apex^®-ultra Sets New Standard for High-Performance FTMS in Top-Down Proteomics and Complex Mixtures Analysis

Bruker Daltonics announced its new apex^®-ultra FTMS mass spectrometer, featuring wider mass range transmission, highest resolving power, even better mass accuracy and faster data acquisition. Bruker’s unique refrigerated FTMS magnet technology is available as an option at 7, 9.4, 12 and now even 15 tesla.

Overall, the novel apex-ultra is the most powerful and flexible FTMS system commercially available for ‘top-down’ proteomics and the analysis of complex mixtures, e.g. in metabolomics or petroleomics.

Top-down proteomics on the apex-ultra requires measuring with superb mass accuracy, excellent dynamic range and ultra-high resolving power at the same time. For the characterization of non-covalent complexes (e.g. drug/protein interactions or protein/protein interactions), a high mass range of greater than 4000 m/z is also required.

The apex-ultra features improved mass accuracy and resolving power through the development of tailored, low noise detection electronics, combined with Bruker’s patented Infinity™ analyzer cell and unique Sidekick™ ion accumulation system. The new apex-ultra is capable of sub-ppm mass accuracy and resolving powers of greater than 900,000 at m/z 400 at 7 tesla, or greater than 1,500,000 at m/z 400 at 9.4 tesla. This represents unparalleled resolution for interrogating proteins and protein fragments, as well as complex mixtures of small molecules in metabolomics or petroleomics. Even higher resolving power and better mass accuracy are available at 12 tesla or 15 tesla.

The apex-ultra also includes improved Q-q-electronics for extended mass range performance from m/z 100 to m/z 10,000. Extending the mass range for ion transmission addresses a wider range of applications, such as the investigation of non-covalent complexes. The apex-ultra data acquisition rates have also been significantly increased with the introduction of the new Nanobay™ console, which incorporates asynchronous data pipelines for FTMS data acquisition faster than one spectrum per second with resolving power of greater than 100,000, suitable for LC-FTMS and LC-MS/FTMS.

A unique feature of the apex-ultra is the mass-selective, continuous enrichment of low abundant species, e.g. selected post-translational modifications (PTMs). This represents an invaluable tool for top-down proteomics, as an enriched protein form can be investigated using fragmentation methods including CID, ECD, and/or IRMPD to produce exceptionally information-rich spectra.

Top-down proteomics requires unique processing tools that can effectively extract mass information from intrinsically very complex spectra. To facilitate this, the powerful Bruker Daltonics Compass™ software suite now includes:

i) SNAP2™, a peak-picking module that accurately determines and extracts monoisotopic mass information from high resolution data for large proteins and protein fragments,

ii) MaxEnt, a charge deconvolution method that is based on the popular Maximum Entropy algorithm for accurate and complete account of charge to produce a neutral-based mass spectrum, and

iii) BioTools™ for de novo sequencing, sequence annotation, and evaluation of results from protein database searches, e.g. using MASCOT.