Multi-parameter optimization of two common proteomics quantification methods for quantifying

To improve the sensitivity and accuracy of label-free quantification and tandem mass tags (TMT) labeling in quantifying low-abundance proteins, multi-parameter optimization was carried out using a complex 2-proteome artificial sample mixture for a series of steps from sample preparation to data analysis, including the desalting of peptides, peptide injection amount for LC-MS/MS, MS1 resolution, the length of LC-MS/MS gradient, AGC targets, ion accumulation time, MS2 resolution, precursor co-isolation threshold, data analysis software, statistical calculation methods and protein fold changes. Five subprojects were included for this project.