Partially isobaric peptide termini labeling assisted proteome quantitation based on MS and MS/MS signals.

Abstract

The partially isobaric peptide termini labeling (PITL) method enabled to simultaneously obtain the quantitative information from MS and MS/MS spectrum, which combined the advantages of these two strategies. Relative quantification could be achieved by comparing the intensities of parent ions in MS spectra and a, b, y ions in the MS/MS spectra. The quantitative analysis for differently labeled yeast digests mixed at various ratios indicated the good accuracy, reproducibility, quantitative coverage and wide dynamic range of the PITL strategy. Finally, we found 84 differentially expressed proteins in mouse hepatocarcinoma ascites syngeneic cell lines with low and high lymph node metastasis rates with PITL strategy and 77 proteins of them were consistently quantified in our previous studies.