FSdb2precursorType: Precursor Types from Fragmentation Spectra DataBase (FSDB)

In IDSL.FSA: Fragmentation Spectra Analysis (FSA)

Precursor Types from Fragmentation Spectra DataBase (FSDB)

Description

This function finds potential ionization pathways for molecular formulas using a vector of InChIKey values from an FSDB. This function only searches for the first 14 InChIKey letters; and therefore, may result with multiple potential precursor types.

Usage

FSdb2precursorType(InChIKeyVector, libFSdb, tableIndicator = "Frequency",
number_processing_threads = 1)

Arguments

InChIKeyVector	A vector of InChIKey values. This value may contain whole InChIKey strings or first 14 InChIKey letters.
libFSdb	A converted MSP library reference file using the 'msp2FSdb' module which is an FSDB produced by the IDSL.FSA package.
tableIndicator	c("Frequency", "PrecursorMZ"). To show frequency or a median of 'PrecursorMZ' values in the output dataframe for each precursor type.
number_processing_threads	Number of processing threads for multi-threaded processing

Value

A matrix of frequency for each InChIKey in the FSDB. The matrix column headers represent precursor types.

Examples

address_input_msp <- system.file("extdata", package = "IDSL.FSA")
MSPfile_vector <- c("Kynurenine_Kynurenic_acid.msp")
libFSdb <- msp2FSdb(path = address_input_msp, MSPfile_vector)
##
InChIKeyVector <- c("HCZHHEIFKROPDY-UHFFFAOYSA-N", "YGPSJZOEDVAXAB-QMMMGPOBSA-N")
precursor_type_table <- FSdb2precursorType(InChIKeyVector, libFSdb,
tableIndicator = "Frequency", number_processing_threads = 1)

IDSL.FSA documentation built on July 9, 2023, 6:45 p.m.