msp2FSdb {IDSL.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, 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)