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Article: Probing SWATH‐MS as a tool for proteome level quantification in a nonmodel fish

TitleProbing SWATH‐MS as a tool for proteome level quantification in a nonmodel fish
Authors
Keywordsclimate change
data‐independent acquisition
fish
quantitative proteomics
spectral libraries
Issue Date2020
PublisherWiley-Blackwell Publishing Ltd.. The Journal's web site is located at http://www.blackwellpublishing.com/journal.asp?ref=1755-098X&site=1
Citation
Molecular Ecology Resources, 2020, v. 20 n. 6, p. 1647-1657 How to Cite?
AbstractQuantitative proteomics via mass spectrometry can provide valuable insight into molecular and phenotypic characteristics of a living system. Recent mass spectrometry developments include data‐independent acquisition (SWATH/DIA‐MS), an accurate, sensitive and reproducible method for analysing the whole proteome. The main requirement for this method is the creation of a comprehensive spectral library. New technologies have emerged producing larger and more accurate species‐specific libraries leading to a progressive collection of proteome references for multiple molecular model species. Here, for the first time, we set out to compare different spectral library constructions using multiple tissues from a coral reef fish to demonstrate its value and feasibility for nonmodel organisms. We created a large spectral library composed of 12,553 protein groups from liver and brain tissues. Via identification of differentially expressed proteins under fish exposure to elevated pCO2 and temperature, we validated the application and usefulness of these different spectral libraries. Successful identification of significant differentially expressed proteins from different environmental exposures occurred using the library with a combination of data‐independent and data‐dependent acquisition methods as well as both tissue types. Further analysis revealed expected patterns of significantly up‐regulated heat shock proteins in a dual condition of ocean warming and acidification indicating the biological accuracy and relevance of the method. This study provides the first reference spectral library for a nonmodel organism. It represents a useful guide for future building of accurate spectral library references in nonmodel organisms allowing the discovery of ecologically relevant changes in the proteome.
Persistent Identifierhttp://hdl.handle.net/10722/287831
ISSN
2023 Impact Factor: 5.5
2023 SCImago Journal Rankings: 2.465
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorMonroe, AA-
dc.contributor.authorZhang, H-
dc.contributor.authorSchunter, C-
dc.contributor.authorRavasi, T-
dc.date.accessioned2020-10-05T12:03:55Z-
dc.date.available2020-10-05T12:03:55Z-
dc.date.issued2020-
dc.identifier.citationMolecular Ecology Resources, 2020, v. 20 n. 6, p. 1647-1657-
dc.identifier.issn1755-098X-
dc.identifier.urihttp://hdl.handle.net/10722/287831-
dc.description.abstractQuantitative proteomics via mass spectrometry can provide valuable insight into molecular and phenotypic characteristics of a living system. Recent mass spectrometry developments include data‐independent acquisition (SWATH/DIA‐MS), an accurate, sensitive and reproducible method for analysing the whole proteome. The main requirement for this method is the creation of a comprehensive spectral library. New technologies have emerged producing larger and more accurate species‐specific libraries leading to a progressive collection of proteome references for multiple molecular model species. Here, for the first time, we set out to compare different spectral library constructions using multiple tissues from a coral reef fish to demonstrate its value and feasibility for nonmodel organisms. We created a large spectral library composed of 12,553 protein groups from liver and brain tissues. Via identification of differentially expressed proteins under fish exposure to elevated pCO2 and temperature, we validated the application and usefulness of these different spectral libraries. Successful identification of significant differentially expressed proteins from different environmental exposures occurred using the library with a combination of data‐independent and data‐dependent acquisition methods as well as both tissue types. Further analysis revealed expected patterns of significantly up‐regulated heat shock proteins in a dual condition of ocean warming and acidification indicating the biological accuracy and relevance of the method. This study provides the first reference spectral library for a nonmodel organism. It represents a useful guide for future building of accurate spectral library references in nonmodel organisms allowing the discovery of ecologically relevant changes in the proteome.-
dc.languageeng-
dc.publisherWiley-Blackwell Publishing Ltd.. The Journal's web site is located at http://www.blackwellpublishing.com/journal.asp?ref=1755-098X&site=1-
dc.relation.ispartofMolecular Ecology Resources-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectclimate change-
dc.subjectdata‐independent acquisition-
dc.subjectfish-
dc.subjectquantitative proteomics-
dc.subjectspectral libraries-
dc.titleProbing SWATH‐MS as a tool for proteome level quantification in a nonmodel fish-
dc.typeArticle-
dc.identifier.emailSchunter, C: schunter@hku.hk-
dc.identifier.authoritySchunter, C=rp02465-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1111/1755-0998.13229-
dc.identifier.pmid32687632-
dc.identifier.pmcidPMC7689905-
dc.identifier.scopuseid_2-s2.0-85088878463-
dc.identifier.hkuros314794-
dc.identifier.volume20-
dc.identifier.issue6-
dc.identifier.spage1647-
dc.identifier.epage1657-
dc.identifier.eissn1755-0998-
dc.identifier.isiWOS:000555296600001-
dc.publisher.placeUnited Kingdom-
dc.identifier.issnl1755-098X-

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