Kalorama: With Biomarkers Harder to Discover, Researchers Go 'Beyond the Shotgun'

NEW YORK, June 22, 2015 /PRNewswire/ -- Protein discovery and mapping has moved rapidly with global protein profiling or 'shotgun' methods, but there are proteins likely that remain "unseen," according to Kalorama Information.   This is driving new targeted approaches healthcare market researcher says that life sciences still has fertile ground to cultivate for biomarkers with these enhancements.  The finding was made in Kalorama Information's recent report, Proteomic Research Markets.

The first two years of the Human Proteome Project (September 2010-October 2012) saw significant progress with at least one peptide for roughly 12,500 protein-encoding gene sequences (contained in Swiss-Prot) identified, leaving roughly 7,500 gene-predicted proteins yet to be discovered with confidence in a proteomics experiment.

"Our research found that a lot of discovery is getting beyond shotgun methods now," said Bruce Carlson, Publisher of Kalorama Information.  "Shotgun proteomics is also inherently limited by its overall scheme as a "bottom-up" method that performs mass analysis on digested proteins or peptide fragments rather than proteins in their original form.

In general terms, proteomics-assisted biomarker discovery relies on the ability of mass spectrometers to determine the mass of ionized proteins, peptides and peptide fragments using their mass/charge (m/z) ratios. The masses of peptides and peptide fragments indicated by their m/z values are compared to the known masses of amino acid sequence fragments; entire protein chain(s) can be discovered or identified through the assembling and association of a combination of mass data from intact proteins, peptides, and peptide fragments. Protein sequence informs identification, structural characterization, and the parameters of targeted analyses for a single protein or set of putative biomarkers in more samples. Numerous strategies exist for proteomic biomarker discovery.  Gel-Based, CE, DIA and Shotgun all have advantages and disadvantages in the quest for new protein targets:

• Shotgun proteomics the use of orthogonal separation or the front-end reduction of sample complexity using a separation or fractionation method before in-line LC, typically high performance.  Advantages quantification of potentially thousands of proteins.  Disadvantages: Loss of some structural information (fragile PTM sites)
• Gel Based Proteomics Difference gel electrophoresis improves upon traditional methods by permitting the loading of multiple samples into the same gel through the use of different dyes.  Advantage: Effective fractionation of protein species and aided analysis with dye and gel imaging platforms  Disadvantage: Added time and labor for experiment, less reproducibility
• Capillary electrophoresis Proteomic Discovery.  Advantages: More efficient separation of intact proteins and large biological molecules; theoretical plate counts approaching 100,000 with digested peptides. Utilizes very small amounts of sample Disadvantages: Little experience in proteomics research compared to LC and gel methods
• Data Independent Acquisition (DIA) methods provide extensive coverage through the systematic fragmentation of all peptides over an assigned range or mass (m/z) window. During DIA, the instrument randomly selects uniformly wide m/z windows that pieced together cover the user-set mass range. The m/z values of all precursors and fragment products are then obtained in switched MS and MS/MS modes.

Kalorama Information's report, Proteomic Research Markets, contains more detail on all of these methods and how they drive instrument purchases, as well as market sizing and forecasts for major instruments used in these methods and for disease areas of research.  The report is available from Kalorama Information at: http://www.kaloramainformation.com/redirect.asp?progid=87538&productid=8989207.

About Kalorama Information
Kalorama Information, a division of MarketResearch.com, supplies the latest in independent medical market research in diagnostics, biotech, pharmaceuticals, medical devices and healthcare; as well as a full range of custom research services. Reports can be purchased through Kalorama's website and are also available on www.marketresearch.com and www.profound.com.

We routinely assist the media with healthcare topics. Follow us on Twitter, LinkedIn and our blog at www.kaloramainformation.com.  

Contact:
Bruce Carlson
(212) 807-2622
[email protected]
www.KaloramaInformation.com

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SOURCE Kalorama Information