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. 2021 Oct 15;12:713400. doi: 10.3389/fgene.2021.713400

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Copyright © 2021 Fijalkowski, Peeters and Van Damme.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Differential analysis of proteins enriched in Amphi+ setup. (A–C) Volcano plots illustrating differential protein abundances between investigated extraction protocols. The 3 total extraction methods (amphi, urea and GuHCl) are pair-wise compared to enriched amphipol samples (Amphi+) and the relation between log of p-value is plotted against fold change in protein abundance. Solid curved lines represent a significance threshold of 1% FDR (S0 = 0.1). SEPs are highlighted in orange. (D) Boxplot illustrating log2 LFQ intensities of SEPs identified in samples across all investigated experimental setups. Significant difference is marked with asterix (p-value <0.01, t-test) (E) Boxplot illustrating log2 LFQ intensities of proteins longer than 100 aa identified in all investigated experimental setups. Significant difference is marked with asterix (p-value <0.01, t-test).