N-Terminal amino acid side-chain cleavage of chemically modified peptides in the gas phase: A mass spectrometry technique for N-terminus identification

peer-reviewed · Bioorganic & Medicinal Chemistry · 2006

peer-reviewed · Bioorganic & Medicinal Chemistry · 2006. Almary Chacon et al. Although genome databases have become the key for proteomic analyses, de novo sequencing remains essential…
Date 2006-09-01
Type peer-reviewed
Venue Bioorganic & Medicinal Chemistry
Publisher Elsevier BV
Contribution adjacent
DOI 10.1016/j.bmc.2006.05.060
Citations (OpenAlex) 28

Abstract

Although genome databases have become the key for proteomic analyses, de novo sequencing remains essential for the study of organisms whose genomes have not been completed. In addition, post-translational modifications present a challenge in database searching. Recognition of the b or y-ion series in a peptide MS/MS spectrum as well as identification of the b1 - and yn-1 -ions can facilitate de novo analyses. Therefore, it is valuable to identify either amino-acid terminus. In previous work, we have demonstrated that peptides modified at the epsilon-amino group of lysine as a t-butyl peroxycarbamate derivative undergo free radical promoted peptide backbone fragmentation under low-energy collision-induced dissociation (CID) conditions. Here we explore the chemistry of the N-terminal amino group modified as a t-butyl peroxycarbamate. The conversion of N-terminal amines to peroxycarbamates of simple amino acids and peptides was studied with aryl t-butyl peroxycarbonates. ESI-MS/MS analysis of the peroxycarbamate adducts gave evidence of a product ion corresponding to the neutral loss of the N-terminal side chain (R), thus identifying this residue. Further fragmentation (MS3) of product ions formed by N-terminal residue side-chain loss (-R) exhibited an m/z shift of the b-ions equal to the neutral loss of R, therefore labeling the b-ion series. The study was extended to the analysis of a protein tryptic digest where the SALSA algorithm was used to identify spectra containing these neutral losses. The method for N-terminus identification presented here has the potential for improvement of de novo analyses as well as in constraining peptide mass mapping database searches.

Authors

  1. Almary Chacon · Vanderbilt University
  2. Douglas S. Masterson · University of Southern Mississippi
  3. Huiyong Yin · Vanderbilt University
  4. Daniel C. Liebler · Vanderbilt University
  5. Ned A. Porter · Vanderbilt University

Methods and tools

  • Peroxycarbamate N-terminal labelling: N-terminal t-butyl peroxycarbamate derivatives lose the N-terminal side chain in CID, identifying that residue and labelling the b-ion series to aid de novo sequencing.

Cites (8)

Cited by (3)

Seen in the charts

Back to the full map

Back to top