mzapy
latest

User Guide

  • Installation
    • From PyPI
    • From Source
    • Dependencies
  • Tech Note Demo
    • Imports
    • Setup
    • Extract and View XIC
    • Extract and View MS1 Spectra
    • Extract and View ATD
    • Mass Calibration
    • CCS Calibration
    • Cleanup

API Reference

  • mzapy.MZA
    • Module Reference
      • Initialization
        • MZA
        • __init__()
        • close()
      • Scan Caching
        • load_scan_cache()
        • save_scan_cache()
      • Metadata
        • metadata()
      • Extracted Ion Chromatograms
        • collect_xic_arrays_by_mz()
        • collect_xic_arrays_by_mz_dt()
      • Arrival Time Distributions
        • collect_atd_arrays_by_rt_mz()
      • MS1 Spectra
        • collect_ms1_arrays_by_rt()
        • collect_ms1_arrays_by_dt()
        • collect_ms1_arrays_by_rt_dt()
        • collect_ms1_df_by_rt()
        • collect_ms1_df_by_rt_dt()
      • MS2 Spectra
        • collect_ms2_arrays_by_rt_dt()
        • collect_ms2_df_by_rt()
        • collect_ms2_df_by_rt_dt()
      • 2-Dimensional Data
        • collect_rtmz_arrays()
        • collect_rtmz_arrays_by_dt()
        • collect_dtmz_arrays_by_rt()
        • collect_rtdt_arrays_by_mz()
  • mzapy.calibration
    • Module Reference
      • Base Object
        • _CalibrationBase
        • fit()
        • transform()
      • Mass Calibration
        • MassCalibration
        • __init__()
        • calibrated_mass()
        • mass_calibration_from_params()
      • DTIMS CCS Calibration (Single-Field)
        • CCSCalibrationDTsf
        • __init__()
        • calibrated_ccs()
        • dtsf_ccs_calibration_from_params()
      • TWIMS CCS Calibration
        • CCSCalibrationTW
        • __init__()
        • calibrated_ccs()
        • tw_ccs_calibration_from_params()
  • mzapy.isotopes
    • The MolecularFormula class
    • The OrderedMolecularFormula class
    • Elements
    • MS Adducts
    • Module Reference
      • Molecular Formula Object
        • MolecularFormula
        • __init__()
      • Ordered Molecular Formula Object
        • OrderedMolecularFormula
        • __init__()
      • Utility Functions
        • valid_element()
        • valid_ms_adduct()
        • monoiso_mass()
        • ms_adduct_formula()
        • ms_adduct_mz()
        • predict_m_m1_m2()
  • mzapy.peaks
    • 1D Peak Fitting
    • Module Reference
      • Interpolation
        • lerp_1d()
        • lerp_2d()
      • Peak Finding
        • find_peaks_1d_localmax()
        • find_peaks_1d_gauss()
      • Miscellaneous
        • calc_gauss_psnr()
        • calc_peak_area()
  • mzapy.view
    • Flexible Plotting System
    • Module Reference
      • Viewing Data
        • plot_spectrum()
        • plot_chrom()
        • plot_atd()
        • add_peaks_to_plot()
        • _setup_and_save_or_show_plot()
      • Calibration Plots
        • plot_mass_calibration()
        • plot_dtsf_ccs_calibration()
        • plot_tw_ccs_calibration()

Project Info

  • License
  • Disclaimer
  • Citing
  • Contributing
    • Feedback
    • Fixing Bugs or Implementing Features
    • Writing Documentation
      • Creating User Guides
    • Submitting a Pull Request
    • Versioning Scheme
    • Coding Style
      • Naming Conventions
      • Docstring Format
      • Adding Entries to Sphinx Documentation
      • Unit Testing
mzapy
  • mzapy 1.7.2
  • Edit on GitHub

mzapy 1.7.2

A Python package that provides an interface to unprocessed MS data in the MZA format.

Source code is available at https://github.com/PNNL-m-q/mzapy

MZA data converter tool is available at https://github.com/PNNL-m-q/mza

User Guide

  • Installation
    • From PyPI
    • From Source
    • Dependencies
  • Tech Note Demo
    • Imports
    • Setup
    • Extract and View XIC
    • Extract and View MS1 Spectra
    • Extract and View ATD
    • Mass Calibration
    • CCS Calibration
    • Cleanup

API Reference

  • mzapy.MZA
    • Module Reference
      • Initialization
      • Scan Caching
      • Metadata
      • Extracted Ion Chromatograms
      • Arrival Time Distributions
      • MS1 Spectra
      • MS2 Spectra
      • 2-Dimensional Data
  • mzapy.calibration
    • Module Reference
      • Base Object
      • Mass Calibration
      • DTIMS CCS Calibration (Single-Field)
      • TWIMS CCS Calibration
  • mzapy.isotopes
    • The MolecularFormula class
    • The OrderedMolecularFormula class
    • Elements
    • MS Adducts
    • Module Reference
      • Molecular Formula Object
      • Ordered Molecular Formula Object
      • Utility Functions
  • mzapy.peaks
    • 1D Peak Fitting
    • Module Reference
      • Interpolation
      • Peak Finding
      • Miscellaneous
  • mzapy.view
    • Flexible Plotting System
    • Module Reference
      • Viewing Data
      • Calibration Plots

Contributors

  • Dylan Ross (dylan.ross@pnnl.gov)

  • Aivett Bilbao (aivett.bilbao@pnnl.gov)

  • Joon-Yong Lee (junyoni@gmail.com)

  • Xueyun Zheng (xueyun.zheng@pnnl.gov)

Project Info

  • License
  • Disclaimer
  • Citing
  • Contributing
    • Feedback
    • Fixing Bugs or Implementing Features
    • Writing Documentation
    • Submitting a Pull Request
    • Versioning Scheme
    • Coding Style
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