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Analysis and visualization of quantitative proteomics data using FragPipe-Analyst.

Yi Hsiao1, Haijian Zhang2, Ginny Xiaohe Li3

  • 1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.

Biorxiv : the Preprint Server for Biology
|March 18, 2024
PubMed
Summary
This summary is machine-generated.

FragPipe-Analyst is a new R shiny web server that provides user-friendly downstream statistical analysis and visualization for quantitative proteomics data. It supports various quantification workflows and offers advanced functionalities for deeper biological insights.

Keywords:
AP-MSFragPipeLiP-MSbioinformaticsdownstream analysisopen sourceprotein phosphorylationsoftware

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • The FragPipe computational proteomics platform is widely adopted for its speed and usability.
  • Existing workflows require user-friendly tools for downstream statistical analysis and visualization of quantitative proteomics data.

Approach:

  • Developed FragPipe-Analyst, an R shiny web server, to facilitate downstream analysis of FragPipe output.
  • Integrated functionalities for label-free quantification, tandem mass tags, and data-independent acquisition.
  • Created FragPipeAnalystR, an R package, for advanced analysis and site-specific post-translational modification analysis.

Key Points:

  • FragPipe-Analyst supports missing value imputation, quality control, clustering, and differential expression analysis (Limma).
  • Includes gene ontology and pathway enrichment analysis via Enrichr.
  • FragPipeAnalystR extends capabilities for customized visualizations and post-translational modification site analysis.

Conclusions:

  • FragPipe-Analyst and FragPipeAnalystR provide accessible, open-source solutions for comprehensive quantitative proteomics data analysis.
  • These tools enhance the utility of FragPipe by enabling robust downstream statistical and visualization methods.