Proteomic workflows for high-quality quantitative proteome and post-translational modification analysis of clinically relevant samples from formalin-fixed paraffin-embedded archives
Abstract
Well-characterized archival formalin-fixed paraffin-embedded (FFPE) tissues are of much value for prospective biomarker discovery studies, and protocols that offer high throughput and good reproducibility are essential in proteomics. Therefore, we implemented efficient paraffin removal and protein extraction from FFPE tissues followed by an optimized two-enzyme digestion using suspension trapping (S-Trap). The protocol was then combined with TMTpro 16plex labeling and applied to lung adenocarcinoma patient samples. In total, 9585 proteins were identified, and proteins related to the clinical outcome were detected. Because acetylation is known to play a major role in cancer development, a fast on-trap acetylation protocol was developed for studying endogenous lysine acetylation, which allows identification and localization of the lysine acetylation together with quantitative comparison between samples. We demonstrated that FFPE tissues are equivalent to frozen tissues to study the degree of acetylation between patients. In summary, we present a reproducible sample preparation workflow optimized for FFPE tissues that resolves known proteomic-related challenges. We demonstrate compatibility of the S-Trap with isobaric labeling and for the first time, we prove that it is feasible to study endogenous lysine acetylation stoichiometry in FFPE tissues, contributing to better utility of the existing global tissue archives. The MS proteomic data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifiers PXD020157, PXD021986, and PXD021964.
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Nagshabandi, L. N., AlHammadi, S. A., Sukkarieh, H. H., Abdelhadi, O. E., & Aljada, A. (2026) · Mass Spectrometry Reviews · doi:10.1002/mas.70047
- Authors
- Kuras, M., Woldmar, N., Kim, Y., Hefner, M., Malm, J., Moldvay, J., Döme, B., Fillinger, J., Pizzatti, L., Gil, J., Marko-Varga, G., & Rezeli, M.
- Affiliations
- Lund University (SE)
- Universidade Federal do Rio de Janeiro (BR)
- Semmelweis University (HU)
- Div. Clinical Protein Science & Imaging, Dept. of Clinical Sciences (Lund) and Dept. of Biomedical Engineering, Lund University, Lund 22100, Sweden
- Corresponding author
- Rezeli, Melinda
- ORCID
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2020-12-10
- Volume
- 20
- Issue
- 1
- Pages
- 1027-1039
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W3111322527
- Cited by
- 36
- References
- 51
- Citations by year
- 2026: 6 · 2025: 7 · 2024: 5 · 2023: 5 · 2022: 5 · 2021: 8
- FWCI
- 1.72
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Journal of Proteome Research (publishedVersion)
- PubMed (publishedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- Funders
- Fru Berta Kamprads Stiftelse
- National Research Foundation of Korea (2015K1A1A2028365, 2016K2A9A1A03904900)
- Ministry of Education and Human Resources Development
- Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior
- Kungliga Fysiografiska S?llskapet i Lund
- Thermo Fischer Scientific
- International Cancer Proteogenome Consortium, National Cancer Institute
- European Cancer Moonshot Lund Center
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced Biosensing Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Keywords
- formalin-fixed paraffin-embedded tissue, paraffin removal, protein extraction, quantitative proteomics, post-translational modification, lysine acetylation, lung adenocarcinoma, biomarker discovery, frozen tissue comparison
- MeSH terms
- Formaldehyde, Humans, Prospective Studies, Protein Processing, Post-Translational, Reproducibility of Results, Paraffin Embedding, Tissue Fixation, Proteome, Proteomics, Workflow
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