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Measurement of Ultrafast Vibrational Coherences in Polyatomic Radical Cations with Strong-Field Adiabatic Ionization
Published on: August 6, 2018
Factorial experimental designs elucidate significant variables affecting data acquisition on a quadrupole Orbitrap
Shan M Randall1, Helene L Cardasis, David C Muddiman
1W. M. Keck Fourier Transform Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA.
Journal of the American Society for Mass Spectrometry
|August 6, 2013
Summary
Optimizing quadrupole Orbitrap mass spectrometer parameters enhances global proteomic analyses. Balancing spectral quality and sequencing speed maximizes proteome coverage for data-dependent acquisition.
Area of Science:
- Mass Spectrometry
- Proteomics
- Analytical Chemistry
Background:
- Global proteomic analyses require optimized instrument parameters for comprehensive data acquisition.
- Data-dependent acquisition strategies are crucial for sequencing complex proteomes but necessitate careful parameter tuning.
Purpose of the Study:
- To optimize instrument parameter values for a quadrupole Orbitrap mass spectrometer for global proteomic analyses.
- To evaluate the influence of fourteen factors on data-dependent acquisition, focusing on sequencing rate and spectral quality.
Main Methods:
- Evaluated fourteen factors influencing data-dependent acquisition using a quadrupole Orbitrap mass spectrometer.
- Maximized unique peptides and protein groups as response variables to assess parameter impact.
- Analyzed MS/MS data based on ion abundance, comparing AGC target percentage with peptide-spectrum matches.
Main Results:
- Twelve of the fourteen evaluated factors showed significant contrast values (P < 0.05) for both response variables.
- Demonstrated that maximum ion injection time, automatic gain control, and minimum MS/MS thresholds significantly affect ion signal, spectra collected, and spectral quality.
- Established ion abundance thresholds for triggering MS/MS isolation and activation by correlating ion abundance with successful peptide-spectrum matches.
Conclusions:
- Achieving a balance between spectral quality and duty cycle is fundamental for maximizing proteome coverage in mass spectrometry.
- Optimized instrument parameters are essential for efficient and high-quality global proteomic data acquisition using data-dependent acquisition.
- Understanding ion abundance effects on MS/MS events aids in establishing effective data acquisition strategies.
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