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EQUIPMENT · New mass spec instrument billed as world's most sensitive for small molecules

By Mark D. Uehling

March 8, 2005 | Many a clinical trial turns on a simple scientific question. Is that a toxic metabolite in a patient's blood sample? A drug? Or bits of benign detritus? It is hardly uncommon for a long-sought chemical signal to be too faint to be detected confidently and reproducibly.

Applied Biosystems believes its new API (atmospheric pressurization ionization) 5000 will set a new threshold of detection for small molecules. Other competitors, of course, will have their own salty interpretations of that claim. But for now, Applied Biosystems machines seem to be the ones to beat, with Bear Stearns on record in a 2004 report that they are the standard throughout the contract research organization (CRO) industry.

In the case of the 5000, ABI bills the instrument as the world's most sensitive LC/MS/MS system. It was designed for absorption, distribution, metabolism, excretion and toxicity (ADMET) projects, as well as studies to identify drug metabolism, pharmacokinetics (DMPK). The API 5000 is basically a small-molecule quantitative analysis tool, the company says.

'Out of the Grass' 

NOZZLE MAGIC: This QJet ion guide, part of the API 5000, uses only radio frequency (RF) to help focus the sample being measured and is designed to be relatively contaminant-free.

Tamara Bond, an Applied Biosystems product manager for the company's quadrupole instruments, notes that customers in pharma and CROs have been keen to test-drive the new machine. "They brought in their hardest samples, the ones they're really struggling with," Bond says. "What we've been able to do is run them on the API 5000 and see a signal. What they say is, 'This pulls it out of the grass.'"

Getting a nice, sharp peak on a piece of paper is not the only benefit of the new machine. It's designed to run unattended, at high throughput. The key isn't only one nice peak, but lots of them, with minimal human intervention. A proprietary algorithm optimizes the peaks, minimizing the need for scientists to play with the parameters to get a perfect result. In one in-house test, just 28 of 360 peaks needed manual re-integration.

ABI reports the machine is approximately 10 times more sensitive than its predecessor, the API 4000, which was introduced in 2001. Because of an orifice that is twice as large and other tweaks, however, the signal-to-noise ratio on the 5000 works out to be four times better than the API 4000.

Sensitivity Training 
With the new API 5000, Applied Biosystems says it has taken pains to maintain as much of the process logic of the earlier machine. That was intended to make the transition to the new machine easier and cheaper, mainly by minimizing downtime due to re-training staff, recalibrating machines, and revalidating methods and workflows.

"All of the improvements are internal to the instruments," Bond notes. "All of the SOPs you currently have in place and the source parameters and the compound-dependent parameters are all virtually identical. There is no learning curve with this instrument."

Bond says ABI is hoping the new machine is so sensitive that it will let customers stretch out the supply of precious analytes by using less in each run. She suggests the greater sensitivity of the machine could be a factor in helping industry move selected compounds into humans earlier — even at microdosages. While these sorts of instruments are often used in clinical research, the company expects that some of the units could find their way into the discovery process as well, helping to keep poor compounds out of trials in the first place.

COMPLETE CONSISTENCY: In a two-day test, the new machine reproducibly and reliably generated data with little noise in analyzing 500 injections that contained Xanax at a few picograms per microliter.
With a list price starting at $450,000, of course, the API 5000 is not an impulse buy. But for project teams struggling to detect a faint signal of efficacy or toxicity, it could produce answers faster.

Included with the purchase price: version 1.4.1 of Applied Biosystem's Analyst software, which is used on a variety of other quadrupole instruments. But this time, the software and the instrument were improved together. "Many of the improvements with the software are directed toward customers who would be quantitive, regulated lab customers," Bond says.

The law under 21 CFR Part 11, she notes, requires that only one live copy of the data be extant at one time. In the past, that required cumbersome saving and deletion of data off the PC attached to the instrument — and onto the company network. Now that can happen in one step, in a fully auditable manner.

The software also has highly adjustable settings for 21 CFR Part 11 compliance, allowing managers to determine which projects and events to track. New projects can be set up based on an "audit map" that was used previously. Security can be handled based on the user, the project, the computer, or all three.

The new machine was produced in a partnership with MDS/Sciex of Canada.

For reprints and/or copyright permission, please contact  Jay Mulhern, (781) 972-1359,