Using the inherent quantitative peak areas of mass signals from peptides analysed by mass spectrometry provides a convenient approach to comparing protein expression in a large number of samples (>10). The average of the peak areas of the three best peptides identifying a protein is used.
With the Orbitrap Fusion, we also have the capability of using data-independent analysis (DIA) approach. For this, we generate a bespoke spectral library of MS/MS for the biological system under study, against which data from experimental samples can be searched for protein identification and quantification. DIA is particularly useful for high throughput analysis of large sample cohorts.