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RATIONALE  Tandem mass (MS/MS) spectra generated by collision‐induced dissociation (CID) typically lack redundant peptide sequence information in the form of e.g. b‐ and y‐ion series due to frequent use of sequence‐specific endopeptidases cleaving C‐ or N‐terminal to Arg or Lys residues.    METHODS  Here we introduce arginyl‐tRNA protein transferase (ATE, EC 2.3.2.8) for proteomics. ATE recognizes acidic amino acids or oxidized Cys at the N‐terminus of a substrate peptide and conjugates an arginine from an aminoacylated tRNA Arg  onto the N‐terminus of the substrate peptide. This enzymatic reaction is carried out under physiological conditions and, in combination with Lys‐C/Asp‐N double digest, results in arginylated peptides with basic amino acids on both termini.    RESULTS  We demonstrate that  in vitro  arginylation of peptides using yeast arginyl tRNA protein transferase 1 (yATE1) is a robust enzymatic reaction, specific to only modifying N‐terminal acidic amino acids. Precursors originating from arginylated peptides generally have an increased protonation state compared with their non‐arginylated forms. Furthermore, the product ion spectra of arginylated peptides show near complete 2× fragment ladders within the same MS/MS spectrum using commonly available electrospray ionization peptide fragmentation modes. Unexpectedly, arginylated peptides generate complete y‐ and c‐ion series using electron transfer dissociation (ETD) despite having an internal proline residue.    CONCLUSIONS  We introduce a rapid enzymatic method to generate peptides flanked on either terminus by basic amino acids, resulting in a rich, redundant MS/MS fragment pattern. © 2014 The Authors.  Rapid Communications in Mass Spectrometry  published by John Wiley & Sons Ltd.

Enzymatic generation of peptides flanked by basic amino acids to obtain MS/MS spectra with 2× sequence coverage