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In mass spectrometry (MS)‐based quantitative proteomics, labeling with isobaric mass tags such as iTRAQ and TMT can substantially improve sample throughput and reduce peptide missing values. Nonetheless, the quantification of labeled peptides tends to suffer from reduced accuracy due to the co‐isolation of co‐eluting precursors of similar mass‐to‐charge. Acquisition approaches such as multistage MS3...