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Triple negative tumors do not benefit from targeted therapies, so further characterization is needed to define subgroups with potential therapeutic value. In this work, the proteomes of 125 formalin\u2010fixed paraffin\u2010embedded samples from patients diagnosed with non\u2010metastatic triple negative breast cancer were analyzed using data\u2010independent acquisition + in a LTQ\u2010Orbitrap Fusion Lumos mass spectrometer coupled to an EASY\u2010nLC 1000. 1206 proteins were identified in at least 66% of the samples. Hierarchical clustering, probabilistic graphical models and Significance Analysis of Microarrays were combined to characterize proteomics\u2010based molecular groups. Two molecular groups were defined with differences in biological processes such as glycolysis, translation and immune response. These two molecular groups showed also several differentially expressed proteins. This clinically homogenous dataset may serve to design new therapeutic strategies in the future.<\/jats:p>","DOI":"10.1002\/pmic.202100110","type":"journal-article","created":{"date-parts":[[2021,10,9]],"date-time":"2021-10-09T06:32:48Z","timestamp":1633761168000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Molecular characterization of triple negative breast cancer formaldehyde\u2010fixed paraffin\u2010embedded samples by data\u2010independent acquisition proteomics"],"prefix":"10.1002","volume":"22","author":[{"given":"Silvia","family":"Garc\u00eda\u2010Adri\u00e1n","sequence":"first","affiliation":[{"name":"Medical Oncology Service Hospital Universitario de M\u00f3stoles  Madrid Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luc\u00eda","family":"Trilla\u2010Fuertes","sequence":"additional","affiliation":[{"name":"Biomedica Molecular Medicine SL  Madrid 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