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While phosphorylation and O‐GlcNAc (cytoplasmic and nuclear glycosylation) are linked to normal and pathological changes in cell states, these post‐translational modifications have been difficult to analyze in proteomic studies. We describe advances in β‐elimination / Michael addition‐based approaches which allow for mass spectrometry‐based identification and comparative quantification of O‐phosphate or O‐GlcNAc‐modified peptides, as well as cysteine‐containing peptides for expression analysis. The method (BEMAD) involves differential isotopic labeling through Michael addition with normal dithiothreitol (DTT) (d0) or deuterated DTT (d6), and enrichment of these peptides by thiol chromatography. BEMAD was comparable to isotope‐coded affinity tags (ICAT; a commercially available differential isotopic quantification technique) in protein expression analysis, but also provided the identity and relative …