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. 2020 Nov 23;7:412. doi: 10.1038/s41597-020-00744-3

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© The Author(s) 2020

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. 3 — SWATH-MS data analysis against human T-cell and Pan human libraries and comparison with DDA-MS data. (a) Experimental protocol used to obtain human CD4⁺ T-cells at different in vitro activated status. Samples were obtained from three different donors. (b) Number of peptides and proteins detected by the analysis of CD4⁺ T-cells by SWATH-MS against human T-cell and pan-human spectral libraries and DDA-MS. (c) Proportional Venn diagram depicting the overlap between quantified SWATH-MS proteins against the two spectral libraries. (d) Proportional Venn diagram depicting the overlap between all the quantified SWATH-MS proteins and DDA-MS proteins. (e) Box plots showing the missing peptide intensity values in SWATH-MS and DDA-MS data (central lines and boxes represent means and 95% confidence intervals respectively while whiskers are 2.5 to 97.5 percentiles). (f) Distribution of Pearson correlation coefficient between protein expression data obtained by SWATH-MS and DDA-MS for human CD4⁺ T-cell time series experiment.