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. 2023 Oct 2;20(10):1530–1536. doi: 10.1038/s41592-023-02007-6

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 1 — a, Titration of number of shapes (10 µm thick) versus proteome depth achieved (n = 3), and measured with the original protocol (single shape, 44 min Evosep gradient, 15 cm column at 500 nL/min, dia-PASEF 27 without optimized windows, library-dependent search in DIA-NN 30). Boxes are first and third quartile, the thick line is median, whiskers are ± 1.5 interquartile range, and outliers are indicated as individual points. b, Protein numbers per five shapes across 230 samples. Line is a smoothing curve. c, Principal component analyses with a color overlay of two indicated zonation markers; n.q. not quantified. d, Unbiased k means clustering of all samples into four bins. Labeled arrows are the top driver proteins of separation. e, Marker expression sorted by central (top) or portal (bottom) markers in the indicated k means clusters in d, expressed as z-score of log2 transformed protein abundances, and sorted according to summed zonal probability across all markers.