ArticleJournal of proteome research2024
Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst.
Article in Journal of proteome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
101 citing papers in PubMed.
- Proteomic and machine learning analysis predicts treatment response signatures in Myasthenia Gravis.Journal of translational medicine · 2026Trial
- A B1 SINE element within the mouseScience advances · 2026Article
- Integrative multi-omics reveals CUL4B as a modulator of macrophage pyroptosis and innate defense againstScience advances · 2026Article
- Host metadherin coordinates hepatic lipid metabolism and CD8Cell metabolism · 2026Article
- MCOD: a memory-constrained deep learning framework for robust outlier detection in quantitative proteomics.Briefings in bioinformatics · 2026Article
- Article
- Proteomic investigation of signaling dynamics: from static maps to network rewiring.Bioscience reports · 2026Review
- Article
- Article
- A conserved vesicular circuit enables metabolic adaptation and maintains systemic heme homeostasis.bioRxiv : the preprint server for biology · 2026Article
- Proteomic Differences Reveal Early Development of Contrasting Energetic Strategies Between Divergent Migratory Ecotypes in Three-Spined Stickleback.Molecular ecology · 2026Article
- PLA2G2F suppresses ferroptosis through phospholipid remodeling.Nature structural & molecular biology · 2026Article
- The regulation of protein phosphatase 4 by FBXO42 is required for cancer cell survival.EMBO reports · 2026Article
- Identification of a conserved gene family with an essential role inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Spinal nociceptive denervation impedes subsequent chronic autonomic remodeling after myocardial infarction in male swine.Nature communications · 2026Article
- Tumor immune cell targeting chimeras reprogram tumor-associated macrophages.Nature chemical biology · 2026Article
- The life history of recessive deleterious alleles as seen through the eyes of a honey bee (Apis mellifera).Molecular biology and evolution · 2026Article
- Prolonged Stagnation Reduces Treated Wastewater Biostability by Altering Microbial Community: Insights From Metaproteomics.Environmental microbiology · 2026Article
- A chemoproteomic biotechnological toolkit for resolving xylanase specificity in decorated xylan.Nature communications · 2026Article
- Coxsackievirus B escapes antiviral CD8Science advances · 2026Article
41 more citing papers are in PubMed but not listed here.
Corrections and comments
- Update of
Authors and funding
9 authors.
Funding
Abstract
The FragPipe computational proteomics platform is gaining widespread popularity among the proteomics research community because of its fast processing speed and user-friendly graphical interface. Although FragPipe produces well-formatted output tables that are ready for analysis, there is still a need for an easy-to-use and user-friendly downstream statistical analysis and visualization tool. FragPipe-Analyst addresses this need by providing an R shiny web server to assist FragPipe users in conducting downstream analyses of the resulting quantitative proteomics data. It supports major quantification workflows, including label-free quantification, tandem mass tags, and data-independent acquisition. FragPipe-Analyst offers a range of useful functionalities, such as various missing value imputation options, data quality control, unsupervised clustering, differential expression (DE) analysis using Limma, and gene ontology and pathway enrichment analysis using Enrichr. To support advanced analysis and customized visualizations, we also developed FragPipeAnalystR, an R package encompassing all FragPipe-Analyst functionalities that is extended to support site-specific analysis of post-translational modifications (PTMs). FragPipe-Analyst and FragPipeAnalystR are both open-source and freely available.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.