Background MS/MS peak detection

Detects background MS/MS peaks by gathering frequently occurring peaks in MS/MS spectra from blanks.

getBGMSMSPeaks(
  anaInfo,
  replicates = NULL,
  MSLevel = 2,
  retentionRange = NULL,
  mobilityRange = NULL,
  minBPIntensity = 5000,
  avgSpectraParams = getDefAvgPListParams(relMinAbundance = 0.1, topMost = 25),
  avgAnalysesParams = getDefAvgPListParams(relMinAbundance = 0.8, topMost = 25)
)

Arguments

anaInfo

The analysis info object with the analyses to be used for background peak detection.

replicates

A character with names of replicates for the analyses used for background peak detection. If NULL then all the analyses defined in anaInfo will be used.

MSLevel

The MS level of the spectra to be used for background peak detection. This should be 1 or 2. This function is only tested with MSLevel=2. And while MSLevel=1 is possible, it may be rather computationally intensive due to the relatively large number of MS peaks to iterate through.

retentionRange, mobilityRange

A two-sized numeric vector with the minimum and maximum retention time and ion mobility to consider, respectively. If NULL then the full range is used.

minBPIntensity

The minimum basepeak intensity of a spectrum to be considered for background peak detection. This is primarily intended to optimize the detection procedure.

avgSpectraParams, avgAnalysesParams

A list with parameters used for averaging the MS spectra within and between analyses, respectively. See getDefAvgPListParams for more details.

Value

A data.table with the detected background peaks and abundance statistics. The table can directly be passed to the removeMZs argument of the filter method for MSPeakLists.

Details

This function iterates through all MS/MS spectra of the given analyses and collects the most frequently occurring peaks. It first averages all spectra within the same analyses, and retains those peaks above an abundance threshold (set by avgSpectraParams). The analyses-averaged spectra are then also averaged, and again peaks with a minimum abundance are kept (set by avgAnalysesParams).

The frequent occurrence of a peak throughout MS/MS spectra, including DDA spectra different isolation m/z values, is often a sign of contamination from the analytical system (e.g. from the mobile phase, MS quadrupoles etc). Hence, the analyses used for blank subtraction are typically just measurements of e.g. ultrapure water or another solvent, and not need to be treated by any extraction procedure.

The output of this function can directly be used to the filter method for MSPeakLists to subsequently remove these background peaks, which possibly improves subsequent feature annotation.

Use of raw HRMS data

The raw data interface of patRoon is used by getBGMSMSPeaks to process HRMS (or IMS-HRMS) data. Please see its documentation for more information on the supported formats and available configuration options.

The use of profile m/z HRMS data (not IMS-HRMS) is currently not supported.

References

Helmus R, Bagdonaite I, de Voogt P, van Bommel MR, Schymanski EL, van Wezel AP, ter Laak TL (2025). “Comprehensive Mass Spectrometry Workflows to Systematically Elucidate Transformation Processes of Organic Micropollutants: A Case Study on the Photodegradation of Four Pharmaceuticals.” Environmental Science & Technology, 59(7), 3723–3736. ISSN 1520-5851, doi:10.1021/acs.est.4c09121 , http://dx.doi.org/10.1021/acs.est.4c09121.