This is the guide to mzQC resources from software libraries, QC software supporting mzQC, to validation.

Core libraries

  • pymzqc: Python library to create, process, and validate mzQC files. It includes a Python object model, (de-)serialisation functions, syntactic validation, and semantic validation of mzQC files.
  • jmzqc: Java library to create, process, and validate mzQC files. It includes a Java object model, (de-)serialisation functions, syntactic validation, and semantic validation of mzQC files.
  • rmzqc: R library to create, process, and validate mzQC files. It includes a R object model, (de-)serialisation functions, syntactic validation, and semantic validation of mzQC files. In development.

QC Software

Metrics generating software with mzQC support:

  • PTXQC: An R package for creation of QC reports from MaxQuant results and OpenMS mzTab files.
  • OpenMS: Open-source software C++ library for LC/MS data management and analyses.
  • QCCalculator: Python tool for base QC metric calculation from mzML, mzIdentML, and MaxQuant input files.
  • Yamato / SwaMe / Prognosticator: SWATH-MS QC metrics generation tools.
  • MsQuality: An R Bioconductor package, which provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics. It supports the calculation of the following metrics.
    • chromatography duration (MS:4000053)
    • TIC quarters RT fraction (MS:4000054)
    • MS1 quarter RT fraction (MS:4000055)
    • MS2 quarter RT fraction (MS:4000056)
    • MS1 TIC-change quartile ratios (MS:4000057)
    • MS1 TIC quartile ratios (MS:4000058)
    • number of MS1 spectra MS:4000059)
    • number of MS2 spectra (MS:4000060)
    • m/z acquisition range (MS:4000069)
    • retention time acquisition range (MS:4000070)
    • MS1 signal jump (10x) count (MS:4000097)
    • MS1 signal fall (10x) count (MS:4000098)
    • number of empty MS1 scans (MS:4000099)
    • number of empty MS2 scans (MS:4000100)
    • number of empty MS3 scans (MS:4000101)
    • MS2 precursor intensity distribution Q1, Q2, Q3 (MS:4000116)
    • MS2 precursor intensity distribution mean (MS:4000117)
    • MS2 precursor intensity distribution sigma (MS:4000118)
    • MS2 precursor median m/z of identified quantification data points (MS:4000152)
    • interquartile RT period for identified quantification data points (MS:4000153)
    • rate of the interquartile RT period for identified quantification data points (MS:4000154)
    • area under TIC (MS:4000155)
    • area under TIC RT quantiles (MS:4000156)
    • extent of identified MS2 precursor intensity (MS:4000157)
    • median of TIC values in the RT range in which the middle half of quantification data points are identified (MS:4000158)
    • median of TIC values in the shortest RT range in which half of the quantification data points are identified (MS:4000159)
    • MS2 precursor intensity range (MS:4000160)
    • identified MS2 precursor intensity distribution Q1, Q2, Q3 (MS:4000161)
    • unidentified MS2 precursor intensity distribution Q1, Q2, Q3 (MS:4000162)
    • identified MS2 precursor intensity distribution mean (MS:4000163)
    • unidentified MS2 precursor intensity distribution mean (MS:4000164)
    • identified MS2 precursor intensity distribution sigma (MS:4000165)
    • unidentified MS2 precursor intensity distribution sigma (MS:4000166)
    • ratio of 1+ over 2+ of all MS2 known precursor charges (MS:4000167)
    • ratio of 1+ over 2+ of identified MS2 known precursor charges (MS:4000168)
    • ratio of 3+ over 2+ of all MS2 known precursor charges (MS:4000169)
    • ratio of 3+ over 2+ of identified MS2 known precursor charges (MS:4000170)
    • ratio of 4+ over 2+ of all MS2 known precursor charges (MS:4000171)
    • ratio of 4+ over 2+ of identified MS2 known precursor charges (MS:4000172)
    • mean MS2 precursor charge in all spectra (MS:4000173)
    • mean MS2 precursor charge in identified spectra (MS:4000174)
    • median MS2 precursor charge in all spectra (MS:4000175)
    • median MS2 precursor charge in identified spectra (MS:4000176)

A Hub for QC

If you are looking for a home to your QC software or library, check out MS-Quality-Hub. All the above libraries have their development home there and some other very useful repositories.