Looking back at this year’s meeting of the American Society for Mass Spectrometry, it seems obvious that proteomics reigned supreme: according to Peter Roepstorff, a proteomics researcher at the University of Southern Denmark in Odense, between 90 and 95 percent of the presentations had to do with proteomics or protein mass spectrometry.
But beneath the glut of protein analysis-related mass spectrometry talks, a larger question remains: Did all the attention given proteomics indicate that researchers have made significant progress in advancing the capabilities of mass spec for analyzing proteins, or merely that many newly minted mass spectrometrists have latched onto the subject for its fashionable status and ability to win grants?
In the past four weeks ProteoMonitor interviewed ASMS speakers, attendees, and session chairs, and the answer is ambiguous. While scientists have made strides in increasing the capabilities of techniques such as Fourier transform and hybrid mass spectrometry for analyzing proteins, the ability to identify posttranslational modifications leaves much to be desired. Further cluttering the equation, some researchers said that in the race to build high-powered instruments, protein mass spectrometrists have forgotten to pose intelligent scientific questions in the first place.
FT/MS Rising?
Cost and complexity notwithstanding, FT/MS techniques for analyzing proteins acquired a larger footprint at this year’s meeting, attendees said. Combined with efforts on the part of mass spectrometry vendors such as Thermo Finnigan and Bruker Daltonics to push the technology into the mainstream, research groups at the Pacific Northwest National Laboratory in Richland, Wash., and MDS Proteomics also presented protein analysis data that showed the advantages in mass accuracy and resolution inherent to the technique.
“A lot of mass spectrometry companies are moving over to FT/MS, because the bottom-line accuracy of the data make it easier for the software [to identify proteins],” said Julian Whitelegge, a researcher at the Pasarow Mass Spectrometry Laboratory at the University of California, Los Angeles, who chaired a session on membrane proteins and hydrophobic peptides at the conference. “I’m looking at an FT/MS [mass spectrometer] with a controllable front end,” he added. “It seems to me to have a strong future.”
The increase in the popularity of FT/MS has come in spite of its shortcomings, which in addition to cost and complexity include limitations on the size of proteins possible to analyze, and currently inflexible front-end ionization sources. Nevertheless, a consensus view was that the method had progressed. “The accuracy is not much better than with a Q-TOF,” said Roepstorff, “but [FT/MS] seems to be more practical now.” It’s moving into the field because of its high mass resolution, he added.
PTM’s Get Short Shrift
On the topic of analyzing posttranslational modifications, however, fewer researchers felt that this year’s ASMS meeting had heralded significant improvements in technology. Roepstorff, who chaired a session on new proteomics technologies, said that he hadn’t received many papers on the analysis of posttranslational modifications by mass spectrometry, even though he had sought them out. “Nearly everyone speaks about [the need for analyzing] posttranslational modifications [in the context of] proteomics, but very few do anything about it,” he said.
Jasna Peter-Katalinic, a glycoprotein researcher at the University of M nster in Germany who chaired a similar session on new proteomics technologies at the ASMS meeting, added her voice to this opinion. In her view, posttranslational modifications are key to understanding protein function, and members of the glycoprotein community have grown concerned over the years that only a few groups have ventured into the field. “All this [protein identification] data needs to lead to function,” she said, “and without the link to glycoproteins we won’t get to function.”
Don’t Break Your Neck
In a larger context, however, some researchers also expressed trepidation at the extraordinary growth in interest in protein mass spectrometry. Given its dominance at the ASMS meeting, it seems likely that alternative targets for analysis by mass spectrometry of potential biological significance might be overlooked, said Roepstorff. “With such a constant increase [in protein mass spectrometry at ASMS], I hope we are peaking now in a way,” he said. “There are a lot of interesting things you can do with mass spectrometry, such as look at carbohydrates and RNA. When such a huge tidal wave approaches, when it breaks you have chaos.”
More importantly, perhaps, Roepstorff and others who have seen proteomics grow from humble beginnings expressed concern that newcomers are relying too much on brute force data collection techniques to provide biological insight without first considering the question they are looking to answer.
High-throughput mass spectrometry gives people “the feeling that they can solve basic problems immediately,” said Peter-Katalinic. “But you finally end up with something with lower information than if you had medium throughput” and fully understood the results, she said.
“The real thing is you need to carefully define your experiment,” added Roepstorff. “Many people who haven’t realized that will break their neck.”
— JSM