Dear ABRF,

I have practical questions for you. Is there someone who has used the ProteoMiner (BioRad) to equalize protein samples and to analyse the equalized product in LC/MS, via tryptic digestion?  

The equalized product is characterized by an acidic pH (5% acetic acid), containing urea (4M) and a low percentage of CHAPS. In your experience, what is the best approach to change the acidic pH of the sample to a basic pH? I can't use "Amicon" or any other cut-off device because I am interesting in the low molecular weight peptide fraction.

In your opinion, is it better to adjust the pH with NaOH or to lyophilize the sample and subsequently to resuspend it in ammonium bicarbonate buffer, pH=8?

The dilution of the sample during the digestion procedure should reduce the percentage of CHAPS to  0.1% approximately. Is this low percentage of CHAPS compatible with an LC-ESI-MSMS analyses?

Thanks in advance,
Donatella