This is probably a poorly phrased question as I am a novice with LC-MS/MS data. I have Agilent Masshunter data that I converted to mzML format via Proteowizard. The data was suppose to be MS/MS but only has (with confirmation from the Proteowizard wizards) MS1 data. I want to use the quantify() method to convert MSnExp to MSnSet, but quantify only uses MS2.
Any ideas? I'm following a tutorial using msmsEDA and msmsTests to create a simple volcano plot.
Thanks. And apologies if this is a dumb question.