Evidence map›Paper›PMID 38496650›Full record

ArticlebioRxiv : the preprint server for biology2024

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

Yi Hsiao, Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood, Joel R Steele, Ralf B Schittenhelm, Alexey I Nesvizhskii

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Yi HsiaoDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.ORCID 0000-0002-9435-0305
Haijian ZhangMonash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.ORCID 0009-0004-8479-8132
Ginny Xiaohe LiDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.ORCID 0000-0001-9260-0414
Yamei DengDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.ORCID 0000-0002-3680-5930
Fengchao YuDepartment of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.ORCID 0000-0002-7695-3698
Hossein Valipour KahroodMonash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.ORCID 0000-0003-4166-0382
Joel R SteeleMonash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.ORCID 0000-0002-3070-9761
Ralf B SchittenhelmMonash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.ORCID 0000-0001-8738-1878
Alexey I NesvizhskiiDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.ORCID 0000-0002-2806-7819

Funding

COMPUTATIONAL TOOLS FOR MASS SPECTROMETRY-BASED INTERACTOME DATAR01GM094231 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Alexey I Nesvizhskii · 2010 to 2026
$5.4M
Michigan Center for Translational Cancer Proteogenomics-Diversity SupplementU24CA271037 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Saravana Mohan Dhanasekaran, Alexey I Nesvizhskii · 2022 to 2026
$4.4M
University of Michigan Proteogenomics Data Analysis CenterU24CA210967 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI CHINNAIYAN, ARUL M, DHANASEKARAN, SARAVANA M · 2016 to 2020
$4.1M
NCI NIH HHS U24 CA210967NCI NIH HHS U24 CA271037NIGMS NIH HHS R01 GM094231
6 · The paper itself

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

AP-MSbioinformaticsdownstream analysisFragPipeLiP-MSopen sourceprotein phosphorylationsoftware

Identifiers

PMID38496650
PMCPMC10942459

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.