I work with peptide/peptidomimetics (1600-1800 Da) and when I perform Mass Analysis (flow injection, ACQUITY Ultra Performance LC; ESI, positive ions, Single Quadrupole analyzer) I often find picks corrisponding to the species without one/two/three Boc groups. Do you have any suggestion to avoid this fragmentation?
Maybe you can try to lower fragmentor. But it seems we can not completely avoid this fragmentation.
To avoid the Boc-cleavage during Mass Analysis, you have to use soft ionization techniques to avoid further cleavages .
Hi Kelly Bugatti , there are few interesting properties of Boc protection. This is not very theall stable. It tends to deprotect when temperature reaches close or higher to 100 degrees. The first doubt I have is whether your peptide is already de protected somehow before the analysis? Do you have any experiment data to support that?
If that so, are you using TFA in your mobile phases by any chance ? Even very low concentration of TFA can induce deprotection of the Boc group. fAs I know, many peptide/protein gradients use TFA in the mobile phases. In Oder to avoid this, you can replace TFA with fomic acid in your gradient.
If neither of these explanation, help you with your doubt, can you try to do a direct inject or perform a MALDI to see whether all Boc groups are intact?
Hope this help!
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