DOI: 10.25345/c5ht2gg46
title: MassIVE MSV000089745 - UBR4 is a key regulator of proteome homeostasis and a vulnerability in aneuploid cancer
title: Proteomes were quantitatively mapped across 16 cancer cell lines upon shRNA-based depletion of UBR4 using two different probes (1 and 2) or control treatment with a scrambled shRNA. All analyses were done in duplicate resulting in a total of 96 mapped proteomes. The 96 samples were divided into 10 TMT sets, and one channel (126) was used as a bridge channel (combined digest of all 96 samples). All data were acquired on an Orbitrap Lumos mass spectrometer using the SPS-MS3 method. Twelve Basic pH reversed-phase liquid chromatography (bRPLC) were analyzed per TMT set. The studied cell lines were (tissues of origin are listed in parentheses): CAL51 (breast) COLO680N (esophageal) CW2 (colon) DETROIT562 (head and neck) DMS53 (lung) EBC1 (lung) GP5D (colon) HCT8 (colon) HCT15 (colon) IGROV1 (ovarian) KURAMOCHI (ovarian) OVCAR3 (ovarian) PA1 (ovarian) PC3 (prostate) SKBR3 (breast) SUM159PT (breast) The TMT labeling scheme for all samples was as follows: TMT1: bridge (126), COLO680N_UBR4shRNA2_replicate2 (127N) DMS53_CTRLshRNA_replicate1 (127C) CAL51_UBR4shRNA1_replicate2 (128N) IGROV1_UBR4shRNA2_replicate2 (128C) KURAMOCHI_CTRLshRNA_replicate2 (129N) GP5D_CTRLshRNA_replicate2 (129C) DETROIT562_CTRLshRNA_replicate1 (130N) EBC1_UBR4shRNA1_replicate2 (130C) DMS53_UBR4shRNA2_replicate2 (131N) PA1_UBR4shRNA2_replicate1 (131C) TMT2: bridge (126) SKBR3_UBR4shRNA1_replicate1 (127N) HCT15_UBR4shRNA1_replicate2 (127C) SKBR3_CTRLshRNA_replicate2 (128N) HCT8_UBR4shRNA2_replicate1 (128C) DETROIT562_UBR4shRNA1_replicate1 (129N) SUM159PT_CTRLshRNA_replicate2 (129C) HCT8_UBR4shRNA1_replicate1 (130N) SUM159PT_UBR4shRNA1_replicate2 (130C) EBC1_UBR4shRNA2_replicate2 (131N) EBC1_CTRLshRNA_replicate2 (131C) TMT3: bridge (126) IGROV1_UBR4shRNA1_replicate1 (127N) SUM159PT_UBR4shRNA1_replicate1 (127C) HCT15_CTRLshRNA_replicate1 (128N) CAL51_UBR4shRNA2_replicate2 (128C) CW2_UBR4shRNA1_replicate1 (129N) OVCAR3_UBR4shRNA2_replicate1 (129C) DMS53_CTRLshRNA_replicate2 (130N) PA1_UBR4shRNA2_replicate2 (130C) IGROV1_UBR4shRNA1_replicate2 (131N) PC3_UBR4shRNA2_replicate1 (131C) TMT4: bridge (126) HCT8_CTRLshRNA_replicate2 (127N) HCT8_UBR4shRNA2_replicate2 (127C) DETROIT562_UBR4shRNA2_replicate2 (128N) SKBR3_CTRLshRNA_replicate1 (128C) KURAMOCHI_UBR4shRNA1_replicate1 (129N) CW2_UBR4shRNA1_replicate2 (129C) COLO680N_UBR4shRNA1_replicate2 (130N) HCT15_UBR4shRNA2_replicate1 (130C) CAL51_UBR4shRNA1_replicate1 (131N) OVCAR3_UBR4shRNA1_replicate2 (131C) TMT5: bridge (126) SUM159PT_UBR4shRNA2_replicate2 (127N) HCT8_CTRLshRNA_replicate1 (127C) PA1_CTRLshRNA_replicate1 (128N) OVCAR3_CTRLshRNA_replicate2 (128C) EBC1_CTRLshRNA_replicate1 (129N) DETROIT562_UBR4shRNA1_replicate2 (129C) CAL51_CTRLshRNA_replicate1 (130N) DMS53_UBR4shRNA2_replicate1 (130C) OVCAR3_UBR4shRNA2_replicate2 (131N) SUM159PT_CTRLshRNA_replicate1 (131C) TMT6: bridge (126) HCT8_UBR4shRNA1_replicate2 (127N) DETROIT562_UBR4shRNA2_replicate1 (127C) GPD5_CTRLshRNA_replicate1 (128N) GPD5_UBR4shRNA2_replicate2 (128C) PC3_UBR4shRNA1_replicate1 (129N) HCT15_UBR4shRNA1_replicate1 (129C) CW2_UBR4shRNA2_replicate2 (130N) EBC1_UBR4shRNA2_replicate1 (130C) PC3_CTRLshRNA_replicate1 (131N) KURAMOCHI_UBR4shRNA2_replicate1 (131C) TMT7: bridge (126) COLO680N_UBR4shRNA1_replicate1 (127N) CAL51_CTRLshRNA_replicate2 (127C) IGROV1_UBR4shRNA2_replicate1 (128N) SKBR3_UBR4shRNA2_replicate1 (128C) PA1_UBR4shRNA1_replicate2 (129N) PC3_UBR4shRNA1_replicate2 (129C) DMS53_UBR4shRNA1_replicate1 (130N) GP5D_UBR4shRNA1_replicate2 (130C) PC3_CTRLshRNA_replicate2 (131N) TMT8: bridge (126) OVCAR3_CTRLshRNA_replicate1 (127N) PC3_UBR4shRNA2_replicate2 (127C) GP5D_UBR4shRNA1_replicate1 (128N) OVCAR3_UBR4shRNA1_replicate1 (128C) KURAMOCHI_UBR4shRNA1_replicate2 (129N) HCT15_CTRLshRNA_replicate2 (129C) CW2_CTRLshRNA_replicate2 (130N) HCT15_UBR4shRNA2_replicate2 (130C) DMS53_UBR4shRNA1_replicate2 (131N) TMT9: bridge (126) GP5D_UBR4shRNA2_replicate1 (127N) COLO680N_CTRLshRNA_replicate2 (127C) DETROIT562_CTRLshRNA_replicate2 (128N) IGROV1_CTRLshRNA_replicate2 (128C) CW2_CTRLshRNA_replicate1 (129N) PA1_CTRLshRNA_replicate2 (129C) CAL51_UBR4shRNA2_replicate1 (130N) EBC1_UBR4shRNA1_replicate1 (130C) KURAMOCHI_CTRLshRNA_replicate1 (131N) TMT10: bridge (126) KURAMOCHI_UBR4shRNA2_replicate2 (127N) SUM159PT_UBR4shRNA2_replicate1 (127C) COLO680N_CTRLshRNA_replicate1 (128N) PA1_UBR4shRNA1_replicate1 (128C) COLO680N_UBR4shRNA2_replicate1 (129N) IGROV1_CTRLshRNA_replicate1 (129C) CW2_UBR4shRNA2_replicate1 (130N) SKBR3_UBR4shRNA1_replicate2 (130C) SKBR3_UBR4shRNA2_replicate2 (131N)