FT-ICR MS optimization for the analysis of intact proteins

Area of Science:

• Analytical Chemistry
• Biochemistry
• Physical Chemistry

Background:

• Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is crucial for top-down proteomics, analyzing intact proteins.
• A novel compensated open cylindrical ion trapping cell was integrated into a 12 T FT-ICR-MS instrument.
• This cell previously enhanced analysis of smaller peptides by approximating ideal harmonic trapping potentials.

Purpose of the Study:

• To optimize the FT-ICR-MS instrument with the new ion trapping cell for analyzing large biomolecular ions, such as proteins.
• To investigate the impact of increased post-excitation cyclotron radii on ion behavior and signal characteristics.
• To evaluate a proposed high-energy ion loss mechanism and its effect on macromolecular ion analysis.

Main Methods:

• Instrument optimization for large biomolecular ion analysis using a compensated open cylindrical ion trapping cell.
• Acquisition of single transient mass spectra for multiply charged bovine ubiquitin ions.
• Evaluation of ion loss mechanisms through experimental comparison with bovine ubiquitin and serum albumin.

Main Results:

• Sub-ppm mass measurement accuracy, improved signal intensity, and increased dynamic range were achieved for bovine ubiquitin ions.
• Increased cyclotron radii led to higher ion kinetic energy, potentially causing fragmentation via ion-neutral collisions.
• Reduced pressure in the ion trapping cell minimized high-energy ion losses, enhancing sensitivity and mass accuracy without sacrificing resolution.

Conclusions:

• The optimized FT-ICR-MS system significantly improves the analysis of large biomolecules.
• Minimizing high-energy ion losses through reduced cell pressure is key for enhanced sensitivity and mass accuracy.
• The findings are broadly applicable to FTMS and likely relevant to Orbitrap mass analyzers.