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. FSDBs are generated from .msp files using the msp2FSdb module in the IDSL.FSA package.

The msp2FSdb 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 files as long as Num Peaks rows are available in the .msp file.

FSDB objects

FSDB objects are R lists consisting of eight primary objects including:

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