I'm currently working on label-free protein quantification from LC-MS data.
Does anyone of you guys know how to calculate p-values for protein regualtions?
Right now Im using a(n unpaired) t-Test, where the input is simply all measured peptide intensities.
Vulcano plots look quite nice but currently we are understimating the significance of regulations.
I'm sure there are more sofisticated ways how to do it.