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Plasma proteome profiling to assess human health and disease
Plasma proteome profiling to assess human health and disease
The majority of diagnostic decisions are made on results from blood-based tests, and protein measurements are prominent among them. However, current assays are restricted to individual proteins, whereas it would be much more desirable to measure all of them in an unbiased, hypothesis-free manner. Therefore, characterization of the plasma proteome by mass spectrometry holds great promise for clinical application. Due to great technological challenges and study design issues, plasma proteomics has not yet lived up to its promises: no new biomarkers have been discovered, plasma proteomics has not entered clinical diagnostics and few biologically meaningful insights have been gained. As a consequence, relatively few groups still continue to pursue plasma proteomics, despite the undiminished clinical need. The overall aim of my PhD thesis was to pave the way for biomarker discovery and clinical applications of proteomics by precision characterization of the human blood plasma proteome. First, we streamlined the standard, time consuming and laborintensive proteomic workflow, and replaced it by a rapid, robust and highly reproducible robotic platform. After optimization of digestion conditions, peptide clean-up procedures and LC-MS/MS procedures, we can now prepare 96 samples in a fully-automated way within 3h and we routinely measure hundreds of plasma proteomes. Our workflow decreases hands-on time and opens the field for a new concept in biomarker discovery, which we termed ‘Plasma Proteome Profiling’. It enables the highly reproducibility (CV<20% for most proteins), and quantitative analysis of several hundred proteins from 1 μl of plasma, reflecting an individual’s physiology. The quantified proteins include inflammatory markers, proteins belonging to the lipid homeostasis system, gender-related proteins, sample quality markers and more than 50 FDA-approved biomarkers. One of my major goals was to demonstrate that MS-based proteomics can be applied to large cohorts and that it is possible to gain biologically and medically relevant information from this. We achieved this aim with our first large scale plasma proteomic study in which we analyzed by far the largest plasma proteomics study with almost 1,300 proteomes, which allowed us to define inflammatory and insulin resistance panels in a weight loss cohort. In summary, this PhD thesis has developed the concept and practice of Plasma Proteome Profiling as a fundamentally new approach in biomarker research and medical diagnostics – the system-wide phenotyping of humans in health and disease.
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Geyer, Philipp
2017
English
Universitätsbibliothek der Ludwig-Maximilians-Universität München
Geyer, Philipp (2017): Plasma proteome profiling to assess human health and disease. Dissertation, LMU München: Faculty of Chemistry and Pharmacy
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Abstract

The majority of diagnostic decisions are made on results from blood-based tests, and protein measurements are prominent among them. However, current assays are restricted to individual proteins, whereas it would be much more desirable to measure all of them in an unbiased, hypothesis-free manner. Therefore, characterization of the plasma proteome by mass spectrometry holds great promise for clinical application. Due to great technological challenges and study design issues, plasma proteomics has not yet lived up to its promises: no new biomarkers have been discovered, plasma proteomics has not entered clinical diagnostics and few biologically meaningful insights have been gained. As a consequence, relatively few groups still continue to pursue plasma proteomics, despite the undiminished clinical need. The overall aim of my PhD thesis was to pave the way for biomarker discovery and clinical applications of proteomics by precision characterization of the human blood plasma proteome. First, we streamlined the standard, time consuming and laborintensive proteomic workflow, and replaced it by a rapid, robust and highly reproducible robotic platform. After optimization of digestion conditions, peptide clean-up procedures and LC-MS/MS procedures, we can now prepare 96 samples in a fully-automated way within 3h and we routinely measure hundreds of plasma proteomes. Our workflow decreases hands-on time and opens the field for a new concept in biomarker discovery, which we termed ‘Plasma Proteome Profiling’. It enables the highly reproducibility (CV<20% for most proteins), and quantitative analysis of several hundred proteins from 1 μl of plasma, reflecting an individual’s physiology. The quantified proteins include inflammatory markers, proteins belonging to the lipid homeostasis system, gender-related proteins, sample quality markers and more than 50 FDA-approved biomarkers. One of my major goals was to demonstrate that MS-based proteomics can be applied to large cohorts and that it is possible to gain biologically and medically relevant information from this. We achieved this aim with our first large scale plasma proteomic study in which we analyzed by far the largest plasma proteomics study with almost 1,300 proteomes, which allowed us to define inflammatory and insulin resistance panels in a weight loss cohort. In summary, this PhD thesis has developed the concept and practice of Plasma Proteome Profiling as a fundamentally new approach in biomarker research and medical diagnostics – the system-wide phenotyping of humans in health and disease.