From 4ca441e674afed8a9de06b1b4f3b14489bd4f0e9 Mon Sep 17 00:00:00 2001 From: Kozo Nishida Date: Tue, 19 Mar 2024 17:47:56 +0900 Subject: [PATCH 1/3] Add MsQuality Bioconductor package. --- docs/pages/resource-guide.md | 44 ++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/docs/pages/resource-guide.md b/docs/pages/resource-guide.md index 3382ef51..1ad65a21 100644 --- a/docs/pages/resource-guide.md +++ b/docs/pages/resource-guide.md @@ -21,6 +21,50 @@ Metrics generating software with mzQC support: - [OpenMS](https://github.com/OpenMS/OpenMS): Open-source software C++ library for LC/MS data management and analyses. - [QCCalculator](https://github.com/bigbio/qccalculator): Python tool for base QC metric calculation from mzML, mzIdentML, and MaxQuant input files. - [Yamato / SwaMe / Prognosticator](https://github.com/PaulBrack/Yamato): 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](https://github.com/MS-Quality-Hub). All the above libraries have their development home there and some other very useful repositories. From b0f5042a1913cee7ebc66fe4fd962c346373756c Mon Sep 17 00:00:00 2001 From: Kozo Nishida Date: Wed, 20 Mar 2024 09:53:21 +0900 Subject: [PATCH 2/3] Correct the MsQuality URL link markdown. --- docs/pages/resource-guide.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/pages/resource-guide.md b/docs/pages/resource-guide.md index 1ad65a21..a720f967 100644 --- a/docs/pages/resource-guide.md +++ b/docs/pages/resource-guide.md @@ -21,7 +21,7 @@ Metrics generating software with mzQC support: - [OpenMS](https://github.com/OpenMS/OpenMS): Open-source software C++ library for LC/MS data management and analyses. - [QCCalculator](https://github.com/bigbio/qccalculator): Python tool for base QC metric calculation from mzML, mzIdentML, and MaxQuant input files. - [Yamato / SwaMe / Prognosticator](https://github.com/PaulBrack/Yamato): 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. +- [MsQuality](https://bioconductor.org/packages/release/bioc/html/MsQuality.html): 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) From f7f555907429f2bb36a31f3e8c4b6d6960c8cc1d Mon Sep 17 00:00:00 2001 From: Mathias Walzer Date: Wed, 20 Mar 2024 05:13:02 +0000 Subject: [PATCH 3/3] Update links in tutorials.md --- docs/pages/tutorials.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/pages/tutorials.md b/docs/pages/tutorials.md index 005211f4..0b3c0430 100644 --- a/docs/pages/tutorials.md +++ b/docs/pages/tutorials.md @@ -7,13 +7,13 @@ permalink: /tutorials/ We have a couple of tutorials and guides to offer, this page will lead you to them: ### with python -* read mzQC: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MS-Quality-hub/pymzqc/blob/v1.0.0rc1/jupyter/colab/read_in_5_minutes.ipynb) -* write mzQC: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MS-Quality-hub/pymzqc/blob/v1.0.0rc1/jupyter/colab/write_in_5_minutes.ipynb) +* read mzQC: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MS-Quality-hub/pymzqc/blob/v1.0.0rc2/jupyter/colab/read_in_5_minutes.ipynb) +* write mzQC: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MS-Quality-hub/pymzqc/blob/v1.0.0rc2/jupyter/colab/write_in_5_minutes.ipynb) * demo video ### with R -* [Rlib for mzQC(TBA)](TBA) +* [rmzQC](https://cran.r-project.org/web/packages/rmzqc/index.html) * PTXQC demo