Bruker Daltonics Announces World’s First Refrigerated 15 Tesla FTMS Magnet with New Tools for Top-down Protein Characterization

At the 2006 ASMS conference, Bruker Daltonics today announces new tools to accelerate the detailed top-down characterization of proteins using the Company’s apex®-Qe line of hybrid Fourier Transform mass spectrometers (Q-q-FTMS). These top-down tools include the world’s first 15.0 Tesla (T) refrigerated (R-series) FTMS magnet, along with a novel and proprietary method of charge deconvolution, based on maximum entropy and an advanced monoisotopic peak finder, called SNAP2™.

FTMS top-down methods of protein characterization are based on two key experimental capabilities: i) highly accurate molecular weight determination of the intact protein, and ii) fragmentation of the intact protein and analysis of the resulting complex mixture of fragments. Both benefit from FTMS detection with simultaneous high mass accuracy, high dynamic range and ultra-high resolution.

Ultimate FTMS performance is largely governed by magnetic field strength. Dynamic range, mass measurement accuracy, and mass resolving power in FTMS improve dramatically with increasing magnetic field. The innovative actively-shielded 15.0T magnet, developed in collaboration with the affiliated Bruker BioSpin group, will enable researchers to investigate larger proteins by top-down analysis, while providing better overall performance on an easy-to-use and easy-to-site platform.

The new 15T magnet is part of Bruker Daltonics’ unique R-series of FTMS magnets that incorporate innovative cryostats equipped with cryocooler refrigeration that replaces the conventional liquid nitrogen reservoir. Besides a smaller footprint, R-series magnets only require cryogens once a year, and annual cryogen costs are minimal.

The unique geometry of the apex-Qe FTMS enables mass-selective efficient enrichment of low abundant protein species, which can then be investigated using a combination of fragmentation methods including CID, ECD, and/or IRMPD. The resulting complex mass spectra are feature-rich and have very high-information content on primary protein structure, as well as on important post-translational modifications. The intrinsic complexity of, for example, ECD spectra requires sophisticated data processing tools that can effectively extract mass information. To facilitate this, Bruker Daltonics has now implemented MaxEnt, a charge deconvolution method that is based on the popular Maximum Entropy algorithm, to calculate a neutral-based mass spectrum that is amenable to data analysis routines such as BioTools™. Moreover, by combining the ion signals represented by multiple charge states, MaxEnt also improves the fidelity of isotopic distributions and increases the overall spectral signal-to-noise ratio.

Another challenge associated with the processing of top-down data is the extraction of monoisotopic masses from the experimentally observed isotopic profiles. The monoisotopic mass is important, because it gives the true molecular weight of the species being observed, but for large proteins the monoisotopic peak is often not observed due to its very low inherent abundance. Bruker Daltonics has developed SNAP2, a new peak-picking module that accurately determines and extracts the monoisotopic mass information from high-resolution spectra of proteins and protein fragments, even when the monoisotopic mass peak cannot experimentally be observed. The combination of these powerful new software features further strengthens the position of the apex-Qeas the preferred platform for detailed, ultra-high resolution top-down protein characterization.

“The ability to accurately extract monoisotopic peak information is crucial to analyzing feature-rich spectra from peptides and proteins. We are excited by the performance of the new SNAP2 algorithm and expect that it will significantly accelerate our biological MS efforts,” said Dr. Jon Amster, Professor of Chemistry at the University of Georgia. The Amster Research Group in the Department of Chemistry uses a 9.4T apex-Qein their laboratory for the investigation of complex biological samples.