Overview
peakPantheR searches specified retention-time and m/z regions, fits chromatographic peaks and reports integration results with diagnostic plots. It supports processing many files in parallel and reviewing parameters through a local Shiny interface. The target list supplies the expected feature annotations; extraction does not independently establish compound identity.
What can this tool do?
Common uses
- Extract a consistent predefined feature panel across LC-MS files.
- Review chromatographic fits and refine target integration windows.
Scientific fit
Primary function
Preprocessing and feature extraction
Analysis types
Targeted metabolomics
Data compatibility
Inputs
Mass spectra, Compound list or annotations
Outputs
Feature or peak table, Human-readable report
Input formats
mzML, Target feature table with retention-time and m/z windows
Output formats
CSV or TSV, Diagnostic chromatographic plots and R annotation objects
Scope and considerations
Designed for
- Targeted extraction from predefined retention-time and m/z regions in profiling data.
Not designed for
- Discovery of all unknown features or de novo metabolite identification.
Important requirements
- A target annotation table with feature identifiers and retention-time/mass windows.
- MS files supported by the underlying R readers and a compatible R/Bioconductor installation.
Considerations
- Chromatographic drift and coelution can compromise extraction within fixed windows.
- Inspect fitting diagnostics and retain target definitions and parameter changes.
- A fitted peak does not replace reference-standard evidence for its assigned identity.
Access and documentation
Open-source Bioconductor R package. Match R and Bioconductor releases and consult the selected release requirements. The Shiny GUI runs from the installed package; it is not a separate hosted analysis service.
License: GPL-3
Evidence and review
Recovered from the corrected public submission after its original ORCID parsing failure. Bioconductor, official project documentation and DOI metadata reviewed on 2026-09-12. No software execution or independent benchmarking performed. Contributor consent and submitted identity preserved; account ownership was not independently authenticated.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Wolfer AM, et al. peakPantheR, an R package for large-scale targeted extraction and integration of annotated metabolic features in LC-MS profiling datasets. Bioinformatics 37, 4886-4888 (2021). doi:10.1093/bioinformatics/btab433
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
Original submission and discussion
- 2026-09-12 · First committed entry
Recover and curate peakPantheR community submission
View change · Entry at this revision