masstrixR: Annotation of MS based metabolomics data

Description Usage Arguments Value Author(s) Examples

This function performs annotation of m/z values with putative metabolites using a previously created SQLite DB. Measured m/z values are compared against theoretical values within a defined error range. This error can be either absolute (in Da) or relative (in ppm). If the database contains RT or CCS values results can be a additionally filtered.

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mzSearch(peakList, dbFileName, mode = "onDisk", mzTol = 0.005,
  mzTolType = "abs", rt = FALSE, rtTol = 0.5, rtTolType = "abs",
  ccs = FALSE, ccsTol = 1, ccsTolType = "rel")

`peakList`	Data frame containing the peaks of interest, minimum column is called mz ($mz) or m.z ($m.z) or mzmed ($mzmed)
`dbFileName`	A .sqlite file containing the DB of interest
`mode`	Defines if the database shall be used from the disk ("onDisk") or in memory ("inMemory"). The second option enhances performances with very large peaks lists and DBs.
`mzTol`	Maximum allowed tolerance in Da or ppm
`mzTolType`	Defines the error type for m/z search, "abs" is used for absolute mass error, "ppm" for relative error
`rt`	Boolean value indicating of RT filtering shall be performed, if this option is true all entries in the DB need a RT value
`rtTol`	Maximum allowed tolerance for RT search in the unit of the DB and peaklist or in relative error
`rtTolType`	Defines the error type for RT search, "abs" is used for absolute RT error, "rel" for relative error
`ccs`	Boolean value indicating of CCS filtering shall be performed, if this option is true all entries in the DB need a CCS value
`ccsTol`	Maximum allowed tolerance for CCS search
`rtTolType`	Defines the error type for CCS search, "abs" is used for absolute CCS error, "rel" for relative error

Returns a data frame with results of the annotation. If for one single m/z value multiple annotations are found, each annotation is represented as individual row.

Michael Witting, michael.witting@helmholtz-muenchen.de