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Updated: Apr 20, 2026
Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
Published on: November 15, 2017
Partially isobaric peptide termini labeling assisted proteome quantitation based on MS and MS/MS signals
Shen Zhang1, Qi Wu1, Yichu Shan2
1National Chromatographic R. and A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China; University of Chinese Academy of Sciences, Beijing, China.
Abstract:
Isotopic labeling and isobaric labeling are two kinds of the typical quantification method that have been widely used in proteomics analysis. Herein, a novel quantitative strategy, partially isobaric peptide termini labeling (PITL), was developed to overcome the drawbacks of each above-mentioned labeling strategy, by simultaneously collecting the quantitative information from both MS and MS/MS spectrum. PITL is based on the site-selective N-terminus dimethylation labeling of peptide α-N-termini and the free ε-amino group of lysines, resulting in the partially isobaric labeling of peptides. The relative quantification can then be achieved by comparing the intensities of precursor ions in MS spectra and a, b and y ions in MS/MS spectra. The quantitative analysis of differently labeled yeast digests pooled with various ratios indicated the good quantitative accuracy, reproducibility, coverage and wide dynamic range of PITL strategy. Furthermore, PITL was applied to the quantitative proteome analysis of two mouse hepatocarcinoma ascites syngeneic cell lines with low and high lymph node metastasis rates (Hca-F and Hca-P). Given its low cost, simple operation and good accuracy, PITL might have great potential in the quantitative proteome analysis of biological samples.
Biological Significance:
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.
