Data independent (DIA) LC-MS/MS quantifies many thousands of proteins in a single experiment, however the unequivocal quality standards have not been established yet.
We developed a simple rationale protocol to validate the DIA LC-MS/MS quantification and optimize major experimental and data processing settings. The protocol relies on the series of proteome mixtures from different organisms and is powered by R-script. The optimized DIA LC-MS/MS offers a demonstrated ability to monitor differential expression and provide data for functional enrichment analysis to decipher the biological significance of proteome-wide perturbations.
Contact: jumel(at)mpi-cbg.de