Benchmarking the Q Exactive HF-X MS for Shotgun Proteomics

Key learning objectives of this seminar:

• Methods for sample preparation and LC and MS methods for high-throughput shotgun proteomics
• MS acquisition methodology used for very deep single-shot proteomics
• Multiplexed tandem mass tag quantification methods on the Thermo Scientific Q Exactive HF-X Hybrid Quadrupole-Orbitrap mass spectrometer for TMT 10-plex

With advances in mass resolution, mass accuracy, fragmentation technology, and speed, bottom-up analysis can identify more proteins in more-complex samples than ever. Moreover, the techniques and principles involved are generally foundational for more complex experiments. Here, we evaluate the performance of the newly introduced Q Exactive HF-X MS. Various MS methods and LC gradient lengths were evaluated for bottom-up proteomics. The largest gains were found at ultrashort gradients with a fast acquisition method resulting in more than 1,100 unique peptide sequences per minute. Additional data will be shown for phosphoproteomics with tandem isobaric mass tag (TMT10-plex) and data-independent acquisition (DIA) analysis on the new Q Exactive HF-X mass spectrometer.

Sign up to watch the webinar and download the executive summary detailing:

• The hardware and software improvements that enable the Q Exactive HF-X MS to push the speed and sensitivity limits of protein identification