Targeted Peak Extraction Ms1

---
name: targeted-peak-extraction-ms1
description: Use when you have raw MS data in a supported instrument format (Agilent .d, Thermo .raw, Bruker .d, mzML) and a predefined list of molecular targets (CSV with m/z and/or retention time) that you need to quantify.
license: CC-BY-4.0
metadata:
  edam_operation: http://edamontology.org/operation_3637
  edam_topics:
  - http://edamontology.org/topic_3520
  - http://edamontology.org/topic_0121
  - http://edamontology.org/topic_3172
  tools:
  - IonToolPack
  - PeakQuant
  - PeakQC
  - Comparador
  techniques:
  - LC-MS
  - direct-infusion-MS
  - ion-mobility-MS
derived_from:
- doi: 10.1021/jasms.4c00146
  title: PeakQC
evidence_spans:
- IonToolPack is a software suite housing tools for mass spectrometry data
- IonToolPack is a software suite housing tools for mass spectrometry data.
- 'PeakQuant: Targeted MS1 peak abundance extraction for quantitation.'
claims: []
provenance:
  collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2
  assembled_by: scripts/collect_metabolomics_collection.py
  sources:
  - build: coll_peakqc_cq
    doi: 10.1021/jasms.4c00146
    title: PeakQC
  dedup_kept_from: coll_peakqc_cq
schema_version: 0.2.0
attribution:
  generator: AgenticScienceBuilder
  original_doi: 10.1021/jasms.4c00146
  all_source_dois:
  - 10.1021/jasms.4c00146
  zenodo_doi: 10.5281/zenodo.20794027
  curators: []
  promoter: Louis-Félix Nothias
  sponsor: CNRS & Université Côte d'Azur
---

# targeted-peak-extraction-ms1

## Summary

Extract targeted MS1 peak abundances from raw mass spectrometry data using user-supplied target lists (m/z, retention time identifiers) for downstream quantitation. This skill converts raw instrument data into a quantitation table suitable for comparative or absolute abundance analysis across samples.

## When to use

You have raw MS data in a supported instrument format (Agilent .d, Thermo .raw, Bruker .d, mzML) and a predefined list of molecular targets (CSV with m/z and/or retention time) that you need to quantify. Use this skill when you want to extract peak abundances only for known targets rather than perform untargeted feature detection, or when you need reproducible quantitation across multiple samples using the same target list.

## When NOT to use

- Input is already a feature table or quantitation matrix (no raw MS data extraction needed).
- You need untargeted feature discovery rather than abundance extraction for known targets.
- Raw MS data is in an unsupported instrument format (not Agilent, Thermo, Bruker, or mzML).

## Inputs

- Raw mass spectrometry data (Agilent .d, Thermo .raw, Bruker .d, or mzML format)
- Target list (CSV file with m/z values, retention times, or other identifiers)
- Mass spectrometry acquisition method metadata (LC-MS, LC-IMS-MS, direct infusion, DDA, or DIA mode)

## Outputs

- Quantitation table (CSV file with rows=targets, columns=samples, values=peak abundances)
- Peak intensity or area values for each target per sample

## How to apply

Load raw MS data into IonToolPack using its simplified GUI, then load your target list in CSV format (containing m/z, retention time, or other identifiers). PeakQuant's targeted extraction algorithm scans the MS1 data for peaks matching each target within user-specified m/z and retention time tolerances, extracts the peak abundance (intensity or area) for each match, and compiles results into a quantitation table. Export the table as CSV for downstream statistical analysis. The workflow is deterministic: the same target list applied to the same raw data should yield identical abundances, making it suitable for large-scale quantitation studies.

## Related tools

- **IonToolPack** (Software suite providing the GUI and data I/O layer for loading raw MS data from multiple instrument formats without installation) — https://github.com/pnnl/IonToolPack
- **PeakQuant** (Core tool that implements the targeted MS1 peak abundance extraction algorithm, matching targets to peaks and computing abundances) — https://github.com/pnnl/IonToolPack
- **PeakQC** (Optional companion tool for quality control assessment of MS1 data before or after targeted extraction via PCA and outlier detection) — https://github.com/pnnl/IonToolPack
- **Comparador** (Optional tool to harmonize and compare quantitation tables generated by PeakQuant across different acquisition methods or processing runs) — https://github.com/pnnl/IonToolPack

## Evaluation signals

- Quantitation table has correct dimensions (number of rows = number of targets; number of columns = number of samples).
- All peak abundance values are positive numbers (intensity or area); no missing or NaN entries for successfully matched targets.
- Reproducibility: applying the same target list to the same raw data file yields identical abundances across runs.
- Peak matching is consistent: targets with expected m/z and retention time in reference samples appear in the output; targets outside data range are absent or flagged.
- CSV export is properly formatted and can be loaded into downstream statistical analysis tools (e.g., R, Python pandas) without parsing errors.

## Limitations

- Extraction is deterministic given fixed tolerances (m/z, RT window), but tolerance choice can affect sensitivity and specificity; no guidance provided in README for threshold selection.
- Tool supports MS1 extraction only; MS/MS or fragment ion quantitation requires alternative workflows or TandemMatch for spectral library matching.
- Success depends on quality and accuracy of the input target list; incorrect or conflicting m/z or RT values may yield missed peaks or false matches.
- No changelog available to track changes across versions, which may affect reproducibility if different versions are used on the same study.
- Requires desktop GUI interaction; no command-line interface mentioned, which may limit automation for large-scale batch processing.

## Evidence

- [readme] PeakQuant: Targeted MS1 peak abundance extraction for quantitation.: "PeakQuant: Targeted MS1 peak abundance extraction for quantitation."
- [other] PeakQuant is designed to perform targeted MS1 peak abundance extraction for quantitation purposes, operating on user-supplied target lists to generate quantitation data.: "PeakQuant is designed to perform targeted MS1 peak abundance extraction for quantitation purposes, operating on user-supplied target lists to generate quantitation data."
- [other] Load raw MS data in a supported instrument format using IonToolPack. Load the target list (CSV format with m/z, retention time, or other identifiers). Extract MS1 peak abundances for each target using PeakQuant's targeted extraction algorithm. Compile extracted abundances into a quantitation table and export as CSV.: "Load raw MS data in a supported instrument format using IonToolPack. Load the target list (CSV format with m/z, retention time, or other identifiers). Extract MS1 peak abundances for each target"
- [readme] It reads data from multiple instrument formats, requires no installation and provides omics agnostic functionalities (metabolomics, lipidomics, proteomics, etc.): "It reads data from multiple instrument formats, requires no installation and provides omics agnostic functionalities (metabolomics, lipidomics, proteomics, etc.)"
- [readme] Supported formats include Agilent 'd', Thermo '.raw', Bruker 'd', and mzML, and for different types of MS acquisition methods: LC-MS, LC-IMS-MS, With/without fragmentation spectra in DDA or DIA mode, Direct infusion: "Supported formats include Agilent 'd', Thermo '.raw', Bruker 'd', and mzML, and for different types of MS acquisition methods: LC-MS, LC-IMS-MS, With/without fragmentation spectra in DDA or DIA mode,"