ArticleAnalytical chemistry2025
Multiplexed Data-Independent Acquisition-Based Proteomics Enabled by TMTpro Complementary Ions.
Article in Analytical chemistry, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
1 citing paper in PubMed.
- Implementation of Nonisobaric TMT Analogs for Accurate Precursor-Level Quantification by plexDIA.Rapid communications in mass spectrometry : RCM · 2026Article
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Authors and funding
4 authors.
Funding
Abstract
Data-independent acquisition (DIA) has emerged as a powerful approach in quantitative proteomics, offering more comprehensive and reproducible proteome coverage than the conventional data-dependent acquisition (DDA) method. However, applying multiplexed isobaric labeling to DIA has been challenging due to ratio distortion caused by coisolation and cofragmentation interference. Here, we present a 3-plex TMTpro complementary ion (TMTproC)-based DIA strategy that leverages complementary ions in isobaric labeling to achieve accurate quantification without increasing spectral complexity. By implementing a 4-Da spacing between complementary ions, we significantly reduce isotopic envelope overlap and simplify deconvolution. We systematically optimized higher-energy collisional dissociation (HCD) settings for complementary ion generation and validated this approach using tryptic bovine serum albumin (BSA) peptides labeled at 1:1:1, 10:5:1, and 1:5:10 ratios, achieving median peptide-level ratios within 10% of expected values and median coefficients of variation (CVs) below 4% across triplicates. We further demonstrated this method by applying TMTproC labeling across a 10-fold dynamic range to the yeast proteome in a strong human proteome background. The results exhibited high quantification precision and minimal ratio distortion. Overall, TMTproC-DIA provides a robust, versatile, and scalable solution for high-throughput DIA-based proteomics.
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