Ion mobility tandem mass spectrometry enhances performance of bottom-up proteomics

We describe a novel method utilizing ion mobility-based concentration of peptide fragment ions on a qTOF mass spectrometer improving the sensitivity of bottom-up proteomics by up to 10-fold. This enabled the identification of 7,500 human proteins within one day and 8,600 phosphorylation sites within 5h of LC-MS/MS time. The method also proved powerful for multiplexed quantification experiments exemplified by the chemoproteomic interaction analysis of HDACs with Trichostatin A.