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. 2021 Nov 18;12:6685. doi: 10.1038/s41467-021-26979-1

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© The Author(s) 2021

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. 4 — a Design of six spectral libraries as defined in Fig. 3b for the RPE1 DIA data analysis (left) and experimental design of the EGF signaling study in the context of MEK inhibition (right). b Number of phosphopeptides and phosphosites that were quantified from the initial search using each library. c Procedure of building a focused library to be used for an iterative search. d Number of phosphopeptides and phosphosites that were quantified from the iterative search using each library. Percentage of the total quantifiable phosphopeptide or phosphosite number is shown for each predicted library relative to Lib 1. The proportions of shared identifications (IDs), gained IDs, lost IDs, and gap IDs yielded by Lib 2 to Lib 7 compared to Lib 1 are indicated in different color. Source data for this figure are provided as a Source data file.