Mass Spectrometry-derived Protein Intensities

Mass spectrometry analysis (data-independent acquisition) derived intensities are reported here for all breast tumor samples (n = 75). RAW data files for these samples are accessible via  ProteomeXchange  with the dataset identifiers PXD032266 (S samples) and PXD037428 (V samples). Protein intensities were Log2 transformed and scaled (samples and proteins). This dataset was used for Figure 5 in the following manuscript: "Proteogenomics decodes the evolution of human ipsilateral breast cancer". De Marchi T, Pyl PT, Sjöström M, Reinsbach SE, DiLorenzo S, Nystedt B, Tran L, Pekar G, Wärnberg F, Fredriksson I, Malmström P, Fernö M, Malmström L, Malmström J, Nimèus E. accepted for publication