msPurity.averageFragSpectra (version 1.16.2+galaxy1)

purityA object:

purityA object saved as 'pa' in a RData file (output from frag4feature tool)

Average and filter fragmentation spectra for each XCMS feature:

Signal-to-noise threshold after averaging or summing:

Relative abundance threshold after averaging or summing:

Minimum fraction (i.e. percentage) of (averaged) scans a fragment peak has to be present in.:

Minimum number of (averaged) fragmentation scans for a fragmentation event (precursor).:

Ppm error tolerance:

Maximum tolerated m/z deviation in parts per million.

Sum intensities across (averaged) scans?:

Function to calculate the average intensity, m/z and SNR values across (averaged) scans after filtering.:

This is ignored for intensities when intensities are summed.

Remove peaks that do not meet the filtering criteria. Otherwise peaks will be flagged instead.:

Average Fragmentation Spectra

Description

Average and filter fragmentation spectra for each XCMS feature using an msPurity purityA object.

The tool uses the msPurity functions averageAllFragSpectra, averageIntraFragSpectra and averageInterFragSpectra.

The fragmentation spectra can be averaged in multiple ways; intra will average fragmentation spectra within an mzML file, inter will average fragmentation spectra across mzML files (requires intra to be run first) and all will average all spectra ignoring the intra and inter relationships.

The averaging is performed using hierarchical clustering of the m/z values of each peaks, where m/z values within a set ppm tolerance will be clustered. The clustered peaks are then averaged (or summed).

The fragmentation can be filtered on the averaged spectra (with the arguments snr, rsd, minfrac, ra)

See Bioconductor documentation for more details, functions: msPurity::averageIntraFragSpectra() msPurity::averageInterFragSpectra() msPurity::averageAllFragSpectra()

Outputs

average_x_fragmentation_spectra_rdata