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PXD020680

PXD020680 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleCombining label-free and label-based accurate quantifications with SWATH-MS: comparison with SRM and PRM for the evaluation of bovine muscle type effects.
DescriptionMass spectrometry has proven to be a valuable tool for the accurate quantification of proteins. In this study, we have evaluated the performances of three targeted approaches, namely Selected Reaction Monitoring (SRM), Parallel Reaction Monitoring (PRM) and Sequential Windowed Acquisition of Theoretical Mass Spectra (SWATH-MS), to accurately quantify ten potential biomarkers of beef meat tenderness or marbling in a cohort of 64 muscle samples. Besides and so as to get the most benefit out of the complete M2 maps that are acquired in SWATH-MS, we developed an original label-free quantification method to estimate protein amounts using an I-spline regression model. Overall, we showed that SWATH-MS outperformed SRM in terms of sensitivity and dynamic range, while PRM still performed the best, and all three strategies showed similar quantification accuracies and precisions for the absolute quantification of targets of interest. This targeted picture was extended by 585 additional proteins for which amounts were estimated using the label-free approach on SWATH-MS, thus offering a more global profiling of muscle proteomes and further insights into muscle type effect on candidate biomarkers of beef meat qualities as well as muscle metabolism.
HostingRepositoryPanoramaPublic
AnnounceDate2021-06-08
AnnouncementXMLSubmission_2021-06-08_09:50:40.421.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterJoanna Bons
SpeciesList scientific name: Bos taurus; NCBI TaxID: 9913;
ModificationListCarbamidomethyl; Oxidation; Label:13C(6)15N(2); Label:13C(6)15N(4)
InstrumentTripleTOF 6600; Q Exactive Plus; TSQ Vantage
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-07-31 21:16:09ID requested
12021-06-08 09:50:41announced
Publication List
Bons J, Husson G, Chion M, Bonnet M, Maumy-Bertrand M, Delalande F, Cianférani S, Bertrand F, Picard B, Carapito C, Combining label-free and label-based accurate quantifications with SWATH-MS: Comparison with SRM and PRM for the evaluation of bovine muscle type effects. Proteomics, 21(10):e2000214(2021) [pubmed]
Keyword List
submitter keyword: Beef meat quality, Data-Independent Acquisition (DIA), Quantitative MS, SWATH-MS, Targeted proteomics
Contact List
Christine Carapito
contact affiliationLaboratoire de Spectrométrie de Masse BioOrganique (LSMBO), University of Strasbourg, CNRS, IPHC, UMR 7178, F-67000 Strasbourg, France
contact emailccarapito@unistra.fr
lab head
Joanna Bons
contact affiliationLaboratoire de Spectrométrie de Masse BioOrganique (LSMBO), University of Strasbourg, CNRS, IPHC, UMR 7178, F-67000 Strasbourg, France
contact emailjoanna.bons@etu.unistra.fr
dataset submitter
Full Dataset Link List
Panorama Public dataset URI