NEWS

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MsQuality 1.11

1.11.3 (2026-03-10)

• Implementation of per-chromatogram metrics for Chromatograms objects: maxIntensity, intensityMean, intensitySd, intensityQuartiles, intensityRange, peakCount, baselineIntensity, signalToNoiseRatio, xicFwhm, peakBoundary, peakWidth, gaussianSimilarity, peakProminence
• Shared functions (chromatographyDuration, rtAcquisitionRange, rtIqr, areaUnderTic, areaUnderTicRtQuantiles, ticQuantileRtFraction, msSignal10xChange, medianTicRtIqr, numberEmptyScans, calculateMetrics) now support both Spectra and Chromatograms
• msSignal10xChange gains minIntensity parameter for noise robustness.
• Renamed argument filterEmptySpectra to filterEmptyObject
• Fixed calculateMetrics() data.frame output
• Fixed shinyMsQuality() documentation example

Changes in version 1.11.2 (2026-03-02)

• replace msdata by MsDataHub package (issue #19)
• adjust all examples, unit tests and vignette to the MsDataHub package

Changes in version 1.11.1 (2026-02-17)

• added conversion to uri from local file to the export function in transformIntoMzQC (contribution by Helge Hecht, PR #20)

Changes in version 1.11.0 (2025-10-29)

• bump version to 1.11.0

MsQuality 1.9

Changes in version 1.9.3 (2025-10-23)

• change unit tests for filterEmptySpectra after update

Changes in version 1.9.2 (2025-08-05)

• resolve NAMESPACE issue of unexported objects

Changes in version 1.9.1 (2025-07-30)

• fix bug due to update in rmzqc package, use $new for constructing R6 objects

MsQuality 1.7

Changes in version 1.7.1 (2025-01-22)

• rename ticQuartersRtFraction to ticQuantileRtFraction
• update tests after update of OBO file / rmzqc

MsQuality 1.3

Changes in version 1.3.2 (2024-02-21)

• bug fix: MS:40000155 in specification file added, adjust tests

Changes in version 1.3.1 (2023-12-14)

• compress data set
• update to new Spectra version

MsQuality 1.1

Changes in version 1.1.3 (2023-08-31)

• update tests after update of OBO file / rmzqc

Changes in version 1.1.2 (2023-08-16)

• Fix implementation of mzAquisitionRange
• add numberEmptyScans in qualityMetrics function
• add unit tests for export in rmzqc format
• add interpretation aid of metrics in vignette

Changes in version 1.1.1 (2023-08-01)

• move msdata from Suggests to Imports
• rename function rtDuration to chromatographyDuration
• rename function rtOverTicQuantiles to ticQuartersRtFraction
• create function numberEmptyScans
• add attributes (MS QC terms) to the output of the Spectra metrics functions if the output matches the described term
• add rmzqc to IMPORTS
• add functionality to export quality metrics as in rmzqc format
• adjust documentation to newest version of PSI MS CV obo file
• add to the vignette information on how the metrics are calculated
• add argument filterEmptySpectra to remove entries of length 0 or that have intensity 0, implement the argument in the functions calculateMetricsFromOneSampleSpectra, calculateMetricsFromSpectra, calculateMetricsFromMsExperiment, and calculateMetrics

MsQuality 0.99

Changes in version 0.99.9 (2023-04-18)

• enable parallel processing in calculateMetricsFromSpectra
• rename ticQuantileToQuantileLogRatio to ticQuartileToQuartileLogRatio
• rename rtOverTicQuantile to rtOverTicQuantiles
• return quartiles instead of quantiles in precursorIntensityQuartiles
• add mzR to Suggests in DESCRIPTION

Changes in version 0.99.8 (2023-09-02)

• adjust behaviour of metrics function when Spectra object of length 0 is presented, return NA values instead of raising an error

Changes in version 0.99.7 (2023-06-02)

• adjust ticQuantileToQuantileLogRatio that it adheres to Quameter calculation

Changes in version 0.99.6 (2022-11-29):

• extend section Description in DESCRIPTION
• add sections BugReports and URL in DESCRIPTION
• update dependency to R version 4.2.0
• transfer source code in R/Lee2019-data.R to inst/sources/Lee2019-data-source.R
• use partial_bundle to reduce the file size of plotly graphics

Changes in version 0.99.5 (2022-10-12):

• add section on alternative software in vignette
• simplify the vignette with regard to dealing with the RPLC and HILIC example data set and adjust the Lee2019-data.R accordingly to keep the RPLC/HILIC information in the dataOrigin slot of the Spectra object

Changes in version 0.99.4 (2022-10-11):

• add missing comma in DESCRIPTION

Changes in version 0.99.3 (2022-10-11):

• delete Maintainer field in DESCRIPTION
• add instructions to install MsQuality in vignette and README.md via remotes/BiocManager instead of devtools

Changes in version 0.99.2 (2022-09-20):

• create branch msexperiment to store infrastructure and functions for MsExperiment objects
• remove MsExperiment objects since this is still in BioC review and solely rely on Spectra objects
• adjust documentation for the implemented changes (removal of MsExperiment)

Changes in version 0.99.1 (2021-11-23)

• simplify calculateMetricsFromSpectra:
  • the function does not any longer match the arguments by the formal arguments of the metric functions
  • the function does not any longer combine the parameters
  • the additional arguments do not take longer the parameter list of arguments but comma-separated arguments given to ...
  • for all metric functions the ... parameter is added
  • adjust the vignette and help pages
• rename functions to camel case

Changes in version 0.99.0 (2021-09-10)

• add quality metrics/functions (metrics based on HUPO-mzQC):
  • rtDuration (QC:4000053),
  • rtOverTICquantile (QC:4000054),
  • rtOverMsQuarters (rtOverMSQuarters),
  • ticQuantileToQuantileLogRatio (QC:4000057, QC:4000058),
  • numberSpectra (QC:4000059, QC:4000060),
  • medianPrecursorMz (QC:4000065),
  • rtIQR (QC:4000072),
  • rtIQRrate (QC:4000073),
  • areaUnderTIC (QC:4000077),
  • areaUnderTICRTquantiles (QC:4000078),
  • extentIdentifiedPrecursorIntensity (QC:4000125),
  • medianTICRTIQR (QC:4000130),
  • medianTICofRTRange (QC:4000132),
  • mzAcquisitionRange (QC:4000138),
  • rtAcquisitionRange (QC:4000139),
  • precursorIntensityRange (QC:4000144),
  • precursorIntensityQuartiles ((QC:4000167, QC:4000228, QC:4000233),
  • precursorIntensityMean (QC:4000168, QC:4000229, QC:4000234),
  • precursorIntensitySD (QC:4000169, QC:4000230, QC:4000235),
  • msSignal10XChange (QC:4000172, QC:4000173),
  • ratioCharge1over2 (QC:4000174, QC:4000179),
  • ratioCharge3over2 (QC:4000175, QC:4000180),
  • ratioCharge4over2 (QC:4000176, QC:4000181),
  • meanCharge (QC:4000177, QC:4000182),
  • medianCharge (QC:4000178, QC:4000183)
  • .rt_order_spectra (helper function)
• add the functions calculateMetricsFromSpectra, calculateMetricsFromMsExperiment to calculate the metrics based on Spectra and MsExperiment objects
• add functions plotMetric, plotMetric_tibble to visualize the metrics
• add shiny application shinyMsQuality to interactively visualize the metrics