Evaluation of analysis methods in mass spectrometry based proteomics

With mass spectrometry leading the field of protein biomarker discovery, constant method development is needed to improve accuracy, reproducibility and data reliability to ensure confidence in findings and enable analysis of large patient cohorts to identify biomarkers which can be successfully validated.
Objectives:
We will compare new technology platforms specifically designed for high resolution data-independent acquisition (DIA) and the different processing and analysis pipelines presently used at the Stoller Biomarker Discovery Centre and also Waters Corporation.
We will carry out analysis on both cell line samples and plasma from the peripheral blood using DIA (SWATH and Waters novel HDMSe and SONAR). In a single measurement, these techniques capture all of the components in a biological sample -a digital proteomic map. These maps allow for the iterative re-mining of the permanent digital record in silico. Data produced will be analysed for both quality and quantity, examining a number of parameters including data missingness and overall quantification.
Potential Outcomes:
Our proposed work programme will produce insights into the bioinformatics pipelines used currently in biomarker discovery, and highlight any disparities between the methods that thwarts data reproducibility. Further conclusions will be made about which of the methods offers the most valuable insights for allowing the investigation of disease processes, to gain a better understanding of the processes underpinning the disease in the correct context. These proposals can be used in the development of new interventions to treat disease. Samples used to facilitate across-method comparison will also be analysed to better understand disease processes.