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San Francisco Mass Spec Conference Seeks to Bridge Gap Between Biologist and Instrument

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A wide spectrum of proteomics scientists, ranging from cell biologists to analytical chemists to instrument engineers, gathered last week in San Francisco to attend the Sixth International Symposium on Mass Spectrometry in the Health and Life Sciences: Molecular and Cellular Proteomics.

The conference, organized by the staff of Molecular and Cellular Proteomics, was intended as a way to help biologists venturing into the realm of mass spectrometry and mass spectrometrists delving into biological questions better understand each other, according to conference co-chair Al Burlingame, deputy editor of MCP and director of the mass spec facility at the University of California, San Francisco.

“If you get a bunch of mass spec people together without diluting them, they will just talk shop,” Burlingame told ProteoMonitor. “We wanted to provide an environment where mass spectrometrists were forced to tell [biologists] what [mass spectra] actually mean.” Burlingame particularly expressed frustration with large technology conferences such as ASMS, an event that he criticized as a “disaster” in the sense that it was too large and was “exclusively populated by technocrats who never had a course in biology.” The intimate environment of this symposium, (there were 300 attendees), allowed for better scientific exchange, said Burlingame. Sessions in which instrument vendors peddled their wares were notably absent from the conference roster.

According to most participants, Burlingame’s goal of intimate exchange was achieved. Mass spectrometrists and biologists alike gave the conference high marks for scientific value and academic exchange, with a few expressing to ProteoMonitor that it was the best conference they had attended this year.

The conference themes reflected current trends in proteomics research, with particular emphasis on the analysis of protein interactions, pathways, and complexes — a topic that the vast majority of the 31 presenters tackled in some fashion. Other common themes included the use of hybrid mass specs (particularly those involving ion traps or FT-ICR components), the analysis of post-translational modifications, the analysis of membrane proteins, expression profiling and quantitation, biomarker discovery, and the need for improvements in front- and back-end tools, particularly in the area of bioinformatics software. Following are some highlights from the first two days of presentations.

Monday, Aug. 25

Charles Cantor, chief scientific officer at San Diego-based Se-quenom, kicked off the proteomics conference by provocatively declaring that proteomics was essentially a waste of time. “I don’t think it makes much sense to do large scale analysis of proteins with a mass spectrometer,” he told a visibly skeptical audience.

Cantor instead plugged his nucleic acid-based gene expression technique, in which he converted RNA to cDNA, amplified it with PCR, and analyzed it with a mass spec to look for differences in expression levels. The DNA pool, Cantor said, could be used as a “first-pass screen” to generate leads for drug candidates that could then be further studied with protein chemistry, without having to screen all the proteins.

Cantor clearly relished his role as antagonist, noting that when working first with DNA, isolating enough pure sample — a major challenge for proteomics — was not an issue. “Wouldn’t you love to do this with proteins?” he asked.

In other presentations, Carol Robinson, a professor at the Cambridge University Chemical Laboratory in Cambridge; Nancy Albritton, associate professor of biomedical engineering at the University of California, Irvine; and David Myszka, research assistant professor at the University of Utah School of Medicine, Salt Lake City, all discussed their efforts to tackle dynamic interactions using mass specs and other techniques. Robinson used a Nanomate from Advion and a modified Q-TOF from Micromass designed to accommodate a 32,000 Da mass range to visualize the role of molecular chaperones in in vivo protein folding, and the dissociation of subunits from a ribosome. In the latter case, Robinson did successive tandem MS on the ribosome as subunits fragmented off, and then analyzed the subunits for member proteins, also by tandem MS.

Roman Zubarev, professor of ion physics at Uppsala University, Sweden, tackled the debate between top-down and bottom-up approaches by combining the two to look at post-translational modifications. He used electron capture dissociation, a “fast and furious” fragmentation technique, along with LC MS/MS on an FT-MS instrument to combine information for both the intact protein and peptides.

Tuesday, Aug. 26

Roland Annan, section head of biological mass spectrometry at GlaxoSmithKline, gave a presentation on using electrospray-MS with triple quads and Q-TOFs, combined with site-directed mutation, to map multiple phosphorylation sites on single substrates. He used N-terminal stable isotopes to quantitate these phosphorylation sites.

Catherine Costello, director of the mass spectrometry resource at Boston University School of Medicine, presented her modified high-pressure MALDI-FTMS machine that she called “cryoFTMS.” By removing the internal insulation on an FT-ICR unit and operating it in a liquid helium environment, she was able to get zeptomolar sensitivity and a huge dynamic range increase. She used the machine to do MS/MS for identification of post-translational modifications. She also probed post-translational modifications with an electrospray Q-Star FTMS hybrid.

In a talk that several conference participants considered to be both significant and controversial, Mathias Uhlen, professor at AlbaNova University Center in Stockholm, introduced Sweden’s Human Proteome Resource Initiative, which he heads. The initiative, funded by the Sweden-based Wallenberg Foundation to the tune of $28 million over four years and officially launched on Jan. 1, has as its aim the systematic gene-based analysis of the entire human proteome within the next 10 years — the results of which are to be stored in a database.

To do this, Uhlen cloned what he termed protein epitope signature tags — fragments of human proteins with minimal overlapping homology to other proteins. He expressed the PrESTs in E. Coli, and captured polyclonal antibodies to the tags. The antibodies could then be put on arrays and later used to probe for protein profiles of different tissues, according to Uhlen.

Images of the expression profiling will be stored in a publicly available database. Using his method of PrEST expression and antibody generation, Uhlen said he was currently able to achieve 50 percent coverage of the proteome, with membrane proteins proving to be the most difficult to express.

Reactions to Uhlen’s presentation were mixed. Stephen Barnes, professor of biochemistry at the University of Alabama Birmingham, called such attempts to “find everything quickly” a “grand seduction,” while Ralf Schoepfer, doctor of pharmacology at University College London, called the database a “huge advance.” Said Schoepfer, “Someone really needed to do this.”

Coming Next Week: San Francisco Conference Report, Part II, plus an interview with Mathias Uhlen.

— KAM

 

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