Treating column with EDTA prior to use on LC/QTOF

So haven't ever really run into specific issues with native MS with SEC methods, though I will assume that the ammonium acetate that you are using is low metal content, so even ACS reagent grade may not be sufficient to ensure no adduct formation. Otherwise, if you have run into this issue and still see trace sodium and potassium, I would suggest flushing the LC front end with 0.1% formic acid and some ACN (5-10%); this should displace most trace metals in the flowpath. Otherwise, avoiding glassware, using high quality vials and such, this is critical as well. 

You can use EDTA in the mobile phase eve, though you don't need a lot, 1-5 µM or so might suffice if it's still an issue. 

Also, note the aforementioned recommendations are typically what I recommend for oligos (ion pair reversed phase). Different application I know, but a lot of the same challenges. That is, the real issue with non-RPLC methods and LC-MS is that, in most RPLC methods, you're basically running formic acid so you are displacing trace metals while running your method. However, with Native MS (or whatever you are using for your SEC-MS method), you are running likely at pH neutral conditions, so effectively you are not"passively passivating" using formate to complex heavy metals, so it's going to cause problems when working with analytes that are prone to adduct formation. 

Hope this is useful!

So haven't ever really run into specific issues with native MS with SEC methods, though I will assume that the ammonium acetate that you are using is low metal content, so even ACS reagent grade may not be sufficient to ensure no adduct formation. Otherwise, if you have run into this issue and still see trace sodium and potassium, I would suggest flushing the LC front end with 0.1% formic acid and some ACN (5-10%); this should displace most trace metals in the flowpath. Otherwise, avoiding glassware, using high quality vials and such, this is critical as well. 

You can use EDTA in the mobile phase eve, though you don't need a lot, 1-5 µM or so might suffice if it's still an issue. 

Also, note the aforementioned recommendations are typically what I recommend for oligos (ion pair reversed phase). Different application I know, but a lot of the same challenges. That is, the real issue with non-RPLC methods and LC-MS is that, in most RPLC methods, you're basically running formic acid so you are displacing trace metals while running your method. However, with Native MS (or whatever you are using for your SEC-MS method), you are running likely at pH neutral conditions, so effectively you are not"passively passivating" using formate to complex heavy metals, so it's going to cause problems when working with analytes that are prone to adduct formation. 

Hope this is useful!