There are several papers where people have used perchlorate/ACN combination in HPLC to resolve peptides. However, it is reported that perchlorate in presence of acetonitrile forms free radicals, So, does this reaction going to harm peptide primary structure? Is it going to produce any additional peaks in the chromatogram ? or is it going to affect column life anyway?
http://www.sciencedirect.com/science/article/pii/S0021967397001507
https://books.google.co.in/books?id=tBxxZclgKyMC&pg=PA273&lpg=PA273&dq=perchlorate+highest+anodic&source=bl&ots=_ZnNqcDS3m&sig=Fa3qmG9Iv2FlUVib4Q5H2FAGZL4&hl=en&sa=X&ved=0ahUKEwi4tbrH3KLMAhVHsJQKHTfuDnYQ6AEIIDAA#v=onepage&q=perchlorate%20highest%20anodic&f=false
I'm not sure that PRIMARY structure will be affected, in that you won't be changing the peptide sequence? But yes, you will modify the pI of the mix, and therefore the elution order, as well as the likely modifications. The paper that you cite specifically refers to this aspect of ion pairing, and you can radically change the elution order.
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