metID.metFrag: metFrag _in silico_ fragmentation query wrapper function

In WMBEdmands/CompMS2miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets

Description

performs metFrag (msbi.ipb-halle.de/MetFrag/) in silico combinatorial fragmentation. Local chemical structure data files (.sdf) are created from most probable annotation canonical SMILES codes. Temporary local sdf files and metfrag parameter files (.txt) are created on a composite spectrum by composite spectrum basis and in silico fragmentation performed. Results are read back into R and stored in the compMS2 class object as results tables. In addition the temporary sdf, .txt and .csv metfrag results files may also optionally be kept (keepTempFiles = TRUE) and are saved in a subdirectory structure (see details). The function will automatically run as a parallel computation is the compMS2 object was created in parallel. The adduct types and codes which MetFrag command line tool will work with are included in a default internal table. See data(metFragAdducts) the following electrospray adducts are contained within: positive mode: '[M+H]+', '[M+NH4]+', '[M+Na]+', '[M+K]+' negative mode: '[M-H]-', '[M+Cl]-', '[M-H+HCOOH]-', '[M-H+CH3COOH]-' All other database annotations of other electrospray adducts will be discarded. If the format of the metFragAdducts table is correctly followed then additional MetFrag adduct types can be added see View(metFragAdducts). This ensures that the adduct types are customizable and can be modified to incorporate future availability. See argument metFragAdducts below.

Usage

metID.metFrag(object, ...)

Arguments

object	a "compMS2" class object.
featureSubSet	character vector of composite spectra names (e.g. CC_1, CC_2 etc.) otherwise the default is to perform metFrag queries on all composite spectra.
adductTable	data.frame containing adduct names, MetFrag number codes and ionization mode. A default data.frame is internal to the package but this table is fully customizable if future adduct types are added. See View(metFragAdducts) to see the format of this table. N.B. The metFrag adduct names must perfectly match those supplied to the adduct2mass function during database annotation using metID.dbAnnotate.
keepTempFiles	logical default = FALSE, txt, sdf and csv results files will be created as temporary files otherwise if TRUE files will be retained in named subdirectories (see details).
maxTreeDepth	numeric maximum tree depth (default = 2). If 2 then fragments of fragments are also considered but will increase computation time.
frag_mzabs	numeric delta predicted-observed fragment mass accuracy for matching.
minMetFragScore	numeric minimum mean total ion current explained and metFrag score (default = 0.9) the candidate with the highest score above this minimum will be automatically added to the Comments table. The argument autoPossId must also be set to TRUE.
autoPossId	logical if TRUE the function will automatically add the name of the top annotation based on mean total ion current explained and metFrag score (default = FALSE). Caution if TRUE this will overwrite any existing possible_identities in the "metID comments" table. This functionality is intended as an automatic annotation identification tool prior to thorough examination of the data in compMS2Explorer. The intention is that automatic annotations can be used in the metID.rtPred retention prediction function as part of a seamless first-pass workflow.
possContam	numeric how many times does a possible annotation have to appear in the automatically generated possible annotations for it to be considered a contaminant and therefore not added to the "metID comment" table (default = 3, i.e. if a database name appears more than 3 times in the automatic annotation table it will be removed).
verbose	logical if TRUE display progress bars.

Details

if keepTempFiles = FALSE, Results directories are generated in the current working directory: for each MS1 feature matched to MS2 data a results directory is created named ("MetFrag_results"). Subdirectories are then created within the results directory named after each composite spectrum name. Assuming MetFrag returned any results the following files should appear within the subdirectories:

1. MetFrag parameters files : MetFrag parameter files (.txt) are saved in each result directory. See http://c-ruttkies.github.io/MetFrag/projects/metfragcl/ for details.

2. localSdf file : the local sdf (chemical structure data files) are saved in each result directory. This file is used as a local database for MetFrag in silico fragmentation.

3. result .csv file: the metFrag results are returned as a comma seperated values text file (.csv).

Value

a compMS2 class object containing metFrag in silico fragmentation results which can be visualized in compMS2Explorer.

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, 10:02 p.m.