Bottom-up protein identification has always been one of the most demanding tasks for biological MS experiments, requiring a combination of peak capacity, speed and sensitivity to sequence as many peptides as possible from a highly complex mixture of digested proteins. Trapped Ion Mobility Spectrometry (TIMS) adds an extra dimension of separation, resulting in unprecedented peak capacity and sensitivity and enabling the PASEF (Parallel Accumulation Serial Fragmentation) workflow for > 100Hz MS/MS with no sensitivity or resolution loss, all while operating at 100% duty cycle.
In a typical shotgun proteomics experiment, peptides from more than a million proteoforms, covering up to 10 orders of magnitude in concentration are separated by nano-LC typically using a 2 hour gradient. This represents a significant challenge for the mass spectrometer which must detect, isolate and fragment as many peptides as possible. Adding ion mobility as an extra dimension of separation has the potential to dramatically increase peak capacity. However, this must not be at the detriment of speed or sensitivity.