TY - JOUR
T1 - DIA-MS proteome analysis of formalin-fixed paraffin-embedded glioblastoma tissues
AU - Weke, Kenneth
AU - Kote, Sachin
AU - Faktor, Jakub
AU - Al Shboul, Sofian
AU - Uwugiaren, Naomi
AU - Brennan, Paul M.
AU - Goodlett, David R.
AU - Hupp, Ted R.
AU - Dapic, Irena
N1 - Funding Information:
This research was funded by the International Research Agenda's Program of the Foundation for Polish Science (MAB/2017/03) (K.W, J.F, N.U, D.R.G, T.R.H, S.K, I.D).This study was funded by the International Research Agenda's Program of the Foundation for Polish Science (MAB/2017/03) (K.W, J.F, N.U, D.R.G, T.R.H, S.K, I.D). The “International Centre for Cancer Vaccine Science” project is carried out within the International Research Agendas programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund. The authors would also like to thank the CI-TASK, Gdansk, and the PL-Grid Infrastructure, Poland for providing their hardware and software resources. 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) (D.R.G). We are grateful to the NHS Lothian Bioresource for facilitating the collection of tissue used in this study (P.M.B).
Funding Information:
This research was funded by the International Research Agenda's Program of the Foundation for Polish Science ( MAB/2017/03 ) (K.W, J.F, N.U, D.R.G, T.R.H, S.K, I.D).
Funding Information:
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) (D.R.G).
Funding Information:
This study was funded by the International Research Agenda's Program of the Foundation for Polish Science ( MAB/2017/03 ) (K.W, J.F, N.U, D.R.G, T.R.H, S.K, I.D). The “International Centre for Cancer Vaccine Science” project is carried out within the International Research Agendas programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund . The authors would also like to thank the CI-TASK, Gdansk, and the PL-Grid Infrastructure, Poland for providing their hardware and software resources.
Publisher Copyright:
© 2022 The Authors
PY - 2022/4/29
Y1 - 2022/4/29
N2 - Developments in quantitative proteomics and data-independent acquisition (DIA) methodology is enabling quantification of proteins in biological samples. Currently, there are a few reports on DIA mass spectrometry (MS) approaches for proteome analysis of formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, to facilitate detection and quantification of immune- and glioblastoma (GBM)-relevant proteins from FFPE patient materials, we established a simple and precise DIA-MS workflow. We first evaluated different lysis buffers for their efficiency in protein extractions from FFPE GBM tissues. Our results showed that more than 1700 proteins were detected and over 1400 proteins were quantified from GBM FFPE tissue microdissections. GBM-relevant proteins (e.g., GFAP, FN1, VIM, and MBP) were quantified with high precision (median coefficient of variation <12%). In addition, immune-related proteins (e.g., ILF2, MIF, and CD38) were consistently detected and quantified. The strategy holds great potential for routinizing protein quantification in FFPE tissue samples.
AB - Developments in quantitative proteomics and data-independent acquisition (DIA) methodology is enabling quantification of proteins in biological samples. Currently, there are a few reports on DIA mass spectrometry (MS) approaches for proteome analysis of formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, to facilitate detection and quantification of immune- and glioblastoma (GBM)-relevant proteins from FFPE patient materials, we established a simple and precise DIA-MS workflow. We first evaluated different lysis buffers for their efficiency in protein extractions from FFPE GBM tissues. Our results showed that more than 1700 proteins were detected and over 1400 proteins were quantified from GBM FFPE tissue microdissections. GBM-relevant proteins (e.g., GFAP, FN1, VIM, and MBP) were quantified with high precision (median coefficient of variation <12%). In addition, immune-related proteins (e.g., ILF2, MIF, and CD38) were consistently detected and quantified. The strategy holds great potential for routinizing protein quantification in FFPE tissue samples.
KW - Data-independent acquisition
KW - Quantitative proteomics
KW - Formalin-fixed paraffin-embedded
KW - Glioblastoma
KW - Mass spectrometry
U2 - 10.1016/j.aca.2022.339695
DO - 10.1016/j.aca.2022.339695
M3 - Article
SN - 0003-2670
VL - 1204
JO - Analytica Chimica Acta
JF - Analytica Chimica Acta
M1 - 339695
ER -