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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
Author(s) -
Bons Joanna,
Husson Gauthier,
Chion Marie,
Bonnet Muriel,
MaumyBertrand Myriam,
Delalande François,
Cianférani Sarah,
Bertrand Frédéric,
Picard Brigitte,
Carapito Christine
Publication year - 2021
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.202000214
Subject(s) - label free quantification , proteome , computer science , mass spectrometry , marbled meat , pattern recognition (psychology) , chemistry , biological system , computational biology , artificial intelligence , quantitative proteomics , chromatography , proteomics , biology , biochemistry , zoology , gene
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 the complete MS2 maps that are acquired in SWATH‐MS, an original label‐free quantification method to estimate protein amounts using an I‐spline regression model was developed. Overall, 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.