biostudies-literatureMakhmut ABundesministerium für Bildung und ForschungBundesministerium fur Bildung und Forschung Dienststelle Berlin100750https://www.ebi.ac.uk/biostudies/studies/S-EPMC11067455biostudies-literatureUnknown23(5)Spatial tissue proteomics integrating whole-slide imaging, laser microdissection, and ultrasensitive mass spectrometry is a powerful approach to link cellular phenotypes to functional proteome states in (patho)physiology. To be applicable to large patient cohorts and low sample input amounts, including single-cell applications, loss-minimized and streamlined end-to-end workflows are key. We here introduce an automated sample preparation protocol for laser microdissected samples utilizing the cellenONE robotic system, which has the capacity to process 192 samples in 3 h. Following laser microdissection collection directly into the proteoCHIP LF 48 or EVO 96 chip, our optimized protocol facilitates lysis, formalin de-crosslinking, and tryptic digest of low-input archival tissue samples. The Molecular & cellular proteomics : MCPAn Automated and Fast Sample Preparation Workflow for Laser Microdissection Guided Ultrasensitive Proteomics.PMC11067455161L0222Seth AHartlmayr DQin DMakhmut ACoscia FfalseAn Automated and Fast Sample Preparation Workflow for Laser Microdissection Guided Ultrasensitive Proteomics.Spatial tissue proteomics integrating whole-slide imaging, laser microdissection, and ultrasensitive mass spectrometry is a powerful approach to link cellular phenotypes to functional proteome states in (patho)physiology. To be applicable to large patient cohorts and low sample input amounts, including single-cell applications, loss-minimized and streamlined end-to-end workflows are key. We here introduce an automated sample preparation protocol for laser microdissected samples utilizing the cellenONE robotic system, which has the capacity to process 192 samples in 3 h. Following laser microdissection collection directly into the proteoCHIP LF 48 or EVO 96 chip, our optimized protocol facilitates lysis, formalin de-crosslinking, and tryptic digest of low-input archival tissue samples. The 2024-01-01T00:00:00Z2024 May2026-07-15T04:50:33.531Z2026-06-29T03:09:50.982ZS-EPMC110674553851389110.1016/j.mcpro.2024.100750