Orbitrap Ascend Structural Biology Tribrid MS

Native MS option facilitates the identification of membrane proteins by top-down MS 
 

With the Orbitrap Ascend Structural Biology Tribrid Mass Spectrometer, it’s now possible to realize the potential of native proteomics to potential of native proteomics to identify individual proteins directly from complexes, including difficult to analyze membrane proteins. Natively prepared samples can be directly injected into the mass spectrometer and the proteins elucidated using their precursor and fragmentation patterns.

At the intact protein level, Proton Transfer Charge Reduction (PTCR) can simplify the spectra produced from complex samples. For top-down analysis, difficult-to-fragment proteins can be dissociated using multiple ion activation options, generating enough sequence coverage for high-confidence identification.

Utilizing PTCR for complex mixture analysis enables more identification across the m/z range  

High-efficiency precursor ion selection, afforded by the Native MS option together with Proton Transfer Charge Reduction (PTCR) allow for highly sensitive and fast PTCR analysis of complex native heterogeneous mixtures. By extending the mass range up to m/z 16,000, the charge state envelope and therefore molecular mass can be elucidated for signals that are buried in the background.

For proteins in membrane mimetics, such as nanodiscs, this allows researchers to gain information on their structure, producing informative results for lipid composition and protein-bound compounds.

Crosslinking experimentation is aided by Real-Time Library Search available on the Orbitrap Ascend Structural Biology MS  

The presence of single peptide with one cross-link (mono-links) complicates the process of true cross-linked peptides identification even after cross-linker enrichment. By analyzing the intensity ratios of specific peaks with enrichable cross-linkers, partial differentiation between true cross-links and mono-links is possible.

Real-Time Library Search-based triggering of high-resolution MS² scans significantly enhances true cross-link identifications, particularly in unenriched samples and when using short LC gradients, proving to be beneficial for higher throughput and sample-constrained biological projects.

Comprehensive disulfide bond mapping analysis using FAIMS and EThcD

Microwave Assisted Acid Hydrolysis (MAAH) effectively digests even non-reduced proteins in a relatively short time, generating massive redundancy in peptides as well as high background noise. FAIMS can effectively remove the chemical noise and bring all desired signals into view.
 

Combining Thermo Scientific FAIMS Pro Duo Interface with EThcD fragmentation generates highly informative spectra for the disulfide-bridged peptides with distinct diagnostic ions. Thermo Scientific Proteome Discoverer Software combined with the XlinkX node (developed in collaboration with Utrecht University) software suite effectively identifies the disulfide bridges and correctly quantifies their occupancy.

Characterize larger proteoforms by top-down proteomics

Top-down proteomics enables scientists to identify and structurally characterize protein sequence variants and post-translation modifications, known collectively as proteoforms, as they occur in the cell. Proton transfer charge reduction (PTCR) and the m/z 16,000 range afforded by native MS option elevate proteoform characterization to a new level, exploring larger proteins or more complex protein mixtures.
 

The same m/z range is isolated and fragmented for proteoform identification and primary structure characterization using Thermo Scientific ProSightPD Software.

Native MS option extends ion detection of large protein complexes

Native protein measurements allow for probing protein-protein interactions as they occur in the cell. Measuring up to m/z 16,000 with the Native MS option enables the analysis of larger and lower charged protein complexes. The Orbitrap Ascend Structural Biology MS can comprehensively characterize large protein complexes and their subunits by deploying alternative fragmentation approaches and MSⁿ capabilities.
 

Here we observe a single scan of GroEL, an 800,000 Da protein complex with a high signal-to-noise ratio made possible by optimized performance in extended m/z range.