@mayank

Indeed PEG will bind to C18. One solution could be to play with ion exchange. At acidic pH (

The concentrate trypsin peptide, do not use any precipitation methods. They work well for proteins ... For peptide, use C18 ZipTip (milipore).

i use C18 but i wanted to remove contamination of PEG from the sample. because PEG is acetone soluble. C18 is unable to remove PEG.

@Mayank

I agree with Stéphane. C18 is the best option to concentrate/or desalt your peptides. Formic acid is OK, it will even help hydrophobic interactions (counter ion) although TFA would perform better. You have different kind and size of C18 (tip, columns, spin,..) Depending on the volume and amount of material you have to choose the one that fits better. to your needs. Elution is done with ACN in the presence of an acid (formic, TFA, acetic,...) You can afterwards get rid of the ACN and the volatile acid by evaporation in e.g a SpeedVac.

Good luck.

thanks for the answer @Stephane and @Didier... do you have any tips for PEG removal from the samples...?

The PEG problem come from tubes and tips use during trypsin digestion and peptide extraction. You need to choose tips without peg release. It is not the more expensive tips. And do not use low bind tubes...

In addition, when I have not enough peptide signal, I have peg contamination and when I have more peptides, I have not...

@mayank

Indeed PEG will bind to C18. One solution could be to play with ion exchange. At acidic pH (

@stephan.. can you suggest any patcular tips and microcentirfuge tubes.. @ Didier, yes, this is entirely feasible.. but my peptides are enriches sialilated peptide menaing SCX would not work but SAX should do the trick.. thanks...

I am trying at the moment mix-mode columns to bind PEG via reverse phase while capturing peptides by IEX and elute sepraately..

Does anybody know the answer to the original question though?  Suppose that I have a good reason to really really want to precipitate short peptides with acetone :)  Does that work?  Whereabouts is the limit? 

John, I think only more hydrophillic peptides will precipitate with mostly the loss of hydrophobic ones. you will loose most of the total peptides in my experience..