ArticleGenomics, proteomics & bioinformatics2025
ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics.
Article in Genomics, proteomics & bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 13 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
13 citing papers in PubMed.
- Profiling of Aggregated Amyloid β42-induced Proteomic Alterations in KOLF2.1J Induced Pluripotent Stem Cell-derived Neurons.bioRxiv : the preprint server for biology · 2026Article
- From functional annotation to functional meaning in microbiome research.Environmental microbiome · 2026Review
- Endothelial Cell Proteins as Biomarkers in Susac Syndrome.Annals of clinical and translational neurology · 2026Article
- SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types.Molecular cell · 2026Article
- Circulating cell type senescence signatures track distinct dimensions of health status and trajectories in human longitudinal cohorts.Cell reports · 2026Article
- IGF2BP3 promotes immune evasion and predicts poor prognosis in head and neck squamous cell carcinoma.Translational cancer research · 2026Article
- Circulating Cell Type Senescence Signatures Reveal High-Resolution Health Status and Trajectories in Human Longitudinal Studies.medRxiv : the preprint server for health sciences · 2026Article
- SenCat: Cataloging human cell senescence through multiomic profiling of multiple senescent primary cell types.bioRxiv : the preprint server for biology · 2026Article
- LanthMS: A Computational Tool for the Structure Elucidation of Lanthipeptides from Tandem Mass Spectrometry Data.Protein and peptide letters · 2026Article
- Altered mRNA transport and local translation in i3Neurons with RNA-binding protein knockdown.Nucleic acids research · 2025Article
- TDP-43 pathology induces CD8bioRxiv : the preprint server for biology · 2025Article
- Altered mRNA transport and local translation in iNeurons with RNA binding protein knockdown.bioRxiv : the preprint server for biology · 2024Article
- Comparative study of enriched dopaminergic neurons from siblings with Gaucher disease discordant for parkinsonism.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
- Erratum issued
- Update of
Authors and funding
24 authors.
Funding
Abstract
Mass spectrometry (MS) is a technique widely employed for the identification and characterization of proteins, with personalized medicine, systems biology, and biomedical applications. The application of MS-based proteomics advances our understanding of protein function, cellular signaling, and complex biological systems. MS data analysis is a critical process that includes identifying and quantifying proteins and peptides and then exploring their biological functions in downstream analyses. To address the complexities associated with MS data analysis, we developed ProtPipe to streamline and automate the processing and analysis of high-throughput proteomics and peptidomics datasets with DIA-NN preinstalled. The pipeline facilitates data quality control, sample filtering, and normalization, ensuring robust and reliable downstream analyses. ProtPipe provides downstream analyses, including protein and peptide differential abundance identification, pathway enrichment analysis, protein-protein interaction analysis, and major histocompatibility complex (MHC)-peptide binding affinity analysis. ProtPipe generates annotated tables and visualizations by performing statistical post-processing and calculating fold changes between predefined pairwise conditions in an experimental design. It is an open-source, well-documented tool available at https://github.com/NIH-CARD/ProtPipe, with a user-friendly web interface.
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.