Mike May, PhD
Scientists know that the proteome holds the answers to many biological and medical questions. In the June 2007 Nature Biotechnology, for example, Jan Eriksson of the Swedish University of Agricultural Sciences and David Fenyö of The Rockefeller University wrote: “Truly comprehensive proteome analysis is highly desirable in systems biology and biomarker discovery efforts.” They added, “But complete proteome characterization has been hindered by the dynamic range and
|Measuring Multiple Proteins
Much of proteomics depends on quantifying the levels of multiple proteins in a single sample. One new way to do that comes from high-throughput Highly Selective Reaction Monitoring (H-SRM) analyses with the Thermo Fisher Scientific TSQ Quantum Ultra triple quadrupole mass spectrometer. This system includes a heated ESI (electrospray ionization) probe and dual desolvation zone technology. In addition, H-SRM scans run fast, in as little as 2 milliseconds. This lets a user quantify hundreds of proteins per second, according to Thermo Fisher Scientific. Company material adds: “The TSQ Quantum Ultra provides enhanced assay sensitivity, selectivity, and robustness enabling researchers to accurately quantify more proteins, more reliably.”
It often takes a combination of technologies to deal with complex mixtures of proteins. For example, Waters recently released its Identity High Definition Proteomics System, which consists of a combination of ultraperformance liquid chromatography and high-bandwidth MS. This works with the Waters Q-Tof Premier or Waters Synapt HDMS, which are both electrospray, tandem mass spectrometers. According to literature from Waters, this system can catalog “complex protein digest mixtures containing tens of thousands of peptides.” To make this system easier to use, Waters provides training, along with defined methods, quality-control standards, and informatics software.
detection sensitivity of experimental designs, which are not adequate to the very wide range of protein abundances.” Consequently, many companies keep making more advanced products to identify and quantify proteins.
One topic that comes up repeatedly is finding the less-abundant proteins. Lester Taylor, marketing director of life sciences mass spectrometry (MS) at Thermo Fisher Scientific, says, “Proteomics researchers are continually looking for MS instrumentation that improves the identification of low-level proteins and the characterization of post-translational modifications.”
Thermo Fisher Scientific recently made some of this easier by adding high-field asymmetric waveform ion mobility spectrometry (FAIMS) to its ion-trap mass spectrometers. “Implementation of FAIMS on ion traps,” says Taylor, “allows the separation of compounds based on their shape and charge in addition to their mass-to-charge properties, which has benefits for proteomics and drug discovery researchers.” The addition of FAIMS also reduces interference, such as that created by ions in the solvent, and increases the selectivity of measurements. This approach also eliminates many of the steps traditionally used to separate a protein from a biological mixture.
Other companies also keep developing new ways to improve the analysis of low-abundance proteins. At the American Society for Mass Spectrometry’s meeting in Indianapolis in June, Agilent Technologies introduced a new version of its Multiple Affinity Removal System, or MARS, called the Human-14 (Hu-14). This technology can remove up to 99 percent of the 14 most abundant proteins in human blood serum or plasma. As a result, it is much easier to study less-abundant proteins.
Getting at the less abundant proteins by eliminating the most abundant ones also forms the basis of other products, such as GE Healthcare‘s Albumin and IgG Removal Kit. This is reported by GE Healthcare to remove more than 95 percent of the albumin and IgG from human serum samples. Likewise, Genomic Solutions makes the ProPrep II, which automatically prepares samples for MS. In just one platform, ProPrep II performs several steps: destaining, washing, reduction and alkylation, digestion, and spotting on MALDI targets or transferring samples to input plates for LC/MS.
These tools help today’s researchers track even low-level proteins, thereby getting a more complete picture of the overall proteome.
About the Author
May is a publishing consultant for science and technology based in Minnesota .
This article was published in Drug Discovery & Development magazine: Vol. 10, No. 9, September, 2007, p. 12.
Filed Under: Drug Discovery