InterpretMSSpectrum (version 1.4.5)

GenerateMetaboliteSQLiteDB: GenerateMetaboliteSQLiteDB.

Description

GenerateMetaboliteSQLiteDB will set up a SQLite data base containing potential metabolite formulas, their masses and isotopic distribution for use with InterpretMSSpectrum.

Usage

GenerateMetaboliteSQLiteDB(
  dbfile = "SQLite_APCI.db",
  ionization = c("APCI", "ESI")[1],
  mass_range = c(100, 105),
  ncores = 1,
  silent = TRUE
)

Value

Returns the resulting data frame invisible. Will write an SQL_DB if 'dbfile' provides a valid path and file name.

Arguments

dbfile

Path and file name of the final SQLiteDB or NULL to return the data frame.

ionization

Has to be specified to account for different plausibility rules and elemental composition.

mass_range

For testing use default range, otherwise use your measurement range.

ncores

Number of cores. Use as many as possible.

silent

Set to FALSE to get progress messages.

Details

The process takes a long time for larger masses (>400 Da). Parallel processing with 8 cores is highly recommended. Alternatively pre-processed versions can be downloaded on request to . To process a 1 Da range (from 900 to 901) for ESI does take approximately 5 minutes on 8 cores.

Examples

# using the default values will compute be relatively fast, but for higher masses it 
# is getting much slower
db <- GenerateMetaboliteSQLiteDB(dbfile = NULL)