Hi David, have you thought about the " wessel & flügge method" (http://www.ncbi.nlm.nih.gov/pubmed/6731838)

It works quiet good for human milk samples. It allows the separation of the lipid, oligosaccharide and protein fraction, but I am not sure if it works for peptides as well.

Robert

I would recommend using membrane filtration, Since you suggested a range as 5 - 50 AA, I assumed a rough-average molecular mass of 30 AA (3.3 kDa). Lactose is 342 Da in molecular mass. You can use a 1 kDa UF membrane (Ultracel PLAC from Millipore) and design a ultra/diafiltration process to retain the peptide but wash out the lactose into the permeate. The method is efficient and non-chromatographic. If you tell me a bit more about your feed, I could give you a more specific design to the UFDF process.

I would recommend to stick to reversed phase/C18, if your method is established & works well.

I don´t know what your intention is to select another method, but if the main issue is speed,  you could switch your method to (reusable) SPE cartridges (available in a huge variety of sizes, up to 10 g /cartrigde, e.g. http://www.waters.com/waters/partDetail.htm?partNumber=WAT043345 or http://www.thermoscientific.com/content/tfs/en/product/hypersep-c18-spe-cartridges.html or many other suppliers.)

Try using the technique of size exclusion chromatography  (SEC) with an adequate column

Hydrophobic Interaction Chromatography (HIC) is good method for separation for protein, based on the reversible interaction between a protein surface and a chromatographic sorbents of hydrophobic nature. The proteins are separated according to differences in the amount of exposed hydrophobic aminoacids.