knitr::opts_chunk$set(echo = TRUE)
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# load required library library(masstrixR) library(MSnbase) # get example file from package pathToMbRecords <- system.file("extdata", "exampleData\\Celegans_ms2\\MassBankRecords", package = 'masstrixR') # read all records in folder mbRecords <- readMassBankFolder(pathToMbRecords) # create MS2 SQLite DB with masstrixR ms2db <- createMs2Db(mbRecords, "example_MS2")
# load required library library(MSnbase) # get example file from package mgfFile <- system.file("extdata", "exampleData\\Celegans_ms2\\exampleMs2.mgf", package = 'masstrixR') # read mgf file with MS2 spectra and isolate all MS2 spectra a list ms2data <- readMgfData(mgfFile) ms2spectra <- spectra(filterMsLevel(ms2data, msLevel = 2)) # adducts to search for adducts <- c("[M+H]+", "[M+Na]+") for(i in 1:length(ms2spectra)) { # create empty Spectra object for results searchResult <- new("Spectra") # perform precursor search # iterate over adducts for(adduct in adducts) { searchResultClipboard <- masstrixR::searchByPrecursor( precursorMz(ms2spectra[[i]]), ms2db, precursorType = adduct, mzTol = 0.005 ) # if 1 or more results were found, add to searchResult if(length(searchResultClipboard) > 0) { searchResult <- append(searchResult, searchResultClipboard) } } if(length(searchResult) > 0) { for(j in 1:length(searchResult)) { forward <- forwardDotProduct(ms2spectra[[i]], searchResult[[j]], align = TRUE, mzTol = 0.005) reserve <- reverseDotProduct(ms2spectra[[i]], searchResult[[j]], align = TRUE, mzTol = 0.005) title <- paste0("forward: ", round(forward * 1000, 0), "/ reverse: ", round(reserve * 1000, 0)) #plot(ms2spectra[[i]], searchResult[[j]]) makeMirrorPlot(ms2spectra[[i]], searchResult[[j]], align = TRUE, mzTol = 0.005, title = title, plotIt = TRUE) } } } plotSpectrum(ms2spectra[[3]], highlight = TRUE, highlightMz = c(69.0667), plotIt = TRUE)
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