Evaluation of a modified Orbitrap Astral Zoom prototype for quantitative proteomics - Beyond identification lists

Mass spectrometry instrumentation continues to evolve rapidly, yet quantifying these advances beyond conventional peptide and protein detections remains challenging. Here, we evaluate a modified Orbitrap Astral Zoom mass spectrometer (MS) prototype and compare its performance to the standard Orbitrap Astral MS. Across a range of acquisition methods and sample inputs, the prototype instrument outperformed the standard Orbitrap Astral MS in precursor and protein identifications, ion accumulation efficiency, and reproducibility of measurements. To enable meaningful cross-platform comparisons, we implemented an ion calibration framework that converts signal intensity from arbitrary units to absolute ion counts (ions/sec). This benchmarking strategy showed that the prototype consistently sampled more ions per peptide, resulting in improved sensitivity and quantitative precision. To make these metrics broadly accessible, we added new metrics to the Skyline document grid to report ion counts directly from data-independent acquisition (DIA) data. Taken together, our results demonstrate the Orbitrap Astral Zoom prototype as a high-performance platform for DIA proteomics and establish a generalizable framework for ion-based evaluation of mass spectrometer performance.