Biomarker Discovery Platform
Predictive Diagnostics (www. predictivediagnostics.com) has combined several technologies into a biomarker discovery platform. This includes: an automated high throughput biomarker enrichment technique with novel membrane chromatography, high-resolution detection via MALDI Orthogonal-TOF mass spectrometry, and biomarker analysis via the company's BAMF (Biomarker Amplification Filter) algorithms.
This platform has been used to identify biomarkers for Alzheimer's disease and lung, prostate, and ovarian cancers. "We start with a normal and a disease blood sample, run these on mass spectrometry and then input the raw data into our BAMF technology processors," Guy della Cioppa, Ph.D., senior vp, business development, explained.
Control spectra versus disease spectra is aligned and analyzed for differences. "We typically look at the low molecular weight proteins and have developed some proprietary ways to enrich the relevant biomarkers in that weight range," he added.
The BAMF platform runs on several large Linnux clusters, essentially parallel supercomputing. "We figured out some proprietary ways to reduce model space so we can integrate these very large marker model sets and build an optimal diagnostic fingerprint."
A new, automated method for scanning LC-MS data sets for peptides and proteins that provides quantitative profiling and interactive confirmation was presented by GE Healthcare (www.gehealthcare.com). The DeCyder MS software provides a two-dimensional representation of LC-MS data.
"This shows mass spectrometrists things they haven't seen before in their data versus conventional software," says Harald Pettersen, Ph.D., scientist, discovery systems. For example, the 2-D representation allows the user to see contaminants and whether the chromatographic resolution is satisfactory.
"It's much faster to look at the data in 2-D, where you can see all the data at once, instead of looking at small portions one at a time," explained Dr. Pettersen. Instead of taking several days, the software provides analyses within an hour because the data is run automatically.
The 2-D image looks similar to a 2-D gel. Algorithms used to match images are adapted from the original DeCyder software (developed by Amersham Biosciences).
"The goal is to find peptides that are up- or downregulated between samples and to quantify them. We show that quantification using LC-MS data without using any chemistry is fully feasible. For researchers working with peptides, where you can't use 2-D gels, this is unique," summarized Dr. Pettersen. The company plans to launch the software in the second quarter of this year.