Proposal for a common nomenclature for fragment ions in mass spectra of lipids

Josch K Pauling, Martin Hermansson, Jürgen Hartler, Klaus Christiansen, Sandra F Gallego, Bing Peng, Robert Ahrends, Christer S Ejsing

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Advances in mass spectrometry-based lipidomics have in recent years prompted efforts to standardize the annotation of the vast number of lipid molecules that can be detected in biological systems. These efforts have focused on cataloguing, naming and drawing chemical structures of intact lipid molecules, but have provided no guidelines for annotation of lipid fragment ions detected using tandem and multi-stage mass spectrometry, albeit these fragment ions are mandatory for structural elucidation and high confidence lipid identification, especially in high throughput lipidomics workflows. Here we propose a nomenclature for the annotation of lipid fragment ions, describe its implementation and present a freely available web application, termed ALEX123 lipid calculator, that can be used to query a comprehensive database featuring curated lipid fragmentation information for more than 430,000 potential lipid molecules from 47 lipid classes covering five lipid categories. We note that the nomenclature is generic, extendable to stable isotope-labeled lipid molecules and applicable to automated annotation of fragment ions detected by most contemporary lipidomics platforms, including LC-MS/MS-based routines.

Original languageEnglish
Pages (from-to)e0188394
Number of pages21
JournalPLoS ONE
Volume12
Issue number11
DOIs
Publication statusPublished - Nov 2017

Fingerprint

Terminology
Ions
ions
Lipids
lipids
Molecules
Mass spectrometry
Mass Spectrometry
Cataloging
mass spectrometry
Workflow
Biological systems
Isotopes
chemical structure
stable isotopes
Throughput
Databases
Guidelines

Keywords

  • Algorithms
  • Databases, Chemical
  • Ions
  • Isotope Labeling
  • Lipids
  • Molecular Structure
  • Tandem Mass Spectrometry
  • Journal Article
  • Lipid fragmentation

Fields of Expertise

  • Human- & Biotechnology

Treatment code (Nähere Zuordnung)

  • Application
  • Basic - Fundamental (Grundlagenforschung)

Cite this

Pauling, J. K., Hermansson, M., Hartler, J., Christiansen, K., Gallego, S. F., Peng, B., ... Ejsing, C. S. (2017). Proposal for a common nomenclature for fragment ions in mass spectra of lipids. PLoS ONE, 12(11), e0188394. https://doi.org/10.1371/journal.pone.0188394

Proposal for a common nomenclature for fragment ions in mass spectra of lipids. / Pauling, Josch K; Hermansson, Martin; Hartler, Jürgen; Christiansen, Klaus; Gallego, Sandra F; Peng, Bing; Ahrends, Robert; Ejsing, Christer S.

In: PLoS ONE, Vol. 12, No. 11, 11.2017, p. e0188394.

Research output: Contribution to journalArticleResearchpeer-review

Pauling, JK, Hermansson, M, Hartler, J, Christiansen, K, Gallego, SF, Peng, B, Ahrends, R & Ejsing, CS 2017, 'Proposal for a common nomenclature for fragment ions in mass spectra of lipids' PLoS ONE, vol. 12, no. 11, pp. e0188394. https://doi.org/10.1371/journal.pone.0188394
Pauling JK, Hermansson M, Hartler J, Christiansen K, Gallego SF, Peng B et al. Proposal for a common nomenclature for fragment ions in mass spectra of lipids. PLoS ONE. 2017 Nov;12(11):e0188394. https://doi.org/10.1371/journal.pone.0188394
Pauling, Josch K ; Hermansson, Martin ; Hartler, Jürgen ; Christiansen, Klaus ; Gallego, Sandra F ; Peng, Bing ; Ahrends, Robert ; Ejsing, Christer S. / Proposal for a common nomenclature for fragment ions in mass spectra of lipids. In: PLoS ONE. 2017 ; Vol. 12, No. 11. pp. e0188394.
@article{a19bd74481de4e4795f981df4edcd929,
title = "Proposal for a common nomenclature for fragment ions in mass spectra of lipids",
abstract = "Advances in mass spectrometry-based lipidomics have in recent years prompted efforts to standardize the annotation of the vast number of lipid molecules that can be detected in biological systems. These efforts have focused on cataloguing, naming and drawing chemical structures of intact lipid molecules, but have provided no guidelines for annotation of lipid fragment ions detected using tandem and multi-stage mass spectrometry, albeit these fragment ions are mandatory for structural elucidation and high confidence lipid identification, especially in high throughput lipidomics workflows. Here we propose a nomenclature for the annotation of lipid fragment ions, describe its implementation and present a freely available web application, termed ALEX123 lipid calculator, that can be used to query a comprehensive database featuring curated lipid fragmentation information for more than 430,000 potential lipid molecules from 47 lipid classes covering five lipid categories. We note that the nomenclature is generic, extendable to stable isotope-labeled lipid molecules and applicable to automated annotation of fragment ions detected by most contemporary lipidomics platforms, including LC-MS/MS-based routines.",
keywords = "Algorithms, Databases, Chemical, Ions, Isotope Labeling, Lipids, Molecular Structure, Tandem Mass Spectrometry, Journal Article, Lipid fragmentation",
author = "Pauling, {Josch K} and Martin Hermansson and J{\"u}rgen Hartler and Klaus Christiansen and Gallego, {Sandra F} and Bing Peng and Robert Ahrends and Ejsing, {Christer S}",
year = "2017",
month = "11",
doi = "10.1371/journal.pone.0188394",
language = "English",
volume = "12",
pages = "e0188394",
journal = "PLoS ONE",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "11",

}

TY - JOUR

T1 - Proposal for a common nomenclature for fragment ions in mass spectra of lipids

AU - Pauling, Josch K

AU - Hermansson, Martin

AU - Hartler, Jürgen

AU - Christiansen, Klaus

AU - Gallego, Sandra F

AU - Peng, Bing

AU - Ahrends, Robert

AU - Ejsing, Christer S

PY - 2017/11

Y1 - 2017/11

N2 - Advances in mass spectrometry-based lipidomics have in recent years prompted efforts to standardize the annotation of the vast number of lipid molecules that can be detected in biological systems. These efforts have focused on cataloguing, naming and drawing chemical structures of intact lipid molecules, but have provided no guidelines for annotation of lipid fragment ions detected using tandem and multi-stage mass spectrometry, albeit these fragment ions are mandatory for structural elucidation and high confidence lipid identification, especially in high throughput lipidomics workflows. Here we propose a nomenclature for the annotation of lipid fragment ions, describe its implementation and present a freely available web application, termed ALEX123 lipid calculator, that can be used to query a comprehensive database featuring curated lipid fragmentation information for more than 430,000 potential lipid molecules from 47 lipid classes covering five lipid categories. We note that the nomenclature is generic, extendable to stable isotope-labeled lipid molecules and applicable to automated annotation of fragment ions detected by most contemporary lipidomics platforms, including LC-MS/MS-based routines.

AB - Advances in mass spectrometry-based lipidomics have in recent years prompted efforts to standardize the annotation of the vast number of lipid molecules that can be detected in biological systems. These efforts have focused on cataloguing, naming and drawing chemical structures of intact lipid molecules, but have provided no guidelines for annotation of lipid fragment ions detected using tandem and multi-stage mass spectrometry, albeit these fragment ions are mandatory for structural elucidation and high confidence lipid identification, especially in high throughput lipidomics workflows. Here we propose a nomenclature for the annotation of lipid fragment ions, describe its implementation and present a freely available web application, termed ALEX123 lipid calculator, that can be used to query a comprehensive database featuring curated lipid fragmentation information for more than 430,000 potential lipid molecules from 47 lipid classes covering five lipid categories. We note that the nomenclature is generic, extendable to stable isotope-labeled lipid molecules and applicable to automated annotation of fragment ions detected by most contemporary lipidomics platforms, including LC-MS/MS-based routines.

KW - Algorithms

KW - Databases, Chemical

KW - Ions

KW - Isotope Labeling

KW - Lipids

KW - Molecular Structure

KW - Tandem Mass Spectrometry

KW - Journal Article

KW - Lipid fragmentation

U2 - 10.1371/journal.pone.0188394

DO - 10.1371/journal.pone.0188394

M3 - Article

VL - 12

SP - e0188394

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 11

ER -