Dimethylated Leucine Isobaric Tags for High-Throughput Proteome Analysis

High-throughput proteome analysis can be improved by using a novel set of isobaric tags called dimethylated leucine complementary ion (DiLeuC) (1). In a recent study published in Analytical and Bioanalytical Chemistry researchers from the University of Wisconsin–Madison proposed that isobaric tags could potentially offer a solution in conducting accurate quantitative analysis in complex samples. Their research offers a glimpse at the potential for DiLeuC to advance proteomic analysis.

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Isobaric tags are a labeling method in tandem mass spectrometry (MS/MS) analysis. These tags are designed to determine the amount of proteins from different sources in a single experiment (1). Conducting accurate high-throughput quantitative analysis of cellular proteomes across conditions such as time points and different perturbations creates a better understanding of treatment-induced responses and disease states (1).

MS analysis has been useful, but existing isobaric labeling methods have several limitations. Some of the main isobaric labeling methods, such as Tandem Mass Tag (TMT) and Isobaric Tags for Relative and Absolute Quantitation (iTRAQ), are incomplete analysis methods because of the indistinguishable low-mass reporter ions used for relative quantitation (1).

DiLeuC relies on complementary ions for relative quantification (1). Unlike traditional methods that suffer from ratio distortion caused by peptide coelution and cofragmentation, DiLeuC's complementary ions are remnant peptide segments in the high-mass range after fragmentation (1). These residual peptide fragments retain relative abundance information in an interference-free manner even within complex sample matrices.

To validate the accuracy of their method, the research team conducted experiments using a two-proteome model. They spiked the yeast proteome with a background human proteome, simulating a complex, real-world scenario. Remarkably, DiLeuC-based quantification demonstrated high precision, overcoming interference challenges, and providing a more accurate representation of protein abundance changes (1).

The researchers also extended the application of DiLeuC to single-cell proteome analysis, revealing its potential for sensitive high-throughput quantitative proteomics (1). The DiLeuC isobaric tags contribute toward advancing studying intricate biological processes and disease mechanisms at the cellular level, opening doors to new discoveries in fields such as cancer research, drug development, and personalized medicine (1).

The future of proteomics research is reliant on novel methods that improve upon existing techniques. The researchers’ introduction of the DiLeuC isobaric tags contributes to the advancement of this field.

Reference

(1) Li, M.; Ma, M.; Li, L. Development of novel isobaric tags enables accurate and sensitive multiplexed proteomics using complementary ions. Anal. Bioanal. Chem. 2023, ASAP. DOI: 10.1007/s00216-023-04877-3