fragmentation_spectra_annotator {IDSL.FSA}

Fragmentation Spectra Annotator

Description

This module annotates fragmentation spectra from .MSP files.

Usage

fragmentation_spectra_annotator(path, MSPfile = "", libFSdb,
libFSdbIDlist, targetedPrecursorType = NA, ratio2basePeak4nSpectraMarkers = 0,
allowedNominalMass = FALSE, allowedWeightedSpectralEntropy = TRUE,
noiseRemovalRatio = 0.01, roundingDigitPrefiltering = 1, minMatchedNumPeaks = 1,
massError = 0, maxNEME = 0, minIonRangeDifference = 0, minCosineSimilarity,
minEntropySimilarity, minRatioMatchedNspectraMarkers,
spectralEntropyDeviationPrefiltering, massErrorPrecursor = NA, RTtolerance = NA,
exportSpectraParameters = NULL, number_processing_threads = 1)

Arguments

path

Address of .msp file(s)

MSPfile

name of the .msp file

libFSdb

A converted .msp library reference file using the 'msp2FSdb' module which is an FSDB produced by the IDSL.FSA package.

libFSdbIDlist

Ion markers object from the FSDB reference

targetedPrecursorType

A vector of targeted precursor types

ratio2basePeak4nSpectraMarkers

Ratio of peaks in fragmentation spectra to the basepeak to calculate minimum qualified number of matched abundant peaks

allowedNominalMass

c(TRUE, FALSE). Select 'TRUE' only for nominal mass analysis.

allowedWeightedSpectralEntropy

c(TRUE, FALSE). Weighted entropy to transform low abundant signals prior to calculating entropy similarity score. Please see the reference for details on wight transformation.

noiseRemovalRatio

noise removal ratio ([0 - 1])relative to the basepeak to measure entropy similarity score.

roundingDigitPrefiltering

Level of pre-filtering

minMatchedNumPeaks

Minimum matched number of peaks

massError

Mass accuracy in Da

maxNEME

Maximum value for Normalized Euclidean Mass Error (NEME) in mDa

minIonRangeDifference

Minimum distance (Da) between lowest and highest matched m/z to prevent matching only isotopic envelopes

minCosineSimilarity

Minimum cosine similarity score

minEntropySimilarity

Minimum entropy similarity score

minRatioMatchedNspectraMarkers

Minimum percentage of detection of abundant library peaks in percentage

spectralEntropyDeviationPrefiltering

Spectral entropy deviation for pre-filtering

massErrorPrecursor

Mass accuracy (Da) to find precursor m/z in .msp files

RTtolerance

Retention time tolerance (min)

exportSpectraParameters

Parameters for export MS/MS match figures

number_processing_threads

Number of processing threads for multi-threaded processing

Value

A dataframe of matched spectra