The standard shotgun proteomics workflow consists of proteolytic digestion of complex protein mixtures and analysis of the resulting peptide mixtures by nano LC-MS/MS. 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 Thermo Scientific Q Exactive HF-X Hybrid Quadrupole-Orbitrap mass spectrometer. 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.

Join us to hear how:

• Professor Jesper Olsen set a new world record identifying 1,100 unique peptides in one minute
• Complex proteomic cell originated from a human HeLa cell line was analyzed by the Q Exactive HF-X mass spectrometer

• 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 Q Exactive HF-X MS for TMT 10-plex

• Scientists performing shotgun proteomics
• Scientists performing TMT workflows
• Scientists performing data-independent acquisition (DIA) workflows