Size exclusion chromatography

[glnegri]

What would be a good search strategy and the best parameters to do a library-free search and quantification of a 20 fractions SEC experiment for which I also have whole cell runs (no separation)? Should I include SEC and whole runs together or run them separately? Library generation mode? Cross-run normalization off?

[vdemichev]

Cross-run normalisation off, library generation set to IDs, RT and IM profiling, run SEC runs independently from bulk.
Running SEC together with bulk will likely increase the IDs numbers in the bulk - if that's the purpose, can do that separately. But this might affect SEC quantities slightly, so better to do SEC quantitation without bulk sample included.