inst/doc/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.R

In msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

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library(msPurity)
mzMLpths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE)
xset <- xcms::xcmsSet(mzMLpths)
xset <- xcms::group(xset)
xset <- xcms::retcor(xset)
xset <- xcms::group(xset)

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pa  <- purityA(mzMLpths)
pa <- frag4feature(pa, xset)

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pa <- filterFragSpectra(pa)

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pa <- averageIntraFragSpectra(pa) # use parameters specific to intra spectra 
pa <- averageInterFragSpectra(pa) # use parameters specific to inter spectra

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pa <- averageAllFragSpectra(pa) 

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td <- tempdir()
q_dbPth <- createDatabase(pa, xset, outDir = td, dbName = 'lcmsms-processing.sqlite')

## -----------------------------------------------------------------------------
result <- spectralMatching(q_dbPth, q_xcmsGroups = c(17, 41), l_accessions=c('CCMSLIB00000577898','CE000616'))
print(result)