Additional file 1 of Trastuzumab-induced upregulation of a protein set in extracellular vesicles emitted by ErbB2-positive breast cancer cells correlates with their trastuzumab sensitivity

Additional file 1: Supplementary Table 1. Liquid chromatography-tandem mass spectrometry analysis of proteins in extracellular vesicles emitted by BT-474 or BT-474TR cells before and after trastuzumab treatment. BT-474 or BT-474TR cells were treated (+) or not (−) with 5 μg/ml trastuzumab (TZ) in 3D culture for 72 h. Extracellular vesicles were isolated from the conditioned media by ultracentrifugation. EV proteins were digested by trypsin and analyzed by LC-MS/MS. The raw data were matched against the latest human SwissProt protein database by use of the Mascot search engine. Label-free TIC quantification was further performed by Scaffold Q+ software. Signal intensities for each of the indicated EV proteins are expressed in TIC units (protein threshold >95.0%, peptide threshold >95.0%, a minimum of two unique peptides identified per protein). The data for five independent experiments are shown.