Accurate classification of breast tumors is vital for patient management decisions and enables more precise cancer treatment. Here, we present a quantitative proteotyping approach based on sequential windowed acquisition of all theoretical fragment ion spectra (SWATH) mass spectrometry and establish key proteins for breast tumor classification. The study is based on 96 tissue samples representing five conventional breast cancer subtypes. SWATH proteotype patterns largely recapitulate these subtypes; however, they also reveal varying heterogeneity within the conventional subtypes, with triple negative tumors being the most heterogeneous. Proteins that contribute most strongly to the proteotype-based classification include INPP4B, CDK1, and ERBB2 and are associated with estrogen receptor (ER) status, tumor grade status, and HER2 status. Although these three key proteins exhibit high levels of correlation with transcript levels (R > 0.67), general correlation did not exceed R = 0.29, indicating the value of protein-level measurements of disease-regulated genes. Overall, this study highlights how cancer tissue proteotyping can lead to more accurate patient stratification.

Department of Biochemistry Faculty of Science Masaryk University Brno Czech Republic

Department of Biochemistry Faculty of Science Masaryk University Brno Czech Republic; Center for Human Genetics University of Leuven Leuven Belgium

Department of Biochemistry Faculty of Science Masaryk University Brno Czech Republic; Regional Centre for Applied Molecular Oncology Masaryk Memorial Cancer Institute Brno Czech Republic

Department of Biology Institute of Molecular Systems Biology Federal Institute of Technology Zurich Zurich Switzerland; Department of Human Genetics University of California Los Angeles Los Angeles CA USA

Department of Biology Institute of Molecular Systems Biology Federal Institute of Technology Zurich Zurich Switzerland; Faculty of Science University of Zurich Zurich Switzerland

Department of Biology Institute of Molecular Systems Biology Federal Institute of Technology Zurich Zurich Switzerland; Systems Biology Ireland University College Dublin Dublin Ireland

Department of Pharmacology Yale Cancer Biology Institute Yale University School of Medicine West Haven CT USA

Regional Centre for Applied Molecular Oncology Masaryk Memorial Cancer Institute Brno Czech Republic

Regional Centre for Applied Molecular Oncology Masaryk Memorial Cancer Institute Brno Czech Republic; Research Centre for Toxic Compounds in the Environment Faculty of Science Masaryk University Brno Czech Republic

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