Proteomic Maps of Breast Cancer Subtypes

Tyanova, S.; Albrechtsen, R.; Kronqvist, P.; et al.

Using MS-based proteomics for systems-wide profiling (instead of genomics and transcriptomics), Geiger, T. et al. employed FFPE filter-aided sample preparation (FASP) in combination with a super-SILAC approach to quantify >10,000 proteins (from >157,000 sequence-unique peptides) in clinical breast cancer tumor samples. The functional networks within and between breast cancer subtypes were examined, while novel cancer regulators and subtype-specific biological processes were discovered. To support clinical translation, a computational workflow based on support vector machine (SVM)-based classification was developed for protein identification according to breast cancer subtype.