A comprehensive investigation of proline fragmentation behavior in low-energy collision-induced dissociation peptide mass spectra

Nai Ping Dong, Liang Xiao Zhang, Yi Zeng Liang

Research output: Journal article publicationJournal articleAcademic researchpeer-review

12 Citations (Scopus)

Abstract

An investigation of more than 130 000 tandem mass spectra of proline-containing peptides extracted from Human and Ecoli peptide libraries in NIST Libraries (http://peptide.nist.gov/) is presented. In this study, fragmentation maps are drawn to show the fragmentation behavior of proline (Pro) in protonated peptides, taking the factors affecting the cleavage N-terminal to Pro as points of the map. In order to quantitatively characterize the fragmentation behavior of proline, probability of occurring selective cleavage at N-terminal side of Pro for each point is calculated. From the fragmentation maps, selective cleavage at N-terminal side of Pro is suppressed when all protons are sequestered by Args except at Asp-Pro and Glu-Pro. When protons are mobile, cleavage at N-terminal side of Pro is determined by pairwise cleavage Xxx-Pro and positions of proline in peptides. For triply and quadruply charged peptides, the Coulombic repulsion between protons affects the fragmentation of peptides and subsequently suppresses the cleavage at N-terminal side of Pro. Other fragmentation pathways influencing the fragmentation such as aspartic acid effect and yN-2/b2 pathway are also found. Investigation of multiple proline containing peptides shows similar influential factors and competition between multiple prolines.

Original languageEnglish
Pages (from-to)89-97
Number of pages9
JournalInternational Journal of Mass Spectrometry
Volume308
Issue number1
DOIs
Publication statusPublished - 1 Nov 2011
Externally publishedYes

Keywords

  • Proline effect
  • Proline fragmentation map
  • Protonated peptides
  • Specific cleavage effect
  • Statistical analysis

ASJC Scopus subject areas

  • Instrumentation
  • Condensed Matter Physics
  • Spectroscopy
  • Physical and Theoretical Chemistry

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