A discovery or shotgun proteomics experiment will most often utilize a form of connected online LC setup which will utilize reverse phase chromatography over a gradient to elute the peptides in the sample. Offline versions of shotgun experiments will often times use a Maldi interface source. In general Discovery based experiments involve a data dependent method that will automatically select which peptide precursor ion to isolate and fragment in MS/MS. The mass spec will generate a survey scan (MS1 mode) for the particular ions detected over scan interval. From this survey scan between 3-7 peptides (possibly more) will be sent to the Ion trap for further fragmentation and creation of MS/MS spectra. Shotgun experiements tend to be more qualitative in design though quantitative analysis from generated data is possible i.e. spectal counting or peptide labeling ITRAQ, ICAT etc.