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. 2017 Aug 11;7:7896. doi: 10.1038/s41598-017-08333-y

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© The Author(s) 2017

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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Representative extracted ion chromatograms for peptides from (a) AI and (b) ADC reference samples, and (c) AI and (d) ADC forced degradation (e.g., 3 mM AAPH) samples. Most peptides, including the unmodified peptide VDNALQSGNSQESVTEQDSK that can be used for normalization, were unaffected by the conjugation of linker drug. On the other hand, the linker-drug-modified peptides such as SFNRGEC were only observed in the ADC. In the ADC, the cysteine in this peptide was observed with carboxymethylation (+58 Da), vcMMAE- (+1315 Da), and vcMMAEhydro (+1333 Da) modifications. In the AI, the cysteine was fully carboxymethylated and no linker-drug modifications were observed. Comparisons of non-linker-drug modifications between reference samples provided negative control for differential site occupancy analysis while comparisons between reference samples versus their forced degradation samples provided positive controls.