Microbore High Throughput Ion Mobility Enabled Mass Spectrometry for Utilisation of Large Cohort Studies

The deployment of proteomic analysis in clinical studies represents a significant opportunity to detect and validate biomarkers in translational medicine, improve disease understanding and provide baseline information on population health. However, comprehensive proteome studies usually employ nano-scale chromatography and often require several hours of analysis/sample. Here we describe a high throughput LC/MS/MS methodology using 1mm scale chromatography requiring only 15 min/sample, coupled to ion mobility-enabled mass spectrometry. The short run time effected a 6 – fold increase in productivity compared with nano-scale LC/MS. The method demonstrated excellent reproducibility with retention time CVs of less than 0.05 % and peak area reproducibility ranging from 5 – 15%. The 1mm system produced similar chromatographic peak capacity values as the miniaturized system, detecting 90% of the E.coli proteins identified by the 75µm LC/MS system. Application to the analysis of serum samples from a human prostate cancer study resulted in the identification of a total of 533 proteins revealing the differential expression of proteins linked to patients receiving hormone-radiotherapy or surgery.