Evaluation of fast and sensitive proteome profiling of FF and FFPE kidney patient tissues
Date
2022
Authors
Dapic, Irena
Uwugiaren, Naomi
Kers, Jesper
Mohammed, Yassene
Goodlett, David R.
Corthals, Garry
Journal Title
Journal ISSN
Volume Title
Publisher
Molecules
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.
Description
Keywords
FF, FFPE, mass spectrometry, kidney, MS-compatible detergents
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