Generate peak lists with Bruker DataAnalysis

Uses Bruker DataAnalysis to read the data needed to generate MS peak lists.

generateMSPeakListsDA(fGroups, ...)

# S4 method for class 'featureGroups'
generateMSPeakListsDA(
  fGroups,
  bgsubtr = TRUE,
  maxMSRtWindow = 5,
  minMSIntensity = 500,
  minMSMSIntensity = 500,
  clear = TRUE,
  close = TRUE,
  save = close,
  MSMSType = "MSMS",
  avgFGroupParams = getDefAvgPListParams()
)

# S4 method for class 'featureGroupsSet'
generateMSPeakListsDA(fGroups, ...)

Arguments

fGroups

The featureGroups object from which MS peak lists should be extracted.

...

(sets workflow) Further arguments passed to the non-sets workflow method.

bgsubtr

If TRUE background will be subtracted using the 'spectral' algorithm.

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.

minMSIntensity, minMSMSIntensity

Minimum intensity for peak lists obtained with DataAnalysis. Highly recommended to set >0 as DA tends to report many very low intensity peaks.

clear

Remove any existing chromatogram traces/mass spectra prior to making new ones.

close, save

If TRUE then Bruker files are closed and saved after processing with DataAnalysis, respectively. Setting close=TRUE prevents that many analyses might be opened simultaneously in DataAnalysis, which otherwise may use excessive memory or become slow. By default save is TRUE when close is TRUE, which is likely what you want as otherwise any processed data is lost.

MSMSType

The type of MS/MS experiment performed: "MSMS" for MRM/AutoMSMS or "BBCID" for broadband CID.

avgFGroupParams

A list with parameters used for averaging of peak lists for feature groups. See getDefAvgPListParams for more details.

Value

A MSPeakLists object.

Details

This function uses Bruker DataAnalysis to generate MS peak lists. This function is called when calling generateMSPeakLists with algorithm="bruker".

The MS data should be in the Bruker data format (.d). This function leverages DataAnalysis functionality to support averaging of spectra, background subtraction and identification of isotopes. In order to obtain mass spectra TICs will be added in DataAnalysis of the MS and relevant MS/MS signals.

Note

The Component column should be active (Method–>Parameters–>Layouts–>Mass List Layout) in order to add isotopologue information.

If any errors related to DCOM appear it might be necessary to terminate DataAnalysis (note that DataAnalysis might still be running as a background process). The ProcessCleaner application installed with DataAnalayis can be used for this.

See also

generateMSPeakLists for more details and other algorithms.