Signal Noise Ratio Improvement Validation

---
name: signal-noise-ratio-improvement-validation
description: Use when after executing multidimensional smoothing, spike removal, or saturation repair on raw TOF-MS or IM-MS data (.d format from Agilent MassHunter) to confirm that signal quality has improved.
license: CC-BY-4.0
metadata:
  edam_operation: http://edamontology.org/operation_3674
  edam_topics:
  - http://edamontology.org/topic_0121
  - http://edamontology.org/topic_3520
  tools:
  - PNNL PreProcessor
  - Agilent MassHunter
  - IM-MS Browser
  techniques:
  - ion-mobility-MS
derived_from:
- doi: 10.1021/jasms.4c00220
  title: PNNL PreProcessor
- doi: 10.1021/acs.jproteome.1c00425
  title: ''
evidence_spans:
- we have developed this user-friendly tool for Agilent MassHunter (.d) and UIMF mass spectrometry data files
- we have developed this user-friendly tool for Agilent MassHunter (.d) and UIMF mass spectrometry data files (MS-files) from drift tube (DT) and structure for lossless ion manipulations (SLIM) IM-MS
- Agilent MassHunter (.d) and UIMF mass spectrometry data files (MS-files)
- Agilent MassHunter (.d) and UIMF mass spectrometry data files
claims: []
provenance:
  collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2
  assembled_by: scripts/collect_metabolomics_collection.py
  sources:
  - build: coll_pnnl_preprocessor_cq
    doi: 10.1021/jasms.4c00220
    title: PNNL PreProcessor
  dedup_kept_from: coll_pnnl_preprocessor_cq
schema_version: 0.2.0
attribution:
  generator: AgenticScienceBuilder
  original_doi: 10.1021/jasms.4c00220
  all_source_dois:
  - 10.1021/jasms.4c00220
  - 10.1021/acs.jproteome.1c00425
  zenodo_doi: 10.5281/zenodo.20794027
  curators: []
  promoter: Louis-Félix Nothias
  sponsor: CNRS & Université Côte d'Azur
---

# signal-noise-ratio-improvement-validation

## Summary

Validates that multidimensional smoothing and noise-filtering preprocessing steps enhance signal quality in ion mobility–mass spectrometry data by removing artifacts from low-abundance ions while preserving real signal peaks. This skill assesses whether preprocessing has successfully reduced background noise and jagged peak artifacts without introducing distortion.

## When to use

Apply this skill after executing multidimensional smoothing, spike removal, or saturation repair on raw TOF-MS or IM-MS data (.d format from Agilent MassHunter) to confirm that signal quality has improved. Use it when low-abundance ions dominate the dataset and jagged peaks are visible in the raw spectra, or when you need to validate that preprocessing artifacts have been removed before proceeding to demultiplexing or peak deconvolution.

## When NOT to use

- Input data has already undergone peak picking or feature extraction; validation should occur on raw/centroided spectra before subsequent processing
- Ions have highly convoluted elution/mobility profiles caused by strong interferences; saturation repair and smoothing may produce incorrect results and mask true signal
- No reference or baseline raw data is available for comparison; validation requires paired before/after datasets

## Inputs

- Raw TOF-MS data file in Agilent MassHunter .d format
- Preprocessed MS-file output (after multidimensional smoothing, spike removal, and/or saturation repair)
- Preprocessing operation log or validation report

## Outputs

- Comparison report of peak quality metrics (before/after)
- Artifact removal verification log
- Signal enhancement validation summary
- Peak morphology assessment (jagged artifact reduction)

## How to apply

Load both the raw input MS-file (.d format) and the preprocessed output MS-file into the PNNL PreProcessor or Agilent MassHunter visualization interface. Compare peak morphology and abundance profiles across the two datasets, focusing on regions with low-abundance ions where jagged artifacts are common. Execute the smoothing verification step in PNNL PreProcessor and review the output log for artifact removal confirmation. Measure the reduction in noise spikes and the sharpness of real signal peaks; real signals should be enhanced while artifacts are flattened. Validate that no saturation distortions or convoluted elution/mobility profiles have been introduced, especially in regions with high ion density or interferences.

## Related tools

- **PNNL PreProcessor** (Primary tool for executing multidimensional smoothing, spike removal, saturation repair, and generating preprocessing logs for validation) — https://github.com/PNNL-Comp-Mass-Spec/PNNL-PreProcessor
- **Agilent MassHunter** (Reference visualization and analysis platform for comparing raw (.d) and preprocessed MS-files, inspecting peak morphology and abundance profiles)
- **IM-MS Browser** (Optional tool for batch visualization of multidimensional ion mobility and mass spectrometry data to assess smoothing quality across large datasets)

## Evaluation signals

- Output log from PNNL PreProcessor confirms artifact removal with no errors or warnings in the multidimensional smoothing step
- Visual inspection shows jagged peaks in low-abundance ion regions of raw data are flattened and smoothed in output without peak broadening or loss of real signal
- Peak signal intensity is maintained or increased for true signals while background noise and spike artifacts are visibly reduced
- No saturation distortions or false convoluted elution/mobility profiles are introduced in regions with high ion density or strong interferences
- Preprocessed output file (.d format) is valid and readable in Agilent MassHunter with consistent metadata export (retention time, m/z, abundance ranges remain coherent)

## Limitations

- Saturation repair software may produce incorrect results for ions with highly convoluted elution/mobility profiles caused by interferences; validation may be ambiguous in such cases
- Smoothing effectiveness depends on peak width and abundance; low-abundance ions with extremely jagged profiles may require manual parameter tuning and iterative validation
- No changelog or version tracking is available in the PNNL PreProcessor repository, making reproducibility and comparison across releases difficult
- Validation relies on visual inspection and log interpretation; quantitative signal-to-noise ratio metrics are not explicitly reported by the tool

## Evidence

- [methods] Smoothing removes artifacts in jagged peaks, which are common in low-abundance ions. Real signals are enhanced: "Smoothing removes artifacts in jagged peaks, which are common in low-abundance ions. Real signals are enhanced"
- [other] Verify smoothing artifacts removal in output log and validate peak quality against input reference: "Verify smoothing artifacts removal in output log and validate peak quality against input reference"
- [methods] the saturation repair software may produce incorrect results for ions with highly convoluted elution/mobility profiles caused by interferences: "the saturation repair software may produce incorrect results for ions with highly convoluted elution/mobility profiles caused by interferences"
- [readme] various algorithms and utilities including data compression and interpolation, ion mobility demultiplexing, multidimensional smoothing, noise filtering by low intensity threshold and spike removal, saturation repair and metadata export: "multidimensional smoothing, noise filtering by low intensity threshold and spike removal, saturation repair and metadata export"
- [other] Load raw TOF-MS data file (.d format from Agilent MassHunter) into PNNL PreProcessor: "Load raw TOF-MS data file (.d format from Agilent MassHunter) into PNNL PreProcessor"