We are trying to identify drug-modified peptides by LC-MS/MS. However, we failed to process the data from LCMSMS- Sciex X500R QTOF System by MZmine2 or Maxquant. Your experience will be helpful.
Before I can help you could you please tell me why did you fail to process the data? does MZmine get stuck? or you did not know what parameters to follow? or what it something else?