When preparing peptides for analycis by LC-MS, I have seen several protocols that use C18 for desalting after detergent removal by MCX. Other groups skip the C18 step. My sample has 0.1% SDS and 1xPBS. MCX (with elution by ammonium hydroxide in methanol) is known to be good at removing non-polar detergents like PEG, but I wonder if large amounts of cations from the SDS and PBS would compete with SCX binding, in which case perhaps C18 would be best before hand. However, since SDS binds to C18, it might compete with peptide binding. If MCX were done first to remove the SDS, then perhaps the cations from SDS and PBS would elute along with the peptides, thus requiring further desalting by C18. Does anyone have experience with this? Is C18 necessary before or after MCX?
It is always good to remove any salts form solution prior to run LC-MS. Mass specs are very sensitive instruments and salts can lower sensitivity of your sample. The best solution is for you to run experiment first with sample desalted and next one without removing salts and compare both.
Personally, I was always removing salts before running LC-MS.
I definitely want salts removed from my sample. So I suppose my question is whether the MCX column removes salts, or if salts are retained on the column and elute with the peptides.
For what it's worth: I use a trap column on my LC, so in effect I am C18 desalting the sample prior to every run. However, I have found that the presence of salt and other compounds that may be in a tryptic digest (especially urea) may cause significant carry-over and even damage to the autosampler, so I find it best to have all salt removed prior to analysis.
Here is Waters notebook about Oasis Sample Preparation. There is a part about MCX Extraction method.
https://www.waters.com/webassets/cms/library/docs/720000609en.pdf
Hopefully will be useful.
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