This application note describes a qualitative and quantitative protein identifications using SONAR mode of acquisition.
A comparative study of DIA methodologies show qualitative improvements with increased protein identification numbers for data acquired using SONAR when compared against SWATH. Results based on varying gradient length showed SONAR to provide significantly more protein identifications than SWATH, particularly when adopting a shorter chromatographic timescale, i.e. the utilization of capillary LC for improved throughput and robustness. Reducing the gradient from 60 to 30 min resulted in only a marginal difference in protein identification rates for SONAR, whereas comparative SWATH data showed a decrease of 23%. The rapidly scanning nature of the quadrupole for SONAR also provides quantitative benefits, with precision being maintained for high throughput analysis.