metFragCl: metFrag command line function for localSDF files

In WMBEdmands/compMS2Miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets

Description

metFrag command line function for localSDF files

Usage

metFragCl(massSpectrum = NULL, precMass = NULL, compSpecName = NULL,
  dbEntryTable = NULL, metFragJar = NULL, SDFtmp = NULL,
  keepTempFiles = FALSE, mode = "pos", frag_mzabs = 0.05,
  esiList = NULL, maxTreeDepth = 1)

Arguments

massSpectrum	data.frame composite spectrum consisting of two columns mass and intensity.
precMass	numeric the MS1 m/z (precursor mass).
compSpecName	character name of composite spectrum for directory and file naming.
dbEntryTable	data.frame with the requisite information for the SDFtmp localSDF database consisting of at least 4 columns named 1. 'WebAddress', 2. 'DBid', 3. 'DBname', 4. 'SMILES'.
metFragJar	character full path to metFragCL.jar file (extdata in compMS2Miner package).
SDFtmp	an "SDFset" class object of SDF file for the localSDF database search of metFragCL.
keepTempFiles	logical default = FALSE, sdf, mf and results files will be created as temporary files otherwise if TRUE files will be retained in named subdirectories (see details).
mode	character ionization polarity (either 'pos' or 'neg').
frag_mzabs	numeric delta predicted-observed fragment mass accuracy for matching.
esiList	named numeric vector of electrospray type numbers for metFrag params file. e.g. positive mode M+H M+NH4 M+Na M+K 1 18 23 39
maxTreeDepth	numeric fragments of fragments? (default = 1 i.e. only direct daughter ions of the structure will be considered). Setting the tree depth to higher values may cause the metFragCL to take longer.

Value

if MetFrag2.3-CL.jar process completed then a data.frame containing any fragments matched to the composite mass spectra are returned. MetFragPreProcessingCandidateFilter = UnconnectedCompoundFilter

Source

http://c-ruttkies.github.io/MetFrag/projects/metfragcl/ developed based on the command line .jar file (MetFrag2.3-CL.jar) downloaded on 2016/07/12

1. MetFrag relaunched: incorporating strategies beyond in silico fragmentation: C Ruttkies, E L Schymanski, S Wolf, J Hollender, S Neumann Journal of Cheminformatics 2016 8:3

2. In silico fragmentation for computer assisted identification of metabolite mass spectra: S Wolf, S Schmidt, M Müller-Hannemann, S Neumann BMC bioinformatics 11 (1), 148

WMBEdmands/compMS2Miner documentation built on May 9, 2019, 10:04 p.m.