Data Independent Label-Free Quantification of Low Abundance Proteins
The quantitative analysis of complex protein mixtures requires tryptic digestion, coupled with a protein identification strategy that accurately identifies proteins with high reproducibility. This has often been overlooked and many quantitative measurements have been based upon spurious identifications. The depth to which a complex sample can be interrogated is also crucial as this defines the lowest abundance limit of proteins that may be quantified. Waters® SYNAPT® G2-S Mass Spectrometry System has substantial improvements in performance: mass resolution and accuracy, dynamic range, and sensitivity. These enable highly accurate protein identifications and label-free, relative protein quantification, which we present here.