Generation of MS Peak Lists

Functionality to convert MS and MS/MS spectra into MS peak lists.

Usage

generateMSPeakLists(fGroups, ...)

# S4 method for class 'featureGroups'
generateMSPeakLists(
  fGroups,
  maxMSRTWindow = defaultLim("retention", "narrow"),
  fixedIsolationWidth = FALSE,
  topMost = NULL,
  avgFeatParams = getDefAvgPListParams(),
  avgFGroupParams = getDefAvgPListParams()
)

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

Arguments

fGroups

The featureGroups object for which MS peak lists should be generated.

...

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

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.

fixedIsolationWidth

Configures how MS/MS spectra are selected for a feature:

• NA: select all spectra unconditionally, i.e. ignoring any precursor information of spectra.

• FALSE: select the spectra that were recorded for the feature m/z, using the instrumental precursor isolation window (e.g. quadrupole m/z width) as the selection tolerance.

• A numeric value: select the spectra that were recorded for the feature m/z within this tolerance window (+/- precursor m/z).

• A two-sized numeric vector: select the spectra that were recorded for the feature m/z within the specified minimum and maximum tolerance window (relative to the precursor m/z).

If no isolation was applied to record MS/MS data (e.g. data-independent MS/MS), then all MS/MS spectra will be always be selected.

NOTE: Sometimes the isolation windows are not exported and cannot be deduced automatically (e.g. Agilent data). In that case, fixedIsolationWidth needs to be set to a numeric or NA value.

topMost

Only extract MS peak lists from a maximum of topMost features with highest intensity. If NULL all features will be used.

avgFeatParams

Parameters used for averaging MS peak lists of individual features. Analogous to avgFGroupParams.

avgFGroupParams

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

Value

An MSPeakLists object.

Details

Data processing steps that use mass spectral data (e.g. formula generation and compound generation) typically use 'MS peak lists', which are tables storing the m/z, intensity and other data from the raw mass spectra. The generateMSPeakLists function generates MS and MS/MS peak lists first for all features (or a subset, if the topMost argument is set). During this step multiple spectra over the feature elution profile are averaged. Subsequently, peak lists will be generated for each feature group by averaging peak lists of the features within the group. The data processing steps that uses peak lists will either use the data from individual features or from group averaged peak lists. For instance, the former may be used by formulae calculation, while compound identification and plotting functionality typically uses group averaged peak lists.

Deprecated algorithms

Prior to patRoon 3.0 the generateMSPeakLists function was a wrapper to the now deprecated functions generateMSPeakListsMzR, generateMSPeakListsDA and generateMSPeakListsDAFMF. These functions are now unmaintained and may not (fully) work anymore. The current interface is much faster and provides most of the previous functionality (and additional). However, please provide feedback if you feel any functionality is missing.

Use of raw HRMS data

The raw data interface of patRoon is used by generateMSPeakLists 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.

Sets workflows

With a sets workflow, the feature group averaged peak lists are made per set. This is important, because for averaging peak lists cannot be mixed, for instance, when different ionization modes were used to generate the sets. The group averaged peaklists are then simply combined and labelled in the final peak lists. However, annotation and most other functionality typically uses only the (uncombined and) set specific peak lists, as most algorithms cannot work with mixed peak lists.