When absolute protein quantification isn't possible, what anaylses work on ranked expression?
I have a DIA-MS proteomic dataset where samples were injected with equal volume (from different concentrations, alhough theoretically the same weight of starting material). We don't have an option to redo this by injecting equal peptide amounts.
Now, aside from basic identification differences, is there a way to compare proteins that are expressed in both groups? Possibly changes in expression ranking? Struggling to find examples that aren't just "re-run the samples".
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I suspect that might be because there are no other legitimate suggestions. That's like when one overcooks the eggs in crème diplomate while making choux pastry. There is no other recourse but to make it again.
Yeah, my first suggestion was also that they redo it... at the, what can I salvage, stage.