Development of Methods to Improve the Efficiency of Proteoform Identification by Mass Spectrometry in Complex Systems

Released on by John Gerrit Pavek
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  • Development of Methods to Improve the Efficiency of Proteoform Identification by Mass Spectrometry in Complex Systems Book Detail

  • Author : John Gerrit Pavek
  • Release Date : 2024
  • Publisher :
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  • Pages : 0
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  • File Size : 36,36 MB
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Development of Methods to Improve the Efficiency of Proteoform Identification by Mass Spectrometry in Complex Systems by John Gerrit Pavek PDF Summary

Book Description: The gap between genotype and phenotype is incredibly difficult to bridge. The complexity of the intervening processes is the reason for this challenge. We believe that proteoforms, the specific molecular products of genes, hold the key to bridging the genotype-phenotype gap with detailed molecular understanding. However, comprehensive proteoform characterization is incredibly difficult due to the wide range in both physicochemical properties and abundances of proteoforms in complex systems. Most commonly, the broad characterization of proteoforms is achieved by top-down proteomics, a technique in which intact proteoforms are analyzed by tandem mass spectrometry. To move towards comprehensive characterization of proteoforms in complex systems requires the development of novel techniques at all aspects of top-down proteomics, from sample preparation to data analysis.Even as deeper proteoform coverage becomes achievable, the practicality of the technique for routine biological analysis remains limited. This is because many of the strategies used to improve proteoform coverage also come with a significant time cost. In this work, I demonstrate our efforts toward developing techniques to make proteoform identification by mass spectrometry more efficient while also achieving reasonable depth. This work centers around the development of strategies for proteoform identification without the need for tandem MS. First, I present a NeuCode chemical labeling strategy that enables the experimental determination of tissue proteoform cysteine counts, which can be used to improve the confidence of proteoform identifications made sans-fragmentation. I then present a proof-of-concept study, where an E.coli proteoform atlas is constructed, and subsequently used to enable efficient proteoform re-identification.

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