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MassSpecSettings_LoadMSPeakLists_patRoon

Source: R/class_MassSpecSettings_LoadMSPeakLists.R
MassSpecSettings_LoadMSPeakLists_patRoon.Rd

Settings for loading MS2 and MS1 spectra for feature groups.

Usage

MassSpecSettings_LoadMSPeakLists_patRoon(
  maxMSRtWindow = 5,
  precursorMzWindow = 4,
  clusterMzWindow = 0.005,
  topMost = 100,
  minIntensityPre = 50,
  minIntensityPost = 50,
  avgFun = "mean",
  method = "hclust",
  retainPrecursorMSMS = TRUE
)

Arguments

maxMSRtWindow

Maximum chromatographic peak window used for spectrum averaging (in seconds, +/- retention time). If NULL all spectra from a feature will be taken into account. Lower to decrease processing time.

precursorMzWindow

The m/z window (in Da) to find MS/MS spectra of a precursor. This is typically used for Data-Dependent like MS/MS data and should correspond to the isolation m/z window (i.e. +/- the precursor m/z) that was used to collect the data. For Data-Independent MS/MS experiments, where precursor ions are not isolated prior to fragmentation (e.g. bbCID, MSe, all-ion, ...) the value should be NULL.

clusterMzWindow

m/z window (in Da) used for clustering m/z values when spectra are averaged. For method="hclust" this corresponds to the cluster height, while for method="distance" this value is used to find nearby masses (+/- window). Too small windows will prevent clustering m/z values (thus erroneously treating equal masses along spectra as different), whereas too big windows may cluster unrelated m/z values from different or even the same spectrum together.

topMost

Only retain this maximum number of MS peaks when generating averaged spectra. Lowering this number may exclude more irrelevant (noisy) MS peaks and decrease processing time, whereas higher values may avoid excluding lower intense MS peaks that may still be of interest.

minIntensityPre

MS peaks with intensities below this value will be removed (applied prior to selection by topMost) before averaging.

minIntensityPost

MS peaks with intensities below this value will be removed after averaging.

avgFun

Function that is used to calculate average m/z values.

method

Method used for producing averaged MS spectra. Valid values are "hclust", used for hierarchical clustering (using the fastcluster package), and "distance", to use the between peak distance. The latter method may reduces processing time and memory requirements, at the potential cost of reduced accuracy.

retainPrecursorMSMS

For MS/MS data only: if TRUE then always retain the precursor mass peak even if is not among the topMost peaks. Note that MS precursor mass peaks are always kept. Furthermore, note that precursor peaks in both MS and MS/MS data may still be removed by intensity thresholds (this is unlike the filter method function).

Value

A MassSpecSettings_LoadMSPeakLists_patRoon object.