Bruker Daltonics Introduces Next-Generation ETD II Top-Down Capability for its Proteomics Market-Leading HCT-Ultra™ High Capacity Ion Trap

At Pittcon 2008, Bruker Daltonics announces ETD II, a next-generation ETD (electron transfer dissociation) module for its HCT-Ultra™ high capacity ion traps. ETD is a very powerful peptide and protein fragmentation technique that preserves functionally important post-translational modifications (PTMs), such as phosphorylations or glycosylations. With ETD in a spherical high-capacity ion trap, the sequencing and identification of proteins, as well as the identification and localization of PTMs are facilitated with greatly improved scores and confidence.

In 2005, Bruker Daltonics introduced the first commercial ion trap equipped with ETD, which quickly became the market leader for ETD-ITMS due to the unique advantages of its spherical geometry, which easily traps positive analyte ions and negative ions in the same small spherical volume for maximum ETD interaction efficiency. This spherical trap geometry yields far improved ETD sensitivity, with a factor of 10-100x better sensitivity than ETD in linear ion traps. ETD also overcomes the low-mass cut-off in ion traps. Due to its superior ion trap mass accuracy, the HCT-Ultra with ETD enables powerful de novo sequencing capabilities, even for difficult to dissociate proteins.

In 2007, the related PTR (Proton Transfer Reaction) technology was first introduced commercially by Bruker. Due to the HCT-Ultra’s inherent greater m/z range of 3,000, and its better mass resolution that can resolve 3+ and 4+ charge states of peptides on-the-fly at full analytical speed, ETD/PTR on the HCT-Ultra can be used for proteins up to and above 12 kDalton, providing an estimated factor of 3x higher effective protein mass range than on linear ion traps.

With proven market and performance leadership in ETD/PTR, Bruker now enhances this key proteomics technology even further with the introduction the improved ETD II accessory. ETD II is based on a novel and compact nCI (negative chemical ionization) source with increased ETD/PTR reactant ion generation, resulting in rapid, sub-fmol sensitivity for the confident characterization of PTMs. In combination with the ETD efficiency and sensitivity advantages of the spherical high capacity trap, ETD II is designed to provide the most sensitive, fastest and robust ETD fragmentation, plus the PTR effective mass range extension for intact protein characterization and top-down PTM characterization.

Dr. Detlev Suckau, Head of Proteomics Applications Development at Bruker Daltonics, commented: "Modern proteomics has moved beyond simple identification, and one of the primary goals of functional proteomics is now the unraveling of the many subtle modifications arising in proteins, which often are very important for their biological activity. By making ETD II available to protein scientists for PTM analyses on the high performance HCT-Ultra, we now can make available to every proteomics laboratory not only easy-to-use, robust, fully automated and exquisitely sensitive PTM analysis capabilities for peptides, but even for proteins up to approximately 12 kDalton in mass."
Frank Laukien, Ph.D., the President of Bruker Daltonics, added: “For any modern proteomics laboratory, we believe that advanced ETD capabilities for PTM analysis, higher protein sequence coverage, and even de novo sequencing, are highly desirable, if not a ‘must have’ today. When fully integrated under our ProteinScape 2.0 software, which is essential for managing any sizeable proteomics project, the combination of the high-performance ultraflex III MALDI-TOF/TOF and the high-capacity spherical HCT-ultra ion trap with ETD/PTR, is perhaps the most powerful combination available today for bottom-up proteomics, quantitative proteomics, PTM discovery and localization, peptide and protein MALDI imaging, as well as for top-down analysis of small low-abundance proteins in proteomics, or of larger recombinant proteins.”

He continued: ”For high-throughput biomarker validation and quantitation, they are complemented by the unique 2 mDalton high-resolution Extracted Ion Chromatogram (hrEIC) capabilities of our new micrOTOF-Q II system. When one is finally ‘drilling’ down on the precise details of a target protein and its isoforms, the unmatched high-resolution ECD top-down capabilities of the apex-ultra ESI/MALDI-FTMS systems with its unique continuous accumulation of selection ions (CASI™) for selective enrichment of top-down pre-cursors is an amazingly powerful problem solver for targeted, detailed protein research.”