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. 2022 Nov 30;13:7242. doi: 10.1038/s41467-022-34824-2

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© The Author(s) 2022

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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Fig. 2 — A The peptide yields of the in-solution, PCT, proExM-MS, and ProteomEx methods applied to the mouse brain tissue (n = 4, 4, 7, 4 biologically independent samples from one, one, two, and one brain slices, respectively, the same samples were used to acquire data shown in panels A–F; dot, individual data point, bar, mean, whiskers, standard deviation (SD), throughout Fig. 2; P-values are estimated by Welch’s t-test (two-sided). Data are presented as mean values ± SD.). B Missed cleavages of the identified peptides prepared using in-solution, PCT, proExM-MS, and ProteomEx methods. Data are presented as mean values ± SD. Number of peptide (C) and protein (D) identifications in seven sample groups (n = 3 and 3 punches from one slice from one mouse for ProteomEx (5.9 nL) and blank hydrogel, n = 3 independent injections for MS buffer; analyzed by DDA). Data are presented as mean values ± SD. E Venn diagram of identified proteins for the bulk samples shown in D. F The subcellular locations of the identified proteins for the samples shown in E. Number of peptide (G) and protein (H) identifications for different tissue volumes processed by ProteomEx and PCT (n = 4 punches per group from 2 mice for ProteomEx, LEF = 6.3, 6.2, 6.3, 5.9; n = 3 tissue dissections per group from 1 mouse for PCT; dot and triangle, individual data point; center of error bar ends, mean; whiskers, SD; solid line, four-parameter logistic fit, dashed line indicates 95% confidence interval border, shaded area represents 95% confidence interval; analyzed by PulseDIA; dot, individual data point; bar, mean; whiskers, SD). Source data are provided as a Source Data file.