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. 2023 Jun 10;14:3428. doi: 10.1038/s41467-023-39149-2

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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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Fig. 1 — a Each individual’s gut microbiome sample was subjected to protein extraction. Then, purified proteins were digested by trypsin. b The resulting peptides were fractionated using a high-pH reversed-phase approach. c 48 micro-fractions were combined into 12 samples prior to LC-MS/MS analysis. d In this study, LC-MS/MS analysis was performed using Exploris 480 with a 1 h gradient for each fraction. e The LC-MS/MS *.RAW files were searched against a protein database using MetaPro-IQ workflow and MetaLab. f When matched metagenomes are available, taxonomic and functional annotations of the metagenomes can be used for PCN generation. Alternatively, a protein-peptide bridge approach can be used for generating the PCNs from MetaLab result tables (see details in Methods and Supplementary Notes 1) without the need of matched metagenomes. g The sample-specific PCN is a bipartite plot linking taxon to their expressed functions, with the links weighed by protein abundances of each taxon. h The PCN can also be converted as functional profiles of each taxon. i The taxon-specific protein biomass contributions (percentage) were calculated from the taxonomy table based on summing up unique peptides of each taxon.