DMSO as an additive for nanoLC proteomics applications is still pretty polarizing. If you want my opinion on it, it is: yes, you get more signal and peptide IDs, but you should anticipate requiring more cleaning and maintenance on your instrument. If you don't mind the downtime and the signal intensity is paramount...well, that's your choice. For me? I would run DMSO if I was doing experiments on your instrument, but I wouldn't use it on mine...
To further investigate the affects of DMSO as an additive Dominika Strzelecka et al., checked to see if adding 3% DMSO would affect their label free quantification. I stole the figure above from the open access paper. In A, you see the ID'ed peptides. In B you see the quantified peptides. In the end they found that DMSO really didn't affect the quality of the quantification, though maybe the increase in signal does help you quantify more.
Me? I'm most interested in the shift in identified peptides!?! Out of ~2500 peptides ID'ed over 1000 were differentially ID'ed by changing the buffers!
Highly recommended paper that adds more info to a very interesting topic.
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