This module annotates fragmentation spectra from .MSP files.
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)A dataframe of matched spectra
Address of .msp file(s)
name of the .msp file
A converted .msp library reference file using the `msp2FSdb` module which is an FSDB produced by the IDSL.FSA package.
Ion markers object from the FSDB reference
A vector of targeted precursor types
Ratio of peaks in fragmentation spectra to the basepeak to calculate minimum qualified number of matched abundant peaks
c(TRUE, FALSE). Select `TRUE` only for nominal mass analysis.
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.
noise removal ratio ([0 - 1])relative to the basepeak to measure entropy similarity score.
Level of pre-filtering
Minimum matched number of peaks
Mass accuracy in Da
Maximum value for Normalized Euclidean Mass Error (NEME) in mDa
Minimum distance (Da) between lowest and highest matched m/z to prevent matching only isotopic envelopes
Minimum cosine similarity score
Minimum entropy similarity score
Minimum percentage of detection of abundant library peaks in percentage
Spectral entropy deviation for pre-filtering
Mass accuracy (Da) to find precursor m/z in .msp files
Retention time tolerance (min)
Parameters for export MS/MS match figures
Number of processing threads for multi-threaded processing