br AUTHOR CONTRIBUTIONS br P
P.B. supervised SWATH-MS analyses at MMCI, analyzed SWATH-MS data, coordinated the study, and wrote the paper; O.T.S. supervised SWATH-MS data analysis and wrote the paper; J.F. performed SWATH-MS analyses at MMCI; L.C. performed data analysis clustering and comparison of gene MDMB-CHMCZCA M 3 at proteome and transcriptome level as well as GSEA pathway an-alyses; H.I. performed validation of selected gene products in independent
datasets; K.Z. performed KEGG pathway analyses; V.P. performed SWATH-MS data analyses in Skyline software; R.H. analyzed p53 status of tumors; Y.L. significantly contributed to SWATH-MS measurements and to manuscript preparation; H.A.E. contributed to SWATH-MS measurements and to manu-script preparation; E.B. constructed the decision tree and co-supervised all data analyses; R.N. designed and selected the set of tissues and contributed to data interpretation; and R.A. approved the joint study, provided computa-tional and instrument capacity, and wrote and approved the manuscript.
DECLARATION OF INTERESTS
The authors declare no competing interests.
Bouchal, P., Roumeliotis, T., Hrstka, R., Nenutil, R., Vojtesek, B., and Garbis, S.D. (2009). Biomarker discovery in low-grade breast cancer using isobaric stable isotope tags and two-dimensional liquid chromatography-tandem mass spectrometry (iTRAQ-2DLC-MS/MS) based quantitative proteomic analysis. J. Proteome Res. 8, 362–373.
Bouchal, P., Dvorakova, M., Scherl, A., Garbis, S.D., Nenutil, R., and Vojtesek, B. (2013). Intact protein profiling in breast cancer biomarker discovery: protein identification issue and the solutions based on 3D protein separation, bottom-up and top-down mass spectrometry. Proteomics 13, 1053–1058.
Brozkova, K., Budinska, E., Bouchal, P., Hernychova, L., Knoflickova, D., Valik, D., Vyzula, R., Vojtesek, B., and Nenutil, R. (2008). Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression. Breast Cancer Res. 10, R48.
Cancer Genome Atlas, N.; Cancer Genome Atlas Network (2012). Comprehen-sive molecular portraits of human breast tumours. Nature 490, 61–70.
mass spectrometry-based proteomic experiments. Bioinformatics 30, 2524– 2526.
Faktor, J., Sucha, R., Paralova, V., Liu, Y., and Bouchal, P. (2017). Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues. Proteomics 17, 1600323.
Nakamura, K., Hirayama-Kurogi, M., Ito, S., Kuno, T., Yoneyama, T., Obuchi, W., Terasaki, T., and Ohtsuki, S. (2016). Large-scale multiplex absolute protein quantification of drug-metabolizing enzymes and transporters in human intes-tine, liver, and kidney microsomes by SWATH-MS: comparison with MRM/ SRM and HR-MRM/PRM. Proteomics 16, 2106–2117.
Parise, C.A., and Caggiano, V. (2014). Breast cancer survival defined by the ER/PR/HER2 subtypes and a surrogate classification according to tumor grade and immunohistochemical biomarkers. J. Cancer Epidemiol. 2014, 469251.
Pavlou, M.P., Dimitromanolakis, A., and Diamandis, E.P. (2013). Coupling pro-teomics and transcriptomics in the quest of subtype-specific proteins in breast cancer. Proteomics 13, 1083–1095.
Pernika´rova´, V., and Bouchal, P. (2015). Targeted proteomics of solid cancers: from quantification of known biomarkers towards reading the digital proteome maps. Expert Rev. Proteomics 12, 651–667.
Nenutil, R., and Bouchal, P. (2017). Targeted proteomics driven verification of biomarker candidates associated with breast cancer aggressiveness. Bio-chim. Biophys. Acta. Proteins Proteomics 1865, 488–498.
Robinson, M.D., McCarthy, D.J., and Smyth, G.K. (2010). edgeR: a bio-conductor package for differential expression analysis of digital gene expres-sion data. Bioinformatics 26, 139–140.
Sequeira, S.J., Wen, H.C., Avivar-Valderas, A., Farias, E.F., and Aguirre-Ghiso, J.A. (2009). Inhibition of eIF2alpha dephosphorylation inhibits ErbB2-induced deregulation of mammary acinar morphogenesis. BMC Cell Biol. 10, 64.
Waldemarson, S., Kurbasic, E., Krogh, M., Cifani, P., Bergga˚rd, T., Borg, A˚., and James, P. (2016). Proteomic analysis of breast tumors confirms the mRNA intrinsic molecular subtypes using different classifiers: a large-scale analysis of fresh frozen tissue samples. Breast Cancer Res. 18, 69.
Wisniewski, J.R., Ostasiewicz, P., and Mann, M. (2011). High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. J. Proteome Res. 10, 3040–3049.