Comparison of MS2, synchronous precursor selection MS3, and real-time search MS3 methodologies for lung proteomes of hydrogen sulfide treated swine

Tandem mass tags (TMTs) have increasingly become an attractive technique for global proteomics. However, its effectiveness for multiplexed quantitation by traditional tandem mass spectrometry (MS²) suffers from ratio distortion. Synchronous precursor selection (SPS) MS³ has been widely accepted for improved quantitation accuracy, but concurrently decreased proteome coverage. Recently, a Real-Time Search algorithm has been integrated with the SPS MS³ pipeline (RTS MS³) to provide accurate quantitation and improved depth of coverage. In this mechanistic study of the impact of exposure to hydrogen sulfide (H₂S) on the respiration of swine, we used TMT-based comparative proteomics of lung tissues from control and H₂S-treated subjects as a test case to evaluate traditional MS², SPS MS³, and RTS MS³ acquisition methods on both the Orbitrap Fusion and Orbitrap Eclipse platforms. Comparison of the results obtained by the MS² with those of SPS MS³ and RTS MS³ methods suggests that the MS³-driven quantitative strategies provided a more accurate global-scale quantitation; however, only RTS MS³ provided proteomic coverage that rivaled that of traditional MS² analysis. RTS MS³ not only yields more productive MS³ spectra than SPS MS³ but also appears to focus the analysis more effectively on unique peptides. Furthermore, pathway enrichment analyses of the H₂S-altered proteins demonstrated that an additional apoptosis pathway was discovered exclusively by RTS MS³. This finding was verified by RT-qPCR, western blotting, and TUNEL staining experiments. We conclude that RTS MS³ workflow enables simultaneous improvement of quantitative accuracy and proteome coverage over alternative approaches (MS² and SPS MS³). Graphical abstract.