MS results for identifying SPINK1-interacting partners

Raw data of mass spectrometry (MS) experiments in "SPINK1-COL18A1 Crosstalk Shapes Epigenome and Drives Cancer Stemness in Pancreatic Ductal Adenocarcinoma" project. A method of proximity dependent biotinylation with UltraID was used in PANC-1 cell line. PANC-1 cells overexpressing SPINK1-UltraID (plasmid plentiSFFV-hSPINK1-UltraID) or Ultra Ctrl (plasmid plentiSFFV-hSPINK1SP-UltraID-ALFA) were allowed to grow to ~90% confluency in 150 mm Petri dish. On the day of the experiment, cells were incubated in 50 µM biotin for 1h at 37℃. Then the biotinylated proteins were pull-down and digested on beads before MS.

Species: Homo sapiens
Tissue: Cell culture
Cell type: Permanent cell line cell (PANC-1 cell line)
Disease: Pancreatic ductal adenocarcinoma
Subcellular: Whole cell lysate
Method: On-beads digestion
Digestion Enzyme: Trypsin
Instrument Type: Affinity purification (AP-MS)
Instrument: Q Executive HF-X

Data was analyzed using Proteome Discoverer (version 2.5)(Thermo Scientific) software and searched in-house using the Mascot algorithm (version 2.8.3) (Matrix Science). Scaffold v5.1.2 (Proteome Software Inc.) was used to validate MS/MS based peptide and protein identifications.

Ultra Ctrl (control group) associated file names: HFX24-1103_Shang_20240313_Control_Digestion.raw; HFX24-1103_Shang_20240313_Control_Digestion.mzid_HFX24-1103_Shang_20240313_Control_Digestion.MGF; HFX24-1103_Shang_20240313_Control_Digestion.mzid

SPINK1-UltraID (experiment group) associated file names: HFX24-1108_Shang_20240313_SPINK1-UltraID_Digestion; HFX24-1108_Shang_20240313_SPINK1-UltraID_Digestion.mzid_HFX24-1108_Shang_20240313_SPINK1-UltraID_Digestion.MGF; HFX24-1108_Shang_20240313_SPINK1-UltraID_Digestion.mzid