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Kraegenbring, J.

Publications and source records attributed to Kraegenbring, J..

2 recordsLinked to original sources
bioRxiv2025

Higher-Throughput Proteome Profiling Enabled by Parallelized Pre-Accumulation and Optimized Ion Processing in the Orbitrap Astral Zoom Mass Spectrometer

High-throughput proteomics is critical for understanding biological processes, enabling large-scale studies such as biomarker discovery and systems biology. However, current mass spectrometry technologies face limitations in speed, sensitivity, and scalability for analyzing large sample cohorts. The Thermo Scientific Orbitrap Astral Zoom mass spectrometer (MS) was developed to address these limitations by improving acquisition speed, ion utilization, and spectral processing, which are all essential for advancing proteome depth in high-throughput proteomics. The Orbitrap Astral Zoom MS achieves ultra-fast MS/MS scan rates of up to 270 Hz with enhanced ion utilization through pre-accumulation, enabling the identification of [~]100,000 unique peptides and >8,400 proteins in a single 300 samples-per-day (SPD) analysis of human cell lysate. The optimized system reduces analysis time by 40%, achieves near-complete proteome coverage (>12,000 proteins) in 2.7 hours, and enables ultra-high-throughput workflows, identifying >7,000 proteins in a 500 SPD method with exceptional reproducibility (Pairwise Pearson correlations >0.99). These advancements establish the Orbitrap Astral Zoom MS as a new benchmark in proteomics, significantly enhancing speed, sensitivity, and scalability, paving the way for routine large-scale proteome studies with applications in clinical research and systems biology. TeaserHigh-Speed Human Proteome Analysis using the Orbitrap Astral Zoom Mass Spectrometer

biochemistry↗
bioRxiv2025

Enhancing tandem MS sensitivity and peptide identification via ion pre-accumulation in an Orbitrap mass spectrometer

High-throughput mass spectrometry-based proteomics has gained increasing interest for both academic and industrial applications. As implementation of faster gradients has facilitated higher sample throughput, mass spectrometers must adapt to shorter analysis times by enhancing scanning speed and sensitivity. For Orbitrap mass spectrometers, faster scan rates are constrained by the need for sufficient ion accumulation time, particularly given limitations on duty cycle at high repetition rate, and transient length, which determines analyzer sensitivity and resolving power. In this context, implementing alternative ion scheduling and better ion signal-processing strategies are needed to unleash the speed of these instruments. Here, we introduce a new scanning strategy termed pre-accumulation, which enables the storage of ions in the bent flatapole in parallel to the operation of the C-trap/IRM, leading to a significant improvement in ion beam utilization and enabling for the first time scanning speeds of >70 Hz on hybrid Orbitrap instruments. The combination of pre-accumulation and increased scan speeds notably enhances peptide and protein group identifications for short LC gradients and improves sensitivity for high-throughput applications. These benefits were further amplified when coupled with the full mass range phase-constrained spectrum deconvolution method ({Phi}SDM), especially for fast, lower-resolving Orbitrap measurements used with short LC gradients. Overall, we demonstrate that pre-accumulation of ions in the bent flatapole offers distinct advantages, particularly for conditions with reduced signal input. Since no hardware changes are required, this approach is highly attractive for Orbitrap mass spectrometers operated with fast MS/MS acquisition methods.

biochemistry↗