msPurity.filterFragSpectra (version 1.16.2+galaxy1)

purityA object with fragmentation linked to XCMS features:

purityA object saved as 'pa' in a RData file where fragmentation has been linked to XCMS features(output from frag4feature tool)

Miniumum precursor ion purity of the associated precursor for fragmentation spectra scan:

Peak instensity threshold:

Relative abundance threshold:

Signal-to-noise threshold:

Function to calculate noise.:

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

Perform filtering on all fragmentation spectra (not just those aligned to XCMS features):

Filter Fragmentation Spectra

Description

Flag and filter features based on signal-to-noise ratio, relative abundance, intensity threshold and precursor ion purity of precursor.

Example LC-MS/MS processing workflow

Purity assessments
- (mzML files) -> purityA -> (pa)
XCMS processing
- (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
Fragmentation processing
- (xset, pa) -> frag4feature -> filterFragSpectra -> averageAllFragSpectra -> createDatabase -> spectralMatching -> (sqlite spectral database)

See Bioconductor documentation for more details, functions: msPurity::filterFragSpectra()

filter_fragmentation_spectra_rdata: RData of the purityA object (pa) with filtered data
peaklist_prec_tsv: precursor peaklist
peaklist_frag_tsv: fragmentation peaklist