FragPipe-Analyst

FragPipe-Analyst is an easy-to-use, interactive web application developed to perform various computational analyses and to visualize quantitative mass spectrometry-based proteomic datasets processed using FragPipe computational pipeline. It is compatible with the LFQ-MBR, spectral counts, TMT, and DIA quantification workflows in FragPipe.

FragPipe-Analyst provides multiple useful analysis features, including differential expression (DE) analysis using Limma, enrichment analysis (GO/Pathways) using Enrichr, and multiple options for missing value imputation. It provides rich data visualization capabilities, including PCA and volcano plot, sample correlation plots, heatmaps, plots for missing value and sample coverage inspection, protein abundance plots for selected protein(s), imputation effect evaluation, and more. The user can also export results in table format for further analysis, such as DE results (FC and p-values), imputed data matrix (protein abundances after performing selected imputation method), and GO/pathway enrichment results.

Public Servers

There are two server instances

• Production (stable) server is available at https://fragpipe-analyst.org/.
• Development server is hosted at http://fragpipe-analyst.nesvilab.org/. It provides the most up to date version, including bug fixes, but may not be stable

Quick Start

• Formatting input files and upload them for analysis
• Interpret the results

Tutorial

• TMT: A clear cell renal cell carcinoma TMT experiment example from CPTAC study published in Cell.
• LFQ: An LFQ AP-MS example of head and neck cancer from Swantey et al. published in Sceince.
• DIA: A tutorial using subset of clear cell renal cell carcinoma data independent acquisition (DIA) experiment. It’s the second part of a tutorial using collection of FragPipe softwares for DIA analysis. You can also find the first part here.
• LFQ Hands-On Tutorial: An hands-on tutorial of analyzing a gliomas data-dependent label-free quantification (LFQ) dataset. It’s the second part of a tutorial using collection of FragPipe softwares for LFQ analysis. You can find the first part here.

Documentation

Detailed information of functionalities are provided for each module. Readers are recommendated to read our manuscript published in Journal of Proteome first for the overview.

• Normalization
• Imputation

Advanced Usage

• GSEA: After getting differential expression analysis result from FragPipe-Analyst, users could perform Gene Set Enrichment Analysis (GSEA) by themselves easily.
• We also recommend advanced users to use FragPipeAnalystR R package for further downstream analysis. It covers the same functionality as FragPipe-Analyst.

Questions, and Technical Support

This repository is intended to provide documentation and a user forum for questions, suggestions, and bug reports. For bug report, please make sure you provide enough details for reproducing the errors. If you feel safer sharing data via email, please email it to yihsiao@umich.edu.

• Questions/Suggestions
• Bug Reports

Reference

Yi Hsiao, Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood, Joel R. Steele, Ralf B. Schittenhelm, and Alexey I. Nesvizhskii Journal of Proteome Research (2024), DOI: 10.1021/acs.jproteome.4c00294

Source Code

The source code of FragPipe-Analyst can be found here. The code is available under GNU General Public License v3.0

Credits

FragPipe-Analyst is being developed by the Nesvizhskii Lab (University of Michigan) in collaboration with the Monash Proteomics and Metabolomics Facility & Monash Bioinformatics Platform, Monash University (PI Ralf Schittenhelm). FragPipe-Analyst is based on the original LFQ-Analyst code developed by the Monash University team.