I performed filter aided sample preparation (FASP) on some protein fractions destined for LC/MS. After FASP, I lyophilized the peptides and dissolved them in 5 % formic acid, before measuring the peptide concentration on nanodrop (by absorbance at 280 nm). The Abs at 280 nm was in the expected range for all the samples, but all of them also contained a big peak (higher in raw absorbance units) at 238-240 nm. I don't think it's SDS (the FASP protocol is designed to remove it - although it hasn't always been effective at that in my hands - and anyway it seems to have a peak at above 400 nm), nor formic acid (seems to have a peak at 210 nm). Would appreciate any tips on what this might be.
It might be caused by EDTA present in your preparation. For more information please see the link below:
http://www.biotek.com/resources/articles/240-nm-absorbance-measurement.html
Thanks! There might very well be EDTA in the trypsin buffer I've used. Desalting should take care of it in that case.
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