Why should I fractionate my biological samples?
The main purpose of fractionation is usually to help obtain a comprehensive protein profile from very complex samples. Samples are fractionated at either the protein or peptide level in order to increase the protein coverage of the resulting analysis.
The choice to fractionate samples is a complicated one, influenced by many factors. Often, it is worth running a comparative study of sample fractionation vs. inclusion-list based analysis to see which is best suited to your lab.
A non-fractionated approach may give results of a comparable quality and depth, but without the extra machine-time and analysis requirements. Where you've detected peptides that have no associated MS2 data, an inclusion list can be used to obtain comparable coverage to that of a fractionated experiment.