Side Chain Cleavage in TEMPO‐assisted Free Radical Initiated Peptide Sequencing (FRIPS): Amino Acid Composition Information^#

Abstract

In tandem mass spectrometry, side‐chain losses are known to provide information on the presence of certain amino acid residues, which can improve peptide identification. In this study, we examine whether side‐chain losses also occur in free‐radical‐initiated peptide sequencing mass spectrometry (FRIPS MS). All four peptides examined here, i.e., ALPMHIR, YRPPGFSPFR, RPPGFSPYR, and YGGFLRRIRPKLK, showed extensive small group losses in the so‐called (M• – X) region. Furthermore, peaks due to small group loss accompanying backbone fragmentations were also extensively observed. The observed small group losses, either radical or neutral side‐chain losses, confirmed the presence of certain amino acids, even exhibiting signature peaks for isoleucine and leucine. In addition, mechanisms for small group losses in FRIPS MS are proposed.