Serum protein profiling using surfactant-aided matrix-assisted laser desorption/ionization mass spectrometry

It has been shown previously that sodium dodecyl sulfate (SDS) can be used at its critical micellar concentration to increase the number of peptides detected in a peptide mixture by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Here we demonstrate that, in a similar fashion, preparation of peptides and low molecular weight proteins from serum using SDS micelles improves the information content in MALDI-MS. In particular, the addition of SDS yielded a 30% increase in the number and a 50% increase in the abundance of low molecular weight (<6000 Da) analytes. C18 ziptips and C18 magnetic beads were used as pre-cleaning steps for comparative analysis and it was found that magnetic beads were more suitable for pre-cleaning prior to combining the eluent with SDS. The non-ionic surfactant n-octyl-β-d-glucopyrinoside yielded improved ion abundances of peptides with masses above 6000 Da, although these increases are less dramatic than those found with SDS. These results demonstrate that surfactant-aided MALDI-MS can lead to an increase in the amount of information obtained from complex mixtures of peptides/proteins. Such improvements may prove advantageous for applications such as those focused on protein profiling.