{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,12]],"date-time":"2026-11-12T21:18:25Z","timestamp":1794518305095,"version":"4.9.1"},"reference-count":54,"publisher":"Springer Science and Business Media LLC","issue":"8067","license":[{"start":{"date-parts":[[2025,4,16]],"date-time":"2025-04-16T00:00:00Z","timestamp":1744761600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,4,16]],"date-time":"2025-04-16T00:00:00Z","timestamp":1744761600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2025,6,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:p>Protein misfolding diseases, including \u03b11-antitrypsin deficiency (AATD), pose substantial health challenges, with their cellular progression still poorly understood<jats:sup>1\u20133<\/jats:sup>. We use spatial proteomics by mass spectrometry and machine learning to map AATD in human liver tissue. Combining Deep Visual Proteomics (DVP) with single-cell analysis<jats:sup>4,5<\/jats:sup>, we probe intact patient biopsies to resolve molecular events during hepatocyte stress in pseudotime across fibrosis stages. We achieve proteome depth of up to 4,300 proteins from one-third of a single cell in formalin-fixed, paraffin-embedded tissue. This dataset reveals a potentially clinically actionable peroxisomal upregulation that precedes the canonical unfolded protein response. Our single-cell proteomics data show \u03b11-antitrypsin accumulation is largely cell-intrinsic, with minimal stress propagation between hepatocytes. We integrated proteomic data with artificial intelligence-guided image-based phenotyping across several disease stages, revealing a late-stage hepatocyte phenotype characterized by globular protein aggregates and distinct proteomic signatures, notably including elevated TNFSF10 (also known as\u00a0TRAIL) amounts. This phenotype may represent a critical disease progression stage. Our study offers new insights into AATD pathogenesis and introduces a powerful methodology for high-resolution, in situ proteomic analysis of complex tissues. This approach holds potential to unravel molecular mechanisms in various protein misfolding disorders, setting a new standard for understanding disease progression at the single-cell level in human tissue.<\/jats:p>","DOI":"10.1038\/s41586-025-08885-4","type":"journal-article","created":{"date-parts":[[2025,4,16]],"date-time":"2025-04-16T15:02:55Z","timestamp":1744815775000},"page":"484-491","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":70,"title":["Deep Visual Proteomics maps proteotoxicity in a genetic liver disease"],"prefix":"10.1038","volume":"642","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4604-6170","authenticated-orcid":false,"given":"Florian A.","family":"Rosenberger","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7817-4180","authenticated-orcid":false,"given":"Sophia C.","family":"M\u00e4dler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0411-0373","authenticated-orcid":false,"given":"Katrine Holtz","family":"Thorhauge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophia","family":"Steigerwald","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0382-5705","authenticated-orcid":false,"given":"Malin","family":"Fromme","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-3646-7899","authenticated-orcid":false,"given":"Mikhail","family":"Lebedev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline A. M.","family":"Weiss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0597-5950","authenticated-orcid":false,"given":"Marc","family":"Oeller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2079-4402","authenticated-orcid":false,"given":"Maria","family":"Wahle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1043-6591","authenticated-orcid":false,"given":"Andreas","family":"Metousis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7005-5619","authenticated-orcid":false,"given":"Maximilian","family":"Zwiebel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3998-1139","authenticated-orcid":false,"given":"Niklas A.","family":"Schmacke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9466-2333","authenticated-orcid":false,"given":"S\u00f6nke","family":"Detlefsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9921-4284","authenticated-orcid":false,"given":"Peter","family":"Boor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ond\u0159ej","family":"Fabi\u00e1n","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"So\u0148a","family":"Fra\u0148kov\u00e1","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9598-4932","authenticated-orcid":false,"given":"Aleksander","family":"Krag","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pavel","family":"Strnad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1292-4799","authenticated-orcid":false,"given":"Matthias","family":"Mann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,4,16]]},"reference":[{"key":"8885_CR1","doi-asserted-by":"publisher","DOI":"10.1038\/nrdp.2016.51","volume":"2","author":"CM Greene","year":"2016","unstructured":"Greene, C. M. et al. \u03b11-Antitrypsin deficiency. Nat. Rev. Dis. Primers 2, 16051 (2016).","journal-title":"Nat. Rev. Dis. Primers"},{"key":"8885_CR2","doi-asserted-by":"publisher","first-page":"1443","DOI":"10.1056\/NEJMra1910234","volume":"382","author":"P Strnad","year":"2020","unstructured":"Strnad, P., McElvaney, N. G. & Lomas, D. A. Alpha1-antitrypsin deficiency. N. Engl. J. Med. 382, 1443\u20131455 (2020).","journal-title":"N. Engl. J. Med."},{"key":"8885_CR3","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1016\/j.tcb.2014.05.003","volume":"24","author":"MS Hipp","year":"2014","unstructured":"Hipp, M. S., Park, S.-H. & Hartl, F. U. Proteostasis impairment in protein-misfolding and -aggregation diseases. Trends Cell Biol. 24, 506\u2013514 (2014).","journal-title":"Trends Cell Biol."},{"key":"8885_CR4","doi-asserted-by":"publisher","first-page":"1231","DOI":"10.1038\/s41587-022-01302-5","volume":"40","author":"A Mund","year":"2022","unstructured":"Mund, A. et al. Deep Visual Proteomics defines single-cell identity and heterogeneity. Nat. Biotechnol. 40, 1231\u20131240 (2022).","journal-title":"Nat. Biotechnol."},{"key":"8885_CR5","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1038\/s41592-023-02007-6","volume":"20","author":"FA Rosenberger","year":"2023","unstructured":"Rosenberger, F. A. et al. Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome. Nat. Methods 20, 1530\u20131536 (2023).","journal-title":"Nat. Methods"},{"key":"8885_CR6","doi-asserted-by":"publisher","unstructured":"Petrosius, V. et al. Evaluating the capabilities of the Astral mass analyzer for single-cell proteomics. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2023.06.06.543943 (2023).","DOI":"10.1101\/2023.06.06.543943"},{"key":"8885_CR7","doi-asserted-by":"publisher","first-page":"1855","DOI":"10.1038\/s41587-023-02099-7","volume":"42","author":"UH Guzman","year":"2024","unstructured":"Guzman, U. H. et al. Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition. Nat. Biotechnol. 42, 1855\u20131866 (2024).","journal-title":"Nat. Biotechnol."},{"key":"8885_CR8","doi-asserted-by":"crossref","unstructured":"Guo, T., Steen, J. A. & Mann, M. Mass-spectrometry-based proteomics: from single cells to clinical applications. Nature 638, 901\u2013911 (2025).","DOI":"10.1038\/s41586-025-08584-0"},{"key":"8885_CR9","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1038\/s41586-024-08061-0","volume":"635","author":"TM Nordmann","year":"2024","unstructured":"Nordmann, T. M. et al. Spatial proteomics identifies JAKi as treatment for a lethal skin disease. Nature 635, 1001\u20131009 (2024).","journal-title":"Nature"},{"key":"8885_CR10","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1146\/annurev-biochem-061516-045115","volume":"86","author":"F Chiti","year":"2017","unstructured":"Chiti, F. & Dobson, C. M. Protein misfolding, amyloid formation, and human disease: a summary of progress over the last decade. Annu. Rev. Biochem. 86, 27\u201368 (2017).","journal-title":"Annu. Rev. Biochem."},{"key":"8885_CR11","doi-asserted-by":"publisher","first-page":"595","DOI":"10.15252\/emmm.201606210","volume":"8","author":"DJ Selkoe","year":"2016","unstructured":"Selkoe, D. J. & Hardy, J. The amyloid hypothesis of Alzheimer\u2019s disease at 25 years. EMBO Mol. Med. 8, 595\u2013608 (2016).","journal-title":"EMBO Mol. Med."},{"key":"8885_CR12","doi-asserted-by":"publisher","first-page":"S51","DOI":"10.3233\/JPD-179005","volume":"7","author":"M Goedert","year":"2017","unstructured":"Goedert, M., Jakes, R. & Spillantini, M. G. The synucleinopathies: twenty years on. J. Parkinsons Dis. 7, S51\u2013S69 (2017).","journal-title":"J. Parkinsons Dis."},{"key":"8885_CR13","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1038\/357605a0","volume":"357","author":"DA Lomas","year":"1992","unstructured":"Lomas, D. A., Evans, D. L., Finch, J. T. & Carrell, R. W. The mechanism of Z alpha 1-antitrypsin accumulation in the liver. Nature 357, 605\u2013607 (1992).","journal-title":"Nature"},{"key":"8885_CR14","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/0002-9343(88)90154-4","volume":"84","author":"M Brantly","year":"1988","unstructured":"Brantly, M., Nukiwa, T. & Crystal, R. G. Molecular basis of alpha-1-antitrypsin deficiency. Am. J. Med. 84, 13\u201331 (1988).","journal-title":"Am. J. Med."},{"key":"8885_CR15","doi-asserted-by":"publisher","first-page":"1357","DOI":"10.1016\/j.jhep.2018.08.005","volume":"69","author":"VC Clark","year":"2018","unstructured":"Clark, V. C. et al. Clinical and histologic features of adults with alpha-1 antitrypsin deficiency in a non-cirrhotic cohort. J. Hepatol. 69, 1357\u20131364 (2018).","journal-title":"J. Hepatol."},{"key":"8885_CR16","doi-asserted-by":"publisher","first-page":"1228","DOI":"10.1002\/hep.21822","volume":"46","author":"D Lindblad","year":"2007","unstructured":"Lindblad, D., Blomenkamp, K. & Teckman, J. Alpha-1-antitrypsin mutant Z protein content in individual hepatocytes correlates with cell death in a mouse model. Hepatology 46, 1228\u20131235 (2007).","journal-title":"Hepatology"},{"key":"8885_CR17","doi-asserted-by":"publisher","first-page":"1048","DOI":"10.1002\/hep.20118","volume":"39","author":"DA Rudnick","year":"2004","unstructured":"Rudnick, D. A. et al. Analyses of hepatocellular proliferation in a mouse model of alpha-1-antitrypsin deficiency. Hepatology 39, 1048\u20131055 (2004).","journal-title":"Hepatology"},{"key":"8885_CR18","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abm2094","volume":"8","author":"JE Chambers","year":"2022","unstructured":"Chambers, J. E. et al. Z-\u03b11-antitrypsin polymers impose molecular filtration in the endoplasmic reticulum after undergoing phase transition to a solid state. Sci. Adv. 8, eabm2094 (2022).","journal-title":"Sci. Adv."},{"key":"8885_CR19","doi-asserted-by":"publisher","first-page":"851","DOI":"10.1016\/j.jhep.2018.05.028","volume":"69","author":"C-P Segeritz","year":"2018","unstructured":"Segeritz, C.-P. et al. hiPSC hepatocyte model demonstrates the role of unfolded protein response and inflammatory networks in \u03b11-antitrypsin deficiency. J. Hepatol. 69, 851\u2013860 (2018).","journal-title":"J. Hepatol."},{"key":"8885_CR20","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1016\/j.jhep.2021.11.022","volume":"76","author":"M Fromme","year":"2022","unstructured":"Fromme, M., Schneider, C. V., Trautwein, C., Brunetti-Pierri, N. & Strnad, P. Alpha-1 antitrypsin deficiency: a re-surfacing adult liver disorder. J. Hepatol. 76, 946\u2013958 (2022).","journal-title":"J. Hepatol."},{"key":"8885_CR21","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1042\/BCJ20220055","volume":"479","author":"Y Zhang","year":"2022","unstructured":"Zhang, Y. et al. LMAN1-MCFD2 complex is a cargo receptor for the ER-Golgi transport of \u03b11-antitrypsin. Biochem. J. 479, 839\u2013855 (2022).","journal-title":"Biochem. J."},{"key":"8885_CR22","doi-asserted-by":"publisher","first-page":"G444","DOI":"10.1152\/ajpgi.00237.2004","volume":"289","author":"BZ Schmidt","year":"2005","unstructured":"Schmidt, B. Z. & Perlmutter, D. H. Grp78, Grp94, and Grp170 interact with alpha1-antitrypsin mutants that are retained in the endoplasmic reticulum. Am. J. Physiol. Gastrointest. Liver Physiol. 289, G444\u2013G455 (2005).","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"8885_CR23","doi-asserted-by":"publisher","first-page":"3219","DOI":"10.1016\/j.ymthe.2021.06.021","volume":"29","author":"RB Werder","year":"2021","unstructured":"Werder, R. B. et al. Adenine base editing reduces misfolded protein accumulation and toxicity in alpha-1 antitrypsin deficient patient iPSC-hepatocytes. Mol. Ther. 29, 3219\u20133229 (2021).","journal-title":"Mol. Ther."},{"key":"8885_CR24","doi-asserted-by":"publisher","DOI":"10.1111\/liv.16207","volume":"45","author":"I Spivak","year":"2025","unstructured":"Spivak, I. et al. Alpha\u20101 antitrypsin inclusions sequester GRP78 in a bile acid\u2013inducible manner. Liver Int. 45, e16207 (2025).","journal-title":"Liver Int."},{"key":"8885_CR25","doi-asserted-by":"publisher","first-page":"1277","DOI":"10.1038\/s41591-022-01850-y","volume":"28","author":"L Niu","year":"2022","unstructured":"Niu, L. et al. Noninvasive proteomic biomarkers for alcohol-related liver disease. Nat. Med. 28, 1277\u20131287 (2022).","journal-title":"Nat. Med."},{"key":"8885_CR26","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1038\/s41420-021-00447-7","volume":"7","author":"S-H Cho","year":"2021","unstructured":"Cho, S.-H. et al. Lgals3bp suppresses colon inflammation and tumorigenesis through the downregulation of TAK1-NF-\u03baB signaling. Cell Death Discov. 7, 65 (2021).","journal-title":"Cell Death Discov."},{"key":"8885_CR27","doi-asserted-by":"publisher","first-page":"G594","DOI":"10.1152\/ajpgi.00207.2022","volume":"323","author":"N Khodayari","year":"2022","unstructured":"Khodayari, N. et al. Characterization of hepatic inflammatory changes in a C57BL\/6J mouse model of alpha1-antitrypsin deficiency. Am. J. Physiol. Gastrointest. Liver Physiol. 323, G594\u2013G608 (2022).","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"8885_CR28","doi-asserted-by":"publisher","DOI":"10.1016\/j.ceb.2023.102292","volume":"86","author":"N Porat-Shliom","year":"2024","unstructured":"Porat-Shliom, N. Compartmentalization, cooperation, and communication: the 3Cs of hepatocyte zonation. Curr. Opin. Cell Biol. 86, 102292 (2024).","journal-title":"Curr. Opin. Cell Biol."},{"key":"8885_CR29","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1002\/hep.29160","volume":"66","author":"P Piccolo","year":"2017","unstructured":"Piccolo, P. et al. Down\u2010regulation of hepatocyte nuclear factor\u20104\u03b1 and defective zonation in livers expressing mutant Z \u03b11\u2010antitrypsin. Hepatology 66, 124 (2017).","journal-title":"Hepatology"},{"key":"8885_CR30","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1038\/sj.ejhg.5201127","volume":"12","author":"DC Crowther","year":"2004","unstructured":"Crowther, D. C. et al. Practical genetics: alpha-1-antitrypsin deficiency and the serpinopathies. Eur. J. Hum. Genet. 12, 167\u2013172 (2004).","journal-title":"Eur. J. Hum. Genet."},{"key":"8885_CR31","doi-asserted-by":"crossref","unstructured":"Liu, Z. et al. A ConvNet for the 2020s. Preprint at https:\/\/arxiv.org\/abs\/2201.03545v2 (2022).","DOI":"10.1109\/CVPR52688.2022.01167"},{"key":"8885_CR32","doi-asserted-by":"publisher","first-page":"867","DOI":"10.4103\/jcrt.JCRT_745_17","volume":"14","author":"C Yang","year":"2018","unstructured":"Yang, C. et al. Increased expression of epidermal growth factor-like domain-containing protein 7 is predictive of poor prognosis in patients with hepatocellular carcinoma. J. Cancer Res. Ther. 14, 867\u2013872 (2018).","journal-title":"J. Cancer Res. Ther."},{"key":"8885_CR33","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1172\/JCI113999","volume":"83","author":"JA Carlson","year":"1989","unstructured":"Carlson, J. A. et al. Accumulation of PiZ alpha 1-antitrypsin causes liver damage in transgenic mice. J. Clin. Invest. 83, 1183\u20131190 (1989).","journal-title":"J. Clin. Invest."},{"key":"8885_CR34","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1038\/nature10424","volume":"478","author":"K Yusa","year":"2011","unstructured":"Yusa, K. et al. Targeted gene correction of \u03b11-antitrypsin deficiency in induced pluripotent stem cells. Nature 478, 391\u2013394 (2011).","journal-title":"Nature"},{"key":"8885_CR35","doi-asserted-by":"publisher","first-page":"39002","DOI":"10.1074\/jbc.M508652200","volume":"280","author":"T Hidvegi","year":"2005","unstructured":"Hidvegi, T., Schmidt, B. Z., Hale, P. & Perlmutter, D. H. Accumulation of mutant alpha1-antitrypsin Z in the endoplasmic reticulum activates caspases-4 and -12, NFkappaB, and BAP31 but not the unfolded protein response. J. Biol. Chem. 280, 39002\u201339015 (2005).","journal-title":"J. Biol. Chem."},{"key":"8885_CR36","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1038\/s41592-023-01771-9","volume":"20","author":"FA Rosenberger","year":"2023","unstructured":"Rosenberger, F. A., Thielert, M. & Mann, M. Making single-cell proteomics biologically relevant. Nat. Methods 20, 320\u2013323 (2023).","journal-title":"Nat. Methods"},{"key":"8885_CR37","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1002\/path.5420","volume":"251","author":"F Coscia","year":"2020","unstructured":"Coscia, F. et al. A streamlined mass spectrometry\u2013based proteomics workflow for large-scale FFPE tissue analysis. J. Pathol. 251, 100\u2013112 (2020).","journal-title":"J. Pathol."},{"key":"8885_CR38","doi-asserted-by":"publisher","first-page":"2223","DOI":"10.1038\/s41592-024-02533-x","volume":"21","author":"R Fan","year":"2024","unstructured":"Fan, R. Integrative spatial protein profiling with multi-omics. Nat. Methods 21, 2223\u20132225 (2024).","journal-title":"Nat. Methods"},{"key":"8885_CR39","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abc2487","volume":"6","author":"MT Henrich","year":"2020","unstructured":"Henrich, M. T. et al. Determinants of seeding and spreading of \u03b1-synuclein pathology in the brain. Sci. Adv. 6, eabc2487 (2020).","journal-title":"Sci. Adv."},{"key":"8885_CR40","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1016\/j.neuron.2019.10.010","volume":"105","author":"F Bassil","year":"2020","unstructured":"Bassil, F. et al. Amyloid-beta (A\u03b2) plaques promote seeding and spreading of alpha-synuclein and tau in a mouse model of Lewy body disorders with A\u03b2 pathology. Neuron 105, 260\u2013275.e6 (2020).","journal-title":"Neuron"},{"key":"8885_CR41","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1053\/j.gastro.2020.04.058","volume":"159","author":"CV Schneider","year":"2020","unstructured":"Schneider, C. V. et al. Liver Phenotypes of European Adults Heterozygous or Homozygous for Pi\u2217Z Variant of AAT (Pi\u2217MZ vs Pi\u2217ZZ genotype) and Noncarriers. Gastroenterology 159, 534\u2013548.e11 (2020).","journal-title":"Gastroenterology"},{"key":"8885_CR42","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1038\/s41592-020-01018-x","volume":"18","author":"C Stringer","year":"2021","unstructured":"Stringer, C., Wang, T., Michaelos, M. & Pachitariu, M. Cellpose: a generalist algorithm for cellular segmentation. Nat. Methods 18, 100\u2013106 (2021).","journal-title":"Nat. Methods"},{"key":"8885_CR43","unstructured":"Wolf, T. et al. HuggingFace\u2019s transformers: state-of-the-art natural language processing. Preprint at https:\/\/arxiv.org\/abs\/1910.03771v5 (2020)."},{"key":"8885_CR44","unstructured":"McInnes, L., Healy, J. & Melville, J. UMAP: uniform manifold approximation and projection for dimension reduction. Preprint at https:\/\/arxiv.org\/abs\/1802.03426v3 (2020)."},{"key":"8885_CR45","first-page":"2825","volume":"12","author":"F Pedregosa","year":"2011","unstructured":"Pedregosa, F. et al. Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825\u20132830 (2011).","journal-title":"J. Mach. Learn. Res."},{"key":"8885_CR46","doi-asserted-by":"publisher","unstructured":"Schmacke, N. A. et al. SPARCS, a platform for genome-scale CRISPR screening for spatial cellular phenotypes. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2023.06.01.542416 (2023).","DOI":"10.1101\/2023.06.01.542416"},{"key":"8885_CR47","doi-asserted-by":"crossref","unstructured":"Thielert, M., Weiss, C. A. M., Mann, M. & Rosenberger, F. A. in Mass Spectrometry Based Single Cell Proteomics (eds. Vegvari, A., Teppo, J. & Zubarev, R. A.) 97\u2013113 (Springer, 2024).","DOI":"10.1007\/978-1-0716-3934-4_9"},{"key":"8885_CR48","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/s41592-019-0638-x","volume":"17","author":"V Demichev","year":"2020","unstructured":"Demichev, V., Messner, C. B., Vernardis, S. I., Lilley, K. S. & Ralser, M. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat. Methods 17, 41\u201344 (2020).","journal-title":"Nat. Methods"},{"key":"8885_CR49","doi-asserted-by":"publisher","first-page":"100581","DOI":"10.1016\/j.mcpro.2023.100581","volume":"22","author":"C Ammar","year":"2023","unstructured":"Ammar, C., Schessner, J. P., Willems, S., Michaelis, A. C. & Mann, M. Accurate label-free quantification by directLFQ to compare unlimited numbers of proteomes. Mol. Cell. Proteomics 22, 100581 (2023).","journal-title":"Mol. Cell. Proteomics"},{"key":"8885_CR50","doi-asserted-by":"publisher","first-page":"W415","DOI":"10.1093\/nar\/gkae456","volume":"52","author":"JM Elizarraras","year":"2024","unstructured":"Elizarraras, J. M. et al. WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics. Nucleic Acids Res. 52, W415\u2013W421 (2024).","journal-title":"Nucleic Acids Res."},{"key":"8885_CR51","doi-asserted-by":"publisher","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","volume":"51","author":"D Szklarczyk","year":"2023","unstructured":"Szklarczyk, D. et al. The STRING database in 2023: protein\u2013protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 51, D638\u2013D646 (2023).","journal-title":"Nucleic Acids Res."},{"key":"8885_CR52","doi-asserted-by":"publisher","DOI":"10.1126\/scisignal.aaz0274","volume":"12","author":"M Uhl\u00e9n","year":"2019","unstructured":"Uhl\u00e9n, M. et al. The human secretome. Sci. Signal. 12, eaaz0274 (2019).","journal-title":"Sci. Signal."},{"key":"8885_CR53","doi-asserted-by":"publisher","first-page":"D543","DOI":"10.1093\/nar\/gkab1038","volume":"50","author":"Y Perez-Riverol","year":"2022","unstructured":"Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 50, D543\u2013D552 (2022).","journal-title":"Nucleic Acids Res."},{"key":"8885_CR54","doi-asserted-by":"publisher","first-page":"D1266","DOI":"10.1093\/nar\/gkx965","volume":"46","author":"U Sarkans","year":"2018","unstructured":"Sarkans, U. et al. The BioStudies database\u2014one stop shop for all data supporting a life sciences study. Nucleic Acids Res. 46, D1266\u2013D1270 (2018).","journal-title":"Nucleic Acids Res."}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-025-08885-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-025-08885-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-025-08885-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,16]],"date-time":"2025-06-16T01:01:44Z","timestamp":1750035704000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-025-08885-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,16]]},"references-count":54,"journal-issue":{"issue":"8067","published-print":{"date-parts":[[2025,6,12]]}},"alternative-id":["8885"],"URL":"https:\/\/doi.org\/10.1038\/s41586-025-08885-4","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,16]]},"assertion":[{"value":"26 August 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 March 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 April 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"M.M. is an indirect investor in Evosep. A patent for treatment of conditions related to \u03b11-antitrypsin deficiency with PPAR\u03b1 agonists has been filed with the European Patent Office (application number EP24205578.8). The other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}