TMT-Based Multiplexed (Chemo)Proteomics on the Orbitrap Astral Mass Spectrometer

Ongoing advancements in instrumentation has established mass spectrometry (MS) as an essential tool in proteomics research and drug discovery. The newly released Asymmetric Track Lossless (Astral) analyzer represents a major step forward in MS instrumentation. Here, we evaluate the Orbitrap Astral mass spectrometer in the context of tandem mass tag (TMT)-based multiplexed proteomics and activity-based proteome profiling, highlighting its sensitivity boost relative to the Orbitrap Tribrid platform-50% at the peptide and 20% at the protein level. We compare TMT data-dependent acquisition and label-free data-independent acquisition on the same instrument, both of which quantify over 10,000 human proteins per sample within 1 h. TMT offers higher quantitative precision and data completeness, while data-independent acquisition is free of ratio compression and is thereby more accurate. Our results suggest that ratio compression is prevalent with the high-resolution MS2-based quantification on the Astral, while real-time search-based MS3 quantification on the Orbitrap Tribrid platform effectively restores accuracy. Additionally, we benchmark TMT-based activity-based proteome profiling by interrogating cysteine ligandability. The Astral measures over 30,000 cysteines in a single-shot experiment, a 54% increase relative to the Orbitrap Eclipse. We further leverage this remarkable sensitivity to profile the target engagement landscape of FDA-approved covalent drugs, including sotorasib and adagrasib. We herein provide a reference for the optimal use of the advanced MS platform.