Preliminary Assessment on Choice of Matrix Based on Hydrophobicity/hydrophilicity of Proteins in Analysis by Maldi Tof-tof Mass Spectrometry

Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) has been extensively used for proteomic profiling of biological samples which contain a mixture of proteins with diverse physico-chemical characteristics. Matrix chemistry therefore plays an essential role in the outcome of profiling. Proteins with different hydrophobicity and hydrophilicity may be detected optimally on distinct matrices. Hence, a preliminary study was conducted in order to optimize the identification strategy based on polarities of the proteins and the matrices used for their analysis by MALDI-MS. Proteins with a wide range of polarities, molecular weights and isoelectric pH were analysed on different MALDI matrices. Proteins were digested with trypsin either in-solution or by in-gel digestion. Based on the scores obtained for peptide mass fingerprinting in MS, the most suitable matrices for identification of proteins were ascertained. The preliminary study suggests that dihydroxybenzoic acid (DHB) efficiently detects hydrophilic as well as hydrophobic proteins over a ten fold concentration range. Thus DHB could be a matrix of choice for profiling of biological samples. This observation would be confirmed by analyzing a large number of diverse proteins.