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We present UFP-MS, an ultra-fast mass spectrometry (MS) proteomics method that integrates narrow-window data-independent acquisition (nDIA) with short-gradient micro-flow chromatography, enabling profiling of &gt;240 samples per day. This optimized MS approach identifies 6,201 and 7,466 human proteins with 1- and 2-min gradients, respectively. Our streamlined sample preparation workflow features high-throughput homogenization, adaptive focused acoustics (AFA)-assisted proteolysis, and Evotip-accelerated desalting, allowing for the processing of up to 96 tissue samples in 5 h. As a practical application, we analyzed 507 samples from 13 mouse tissues treated with the enzyme-drug L-asparaginase (ASNase) or its glutaminase-free Q59L mutant, generating a quantitative profile of 11,472 proteins following drug treatment. The MS results confirmed the impact of ASNase on amino acid metabolism in solid tissues. Further analysis revealed broad suppression of anticoagulants and cholesterol metabolism and uncovered numerous tissue-specific dysregulated pathways. In summary, the UFP-MS method greatly accelerates the generation of biological insights and clinically actionable hypotheses into tissue-specific vulnerabilities targeted by ASNase.<\/jats:p>","DOI":"10.1101\/2024.09.25.615060","type":"posted-content","created":{"date-parts":[[2024,9,27]],"date-time":"2024-09-27T19:25:13Z","timestamp":1727465113000},"source":"Crossref","is-referenced-by-count":5,"title":["Ultra-Fast Multi-Organ Proteomics Unveils Tissue-Specific Mechanisms of Drug Efficacy and Toxicity"],"prefix":"10.64898","author":[{"given":"Yun","family":"Xiong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin","family":"Tan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wai-kin","family":"Chan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric S.","family":"Yin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sri Ramya","family":"Donepudi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jibin","family":"Ding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bao","family":"Tran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Martinez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iqbal","family":"Mahmud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hamish I.","family":"Stewart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel J.","family":"Hermanson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John N.","family":"Weinstein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip L.","family":"Lorenzi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2024100907350688000_2024.09.25.615060v2.1","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/nrclinonc.2014.6","article-title":"Cancer Systems Biology: a peek into the future of patient care?","volume":"11","year":"2014","journal-title":"Nature Reviews Clinical Oncology"},{"key":"2024100907350688000_2024.09.25.615060v2.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41568-020-0240-7"},{"key":"2024100907350688000_2024.09.25.615060v2.3","doi-asserted-by":"publisher","DOI":"10.1038\/nrg.2016.49"},{"key":"2024100907350688000_2024.09.25.615060v2.4","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1486"},{"key":"2024100907350688000_2024.09.25.615060v2.5","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/s41573-022-00409-3","article-title":"The emerging role of mass spectrometry-based proteomics in drug discovery","volume":"21","year":"2022","journal-title":"Nat Rev Drug Discov"},{"key":"2024100907350688000_2024.09.25.615060v2.6","doi-asserted-by":"publisher","DOI":"10.1038\/nature19949"},{"key":"2024100907350688000_2024.09.25.615060v2.7","doi-asserted-by":"publisher","DOI":"10.1016\/j.mcpro.2023.100577"},{"key":"2024100907350688000_2024.09.25.615060v2.8","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/s41592-019-0638-x","article-title":"DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput","volume":"17","year":"2020","journal-title":"Nature methods"},{"key":"2024100907350688000_2024.09.25.615060v2.9","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2021.06.006"},{"key":"2024100907350688000_2024.09.25.615060v2.10","doi-asserted-by":"publisher","DOI":"10.1038\/S41592-019-0426-7"},{"key":"2024100907350688000_2024.09.25.615060v2.11","first-page":"95","article-title":"Data Processing and Analysis for DIA-Based Phosphoproteomics Using Spectronaut","volume":"2361","year":"2021","journal-title":"Proteomics Data Analysis"},{"key":"2024100907350688000_2024.09.25.615060v2.12","doi-asserted-by":"crossref","unstructured":"R. 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