msp2FSdb: msp to Fragmentation Spectra DataBase (FSDB)

In IDSL.FSA: Fragmentation Spectra Analysis (FSA)

msp to Fragmentation Spectra DataBase (FSDB)

Description

This function converts .msp (mass spectra format) files into a readable R object.

Usage

msp2FSdb(path, MSPfile_vector = "", massIntegrationWindow = 0,
allowedNominalMass = FALSE, allowedWeightedSpectralEntropy = TRUE,
noiseRemovalRatio = 0.01, number_processing_threads = 1)

Arguments

path	Address of .msp file(s)
MSPfile_vector	A vector of names of .msp files or one .msp file name.
massIntegrationWindow	Mass window in Da to integrate adjacent peaks in the fragmentation spectra
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.
number_processing_threads	Number of processing threads for multi-threaded processing

Value

logFSdb	Parameters used to create the FSDB object
PrecursorMZ	A vector of precursor m/z values
Precursor Type	A vector of precursor adduct types
Retention Time	A vector of retention time values
Num Peaks	A vector of num peaks values indicating number of ions for each fragment spectra
Spectral Entropy	A vector of spectral entropy values
FragmentList	A list of fragment ions
MSPLibraryParameters	A dataframe of tabulated headers and their values for each msp block

Note

This function was designed not only to achieve the fastest computational speed; but also can standardize .msp files that were generated by inconsistent settings.

References

Li, Y., Kind, T., Folz, J., Vaniya, A., Mehta, S.S. and Fiehn, O. (2021). Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification. Nature methods, 18(12), 1524-1531, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41592-021-01331-z")}

Examples

path_extdata <- system.file("extdata", package = "IDSL.FSA")
MSPfile <- c("Kynurenine_Kynurenic_acid.msp")
sampleFSdb <- msp2FSdb(path = path_extdata, MSPfile)

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