Evaluation of fast and sensitive proteome profiling of FF and FFPE kidney patient tissues
| dc.contributor.author | Dapic, Irena | |
| dc.contributor.author | Uwugiaren, Naomi | |
| dc.contributor.author | Kers, Jesper | |
| dc.contributor.author | Mohammed, Yassene | |
| dc.contributor.author | Goodlett, David R. | |
| dc.contributor.author | Corthals, Garry | |
| dc.date.accessioned | 2022-10-25T16:14:27Z | |
| dc.date.available | 2022-10-25T16:14:27Z | |
| dc.date.copyright | 2022 | en_US |
| dc.date.issued | 2022 | |
| dc.description.abstract | The application of proteomics to fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) human tissues is an important development spurred on by requests from stakeholder groups in clinical fields. One objective is to complement current diagnostic methods with new specific molecular information. An important goal is to achieve adequate and consistent protein recovery across and within large-scale studies. Here, we describe development of several protocols incorporating mass spectrometry compatible detergents, including Rapigest, PPS, and ProteaseMax. Methods were applied on 4 and 15 micrometer thick FF tissues, and 4 micrometer thick FFPE tissues. We evaluated sensitivity and repeatability of the methods and found that the protocol containing Rapigest enabled detection of 630 proteins from FF tissue of 1 mm2 and 15 micrometers thick, whereas 498 and 297 proteins were detected with the protocols containing ProteaseMax and PPS, respectively. Surprisingly, PPS-containing buffer showed good extraction of the proteins from 4 micrometer thick FFPE tissue with the average of 270 protein identifications (1 mm2), similar to the results on 4 micrometer thick FF. Moreover, we found that temperature increases during incubation with urea on 4 micrometer thick FF tissue revealed a decrease in the number of identified proteins and increase in the number of the carbamylated peptides. | en_US |
| dc.description.reviewstatus | Reviewed | en_US |
| dc.description.scholarlevel | Faculty | en_US |
| dc.description.sponsorship | This work was supported by the International Centre for Cancer Vaccine Science, carried out within the International Research Agendas program of the Foundation for Polish Science cofinanced by the European Union under the European Regional Development Fund. The authors also thank Dutch National Sectorplan Natuur-en Scheikunde (SNS-10.0119/D). J. Kers was financially supported by a grant from the Dutch Kidney Foundation (grant number 17OKG23). We are grateful for funding for technology development and platform support for The Pan-Canadian Proteomics Centre (PCPC), from Genome Canada, and Genome British Columbia through the Genomics Technology Platform (GTP) program for operations and technology development (264PRO). The University of Victoria- Genome BC Proteomics Center is grateful to Genome Canada and Genome British Columbia for financial support (project code 282PQP). | en_US |
| dc.identifier.citation | Dapic, I., Uwugiaren, N., Kers, J., Mohammed, Y., Goodlett, D., & Corthals, G. (2022). “Evaluation of fast and sensitive proteome profiling of FF and FFPE kidney patient tissues.” Molecules, 27(3), 1137. https://doi.org/10.3390/molecules27031137 | en_US |
| dc.identifier.uri | https://doi.org/10.3390/molecules27031137 | |
| dc.identifier.uri | http://hdl.handle.net/1828/14308 | |
| dc.language.iso | en | en_US |
| dc.publisher | Molecules | en_US |
| dc.subject | FF | |
| dc.subject | FFPE | |
| dc.subject | mass spectrometry | |
| dc.subject | kidney | |
| dc.subject | MS-compatible detergents | |
| dc.subject | UVic Genome BC Proteomics Centre | |
| dc.subject.department | Department of Biochemistry and Microbiology | |
| dc.title | Evaluation of fast and sensitive proteome profiling of FF and FFPE kidney patient tissues | en_US |
| dc.type | Article | en_US |