I am preparing a peptide from a fusion protein digest using a combination or proteases. The result mixture contains peptides range from 1-7 KDa and a acouple of proteins, all above 20 KDa. It seems that the molecular weight cut off column of 10 Kda are retaining the peptides. I wonder if there is another quick method to perform this separation. I do not mind a sub-optimal recovery of the peptides, as long as I get enough to perform LC-MS analysis
Thank you
Reverse-phase chromatography by HPLC or UPLC with an ion pairing reagent is a good way to separate a mixture of peptides. The separation is on the basis of hydrophobicity.
A suitable HPLC size exclusion column is another good method, separating on the basis of size.
Dear Abdullateef Nashed
Are you interested to analize the peptide or the proteins by LC-MS?
Because if you are interested to analize the proteins, probably the SDS-page, as suggested from Omar Gonzalez-Ortega could be fine
https://pmc.ncbi.nlm.nih.gov/articles/PMC4416643/
on the contrary if you are interested to analize the peptides is possible that so small MW will be lost in SDS-page and probably or reverse phase chromatograpy using a C18 coloumn or a size exclusion chtomatography using a coloumn with low exclusion limits, eg supedex30, may work better in your case.
Good luck
Manuele
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