FragPipe-Analyst: Advancing Quantitative Proteomics Analysis
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CPTAC researchers from the University of Michigan and researchers from Monash University, Australia have developed a new software tool to complement the widely used FragPipe computational proteomics platform. FragPipe-Analyst (FP-A) is designed to streamline downstream statistical analysis and data visualization, simplifying the exploration of dense proteomics datasets.
FragPipe is an open-source software pipeline for mass spectrometry-based proteomics, offering tools like MSFragger for peptide identification, IonQuant for label-free quantification, and PTM-Shepherd for modification analysis. While FragPipe provides a robust platform for upstream data processing, downstream statistical and visualization steps remain critical for deriving insights in proteomics.
FP-A is a web-based application with a user-friendly interface that allows users to directly upload FragPipe-generated files from a variety of quantification workflows (DDA, DIA, TMT, etc.) for downstream analysis and visualization. Like FragPipe, FP-A is completely open-source and freely available, with extensive documentation and tutorials for new users.
FP-A includes a range of downstream data processing features such as missing value filtering, data normalization, and missing value imputation. Once the data is processed, FP-A can automatically identify significant changes and patterns through differential expression analysis and sample clustering. After data processing and analysis, FP-A readily visualizes data (PCA plots, volcano plots, heatmaps) to facilitate quality assessment, enhance data interpretation, and aid in the sharing of results.
Yi Hsiao, a Ph.D. candidate from University of Michigan who led the project commented on FP-A’s value and ease of use, saying “the tools are used by graduate students who are beginners in proteomics and don’t have much programming experience. As a bioinformatics student, it’s always thrilling to have tools be useful for many users.”
FP-A’s companion program, FragPipeAnalystR (FPAR), is an R package that maintains the same functionality while allowing for further modification of analysis workflows and integration with other R packages. So far, FP-A/FPAR has demonstrated its capabilities through reanalysis of existing proteomics studies, including CPTAC research on clear cell renal cell carcinoma. As FP-A/FPAR continues to be developed, the team plans to expand support for additional PTMs and improve integration with multiomics workflows.