dozen lasers bouncing off the analyte at once. The company announced its new Heleos instrument, with 100 times the dynamic range of the previous model.

Wyatt takes its software as seriously as its instruments. “We have a patented algorithm that can determine numbers of organisms and viruses using just a light scattering instrument,” notes Miles Weida, senior scientist at Wyatt.

But Wyatt’s 21 CFR part 11 compliant application also can integrate with the Empower suite from Waters. That grew out of the realization that most customers in industry have equipment from a variety of sources. “Every chromatography company has their own software,” says Weida. “They really don’t talk to each other. Our hope is to extend to other software packages.”

New Tools from Waters
There was a similar sentiment at Waters. “One software solution is not going to provide all the answers,” says Mark Harnois, senior product marketing manager.

Waters released a new version of its Empower application, which is already tied to both its eLab Notebook software and SDMS (Scientific Data Management System). The Empower program acquires, processes and archives data generated by liquid chromatography, gas chromatography, MS and photo diode arrays. “We can do IQ, OQ, and PQ,” says Harnois. “What used to take an engineer 4-12 hours, we’re doing in 30 minutes.”

Waters also released a new version of SDMS. The software now includes Lightweight Directory Access Protocol (LDAP) that will help IT departments easily implement a single sign-on across large organizations. The software also has a new tool to convert raw file data into JCAMP and other standard formats to facilitate data mining.

On the equipment side, Waters’ new Acquity UPLC ELSD detector delivers results up to nine times faster than conventional HPLC for demanding separations — and routine sensitivity three times better than traditional systems. The Acquity machine is part of a new Waters Protein Expression system, which the company says is the first end-to-end LC/MS solution to quantitatively assess changes in protein expression in the midst of an identification. No labeling isotopes are required.

Shotgun Proteomics
There were hints at PittCon that academics and government scientists are finally making headway in working with proteins in larger batches. In “shotgun” methods, to take just one example, proteins are chewed up with enzymes and identified en masse from databases.

Neil Kelleher of the University of Illinois demonstrated shotgun annotation using top-down tandem MS and his own ProSight PTM (post-translational modification) software. The program is free, with a commercial version in the works. Kelleher calls it the first search engine for top-down proteomics, already used in 70 other labs.

“You don’t have to look at this data,” Kelleher said. “What shotgun annotation allows is automatic interpretation of this data and short-circuiting straight to protein characterization. That’s the kind of efficiency that will really boost the proliferation of tandem MS.”

But Tracie Williams (FDA) can probably be categorized as a more frustrated user. All she wanted to do was to use MS to identify a few pathogenic bacteria where no genome-wide data were available. Said Williams: “We tried 2-D gels, we tried MALDI, we tried bottom-up. For our purposes, they don’t work.” The analytical tools available, she said, need refinement. “There is a lack of data analysis tools needed for automating this process. This is not high throughput. We are trying to make it higher throughput.”

Williams praised Peter Leopold and his company, Bioanalyte, Inc., whose ProteinTrawler software was partly developed with FDA funding and was recently used to identify a biomarker.  l

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