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A software tool for omics-agnostic automated quality control of mass spectrometry data.

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IonToolPack | PeakQC

IonToolPack is a software suite for housing tools for mass spectrometry. The first one is PeakQC, a software a tool for automated quality control (QC) of mass spectrometry (MS) data which is is omics-agnostic (works for any ion type, e.g.: metabolomics, lipidomics, proteomics, etc.), supports various instrument platforms and acquisition modes and has a simple graphical user interface.

Usage

  1. Download the latest version (Release section, right panel) and decompress it
  2. Double click IonToolPack.exe
  3. Import raw MS files and click “Process”
  4. See more details and examples in PeakQC_User-guide_*.pdf

MS data supported

Supported formats include Agilent 'd', Bruker 'd' (improvements in progress), Thermo '.raw', 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

Contact

aivett.bilbao@pnnl.gov

References

If you this tool or any portions of this code please cite:

  • Harrison et al. "PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data". Journal of the American Society for Mass Spectrometry 2024 https://doi.org/10.1021/jasms.4c00146.
  • Bilbao et al. "MZA: A Data Conversion Tool to Facilitate Software Development and Artificial Intelligence Research in Multidimensional Mass Spectrometry". Journal of Proteome Research 2023 https://doi.org/10.1021/acs.jproteome.2c00313.