We routinely purify peptides for MS on C-18 spin columns. They work fine, however they capture preferentially hydrophobic peptides. I would like to ask if anybody has compared C18 with graphite columns (e.g. from Pierce) that should capture hydrophilic peptides better than C-18. I am concerned about contamination of LC column by substances that could be potentially co-purified with peptide on graphite column. Thank you for reply
You might consider Sep-Pak type (short 1 cm) columns to do this batch separation then analyze each group separately. Samples are available from several companies, and a program helps suggest which media for various polarities.
you can try to add hydrophobic ion-pairing agent to your sample, which is always effective in our Lab.
I have just started to experiment with graphite spin columns to enrich for hydrophilic proteins. Just now I am trying to purify the proteins and remove some colour. I have had a lot more success using the graphite columns first , collecting the run-off and then putting this through C18. I have only seen a few small runs on the mass spectrometer. the graphite column purity looks good.
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