Application of SAMDI Mass Spectrometry for Molecular Data Storage and Random Peptide Arrays


Self-Assembled Monolayers for MALDI-TOF Mass Spectrometry (SAMDI-MS) is a technique that combines self-assembling molecules of alkane disulfides on gold and MALDI-TOF mass spectrometry. By using well-defined monolayers with functionalizations that both prevent non-specific adsorption onto the surface and presents immobilization handles, it is possible to pull out analytes of interest, selectively, onto the surface from reaction mixtures. The use of the MALDI-TOF enables rapid and quantitative characterization of immobilized molecules, by their mass, enabling quantification of both reactants and products, of reactions that incur a mass change. In this work I will demonstrate the utility of SAMDI-MS with peptides and peptide arrays to demonstrate two novel uses of this method. First, I will demonstrate an approach that uses peptide mixtures with SAMDI to store digital information in molecules. Currently, digital information is stored on many different media, including magnetic tape, optical discs, hard disks, and flash. Although each of these methods has its benefits, they also have drawbacks. To combat some of these possible drawbacks, such as longevity, the use of molecules to storage information has been proposed. The molecules predominantly considered when information storage is uttered is DNA. DNA has been used by nature to store genetic information for billions of years, and now with the advances in DNA synthesis and sequencing technology it is possible to synthesize artificial strands of DNA to encode digital data, albeit at a cost many times more expensive than currently available technology. To provide another possible method for storing information using molecules, I will demonstrate how it is possible to use the feature of SAMDI surfaces to pull out all analytes with the proper handles out of a solution and distinguish them by mass. I use this feature and show that it is possible to immobilize 32 peptides onto a single spot, giving us an information density of 4 bytes/spot in binary. I will further expand on this ability and incorporate SAMDI's ability to quantitate molecule abundance in solution and demonstrate that through the use of concentrations it is also possible to store information in higher-than-binary manner. In the second portion of this work I will show two novel applications of SAMDI and peptide arrays, as well as introduce a method for the synthesis, analysis, and utilization of random peptide arrays with a novel capping scheme. The two novel applications of SAMDI are to first study the proteases contained within detergents, and second, to look at initial rates of related isoforms of KDACs, on a peptide library, to provide a method to distinguish activity profiles of these isoforms that have similar activity. The final approach will provide a method to utilize a split-pool synthesis method to synthesize random peptide libraries. I will show that it is possible to combine this method with a novel capping scheme, which uses only 4 capping groups, and SAMDI to fully decode a library of peptides without any ambiguity, which has been the drawback of previous applications. I will also demonstrate the use of these random arrays with SAMDI surfaces in an attempt to discover a novel short peptide adhesion ligand using a 5,832-member library.

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