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Amassing Mass Spectrometry Tools

By Robert M. Frederickson

July 20, 2005 | Mass spectrometry is a key tool in the effort to identify protein biomarkers of human disease. Manufacturers have met major challenges in adapting this technology to protein discovery, both qualitatively and quantitatively. Several new products of interest were announced at the  American Society for Mass Spectrometry meeting in June.

Many key protein biomarkers are present in vanishingly small quantities within complex mixtures, which challenges detection methods. Strategies that deplete abundant proteins from the samples can lead to the loss or dilution of associated low-abundance proteins and often involve methods ill suited to high-throughput automation.

To address this problem, Ciphergen Biosystems introduced Deep Proteome Research Services including Equalizer bead technology, which makes use of a random combinatorial peptide ligand library synthesized directly on the surface of beads. Each 70-µm hydrogel bead contains a 6-mer peptide of distinct sequence on its surface and therefore binds a distinct protein or set of proteins. When these beads bind proteins within an excess of sample, excess abundant proteins can be washed away, essentially compressing the dynamic range of protein concentrations by several orders of magnitude while maintaining the diversity and differential levels of expression of the proteome. When used together with Ciphergen’s automated MultiSelect protein-profiling technology, trace protein detection and total protein count can be improved.

Bruker Daltonics also addressed the issue of sample enrichment with the expansion of its ClinProt sample prefractionation technology. ClinProt uses magnetic beads with functionalized surfaces that capture and enrich proteins and peptides for analysis on Bruker’s AnchorChip. Assays include various types of bead, including hydrophobic beads, weak anion exchange and weak cation exchange beads, immobilized metal affinity capture beads, and antibody-based beads that specifically enrich particular clinical antigens. The portfolio of beads has been further expanded to address the analysis of large proteins and glycoproteins and antigen-specific enrichment of selected biomarker molecules.

“Large-protein beads” are designed to overcome previous limitations of biomarker discovery to peptide and small proteins and to exploit a mass range of up to several-hundred kilodaltons. Such beads are complemented by a DHAP matrix optimized for high-molecular-weight proteins. Profiling of glycosylated peptides or proteins or of selected glycan structures can be informative in cancer research and diagnostics, as many tumor cells show altered glycans on their surface. The new Glyco-beads include chemical capture or lectin capture strategies. “Antibody-capture beads” enrich for specific antigens, thus enhancing access to specific low-abundance proteins in plasma.

Software Salutations
Several new software packages for analysis of mass spectrometry data were also presented at the meeting. Bruker Daltonics’ ProfileAnalysis 1.0 software expands the use of electrospray ionization time-of-flight (ESI-TOF) mass spectrometry for clinical research and pharmaceutical development and is suited for small-molecule profiling of complex biological fluids such as urine.

Applied Biosystems Group and MDS Sciex introduced MarkerView software for metabolomics and biomarker profiling analysis. It is hoped that metabolomics, the study of changes in the metabolic profiles of cells in response to a drug or disease, may facilitate both disease diagnosis and toxicology studies. MarkerView, which is compatible with all Applied Biosystems/MDS Sciex mass spectrometers, incorporates statistical analysis to allow researchers performing global metabolomics and protein biomarker profiling studies to mine very large and complex mass spectrometry data sets for changes in protein, peptide, and metabolites resulting from disease, drug treatment, or drug toxicity.

Thermo Electron launched the LTQ Orbitrap, a hybrid mass spectrometer that is claimed to offer superior mass resolution and accuracy, detection power, and dynamic range when compared to existing time-of-flight technology. Thermo also launched the H-ESI (heated electrospray ionization) probe with dual desolvation zone technology for the Finnigan TSQ Quantum triple quadrupole instruments. This probe enhances liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) assay sensitivity up to 8-fold, providing potential advantages for drug metabolism and pharmacokinetics applications.

Robert M. Frederickson is a biotech writer based in Seattle. E-mail:

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