Package: MsQuality 1.5.0

Thomas Naake

MsQuality: MsQuality - Quality metric calculation from Spectra and MsExperiment objects

The MsQuality 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 defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.

Authors:Thomas Naake [aut, cre], Johannes Rainer [aut]

MsQuality_1.5.0.tar.gz
MsQuality_1.5.0.zip(r-4.5)MsQuality_1.5.0.zip(r-4.4)MsQuality_1.5.0.zip(r-4.3)
MsQuality_1.5.0.tgz(r-4.4-any)MsQuality_1.5.0.tgz(r-4.3-any)
MsQuality_1.5.0.tar.gz(r-4.5-noble)MsQuality_1.5.0.tar.gz(r-4.4-noble)
MsQuality_1.5.0.tgz(r-4.4-emscripten)MsQuality_1.5.0.tgz(r-4.3-emscripten)
MsQuality.pdf |MsQuality.html✨
MsQuality/json (API)
NEWS

# Install 'MsQuality' in R:
install.packages('MsQuality', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/tnaake/msquality/issues

Datasets:
  • meta - Example data for 'MsQuality': data set of Lee et al.
  • msexp_hilic - Example data for 'MsQuality': data set of Lee et al.
  • msexp_rplc - Example data for 'MsQuality': data set of Lee et al.
  • sps_hilic - Example data for 'MsQuality': data set of Lee et al.
  • sps_rplc - Example data for 'MsQuality': data set of Lee et al.
  • vals - Example data for 'MsQuality': data set of Lee et al.

On BioConductor:MsQuality-1.5.0(bioc 3.20)MsQuality-1.4.0(bioc 3.19)

bioconductor-package

33 exports 1.31 score 137 dependencies

Last updated 2 months agofrom:8e3581c2ba

Exports:areaUnderTicareaUnderTicRtQuantilescalculateMetricscalculateMetricsFromMsExperimentcalculateMetricsFromSpectrachromatographyDurationextentIdentifiedPrecursorIntensitymeanChargemedianChargemedianPrecursorMzmedianTicOfRtRangemedianTicRtIqrmsSignal10xChangemzAcquisitionRangenumberEmptyScansnumberSpectraplotMetricplotMetricTibbleprecursorIntensityMeanprecursorIntensityQuartilesprecursorIntensityRangeprecursorIntensitySdqualityMetricsratioCharge1over2ratioCharge3over2ratioCharge4over2rtAcquisitionRangertIqrrtIqrRatertOverMsQuartersshinyMsQualityticQuartersRtFractionticQuartileToQuartileLogRatio

Dependencies:abindAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbriobslibcachemcallrcliclueclustercodetoolscollectionscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydescdiffobjdigestdplyrevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobandjquerylibjsonlitejsonvalidateknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmgcvmimeMsCoreUtilsmsdataMsExperimentMultiAssayExperimentmunsellnlmeontologyIndexopensslpillarpkgbuildpkgconfigpkgloadplotlyplyrpraiseprocessxpromisesProtGenericspspurrrQFeaturesR6R6PrappdirsRColorBrewerRcpprematch2reshape2rlangrmarkdownrmzqcrprojrootS4ArraysS4VectorssassscalesshinyshinydashboardsnowsourcetoolsSparseArraySpectrastringistringrSummarizedExperimentsystestthattibbletidyrtidyselecttinytexUCSC.utilsutf8V8vctrsviridisLitewaldowithrxfunxtableXVectoryamlzlibbioc

MsQuality: Calculation of QC metrics from mass spectrometry data

Thomas Naake and Johannes Rainer

Rendered fromMsQuality.Rmdusingknitr::rmarkdownon Jun 15 2024.

Last update: 2023-09-01
Started: 2021-09-09

Readme and manuals

Help Manual

Help pageTopics
MsQuality - Quality metric calculation from Spectra and MsExperiment objectsMsQuality-package MsQuality
Order Spectra according to increasing retention time.rtOrderSpectra
area under TIC (MS:4000155)areaUnderTic
area under TIC RT quantiles (MS:4000156)areaUnderTicRtQuantiles
Calculate QC metrics from a Spectra or MsExperiment objectcalculateMetrics
Calculate QC metrics from a MsExperiment objectcalculateMetricsFromMsExperiment
Calculate QC metrics from a Spectra object containing only spectral data from one samplecalculateMetricsFromOneSampleSpectra
Calculate QC metrics from a Spectra objectcalculateMetricsFromSpectra
chromatography duration (MS:4000053)chromatographyDuration
extent of identified MS2 precursor intensity (MS:4000157)extentIdentifiedPrecursorIntensity
Example data for 'MsQuality': data set of Lee et al. (2019)Lee_2019 msexp_hilic msexp_rplc sps_hilic sps_rplc
Example data for 'MsQuality': data set of Lee et al. (2019)Lee_2019_meta_vals meta vals
mean MS2 precursor charge in all spectra (MS:4000173) or mean MS2 precursor charge in identified spectra (MS:4000174)meanCharge
median MS2 precursor charge in all spectra (MS:4000175) or median MS2 precursor charge in identified spectra (MS:4000176)medianCharge
MS2 precursor median m/z of identified quantification data points (MS:4000152)medianPrecursorMz
median of TIC values in the shortest RT range in which half of the quantification data points are identified (MS:4000159)medianTicOfRtRange
median of TIC values in the RT range in which the middle half of quantification data points are identified (MS:4000158)medianTicRtIqr
MS1 signal jump (10x) count (MS:4000097) or MS1 signal fall (10x) count (MS:4000098)msSignal10xChange
m/z acquisition range (MS:4000069)mzAcquisitionRange
number of empty MS1 scans (MS:4000099), number of empty MS2 scans (MS:4000100), or number of empty MS3 scans (MS:4000101)numberEmptyScans
number of MS1 spectra (MS:4000059) or number of MS2 spectra (MS:4000060)numberSpectra
Visualize a quality metricplotMetric
Helper function for plotMetricplotMetricTibble
MS2 precursor intensity distribution mean (MS:4000117), identified MS2 precursor intensity distribution mean (MS:4000163), or unidentified MS2 precursor intensity distribution mean (MS:4000164)precursorIntensityMean
MS2 precursor intensity distribution (MS:4000116), identified MS2 precursor intensity distribution (MS:4000161), or unidentified MS2 precursor intensity distribution (MS:4000162)precursorIntensityQuartiles
MS2 precursor intensity range (MS:4000160)precursorIntensityRange
MS2 precursor intensity distribution sigma (MS:4000118), identified MS2 precursor intensity distribution sigma (MS:4000165), or unidentified MS2 precursor intensity distribution sigma (MS:4000166)precursorIntensitySd
Get a vector of quality metrics than can be applied to 'object'qualityMetrics
ratio of 1+ over 2+ of all MS2 known precursor charges (MS:4000167) or ratio of 1+ over 2+ of identified MS2 known precursor charges (MS:4000168)ratioCharge1over2
ratio of 3+ over 2+ of all MS2 known precursor charges (MS:4000169) or ratio of 3+ over 2+ of identified MS2 known precursor charges (MS:4000170)ratioCharge3over2
ratio of 4+ over 2+ of all MS2 known precursor charges (MS:4000171) or ratio of 4+ over 2+ of identified MS2 known precursor charges (MS:4000172)ratioCharge4over2
retention time acquisition range (MS:4000070)rtAcquisitionRange
interquartile RT period for identified quantification data points (MS:4000153)rtIqr
rate of the interquartile RT period for identified quantification data points (MS:4000154)rtIqrRate
MS1 quarter RT fraction (MS:4000055) or MS2 quarter RT fraction (MS:4000056)rtOverMsQuarters
Shiny application to visualize quality metricsshinyMsQuality
TIC quarters RT fraction (MS:4000054)ticQuartersRtFraction
MS1 TIC-change quartile ratios (MS:4000057) or MS1 TIC quartile ratios (MS:4000058)ticQuartileToQuartileLogRatio
Transform the metrics into a list of 'MzQCmzQC' objectstransformIntoMzQC