Helmholtz Gemeinschaft


Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories

PDF (Original Article) - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
[img] Other (Supplementary Material)

Item Type:Article
Title:Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories
Creators Name:Friedrich, C. and Schallenberg, S. and Kirchner, M. and Ziehm, M. and Niquet, S. and Haji, M. and Beier, C. and Neudecker, J. and Klauschen, F. and Mertins, P.
Abstract:Formalin-fixed paraffin-embedded (FFPE) tissues are a valuable resource for retrospective clinical studies. Here, we evaluate the feasibility of (phospho-)proteomics on FFPE lung tissue regarding protein extraction, quantification, pre-analytics, and sample size. After comparing protein extraction protocols, we use the best-performing protocol for the acquisition of deep (phospho-)proteomes from lung squamous cell and adenocarcinoma with >8,000 quantified proteins and >14,000 phosphosites with a tandem mass tag (TMT) approach. With a microscaled approach, we quantify 7,000 phosphosites, enabling the analysis of FFPE biopsies with limited tissue amounts. We also investigate the influence of pre-analytical variables including fixation time and heat-assisted de-crosslinking on protein extraction efficiency and proteome coverage. Our improved workflows provide quantitative information on protein abundance and phosphosite regulation for the most relevant oncogenes, tumor suppressors, and signaling pathways in lung cancer. Finally, we present general guidelines to which methods are best suited for different applications, highlighting TMT methods for comprehensive (phospho-)proteome profiling for focused clinical studies and label-free methods for large cohorts.
Keywords:Biopsy, Epithelial Cells, Gene Expression Profiling, HEK293 Cells, Lung Neoplasms, Neoplasms, Paraffin Embedding, Phosphorylation, Proteome, Proteomics, Retrospective Studies, Tandem Mass Spectrometry, Tissue Fixation, Tumor Biomarkers
Source:Nature Communications
Publisher:Nature Publishing Group
Page Range:3576
Date:11 June 2021
Official Publication:https://doi.org/10.1038/s41467-021-23855-w
PubMed:View item in PubMed

Repository Staff Only: item control page


Downloads per month over past year

Open Access
MDC Library