For regular IPs, use uPU-60mingradTOP20-highload_Luciano_IP_gradient_375_1500
For Lyso IPs and WCL or Hela searches, use uPU-90mingradTOP20-highload_Luciano_375_1500
For any other type of sample, or if there are any specific aims (e. g. DIA, crosslinked samples, TMT, etc) ASK LUCIANO.
For any given queue of samples, run all replicates together and run a blank (Moderate_seesaw or Intense_seesaw) in between two groups of replicates. Always queue up a Hela at the beginning and the end of each set of samples and compare BPI (>1E+09) and Protein Groups ID number (>2000) to check that the MS is performing well. To quickly do a Hela search, go to PD daemon and use PWF_QE_Basic_SequestHT_Homo_sapiens_label-free_quantitation as processing workflow and CFW_Basic_Label-free as Consensus workflow.