Information on interpretability of the metrics

[tnaake]

Add interpretation of the metrics in the vignette. Currently the interpretation is still lacking for the metrics

• [x] chromatographyDuration
• [x] ticQuartersRtFraction
• [x] rtOverMsQuarters
• [ ] ticQuartileToQuartileLogRatio
• [ ] numberSpectra
• [x] mzAcquisitionRange
• [ ] rtAcquisitionRange
• [x] numberEmptyScans
• [ ] medianPrecursorMz
• [x] areaUnderTic
• [x] areaUnderTicRtQuantiles
• [ ] medianTicRtIqr
• [ ] medianTicOfRtRange
• [ ] meanCharge
• [ ] medianCharge

Should these interpretations be added to the mzQC obo file? @jorainer

Let's keep it rather basic (as this was also previously done for other metrics in the mzQC obo file). I have added some suggestions for each metric that we can discuss separately.

[tnaake]

Suggestions: chromatographyDuration: Longer times indicate better chromatographic separation.

[tnaake]

ticQuartersRtFraction: The metric informs about the dynamic range of the acquisition along the chromatographic separation.

[tnaake]

rtOverMsQuarters: The metric informs about the dynamic range of the acquisition along the chromatographic separation.

[tnaake]

ticQuartileToQuartileLogRatio: The metric informs about the dynamic range of the acquisition along the chromatographic separation.

[tnaake]

numberSpectra: An unusual low number may indicate incomplete sampling.

[tnaake]

mzAcquisitionRange: The metric informs about the dynamic range of the acquisition.

[tnaake]

rtAcquisitionRange: An unusual low range may indicate incomplete sampling.

[tnaake]

numberEmptyScans: An unusual high number may indicate incomplete sampling.

[tnaake]

medianPrecursorMz. The m/z distribution informs about the dynamic range of the acquisition.

[tnaake]

areaUnderTic: The metric informs about the dynamic range of the acquisition.

[tnaake]

areaUnderTicRtQuantiles: The metric informs about the dynamic range of the acquisition along the chromatographic separation.

[tnaake]

medianTicRtIqr: The metric informs about the dynamic range of the acquisition along the chromatographic separation.

[tnaake]

medianTicOfRtRange: The metric informs about the dynamic range of the acquisition along the chromatographic separation.

[tnaake]

meanCharge/medianCharge: Higher charges may indicate inefficient ionization or preference for e.g. longer peptides.

[jorainer]

Suggestions for some:

chromatographyDuration: the duration of the chromatography of a sample (in seconds). Longer duration could indicate a better separation of compounds which depends however also on the sampling/scan rate of the MS instrument. The duration of chromatographic runs for files/samples in an experiment should be very similar.

mzAcquisitionRange: the range of precursor m/z values for MSn scans within a sample. Depending on the used MS instrument configuration, these ranges should be similar. They might however differ between data files with DDA acquisition.

[jorainer]

ticQuartersRtFraction: The metric informs about the dynamic range of the acquisition along the chromatographic separation. This provides information on the sample (compound) flow along the chromatographic run and could indicate poor chromatographic runs (e.g. if no signal is measured for a big part of the chromatographic run).

[jorainer]

rtOverMsQuarters: The metric provides information on the retention times at which a certain proportion of MS scans (of the specified MS level) was measured. For MS1 scans the values are expected to be comparable across samples. For MS2 scans it depends on the acquisition mode and setting to select ions for fragmentation.

[jorainer]

numberEmptyScans: An unusual high number may indicate incomplete sampling, low sample volume or failed injection of a sample. The number of empty scans should be comparable across samples of an experiment.

[jorainer]

areaUnderTic: provides information about the total signal measured for a sample. These values should be (depending on the samples of the experiment) comparable across samples of an experiment.

[jorainer]

areaUnderTicRtQuantiles: The metric informs about the dynamic range of the acquisition along the chromatographic separation. Differences between samples of an experiment could indicate differences in chromatographic performance, or differences in sample content.