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Combining label-free and label-based accurate quantifications with SWATH-MS: comparison with SRM and PRM for the evaluation of bovine muscle type effects

ABSTRACT: The performances of label-based SWATH-MS, SRM and PRM to accurately quantify ten candidate biomarkers of beef meat tenderness or marbling, in a cohort of 64 bovine muscle tissues expected to cover a wide biological range of these traits, were evaluated. Limits of quantification, dynamic range and quantification performances were assessed. Moreover, protein amounts for all proteins detected in SWATH-MS were estimated in a label-free manner.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Bos Taurus (bovine)

TISSUE(S): Muscle

SUBMITTER: Joanna Bons

LAB HEAD: Christine Carapito

PROVIDER: PXD020638 | Pride | 2021-06-09

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	BosTaurusiRT_DCpUN_BJ_20171206.fasta	Fasta
	F051328.dat	Other
	F053256.dat	Other
	F053257.dat	Other
	F053258.dat	Other

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Publications

Combining label-free and label-based accurate quantifications with SWATH-MS: Comparison with SRM and PRM for the evaluation of bovine muscle type effects.

Bons Joanna J Husson Gauthier G Chion Marie M Bonnet Muriel M Maumy-Bertrand Myriam M Delalande François F Cianférani Sarah S Bertrand Frédéric F Picard Brigitte B Carapito Christine C

Proteomics 20210330 10

Mass spectrometry has proven to be a valuable tool for the accurate quantification of proteins. In this study, the performances of three targeted approaches, namely selected reaction monitoring (SRM), parallel reaction monitoring (PRM) and sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS), to accurately quantify ten potential biomarkers of beef meat tenderness or marbling in a cohort of 64 muscle samples were evaluated. So as to get the most benefit out of t ...[more]

PMID: 33733615

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Combining label-free and label-based accurate quantifications with SWATH-MS: comparison with SRM and PRM for the evaluation of bovine muscle type effects.

Project description:Mass 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.

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Chip-SIP analysis of Monterey Bay surface waters incubated with organic carbon substrates

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Magnitude of ubiquitination determines the fate of activated epidermal growth factor receptor and downstream cellular effects

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Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS: PTM-SWATH-MS Gold Standard data set

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Label-free SRM-based relative quantification of antibiotic resistance mechanisms in Pseudomonas aeruginosa clinical isolates.

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