Advancing Mass Spectrometry-based Discovery and Targeted Approaches for Disease Proteomic and Ptm Analyses

Download or read book Advancing Mass Spectrometry-based Discovery and Targeted Approaches for Disease Proteomic and Ptm Analyses written by Xiaofang Zhong (Ph.D.) and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Stable-isotope labeling coupled with mass spectrometry (MS) has emerged as the central technology for proteome quantification. Chemical stable isotope labels can be categorized into two major classes, namely mass difference labels and isobaric labels. Based on the various labeling approaches, we firstly develop a strategy for discovery and verification of candidate biomarkers in cerebrospinal fluid of preclinical Alzheimer's disease (AD), an asymptomatic phase with neuropathological abnormalities but no cognitive impairment. To further improve quantification accuracy, we develop 5-plex mass defect-based N,N-dimethyl leucine (mdDiLeu) tags for quantitative proteomics as an MS1-centric quantification method. The limitations of current quantification methods used for biomarker verification include low specificity in complex backgrounds, limited analytical throughput, and wide dynamic range, we developed a hybrid offset-triggered multiplex absolute quantification (HOTMAQ) strategy for targeted proteomics. HOTMAQ combines cost-effective mass difference and isobaric tags to address these issues simultaneously. Given the controversial discovery of protein biomarkers in AD and no reliable protein biomarkers for early detection are available in mild cognitive impairment (MCI, a symptomatic predementia phase) or AD so far, it is pivotal to define new players to aid in accurate diagnosis of this devastating disease. Protein glycosylation is one of the most common and complex post-translational modifications (PTMs), playing a fundamental role in many key biological processes. we develop large-scale comparative N-glycoproteomics of cerebrospinal fluid to elucidate glycoprotein microheterogeneity and relate the subtle changes in glycan structural repertoire to disease progression of AD. Phosphorylation, another common PTM, has been revealed to regulate cell dedifferentiation in restenosis. Transforming growth factor beta (TGF-[beta]) and its signaling protein Smad3 play important roles in vascular restenosis, but very little is yet known about the downstream regulation in response to elevated TGF-[beta]/Smad3 in smooth muscle cell (SMC). We develop a highly multiplexed quantitative proteomics and phosphoproteomics approach to assess dynamic protein expression and phosphorylation changes in SMC. Taken together, this work not only improves the quantification strategies for discovery and targeted proteomics and global PTM analyses, but also presents a useful platform to discover biomarkers and explore the underlying molecular mechanism of several diseases.