Large-protein beads are designed to overcome previous limitations of biomarker discovery to peptide and small proteins, and to exploit the full mass range of up to several hundred kDaltons
Bruker Daltonics has announced the introduction of the next level of its ClinProt system for advanced biomarker discovery, identification and validation in clinical proteomics.
The ClinProt portfolio of magnetic beads for sample pre-fractionation has now been further expanded with novel capabilities to address biomarker analysis of large proteins, targeted glyco-protein analysis, and antigen- specific enrichment of selected biomarker molecules, combined with high- performance Maldi-Tof read-out.
New ClinProt large-protein beads are designed to overcome previous limitations of biomarker discovery to peptide and small proteins, and to exploit the full mass range of up to several hundred kDaltons supported by Bruker Daltonics's cutting-edge Maldi-Tof mass spectrometers.
These novel large protein beads are complemented by a new DHAP matrix product, which is optimised for high molecular weight proteins.
In addition, new ClinProt Glyco-Beads bridge the gap between clinical proteomics and the important field of glycomics.
The unique Glyco-Beads offer multiple methods for glyco-protein enrichment, including both chemical capture or lectin-capture strategies.
After glyco-protein enrichment, the ClinProt solution now offers multiple glycomics workflows: for example, profiling of all glycosylated peptides or proteins, or of selected glycan-structures can be very informative in cancer research, as many cancer cells show altered glycans on their surface.
In-depth structural analysis and identification of specific glycoproteins can then be accomplished using Proteineer for expression proteomics, involving Maldi-Tof/Tof and/or LC-ESI-MS/MS workflows.
Finally, novel ClinProt Antibody-Capture Beads allow the specific enrichment of different protein groups with the same antigen specificity or even of specific proteins, thus giving access to low-abundance proteins in plasma.
Enriching specific proteins via coupling of customer-selected antibodies can give the specificity of an immunoassay, combined with the confidence of a mass spectrometry read-out.
This allows scientists to see all proteins bound to an antibody at once, and to distinguish the specific protein from other isoforms, or from undesired cross-contamination, thereby considerably increasing the confidence in any antibody-based assay.
The new ClinProt bead products are complemented by the ClinProTools 2.0 bioinformatics package for streamlined data interpretation.
ClinProTools 2.0 combines intuitive data visualisation with sophisticated pattern recognition algorithms for the determination of predictive biomarker panels.
Spectra not reaching the desired quality standard can be excluded from the analysis in the graphical user interface.
The new proprietary QuickClassifier algorithm circumvents the common problem of model generation being extremely time-consuming.
The QuickClassifier provides a classification result in a few seconds, even for large data sets.
This is further complemented by a new multi-class support vector machine (mSVM) for high-end classifications.
Multiple sample classes, for example originating from different control groups or from staging of a disease, are supported by the algorithms and likewise by the visualisation tools.
A correlation matrix gives an overview of all positively or negatively correlated peaks, even if they have not been selected for a predictive pattern.
This gives an optimal overview of co-expressed signals in a set of profiling samples.
In addition, newly introduced ProfileAnalysis 1.0 software further expands the use of electrospray ionisation (ESI) time-of-flight (Tof) mass spectrometry for clinical research and pharmaceutical development applications, using Bruker Daltonics's Microtof ESI-Tof systems.
ProfileAnalysis software is well- suited for small molecule profiling of complex biological fluids, eg urine.
The pattern recognition process is supported by principle component analysis, and optimized visualisation tools support the researcher during the application of these sophisticated mathematical approaches.
Professor Thiery, head of the Institute for Clinical Chemistry and Laboratory Medicine in Leipzig, Germany, commented on the new ClinProt products: "In our laboratory, the ClinProt system has recently been shown to overcome reproducibility problems which were reported for chip-based pre-fractionation techniques.
"Maldi-Tof mass spectrometry-based profile analysis in our hands has proved to be a promising tool for future routine applications in the clinical laboratory.
"Our recently published standard operating procedures (Baumann et al, Clinical Chemistry 2005; 51: 973-980) for standardised sample preparation give every researcher access to proven pre- fractionation techniques when starting research in clinical proteomics".
Frank Laukien, president and CEO of Bruker Daltonics, stated: "The introduction of our next level of ClinProt sample preparation beads and analysis software drives biomarker analysis one step further, as it gives access to novel applications and important assays that previously could not be addressed efficiently.
"Moreover, our next-generation ClinProt and Proteineer solutions now also are applicable to new fields like glyco-biology, which is expected to have significant impact in cancer research".
