Reporter ion-based mass spectrometry approaches for the detection of non-enzymatic protein modifications in biological samples

Research output: Contribution to journalArticle

Abstract

Development of mass spectrometry techniques to detect protein oxidation, which contributes to signalling and inflammation, is important. Label-free approaches have the advantage of reduced sample manipulation, but are challenging in complex samples owing to undirected analysis of large data sets using statistical search engines. To identify oxidised proteins in biological samples, we previously developed a targeted approach involving precursor ion scanning for diagnostic MS3 ions from oxidised residues. Here, we tested this approach for other oxidations, and compared it with an alternative approach involving the use of extracted ion chromatograms (XICs) generated from high-resolution MSMS data using very narrow mass windows. This accurate mass XIC data methodology was effective at identifying nitrotyrosine, chlorotyrosine, and oxidative deamination of lysine, and for tyrosine oxidations highlighted more modified peptide species than precursor ion scanning or statistical database searches. Although some false positive peaks still occurred in the XICs, these could be identified by comparative assessment of the peak intensities. The method has the advantage that a number of different modifications can be analysed simultaneously in a single LC-MSMS run. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine. Biological significance: The use of accurate mass extracted product ion chromatograms to detect oxidised peptides could improve the identification of oxidatively damaged proteins in inflammatory conditions. © 2013 Elsevier B.V.

LanguageEnglish
Pages71-79
Number of pages9
JournalJournal of Proteomics
Volume92
Early online date17 Apr 2013
DOIs
Publication statusPublished - 30 Oct 2013

Fingerprint

Mass spectrometry
Mass Spectrometry
Ions
Proteins
Oxidation
Scanning
Search Engine
Peptides
Deamination
Post Translational Protein Processing
Search engines
Lysine
Medicine
Tyrosine
Labels
Databases
Inflammation

Bibliographical note

Funding: Proxomics Project funded by EP/I017887/1 Cross-Disciplinary Research
Landscape Award. PIEF-GA-2009-255076for the project ATHERO_MASS.

Supplementary data to this article can be found online at
http://dx.doi.org/10.1016/j.jprot.2013.03.033

Keywords

  • accurate mass XIC
  • allysine
  • human serum albumin
  • precursor ion scanning
  • tyrosine chlorination
  • tyrosine nitration

Cite this

@article{8bcfc2ab7219478ca5fa9a1d7d4a4892,
title = "Reporter ion-based mass spectrometry approaches for the detection of non-enzymatic protein modifications in biological samples",
abstract = "Development of mass spectrometry techniques to detect protein oxidation, which contributes to signalling and inflammation, is important. Label-free approaches have the advantage of reduced sample manipulation, but are challenging in complex samples owing to undirected analysis of large data sets using statistical search engines. To identify oxidised proteins in biological samples, we previously developed a targeted approach involving precursor ion scanning for diagnostic MS3 ions from oxidised residues. Here, we tested this approach for other oxidations, and compared it with an alternative approach involving the use of extracted ion chromatograms (XICs) generated from high-resolution MSMS data using very narrow mass windows. This accurate mass XIC data methodology was effective at identifying nitrotyrosine, chlorotyrosine, and oxidative deamination of lysine, and for tyrosine oxidations highlighted more modified peptide species than precursor ion scanning or statistical database searches. Although some false positive peaks still occurred in the XICs, these could be identified by comparative assessment of the peak intensities. The method has the advantage that a number of different modifications can be analysed simultaneously in a single LC-MSMS run. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine. Biological significance: The use of accurate mass extracted product ion chromatograms to detect oxidised peptides could improve the identification of oxidatively damaged proteins in inflammatory conditions. {\circledC} 2013 Elsevier B.V.",
keywords = "accurate mass XIC, allysine, human serum albumin, precursor ion scanning, tyrosine chlorination, tyrosine nitration",
author = "{Tveen Jensen}, Karina and Ana Reis and Laetitia Mouls and Pitt, {Andrew R.} and Spickett, {Corinne M.}",
note = "Funding: Proxomics Project funded by EP/I017887/1 Cross-Disciplinary Research Landscape Award. PIEF-GA-2009-255076for the project ATHERO_MASS. Supplementary data to this article can be found online at http://dx.doi.org/10.1016/j.jprot.2013.03.033",
year = "2013",
month = "10",
day = "30",
doi = "10.1016/j.jprot.2013.03.033",
language = "English",
volume = "92",
pages = "71--79",
journal = "Journal of Proteomics",
issn = "1874-3919",
publisher = "Elsevier",

}

TY - JOUR

T1 - Reporter ion-based mass spectrometry approaches for the detection of non-enzymatic protein modifications in biological samples

AU - Tveen Jensen, Karina

AU - Reis, Ana

AU - Mouls, Laetitia

AU - Pitt, Andrew R.

AU - Spickett, Corinne M.

N1 - Funding: Proxomics Project funded by EP/I017887/1 Cross-Disciplinary Research Landscape Award. PIEF-GA-2009-255076for the project ATHERO_MASS. Supplementary data to this article can be found online at http://dx.doi.org/10.1016/j.jprot.2013.03.033

PY - 2013/10/30

Y1 - 2013/10/30

N2 - Development of mass spectrometry techniques to detect protein oxidation, which contributes to signalling and inflammation, is important. Label-free approaches have the advantage of reduced sample manipulation, but are challenging in complex samples owing to undirected analysis of large data sets using statistical search engines. To identify oxidised proteins in biological samples, we previously developed a targeted approach involving precursor ion scanning for diagnostic MS3 ions from oxidised residues. Here, we tested this approach for other oxidations, and compared it with an alternative approach involving the use of extracted ion chromatograms (XICs) generated from high-resolution MSMS data using very narrow mass windows. This accurate mass XIC data methodology was effective at identifying nitrotyrosine, chlorotyrosine, and oxidative deamination of lysine, and for tyrosine oxidations highlighted more modified peptide species than precursor ion scanning or statistical database searches. Although some false positive peaks still occurred in the XICs, these could be identified by comparative assessment of the peak intensities. The method has the advantage that a number of different modifications can be analysed simultaneously in a single LC-MSMS run. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine. Biological significance: The use of accurate mass extracted product ion chromatograms to detect oxidised peptides could improve the identification of oxidatively damaged proteins in inflammatory conditions. © 2013 Elsevier B.V.

AB - Development of mass spectrometry techniques to detect protein oxidation, which contributes to signalling and inflammation, is important. Label-free approaches have the advantage of reduced sample manipulation, but are challenging in complex samples owing to undirected analysis of large data sets using statistical search engines. To identify oxidised proteins in biological samples, we previously developed a targeted approach involving precursor ion scanning for diagnostic MS3 ions from oxidised residues. Here, we tested this approach for other oxidations, and compared it with an alternative approach involving the use of extracted ion chromatograms (XICs) generated from high-resolution MSMS data using very narrow mass windows. This accurate mass XIC data methodology was effective at identifying nitrotyrosine, chlorotyrosine, and oxidative deamination of lysine, and for tyrosine oxidations highlighted more modified peptide species than precursor ion scanning or statistical database searches. Although some false positive peaks still occurred in the XICs, these could be identified by comparative assessment of the peak intensities. The method has the advantage that a number of different modifications can be analysed simultaneously in a single LC-MSMS run. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine. Biological significance: The use of accurate mass extracted product ion chromatograms to detect oxidised peptides could improve the identification of oxidatively damaged proteins in inflammatory conditions. © 2013 Elsevier B.V.

KW - accurate mass XIC

KW - allysine

KW - human serum albumin

KW - precursor ion scanning

KW - tyrosine chlorination

KW - tyrosine nitration

UR - http://www.scopus.com/inward/record.url?scp=84886952989&partnerID=8YFLogxK

U2 - 10.1016/j.jprot.2013.03.033

DO - 10.1016/j.jprot.2013.03.033

M3 - Article

VL - 92

SP - 71

EP - 79

JO - Journal of Proteomics

T2 - Journal of Proteomics

JF - Journal of Proteomics

SN - 1874-3919

ER -