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: 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.

ORGANISM(S): Bos Taurus

SUBMITTER: Joanna Bons  

PROVIDER: PXD020680 | panorama | Tue Jun 08 00:00:00 BST 2021

REPOSITORIES: PanoramaPublic