compMS2-class: compMS2-class

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

Description

The compMS2 class matches MS1 data to MS2 precursors, extracts both MS1 and MS2 spectral data, noise filters and annotates both MS1 features and MS2 substructures.

Slots

compSpectra

list containing the composite MS/MS spectra

metaData

list containing the combined scan header information and other information for each composite spectrum.

network

list containing the correlation and spectral similarity network graphs added by metID.corrNetwork and/or metID.specSimNetwork.

DBanno

list of dataframes one for each composite spectrum containing all monoisotopic mass accuracy based database matches added by metID.dbAnnotate.

BestAnno

list of dataframes one for each composite spectrum containing all monoisotopic mass accuracy based database matches taken from the DBanno list subset by presence of substructure type detected by subStructure.Annotate and subStructure.prob and then added by metID.dbProb.

subStrAnno

data.frame of most likely MS/MS fragmentation substructures detected added by subStructure.prob.

spectralDB

list of lists one for each composite spectrum. If a match to a spectral database file has been made for a composite spectrum using metID.matchSpectralDB then within the list there are two lists, dbSpectra containing match information and entryInfo containing the database entry information for each match.

Comments

data.frame containing all user made comments or annotations automatically added using metID.chemSim, metID.buildConsensus or metID.optimConsensus.

filePaths

character vector with absolute path names of each MS/MS mzXML file.

Parameters

data.frame containing user supplied parameters for compMS2Miner functions for reproducibility purposes.

inSilico

list containing two lists MetFrag and CFM. Within each of these lists are contained any matches made to in silico fragmentation data derived from the command line versions of MetFrag and CFM added by metID.metFrag and metID.CFM.

rtPred

list containing the randomForest recursive feature elimination model added by metID.rtPred.

Methods

compSpectra<-

signature(object = "compMS2"): set compSpectra slot

compSpectra

signature(object = "compMS2"): get compSpectra slot

BestAnno<-

signature(object = "compMS2"): set BestAnno slot

BestAnno

signature(object = "compMS2"): get BestAnno slot

CFM<-

signature(object = "compMS2"): set the CFM list in the inSilico slot

CFM

signature(object = "compMS2"): get the CFM list in the inSilico slot

Comments<-

signature(object = "compMS2"): set Comments slot

Comments

signature(object = "compMS2"): get Comments slot

combineMS2

signature(object = "compMS2"): various methods for grouping and signal summation of fragment ions between MS/MS scans and removal of possible contaminant ions.

compMS2Explorer

signature(object = "compMS2"): shiny application for visualization of compMS2Miner results.

couchDBconn<-

signature(object = "compMS2"): set couchDBconn slot

couchDBconn

signature(object = "compMS2"): get couchDBconn slot

DBanno<-

signature(object = "compMS2"): set DBanno slot

DBanno

signature(object = "compMS2"): get DBanno slot

deconvNoise

signature(object = "compMS2"): ion fragment noise filtration methods such as dynamic noise filtration.

filePaths<-

signature(object = "compMS2"): set filePaths slot

filePaths

signature(object = "compMS2"): get filePaths slot

metaData<-

signature(object = "compMS2"): set metaData slot

metaData

signature(object = "compMS2"): get metaData slot

MetFrag<-

signature(object = "compMS2"): set the MetFrag list in the inSilico slot

MetFrag

signature(object = "compMS2"): get the MetFrag list in the inSilico slot

metID

signature(object = "compMS2"): various methods for metabolite identification including:

1. monoisotopic mass based precursor MS1 to database matching with customisable ESI adduct generation. metID(object, method='dbAnnotate').

2. subset database annotations to BestAnno(object) slot based on customizable substructures identified by subStructure. metID(object, method='dbProb').

3. match to spectral database resources such as lipidBlast and massbank using the NIST (National Institute of Standards and Technology) ASCII text database format based on dot product similarity and proportion of spectrum explained. metID(object, method='matchSpectralDB').

4. predict Phase II biotransformation metabolites from SMILES codes contained in the BestAnno(object) slot (currently glucuronides, sulfates and glycine conjugates). metID(object, method='predSMILES').

5. in silico fragmentation prediction using the command line versions of both the MetFrag metID(object, method='MetFrag') and CFM (competitive fragmentation modelling) metID(object, method='CFM') softwares internal to compMS2Miner.

6. spectral similarity network calculation, both ion fragment and neutral loss patterns are used to calculate dot product similarity scores metID(object, method='specSimNetwork').

7. correlation network, MS1 level peak areas can be used to calculate a correlation network. metID(object, method='corrNetwork').

8. 1st network (spectral similarity and/or correlation) neighbour mean maximum chemical similarity scoring (tanimoto) and automated first pass metabolite identification metID(object, method='chemSim').

9. retention time prediction using randomForest and molecular descriptors.metID(object, method='rtPred').

10. build metabolite consensus based on optional combinations of mass accuracy, spectral database matching, in silico fragmentation matching, predicted retention time, 1st network neighbour mean maximum chemical similarity and number of pubMed citations.

11. optimize weighted mean consensus metabolite scoring using differential evolution algorithm. metID(object, method='optimConsensus')

network<-

signature(object = "compMS2"): set network slot

network

signature(object = "compMS2"): get network slot

Parameters<-

signature(object = "compMS2"): set Parameters slot

Parameters

signature(object = "compMS2"): get Parameters slot

publishApp

signature(object = "compMS2"): publish compMS2 object to shinyapps.io account or as a self-contained zip file.

rtPred<-

signature(object = "compMS2"): set rtPred slot

rtPred

signature(object = "compMS2"): get rtPred slot

spectralDB<-

signature(object = "compMS2"): set spectralDB slot

spectralDB

signature(object = "compMS2"): get spectralDB slot

subsetCompMS2

signature(object = "compMS2"): subset a compMS2 object according to a character vector of compSpectra names. Retains all corresponding slot names except networks derived from corrNetwork and specSimNetwork which must be recalculated. This can be used to quickly remove any unwanted spectra by name.

subStrAnno<-

signature(object = "compMS2"): set subStrAnno slot

subStrAnno

signature(object = "compMS2"): get subStrAnno slot

subStructure

signature(object = "compMS2"): identify ion fragment substructures and neutral losses and identify the most probable substructure.

Author(s)

WMB Edmands

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