I am working with SILAC-labeled protein samples of S. aureus and doing the quantification with MaxQuant and various databases. Usually I'm doing a labeled quantification with multiplicity 2 with heavy labels at Arg6 and Lys6. Now I'm wondering if it would make sense to do a LFQ and, if so the results could be compared to the LFQ of my protein samples without SILAC?
Thanks in advance for your time and answers.