Removal of sodium dodecyl sulfate from protein samples prior to matrix-assisted laser desorption/ionization mass spectrometry

Sodium dodecyl sulfate (SDS) is widely used for protein solubilization and for separation of proteins by SDS polyacrylamide gel electrophoresis (SDS-P AGE), However, SDS interferes with other techniques used for characterizati on of proteins, such as mass spectrometry (MS) and amino acid sequencing. I n this paper, we have compared three procedures to remove SDS from proteins , including chloroform/methanol/water extraction (C/M/W), cold acetone extr action and desalting columns, in order to find a rapid and reproducible pro cedure that provides sufficient reduction of SDS and high recovery rates fo r proteins prior to matrix-assisted laser desorption/ionization time-of-fli ght mass spectrometry (MALDI-TOFMS), A 1000-fold reduction of SDS concentra tion and a protein recovery at approximately 50% were obtained with the C/M /W procedure. The cold acetone procedure gave a 100-fold reduction of SDS a nd a protein recovery of approximately 80%, By using desalting columns, the removal of SDS was 100-fold, with a protein recovery of nearly 50%, Both t he C/M/W and the cold acetone methods provided sufficient reduction of SDS, high recovery rates of protein and allowed the acquisition of MALDI spectr a, The use of n-octyl-beta-D-glucopyranoside in the protein sample preparat ion enhanced the MALDI signal for protein samples containing more than 2 10 (-4)% SDS, after the C/M/W extraction. Following the cold acetone procedure , the use of n-octylglucoside was found to be necessary in order to obtain spectra, but they were of lower quality than those obtained with the C/M/W method, probably due to higher residual amounts of SDS, Copyright (C) 1999 John Whey & Sons, Ltd.