Recent advances in isobaric labeling and applications in quantitative proteomics

Mass spectrometry (MS) has emerged at the forefront of quantitative proteomic techniques. Liquid chromatography-mass spectrometry (LC-MS) can be used to determine abundances of proteins and peptides in complex biological samples. Several methods have been developed and adapted for accurate quantification based on chemical isotopic labeling. Among various chemical isotopic labeling techniques, isobaric tagging approaches rely on the analysis of peptides from MS2-based quantification rather than MS1-based quantification. In this review, we will provide an overview of several isobaric tags along with some recent developments including complementary ion tags, improvements in sensitive quantitation of analytes with lower abundance, strategies to increase multiplexing capabilities, and targeted analysis strategies. We will also discuss limitations of isobaric tags and approaches to alleviate these restrictions through bioinformatic tools and data acquisition methods. This review will highlight several applications of isobaric tags, including biomarker discovery and validation, thermal proteome profiling, cross-linking for structural investigations, single-cell analysis, top-down proteomics, along with applications to different molecules including neuropeptides, glycans, metabolites, and lipids, while providing considerations and evaluations to each application.

Automated summary

This article provides an overview of the application of mass spectrometry (MS) in quantitative proteomics. Liquid chromatography-mass spectrometry (LC-MS) is a powerful technique for accurately quantifying proteins and peptides in complex biological samples. Isobaric tagging, a commonly used chemical isotopic labeling technique, allows for quantification based on MS2 peptide analysis. The article also discusses recent developments in isobaric tagging methods and improvements, as well as limitations and approaches to address them. The review highlights the diverse applications of isobaric tags in biomarker discovery, thermal proteome profiling, cross-linking structural investigations, single-cell analysis, top-down proteomics, and analysis of neuropeptides, glycans, metabolites, and lipids. Considerations and evaluations are provided for each application.