Digital Commons Network^™

Analysis Of Post-Translational Modifications (Ptm) Crosstalk, Amit Das

Theses and Dissertations

Mass spectrometry-based proteomics is a powerful tool for identifying post-translational modifications (PTMs) across the proteome. O-GlcNAcylation and phosphorylation are two PTMs that play crucial roles in regulating cellular processes, including cardiac contractile function. Dysregulation of these PTMs has been implicated in the development and progression of diabetic cardiomyopathy. In this study, we aimed to investigate the interplay between O-GlcNAcylation and phosphorylation in healthy and type 2 diabetic hearts, with a specific focus on the functional relationships between these PTMs and their potential therapeutic implications.

Utilizing mass spectrometry data, we identified and quantified specific PTMs on myofilament proteins, uncovering 1354 O-GlcNAcylated …

Ensemble Protein Inference Evaluation, Kyle Lee Lucke

Graduate Student Theses, Dissertations, & Professional Papers

The Protein inference problem is becoming an increasingly important tool that aids in the characterization of complex proteomes and analysis of complex protein samples. In bottom-up shotgun proteomics experiments the metrics for evaluation (like AUC and calibration error) are based on an often imperfect target-decoy database. These metrics make the inherent assumption that all of the proteins in the target set are present in the sample being analyzed. In general, this is not the case, they are typically a mix of present and absent proteins. To objectively evaluate inference methods, protein standard datasets are used. These datasets are special in …

High-Performance Reductive Strategies For Big Data From Lc-Ms/Ms Proteomics, Muaaz Gul Awan

Dissertations

Mass Spectrometry (MS)-based proteomics utilizes high performance liquid chromatography in tandem with high-throughput mass spectrometers. These experiments can produce MS data sets with astonishing speed and volume that can easily reach peta-scale level, creating storage and computational problems for large-scale systems biology studies. Each spectrum output by a mass spectrometer may consist of thousands of peaks, which must all be processed to deduce the corresponding peptide. However, only a small percentage of peaks in a spectrum are useful for further processing, as most of the peaks are either noise or are not useful. Our experiments have shown that 90 to …

A Holistic Computational Approach To Boosting The Performance Of Protein Search Engines, Majdi Ahmad Mosa Maabreh

Dissertations

Despite availability of several proteins search engines, due to the increasing amounts of MS/MS data and database sizes, more efficient data analysis and reduction methods are important. Improving accuracy and performance of protein identification is a main goal in the community of proteomic research. In this research, a holistic solution for improvement in search performance is developed.

Most current search engines apply the SEQUEST style of searching protein databases to define MS/MS spectra. SEQUEST involves three main phases: (i) Indexing the protein databases, (ii) Matching and Ranking the MS/MS spectra and (iii) Filtering the matches and reporting the final proteins. …

Nbpmf: Novel Network-Based Inference Methods For Peptide Mass Fingerprinting, Zhewei Liang

Electronic Thesis and Dissertation Repository

Proteins are large, complex molecules that perform a vast array of functions in every living cell. A proteome is a set of proteins produced in an organism, and proteomics is the large-scale study of proteomes. Several high-throughput technologies have been developed in proteomics, where the most commonly applied are mass spectrometry (MS) based approaches. MS is an analytical technique for determining the composition of a sample. Recently it has become a primary tool for protein identification, quantification, and post translational modification (PTM) characterization in proteomics research. There are usually two different ways to identify proteins: top-down and bottom-up. Top-down approaches …