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Fragmentation Spectra DataBase (FSDB)
Fragmentation Spectra DataBases (FSDBs) are R readable objects from one or several .msp files. FSDB objects facilitate .msp file annotation and data parsing in the R environment. FSDB files for GNPS and MoNA public libraries can be accessed from this link.
The msp2FSdb module of the IDSL.FSA is used to generate FSDB objects. This module was designed to be consistent with various .msp files structures particularly from NIST, GNPS, MoNA, IDSL.CSA libraries. The msp2FSdb module generally can work for any .msp file as long as Num Peaks lines are available in the .msp file.
FSDB objects are R lists consisting of seven primary objects including:
logFSdb: parameters used to create the FSDB object
PrecursorMZ: A vector of precursor m/z values
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