Collision‐induced fragmentations of the (M‐H)− parent anions of underivatized peptides: An aid to structure determination and some unusual negative ion cleavages

Abstract I. Introduction 87 II. Discussion 88 A. The Backbone Cleavages of (M‐H) − Parent Anions of Peptides 88 1. α‐ and β‐Backbone Cleavages 89 2. The β′ Cleavage 92 3. The Asp and Asn γ and δ Backbone Cleavages (Also Phe, Tyr, His, and Trp) 94 4. The δ‐ and γ‐Cleavages of Glu and Gln 96 5. Ser and Thr Cleavages: Side Chain and Backbone Fragmentations 99 a. The side chain cleavages 99 b. The backbone cleavage reactions of Ser and Thr 100 6. Other Backbone Cleavage Processes 102 Acknowledgments 105 References 105 This article describes the fundamental cleavage reactions of (M‐H) − anions of underivatized peptides that contain up to 25 amino acid residues. The experimental observations of these cleavages have been backed up by molecular modeling, generally at the AM1 level of theory. The basic cleavages are the ubiquitous α‐ and β‐backbone cleavage reactions, which provide information similar to that of the B and Y + 2 cleavages of MH + ions of peptides. The residues Asp and Asn also effect cleavages of the backbone (called δ‐ and γ‐cleavages), by reactions initiated from side chain enolate anions, causing elimination reactions that cleave the backbone between the Asp (Asn) NC backbone bond. Glu and Gln also direct analogous δ‐ and γ‐cleavages of the backbone, but in this case the processes are initiated by attack of the side chain CO 2 − (CONH − ) to form a lactone (lactam). Ser and Thr residues undergo characteristic fragmentations of the side chain. These processes, losses of CH 2 O (Ser) and MeCHO (Thr), convert these residues into Gly. In larger peptides, Ser and Thr can effect two backbone cleavage reactions, called γ‐ and ε‐processes. The C‐terminal CO 2 − (or CONH − ) forms a hydrogen bond with the side chain OH (of Ser or Thr), placing the C‐terminal residue in a position where it may affect S N 2 attack at the electrophilic backbone CH of Ser, with concomitant cleavage of the backbone. All of the above negative ion cleavages require the peptide backbone to be conformationally flexible. However, there is a backbone cleavage that requires the peptide to have an alpha‐helical conformation in order for the two reacting centers to approach. This cleavage is illustrated for the Glu23‐initiated backbone cleavage at Ile21 for the (M‐H) − anion of the antimicrobial peptide caerin 1.1. © 2002 Wiley Periodicals, Inc., Mass Spec Rev 21:87–107, 2002; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/mas.10022