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Full-Text Articles in Physical Sciences and Mathematics
Algorithms For Peptide Identification From Mixture Tandem Mass Spectra, Yi Liu
Algorithms For Peptide Identification From Mixture Tandem Mass Spectra, Yi Liu
Electronic Thesis and Dissertation Repository
The large amount of data collected in an mass spectrometry experiment requires effective computational approaches for the automated analysis of those data. Though extensive research has been conducted for such purpose by the proteomics community, there are still remaining challenges, among which, one particular challenge is that the identification rate of the MS/MS spectra collected is rather low. One significant reason that contributes to this situation is the frequently observed mixture spectra, which result from the concurrent fragmentation of multiple precursors in a single MS/MS spectrum. However, nearly all the mainstream computational methods still take the assumption that the acquired …
From Solution Into The Gas Phase: Studying Protein Hydrogen Exchange And Electrospray Ionization Using Molecular Dynamics Simulation, Robert G. Mcallister
From Solution Into The Gas Phase: Studying Protein Hydrogen Exchange And Electrospray Ionization Using Molecular Dynamics Simulation, Robert G. Mcallister
Electronic Thesis and Dissertation Repository
Here, we apply Molecular Dynamics (MD) simulations to investigate fundamental aspects of structural mass spectrometry (MS). We first examine microscopic phenomena underlying Hydrogen/Deuterium exchange (HDX). HDX interrogates structural dynamics of proteins by measuring the rate of Deuterium uptake into backbone amides. We perform microsecond MD simulations on ubiquitin to investigate this process. We find that HDX protection often cannot be explained by H‑bonding or solvent accessibility considerations. These findings caution against non-critical use of HDX data in structural contexts. We next use MD to examine the Electrospray ionization (ESI) mechanism of proteins. ESI is a soft ionization technique resulting in …