In michaelwitting/masstrixR: Annotation of MS based metabolomics data

knitr::opts_chunk$set(echo = TRUE)

Introduction

blablabla

# 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")

Including Plots

# 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)