A modified database search strategy leads to improved identification of in vitro brominated peptides spiked into a complex proteomic sample

Huiling Liu, Cheryl F. Lichti, Barsam Mirfattah, Jennifer Frahm, Carol L. Nilsson

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Inflammation leads to activation of immune cells, resulting in production of hypobromous acid. Few investigations have been performed on protein bromination on a proteomic scale, even though bromination is a relatively abundant protein modification in endogenously brominated proteomes. Such studies have been hampered by the lack of an optimized database search strategy. In order to address this issue, we performed nano-LC-MS/MS analysis of an in vitro generated, trypsin-digested brominated human serum albumin standard, spiked into a complex trypsin-digested proteomic background, in an LTQ-Orbitrap instrument. We found that brominated peptides spiked in at a 1-10% ratio (mass:mass) were easily identified by manual inspection when higher-energy collisional dissociation (HCD) and collision induced dissociation (CID) were employed as the dissociation mode; however, confident assignment of brominated peptides from protein database searches required a novel approach. By addition of a custom modification, corresponding to the substitution of a single bromine with 81Br rather than 79Br for dibromotyrosine ( 79Br81BrY), the number of validated assignments for peptides containing dibromotyrosine increased significantly when analyzing both high resolution and low resolution MS/MS data. This new approach will facilitate the identification of proteins derived from endogenously brominated proteomes, providing further knowledge about the role of protein bromination in various pathological states.

Original languageEnglish (US)
Pages (from-to)4248-4254
Number of pages7
JournalJournal of Proteome Research
Volume12
Issue number9
DOIs
StatePublished - Sep 6 2013

Fingerprint

Proteomics
Halogenation
Databases
Peptides
Proteome
Trypsin
Proteins
Bromine
Protein Databases
Serum Albumin
Inflammation
Substitution reactions
Inspection
Chemical activation
In Vitro Techniques

Keywords

  • bioinformatics
  • CID
  • HCD
  • mass spectrometry
  • post-translational modification
  • protein bromination
  • proteomics

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

A modified database search strategy leads to improved identification of in vitro brominated peptides spiked into a complex proteomic sample. / Liu, Huiling; Lichti, Cheryl F.; Mirfattah, Barsam; Frahm, Jennifer; Nilsson, Carol L.

In: Journal of Proteome Research, Vol. 12, No. 9, 06.09.2013, p. 4248-4254.

Research output: Contribution to journalArticle

Liu, Huiling ; Lichti, Cheryl F. ; Mirfattah, Barsam ; Frahm, Jennifer ; Nilsson, Carol L. / A modified database search strategy leads to improved identification of in vitro brominated peptides spiked into a complex proteomic sample. In: Journal of Proteome Research. 2013 ; Vol. 12, No. 9. pp. 4248-4254.
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abstract = "Inflammation leads to activation of immune cells, resulting in production of hypobromous acid. Few investigations have been performed on protein bromination on a proteomic scale, even though bromination is a relatively abundant protein modification in endogenously brominated proteomes. Such studies have been hampered by the lack of an optimized database search strategy. In order to address this issue, we performed nano-LC-MS/MS analysis of an in vitro generated, trypsin-digested brominated human serum albumin standard, spiked into a complex trypsin-digested proteomic background, in an LTQ-Orbitrap instrument. We found that brominated peptides spiked in at a 1-10{\%} ratio (mass:mass) were easily identified by manual inspection when higher-energy collisional dissociation (HCD) and collision induced dissociation (CID) were employed as the dissociation mode; however, confident assignment of brominated peptides from protein database searches required a novel approach. By addition of a custom modification, corresponding to the substitution of a single bromine with 81Br rather than 79Br for dibromotyrosine ( 79Br81BrY), the number of validated assignments for peptides containing dibromotyrosine increased significantly when analyzing both high resolution and low resolution MS/MS data. This new approach will facilitate the identification of proteins derived from endogenously brominated proteomes, providing further knowledge about the role of protein bromination in various pathological states.",
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