Here we have examined the effect of sodium dodecyl sulfate (SDS) at various concentrations on matrix-assisted laser desorption/ionization (MALDI) peptide mass fingerprinting experiments. Several model proteins were digested with trypsin and then various amounts of SDS were added prior to MALDI mass spectrometry. Evaluation of the data was made by calculating the amino acid sequence coverage within each analysis. It was found that addition of 0.1-0.3% w/v SDS prior to MALDI analysis results in an increase in the number of tryptic peptides detected thereby improving the total sequence coverage of the analysis. The use of SDS at concentrations near its critical micelle concentration can improve sequence coverage from MALDI peptide mass fingerprinting analyses allowing for increased confidence in protein identification or additional opportunities to identify putative regions of posttranslational modification.
Although sodium dodecyl sulfate (SDS) is routinely used as a denaturing agent for proteins, its presence is highly detrimental on the analysis of peptides and proteins by mass spectrometry. It has been found, however, that when SDS is present in concentrations near to or above its critical micelle concentration (CMC), improvements in the matrix-assisted laser desorption/ ionization mass spectrometry (MALDI-MS) analysis of peptide mixtures or hydrophobic proteins are obtained. To elucidate possible explanations for such improvements, here we have undertaken a study examining the effect of SDS micelles on peptide mixtures. Fluorescently labeled peptides were used as probes to determine whether hydrophobic or hydrophilic peptides interact exclusively with SDS micelles. In addition, four globular proteins were digested with trypsin and then various amounts of SDS were added before MALDI mass spectrometry. To examine the role of mixture complexity on the mass spectral results, the tryptic digest of bovine serum albumin was also fractionated according to hydrophobicity before SDS treatment. Results from these experiments suggest that micelle-peptide interactions increase peptide-matrix cocrystallization irrespective of analyte hydrophobicity. As these studies were performed using the dried-droplet method of sample spotting, the presence of micelles is also hypothesized to reduce Marangoni effects during the crystallization process. (J Am Soc Mass Spectrom 2005, 16, 1438 -1446
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is a popular analytical tool for the analysis of large biomolecules such as proteins, oligonucleotides and oligosaccharides. This method has proven to be extremely useful for the analysis ofwater soluble proteins. However, analysis ofhydrophobic proteins using MALDI-MS has been more ofa challenge. The difficulty arises due to the limited solubility ofthese compounds in the aqueous solutions used to prepare the MALDI matrix. This study has investigated the effect of surfactants on the MALDI-MS data obtained from hydrophobic peptides and tryptic digests of hydrophobic and hydrophilic proteins. The surfactant sodium dodecylsulfate (SDS) was found to improve the information content obtained during MALDI-MS analysis of such molecules. Preliminary results which examine the applicability of surfactant-aided MALDI-TOFMS for the characterization ofproteolytic digests of proteins will be presented. and the potential use of this analytical strategy in a proteomics-based examination of intrinsic membrane proteins will be discussed.
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