An Ultrasensitive Spatial Tissue Proteomics Workflow Exceeding 100 Proteomes Per Day.

ABSTRACT: Achieving high-resolution spatial tissue proteomes requires careful balancing and integration of optimized sample processing, chromatography, and MS acquisition. Here, we present an advanced cellenONE protocol for loss-reduced tissue processing and compare all Evosep ONE Whisper Zoom gradients (20, 40, 80, and 120 samples per day), along with three common data-independent acquisition schemes on a timsUltra athena ion processor mass spectrometer. We found that tissue type was as important as gradient length and sample amount in determining proteome coverage. Moreover, the benefit of increased tissue sampling was gradient- and dynamic range-dependent. Analyzing mouse liver, a high dynamic range tissue, over tenfold more tissue sampling led to only ∼30% gain in protein identification for shor

SUBMITTER: Klingeberg M 

PROVIDER: S-EPMC12828817 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature