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Proteomic Scientists Ask, Where Are Cell Biologists?

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Poor sample preparation, inexact results, a relative inability to show dynamic processes, and a number of other factors have all contributed to the paucity of mass spec-based proteomics work by cell biologists, according to researchers at McGill University and Göteborg University.

As proteomics lurches out of its infancy as a research field, many say they are seeing more biologists, especially cell biologists, entering the fray. But mass spec proteomics is still dominated by analytical chemists with biologists distinctly in the minority.

In a paper published in Nature Methods, researchers from McGill in Toronto and Göteborg in Sweden examine why biologists continue to have an aversion to proteomics in general, and mass spec-based proteomics research specifically.

The paper is one of several in that issue of the journal exploring the use of mass spec for proteomics research.

In the paper, the researchers say there is no one overarching reason why cell biologists continue to have little presence in mass spec-based proteomics. Rather, a number of factors have prevented cell biologists from embracing proteomics. First, they say mass spectrometry lacks the “charm” of technology more often found in cell biology, such as live-cell video microscopy, that puts the instrument at an immediate disadvantage.

“With imaging we can observe dynamic processes — something that proteomics has a hard time rivaling,” they write.

But aside from a missing coolness quotient, the quality of current proteomics research may be a barrier to recruiting more cell biologists into the field. In particular, the authors write, shoddy sample preparation has resulted in a skeptical view of proteomics among cell biologists.

While issues with sample preparation are “well-founded,” rather than trying to address the problem head-on, “the proteomics community has instead attempted to circumvent the need for rigorous sample preparation by developing advanced bioinformatics tools,” the authors write.

—Tony Fong

Short reads

The test samples for the Association of Biomolecular Resource Facilities’ 2008 study are available. This study hopes to determine how difficult it is to sequence through an N-terminal His-tag and still ascertain the protein’s identity. The results will be presented at ABRF’s February meeting in Salt Lake City.
 
MissionCouver and GWC Technologies signed a distribution agreement. Under its terms, MissionCouver will be the exclusive distributor of GWC Technologies’ label-free array systems in China. The agreement also addresses the marketing of GWC’s SPRimager II label-free detection system.
 
Japan’s National Cancer Research Institute is using Nonlinear Dynamics’ 2D gel analysis software for cancer biomarker discovery and validation. In particular, the NCRI is using Nonlinear’s Progenesis SameSpots image analysis platform to uncover biomarker candidates that predict patient response to gefitinib in lung adenocarcinoma. They also plan to look for markers that indicate a risk of recurrence.

The third version of the Human Protein Atlas was released at the Human Proteome Organization’s 6th Annual World Congress. HPA 3 contains 2.8 million images corresponding to 2,618 proteins and 3,015 antibodies. New features for the atlas include validation data for the antibodies based on protein arrays and western blots, as well as an advanced search function allowing tissue-specific profiling.

Patents

US Patent 7,271,397. Combined chemical/biological agent detection system and method utilizing mass spectrometry. Inventors: Wayne Bryden, Robert Cotter, Scott Ecelberger. Assignee: Johns Hopkins University. Issued: September 18, 2007.

This patent describes a mass spectrometer with two ionization sources.  The first ionization source, most likely MALDI, ESI, or some similar source, would be capable of providing not only ions, but also a set of normally intractable desorbed neutrals. Those neutrals are then ionized by a second EI source that is coupled to the first source.

US Patent 7,265,349. Method and apparatus for a multiple part capillary device for use in mass spectrometry. Inventor: Melvin Park. Assignee: Bruker Daltonics. Issued: September 4, 2007.

This patent is for a multi-part capillary to be used in mass analysis instruments. This is, says the abstract, “specifically, a multiple part capillary comprising at least two capillary sections joined with airtight seal by a union for use in mass spectrometry (particularly with ionization sources) to transport ions between pressure regions of a mass spectrometer for analysis.”

Data point

$1.94 million

The Advanced Technology Program granted Anima Cell Metrology $1.94 million to develop a platform to study and identify proteins in live cells in real time.

The Scan

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