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Providing Training in Protein MS Isn t Easy, But Help May Be on the Way


In marked contrast to recent macroeconomic trends, the proteomics field over the past few years has experienced a remarkable period of growth, as most proteomics observers are well aware. The number of attendees interested in proteomics at the American Society for Mass Spectrometry conference, for instance, has grown exponentially, as has the number of industry conferences choosing the topic as a central theme.

But beneath the well-spring of interest, the question remains as to whether new entrants to the field really know what they're doing. After all, not every industry researcher with a burning desire to study proteins en masse is willing to become a postdoc to learn the secrets of protein mass spectrometry, nor would some even want to if they could. As a result, scientists are searching for alternative means of acquiring skills in proteomics, and for the most part their options have been limited.

“There’s really not a lot out there on offer from a formal perspective,” said Steve Naylor, Beyond Genomics’ chief technology officer. “People don’t have the skill sets to do fairly complicated proteomics analysis, and it’s remarkable how little opportunity there is [to acquire them].”

But that may be changing. In addition to the existing sources of training available through vendors and specialized consultants, professional societies such as ASMS and the American Chemical Society are starting to shoulder the responsibility for offering hands-on courses in protein mass spectrometry. In addition, public-sector organizations – both independent and within large research institutions such as NIH – are offering newcomers to the field up-close access to product tutorials and theoretical developments through seminars.

First Stop for Training: Mass Spec Vendors

Before committing to a week-long training course, many industry experts recommend turning to the most immediate source of instrument-specific know-how: the mass spectrometer vendors themselves. Typically, when a lab purchases a new instrument, a field application specialist with some knowledge of how to perform protein identification pays the new customer a visit to aid in setting up the instrument, performing calibrations, and demonstrating the instrument’s capabilities in biological mass spectrometry.

Bruker Daltonics, for example, normally sells all of its instruments as a part of a package that includes a three- to five-day training course, held at the company’s demonstration labs. The course includes “all kinds of attributes of sample prep, working over the data, performing bioinformatics searches, and checking MS/MS sequences,” said Victor Fursey, Bruker’s sales manager for North America. This type of course, if purchased separately, might cost on the order of $2,500, Fursey said.

If a customer requires more specialized training, vendors also offer the services of their application specialists, who for a fee will visit a customer’s lab to diagnose specific problems or provide instruction in more intricate protein analysis experiments. Applied Biosystems, for example, trains its application specialists to teach users the protocols for performing experiments using the ICAT reagents, said Keith Waddell, the company’s application training manager. In addition, some mass spectrometry vendors, including ABI and Agilent Technologies, offer seminars at various regional centers that feature prominent scientists giving instruction in specific protein mass spectrometry techniques.

“Vendors weren’t doing such a great job [providing training] five years ago, but they’re now starting to catch up,” said Matt Sweeney, an independent mass spectrometry consultant with particular experience in LC/MS and Thermo Finnigan instrumentation. “Now I tell potential customers I don’t want to see them until they have seen the vendor.”

But that doesn’t mean a vendor can satisfy everyone’s desire for specialized training in proteomics applications. Beyond learning the basic capabilities of a particular instrument, many biochemists or molecular biologists are looking to expand their knowledge of the intricacies of protein mass spectrometry, skills they would have to learn either by trial and error or from specialists with many years experience in the field.

Consultants such as Sweeney represent one potential source of this type of expertise. Typically, customers will approach a consultant if they’ve run into difficulties that the vendor cannot solve or simply can’t afford to pay the vendor to solve on a tight, typically academic, budget, Sweeney said.

The advantages to working with a consultant, Sweeney said, lie in the close working relationship that can develop, as well as in the cost of providing that training relationship. In most cases, “I tend to be the kind of person to teach [the customer] how to fish,” he said, rather than just demonstrating a particular technique.

ASMS, Others Step In

Yet when it comes to cost-effectiveness, many proteomics observers stressed that professional organizations have the resources – both in skilled instructors and infrastructure – to make an attempt at addressing the demand for proteomics training. And looking ahead to the fall, several organizations appear to be taking their first swing at bat. In addition to ASMS, which will feature a two-day proteomics course in November as part of its annual fall workshop session, ACS held a two-day training session last week in Boston as part of its annual meeting and plans to offer additional proteomics training throughout the fall. Even for-profit conference promoter IBC is advertising two-day courses to be held in December, January, and February. The cost of attending a course through the professional organizations ranges from about $500 to $1,000; an IBC course costs $1,500, or $800 for academics.

But besides cost, the organizers of such training sessions say their approach to proteomics instruction offers the advantage of providing a comprehensive introduction to protein mass spectrometry for those new to the field. “Starting with sample prep, separations, the various mass spectrometry approaches, and all the way through to the bioinformatics, we really want to make certain [attendees] understand the logic of why people do [proteomics] that way, as well as how,” said Beyond Genomics’ Naylor, who is organizing the November ASMS workshop.

But even Naylor admits that his course wouldn’t provide all the answers, and he wouldn’t expect a novice to come away from the experience with the skills to jump into state-of-the-art proteomics analysis. Says Sweeney: “Classes are good for a nice theoretical overview, but there’s something to be said for someone to come and work in front of your system.”

Nevertheless, the attempts of ASMS and others are just the beginning of what’s necessary to provide enthusiastic researchers with the tools they need to get started. “We within the ASMS community have not done enough to guide people who are not trained mass spectrometrists,” said Naylor. “I’ve argued that we need to.”


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