Acid Cleavable\nBiotin-Alkyne Improves Sensitivity\nfor Direct Detection of Biotin Labeled Peptides in Biorthogonal Noncanonical\nAmino Acid Tagging Analysis

Biorthogonal noncanonical amino acid tagging is a labeling\nstrategy\nthat covalently adds a biotin-alkyne (BA) to methionine analogs via\na click reaction. When methionine analogs are incorporated into a\nproteome, enrichment of the BA-labeled proteins allows the detection\nof newly synthesized proteins (NSP) by mass spectrometry. We previously\nreported that our direct detection of biotin-containing tags strategy\nincreased protein identifications by enriching for BA-peptides instead\nof BA-proteins. We compared the performance of cleavable BA (DADPS)\nand uncleavable BA in the identification and TMT quantification of\nthe NSP. DADPS identified and quantified more than double the number\nof peptides than uncleavable BA. Interrogation of the data revealed\nthat multiple factors are responsible for the superior performance\nof DADPS.