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. 2022 Apr 18;23(8):4443. doi: 10.3390/ijms23084443

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© 2022 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Experimental Design. Xenografts were generated from human DCIS cells and tumors were resected after 1.5 weeks, followed by formalin-fixation and paraffin-embedding, as described in [17]. One-millimeter-diameter FFPE cores were used to optimize individual steps of the FFPE sample preparation: (1) deparaffinization, (2) homogenization, (3) extraction, and (4) digestion. Peptide samples were analyzed by nano-LC-MS/MS label-free quantitation (LFQ) to compare the performance of the evaluated protocols for each step of the sample preparation workflow.