Cargando…
An in silico MS/MS library for automatic annotation of novel FAHFA lipids
BACKGROUND: A new lipid class named ‘fatty acid esters of hydroxyl fatty acids’ (FAHFA) was recently discovered in mammalian adipose tissue and in blood plasma and some FAHFAs were found to be associated with type 2 diabetes. To facilitate the automatic annotation of FAHFAs in biological specimens,...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer International Publishing
2015
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4646931/ https://www.ncbi.nlm.nih.gov/pubmed/26579213 http://dx.doi.org/10.1186/s13321-015-0104-4 |
_version_ | 1782401001552084992 |
---|---|
author | Ma, Yan Kind, Tobias Vaniya, Arpana Gennity, Ingrid Fahrmann, Johannes F. Fiehn, Oliver |
author_facet | Ma, Yan Kind, Tobias Vaniya, Arpana Gennity, Ingrid Fahrmann, Johannes F. Fiehn, Oliver |
author_sort | Ma, Yan |
collection | PubMed |
description | BACKGROUND: A new lipid class named ‘fatty acid esters of hydroxyl fatty acids’ (FAHFA) was recently discovered in mammalian adipose tissue and in blood plasma and some FAHFAs were found to be associated with type 2 diabetes. To facilitate the automatic annotation of FAHFAs in biological specimens, a tandem mass spectra (MS/MS) library is needed. Due to the limitation of the commercial available standard compounds, we proposed building an in silico MS/MS library to extend the coverage of molecules. RESULTS: We developed a computer-generated library with 3267 tandem mass spectra (MS/MS) for 1089 FAHFA species. FAHFA spectra were generated based on authentic standards with negative mode electrospray ionization and 10, 20, and 40 V collision induced dissociation at 4 spectra/s as used in in ultra-high performance liquid chromatography-QTOF mass spectrometry studies. However, positional information of the hydroxyl group is only obtained either at lower QTOF spectra acquisition rates of 1 spectrum/s or at the MS(3) level in ion trap instruments. Therefore, an additional set of 4290 fragment-rich MS/MS spectra was created to enable distinguishing positional FAHFA isomers. The library was generated based on ion fragmentations and ion intensities of FAHFA external reference standards, developing a heuristic model for fragmentation rules and extending these rules to large swaths of computer-generated structures of FAHFAs with varying chain lengths, degrees of unsaturation and hydroxyl group positions. Subsequently, we validated the new in silico library by discovering several new FAHFA species in egg yolk, showing that this library enables high-throughput screening of FAHFA lipids in various biological matrices. CONCLUSIONS: The developed library and templates are freely available for commercial or noncommercial use at http://fiehnlab.ucdavis.edu/staff/yanma/fahfa-lipid-library. This in silico MS/MS library allows users to annotate FAHFAs from accurate mass tandem mass spectra in an easy and fast manner with NIST MS Search or PepSearch software. The developing template is provided for advanced users to modify the parameters and export customized libraries according to their instrument features. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13321-015-0104-4) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4646931 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Springer International Publishing |
record_format | MEDLINE/PubMed |
spelling | pubmed-46469312015-11-18 An in silico MS/MS library for automatic annotation of novel FAHFA lipids Ma, Yan Kind, Tobias Vaniya, Arpana Gennity, Ingrid Fahrmann, Johannes F. Fiehn, Oliver J Cheminform Research Article BACKGROUND: A new lipid class named ‘fatty acid esters of hydroxyl fatty acids’ (FAHFA) was recently discovered in mammalian adipose tissue and in blood plasma and some FAHFAs were found to be associated with type 2 diabetes. To facilitate the automatic annotation of FAHFAs in biological specimens, a tandem mass spectra (MS/MS) library is needed. Due to the limitation of the commercial available standard compounds, we proposed building an in silico MS/MS library to extend the coverage of molecules. RESULTS: We developed a computer-generated library with 3267 tandem mass spectra (MS/MS) for 1089 FAHFA species. FAHFA spectra were generated based on authentic standards with negative mode electrospray ionization and 10, 20, and 40 V collision induced dissociation at 4 spectra/s as used in in ultra-high performance liquid chromatography-QTOF mass spectrometry studies. However, positional information of the hydroxyl group is only obtained either at lower QTOF spectra acquisition rates of 1 spectrum/s or at the MS(3) level in ion trap instruments. Therefore, an additional set of 4290 fragment-rich MS/MS spectra was created to enable distinguishing positional FAHFA isomers. The library was generated based on ion fragmentations and ion intensities of FAHFA external reference standards, developing a heuristic model for fragmentation rules and extending these rules to large swaths of computer-generated structures of FAHFAs with varying chain lengths, degrees of unsaturation and hydroxyl group positions. Subsequently, we validated the new in silico library by discovering several new FAHFA species in egg yolk, showing that this library enables high-throughput screening of FAHFA lipids in various biological matrices. CONCLUSIONS: The developed library and templates are freely available for commercial or noncommercial use at http://fiehnlab.ucdavis.edu/staff/yanma/fahfa-lipid-library. This in silico MS/MS library allows users to annotate FAHFAs from accurate mass tandem mass spectra in an easy and fast manner with NIST MS Search or PepSearch software. The developing template is provided for advanced users to modify the parameters and export customized libraries according to their instrument features. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13321-015-0104-4) contains supplementary material, which is available to authorized users. Springer International Publishing 2015-11-16 /pmc/articles/PMC4646931/ /pubmed/26579213 http://dx.doi.org/10.1186/s13321-015-0104-4 Text en © Ma et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Ma, Yan Kind, Tobias Vaniya, Arpana Gennity, Ingrid Fahrmann, Johannes F. Fiehn, Oliver An in silico MS/MS library for automatic annotation of novel FAHFA lipids |
title | An in silico MS/MS library for automatic annotation of novel FAHFA lipids |
title_full | An in silico MS/MS library for automatic annotation of novel FAHFA lipids |
title_fullStr | An in silico MS/MS library for automatic annotation of novel FAHFA lipids |
title_full_unstemmed | An in silico MS/MS library for automatic annotation of novel FAHFA lipids |
title_short | An in silico MS/MS library for automatic annotation of novel FAHFA lipids |
title_sort | in silico ms/ms library for automatic annotation of novel fahfa lipids |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4646931/ https://www.ncbi.nlm.nih.gov/pubmed/26579213 http://dx.doi.org/10.1186/s13321-015-0104-4 |
work_keys_str_mv | AT mayan aninsilicomsmslibraryforautomaticannotationofnovelfahfalipids AT kindtobias aninsilicomsmslibraryforautomaticannotationofnovelfahfalipids AT vaniyaarpana aninsilicomsmslibraryforautomaticannotationofnovelfahfalipids AT gennityingrid aninsilicomsmslibraryforautomaticannotationofnovelfahfalipids AT fahrmannjohannesf aninsilicomsmslibraryforautomaticannotationofnovelfahfalipids AT fiehnoliver aninsilicomsmslibraryforautomaticannotationofnovelfahfalipids AT mayan insilicomsmslibraryforautomaticannotationofnovelfahfalipids AT kindtobias insilicomsmslibraryforautomaticannotationofnovelfahfalipids AT vaniyaarpana insilicomsmslibraryforautomaticannotationofnovelfahfalipids AT gennityingrid insilicomsmslibraryforautomaticannotationofnovelfahfalipids AT fahrmannjohannesf insilicomsmslibraryforautomaticannotationofnovelfahfalipids AT fiehnoliver insilicomsmslibraryforautomaticannotationofnovelfahfalipids |