Bruker Daltronics (www. bdal.com) introduced an improvement to its ion trap mass spectrometry (ITMS) system, according to Catherine Stacey, Ph.D, director of proteomics systems. The HCTultra PTM discovery system includes both convention CID (collision-induced dissociation) and ETD (electron transfer dissociation) fragmentation on a high-resolution ion trap instrument making this product unique.
The quadrupole ion trap mass spectrometer has been recognized for the last decade as a superior tool for biomolecular analysis, capable of identifying and describing a variety of molecules.
The fundamental difference of the ion trap is that all ions created over a given time period are trapped and then ejected into a conventional electron multiplier detector. This new method allows faster and more efficient ejection of the ion packet, thus greatly improving resolution.
Brukers Protein Post-Translational Modification (PTM) Discovery Tool represents a commercial application of electron transfer dissociation to the ion trap spectrophotometer. The module is a protein and peptide fragmentation technique that preserves glycosylation, phosphorylation, and other significant post-translational modifications. This provides an important step forward in deciphering the subtle modifications of proteins, which are known to have profound effects on phenotypic expression.
Peptide modifications are detected by various MS/MS approaches of which ETD has the advantage of preserving the modification on the amino acid during the fragmentation. The sequence, including the position of the modification, is easily confirmed by de novo sequencing or database searching, explained Dr. Stacey. Standard sequencing techniques will fail to identify many secondary modifications of proteins, so there is a strong demand for the Bruker technology.
Another platform, referred to as Clinprot and Clinprot micro, ties the companys mass spectrometry-based biomarker analysis technology to a collaborative in vitro diagnostics program with HealthLinx (Melbourne, Australia). This system is an integrated set of tools for biomarker discovery and clinical proteomics research, including software packages to advance clinical research and shorten timelines in biomarker discovery.
The Clinport workflow measures peptides and proteins that can be used to discover multimarker panels or profile patterns indicative of specific diseases. These multimarker panels or patterns have potentially better diagnostic specificity than single biomarkers.
The partnership is focused on discovery of potential biomarkers for malignancy in serum, plasma, urine, saliva, cerebral spinal fluid, or cell lysates. Clinprot supports a profiling workflow to detect patterns indicative of specific diseases in biological fluids. In a second workflow, individual biomarker candidates can be identified by means of the Bruker Daltonics TOF/TOF technology.
Sample preparation takes advantage of magnetic bead capture. These are microparticles with functional surfaces able to bind proteins and peptides. After elution the captured proteins and peptides are transferred to AnchorChips (a specialized sample support).
Profile spectra of the separated protein/peptide fractions are acquired using the FLEX-series MALDI-TOF instrument, taking advantage of bioinformatics for all major functionalities in biomarker detection and evaluation. This includes data on pretreatment, peak statistics, pattern recognition with direct feedback to the visualization, cross validation of the cluster analysis, and determination of sensitivity and specificity with independent test data.
Any future use of biomarker candidates in clinical environments requires identification of the respective peptides. The TOF/TOF functionality offered by Clinprot addresses this important task in clinical proteomics.
Biomarker candidates detected by ClinProTools can be subjected to TOF/TOF analysis. Metastable fragment ions of the respective precursor ion are analyzed after a second acceleration step, and a software package known as BioTools interprets the resulting fragment pattern and is used for peptide identification via database search.
The Clinprot micro solution is designed for cancer research and other clinical and diagnostics research laboratories engaged in biomarker discovery across a range of samples.
It represents a compact clinical system dedicated to peptide and protein profiling, biomarker discovery, and biomarker validation. It is derived from benchtop MALDI-TOF mass spectrometer from Bruker Daltonics FLEX series, providing biomarker detection sensitivity and resolution, as well as the reliability and reproducibility needed for validation studies of putative biomarkers for cancer and other diseases, according to the company.
The Clinprot micro system offers integrated sample-preparation tools for biological fluids and tissue extracts with comprehensive analysis, visualization, and model-building software.
Dr. Stacey considered the direction of technological developments in the companys product line. All mass spec vendors continue to innovate with technical enhancements to their existing products and introduce new products continuously.
The demand from customers tends to be for more performance, sensitivity, resolution, and better fragmentation, at a given price point, rather than for price or size reduction, she stated.
Diagnostic tests, via biomarker detection, using MALDI-TOF or ESI methods in combination with upfront sample preparation such as our ClinProt magnetic beads, is an emerging market for our company. We expect biomarker detection to grow in the clinical research world, although routine diagnostic testing is some where in the future.