Description: Hps4 disease LysoIPs; to determine how this disease alters the lung lysosomal proteome. After sample prep, 20% of the material was used to do TMT labelling as described in the manual provided by thermo. The table with the labeling can be found in https://rockefeller.box.com/s/z94ez3mqop99180u3c89yuadclikn3xy Samples were reinjected in order to generate a set of data that let us compare DDA to DIA on Lyso IP samples using a 1 h gradient. Thermo’s TMT user manual: https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2FMAN0016969_2162457_TMT10plex_UG.pdf
Link to sample prep: https://macromolecule-child.rockefeller.edu/#13%2F11%2F2020_S-Trap%20Micro%20Protocol%20(Raghu%20Chivukula's%20LysoIP%20samples%2C%20RC10-30%2C%20changed%20protocol)
Resuspension solvent: 94.9:5.0:0.1 water:MeOH:FA
Resuspension volume: 25 uL (100%)
Injection volume: 1 uL
MS method: uPU-90mingradTOP20-highload_Luciano_375_1500, uPU-90mingradTOP25-TMT-1microscan-375_1500, uPU-60mingrad_Hload_DIA_375_1500_window_15, uPU-60mingradTOP20-highload_Luciano_IP_gradient_375_1500
Link to RAW files: https://www.dropbox.com/sh/98ardhi8xfbmiz0/AACX1rfToegDqrMiKw4WSXW6a?dl=0