Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Evaluating the Performance of Photon- and Electron-Based Fragmentation Methods in Omnitrap-LCMS Analysis of <i>N</i>-Glycopeptides.

Analytical chemistry·2026
Same author

Spatial distribution of the proteome in the human body and in cancers.

Nature·2026
Same author

Integrated proteogenomic and metabolomic profiling of acute myeloid leukemias to identify molecular subtypes and associated therapy targets.

Nature cancer·2026
Same author

Aerobic soil bacteria adapt to hypoxia by hybridizing fermentation with carbon storage.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Investigating the P450-Mediated Cross-Linking of the Atypical GPA Complestatin Using Alternate Peptide Probes.

The Journal of organic chemistry·2026
Same author

Monocyte Migration Emerges from a Divergent Chemokine Signaling Network.

bioRxiv : the preprint server for biology·2026
Same journal

From Method-Defined Signals to Reference Measurement Procedures: Two Decades of Mass Spectrometry-Based ProGRP Quantification.

Journal of proteome research·2026
Same journal

Proteomic Profiling of Extracellular Vesicle-Enriched Plasma Using Mag-Net for Biomarker Discovery in Pancreatic Ductal Adenocarcinoma.

Journal of proteome research·2026
Same journal

Computationally Efficient Bayesian Estimation of Graphical Networks for Omics Data.

Journal of proteome research·2026
Same journal

Hierarchy of MS-Based Evidence.

Journal of proteome research·2026
Same journal

Proteomic Profiling of Exosomes from HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinoma: Selective Cargo Packaging.

Journal of proteome research·2026
Same journal

Proteomic Analysis Identifies ATE1-Dependent Arginylation Dysregulation across Meningioma Grades.

Journal of proteome research·2026
See all related articles

Related Experiment Video

Updated: Jun 13, 2025

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
08:37

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

Published on: November 2, 2021

2.2K

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, Michigan 48109, United States.

Journal of Proteome Research
|September 10, 2024
PubMed
Summary
This summary is machine-generated.

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

Keywords:
AP-MSFragPipeLiP-MSbioinformaticsdownstream analysisopen sourceprotein phosphorylationsoftware

More Related Videos

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

6.8K
Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
07:38

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

12.7K

Related Experiment Videos

Last Updated: Jun 13, 2025

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
08:37

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

Published on: November 2, 2021

2.2K
Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

6.8K
Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
07:38

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

12.7K

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • FragPipe is a popular computational proteomics platform known for speed and usability.
  • Existing workflows require separate tools for downstream statistical analysis and visualization of quantitative proteomics data.

Purpose of the Study:

  • To develop an easy-to-use downstream analysis and visualization tool for FragPipe users.
  • To provide comprehensive statistical analysis and visualization capabilities for quantitative proteomics data.

Main Methods:

  • Developed FragPipe-Analyst, an R shiny web server.
  • Created FragPipeAnalystR, an R package extending functionalities.
  • Supported label-free quantification, tandem mass tags, and data-independent acquisition workflows.
  • Implemented missing value imputation, quality control, clustering, differential expression analysis (Limma), and enrichment analysis (Enrichr).

Main Results:

  • FragPipe-Analyst offers a user-friendly interface for downstream proteomics data analysis.
  • The tool supports major quantification workflows and includes advanced statistical methods.
  • FragPipeAnalystR package enables site-specific analysis of post-translational modifications (PTMs).

Conclusions:

  • FragPipe-Analyst and FragPipeAnalystR provide essential tools for comprehensive quantitative proteomics data analysis.
  • These open-source resources enhance the utility of the FragPipe platform for the research community.
  • The tools facilitate advanced analysis and customized visualizations, including PTM site-specific analysis.