Hi to all, I have to analyze an in-solution tryptic digest performed in the presence of 0.1% sds. I'm wandering if I can directly analyze it by means of rphplc ms w/o desalt it with zip tip since I need the maximum peptide coverage. Thanks
Antonio, it is always desirable to have your sample be as "clean" as possible when injecting it for LC-MS analysis. Depending on the column and mobile phase you use, the SDS could co-elute with your analyte of interest, potentially causing ion suppression. I've found a very relevant journal article from the journal Analytical Chemistry that has lots of information relating to your question:
Anal Chem. 2012 Mar 20; 84(6): 2862–2867
DOI: 10.1021/ac203394r
Good luck in your analysis and come back and let us know how it went!
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310275/
If SDS gets on your separation column, you will be doing ion pairing chromatography instead of reversed phase chromatography, which I guess is not your intention.
http://www.chromatographyonline.com/ion-pairing-blessing-or-curse?rel=canonical
Furthermore, SDS at 0.1% will also retard digestion with trypsin. I once had a directed study student compare tryptic digests of albumin at 0%, 0.01%, 0.02%, 0.05% and 0.1% SDS. Even 0.01% SDS saw a significant drop in performance as measured by declining counts of peptide-spectrum matches and increased missed cleavages. In all cases, mixed-mode SCX/RP (MCX) cartridges were used for SDS removal before MS.
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