createMSP-purityA-method: Using a purityA object, create an MSP file of fragmentation...

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

Using a purityA object, create an MSP file of fragmentation spectra

Description

General

Create an MSP file for all the fragmentation spectra that has been linked to an XCMS feature via frag4feature. Can export all the associated scans individually or the averaged fragmentation spectra can be exported.

Additional metadata can be included in a dataframe (each column will be added to metadata of the MSP spectra). The dataframe must contain the column "grpid" corresponding to the XCMS grouped feature.

Example LC-MS/MS processing workflow

• Purity assessments

  • (mzML files) -> purityA -> (pa)

• XCMS processing

  • (mzML files) -> xcms.findChromPeaks -> (optionally) xcms.adjustRtime -> xcms.groupChromPeaks -> (xcmsObj)

  • — Older versions of XCMS — (mzML files) -> xcms.xcmsSet -> xcms.group -> xcms.retcor -> xcms.group -> (xcmsObj)

• Fragmentation processing

  • (xcmsObj, pa) -> frag4feature -> filterFragSpectra -> averageIntraFragSpectra -> averageIntraFragSpectra -> createMSP -> (MSP file)

Usage

## S4 method for signature 'purityA'
createMSP(
  pa,
  msp_file_pth = NULL,
  metadata = NULL,
  metadata_cols = NULL,
  xcms_groupids = NULL,
  method = "all",
  adduct_split = TRUE,
  filter = TRUE,
  msp_schema = "massbank",
  intensity_ra = "intensity_ra",
  include_adducts = ""
)

Arguments

pa	object; purityA object
msp_file_pth	character; Name of the output msp file, if NULL the file "frag_spectra_time stamp.msp" will be created in the current directory
metadata	data.frame; Data frame with additional coumpound infomation to include in msp output
metadata_cols	vector; Column names of meta data to incorporate into name
xcms_groupids	vector; XCMS group id's to extract ms/ms data for
method	character; "all" will export all matching ms/ms spectra to xcms features, "max" will use spectra with the highest inensity, "av_intra" will use the intra file averaged spectra (within file), "av_inter" will use the inter file (across file) averaged spectra, "av_all" will use the averaged spectra (ignoring inter and intra)
adduct_split	boolean; If either "adduct" or MS$FOCUSED_ION: PRECURSOR_TYPE column is in metadata then each adduct will have it's own MSP spectra. (Useful, if the MSP file will be used for further annotation)
filter	boolean; TRUE if filtered peaks are to be removed
msp_schema	character; Either MassBank (Europe) or MoNA style of MSP file format to be used ('massbank' or 'mona')
intensity_ra	character; Either 'intensity', 'ra' (relative abundance) or 'intensity_ra' (intensity and relative abundance) to be written to the MSP file
include_adducts	character; Additional adducts to include as a string seperated by white a space (e.g. [M+H]+ [M+Na]+)

Value

Returns a MSP file with the selected spectra and metadata

Examples

#====== XCMS =================================
## Read in MS data
#msmsPths <- list.files(system.file("extdata", "lcms", "mzML",
#           package="msPurityData"), full.names = TRUE, pattern = "MSMS")
#ms_data = readMSData(msmsPths, mode = 'onDisk', msLevel. = 1)

## Find peaks in each file
#cwp <- CentWaveParam(snthresh = 5, noise = 100, ppm = 10, peakwidth = c(3, 30))
#xcmsObj  <- xcms::findChromPeaks(ms_data, param = cwp)

## Optionally adjust retention time
#xcmsObj  <- adjustRtime(xcmsObj , param = ObiwarpParam(binSize = 0.6))

## Group features across samples
#pdp <- PeakDensityParam(sampleGroups = c(1, 1), minFraction = 0, bw = 30)
#xcmsObj <- groupChromPeaks(xcmsObj , param = pdp)

#====== msPurity ============================
#pa  <- purityA(msmsPths)
#pa <- frag4feature(pa = pa, xcmsObj = xcmsObj)
#pa <- filterFragSpectra(pa, allfrag=TRUE)
#pa <- averageAllFragSpectra(pa)
#createMSP(pa)

pa <- readRDS(system.file("extdata", "tests", "purityA",
                          "9_averageAllFragSpectra_with_filter_pa.rds",
                          package="msPurity"))
createMSP(pa)

Viant-Metabolomics/msPurity documentation built on May 13, 2024, 8:23 a.m.