Whole Proteome and Methyl Proteome Alterations Due to Methyl Donor Abundance Changes
This analysis characterized global changes in protein abundance and alterations in post-translational modification (PTM) patterns in Saccharomyces cerevisiae using LC-MS/MS proteomics data. The study included three experimental conditions: a wild-type control and two separate mutant conditions targeting key methyl-donor synthesis genes.
A custom R-based workflow was developed to process PEAKS Studio output generated by a university proteomics core facility. The pipeline performed data cleaning, annotation, PTM identification, and differential analyses of protein abundance and PTMs across experimental conditions. To place these molecular changes in a biological context, pathway enrichment and Gene Ontology (GO) analyses were also performed.
Deliverables
- Interactive HTML Report: An interactive HTML report summarizing the data cleaning workflow, analytical methods, and key findings, including publication-quality graphics, enabling researchers to efficiently explore and interpret the results.
- Spreadsheet Results: A multi-sheet Excel workbook containing differential protein abundance results, PTM analyses, and enrichment findings across all experimental conditions.
- Data Dictionary: A structured data dictionary defining key features and data mappings.
Publications
- Manuscript in progress