ESI-MS data
In CAMERA: Collection of annotation related methods for mass spectrometry data

Description Usage Arguments Details Author(s) References See Also Examples

Annotate validated isotope clusters for a xsAnnotate object. Returns a xsAnnotate object with annotated isotopes. Validation of isotope clusters is based on statistics of the KEGG database implemented in S4 class object compoundQuantiles.

1	findIsotopesWithValidation(object, maxcharge=3, ppm=5, mzabs=0.01, intval=c("maxo","into","intb"), validateIsotopePatterns = TRUE, database="kegg")

`object`	the `xsAnnotate` object
`maxcharge`	max. number of the isotope charge
`ppm`	ppm error for the search
`mzabs`	allowed variance for the search
`intval`	choose intensity values for C12/C13 check. Allowed values are into, maxo, intb
`validateIsotopePatterns`	logical, if TRUE putative isotope clusters are validated based on KEGG database statistics.
`database`	the database which is the basis for isotope cluster validation. One of `compoundLibraries()`.

Isotope peaks are annotated for a xsAnnotate object according to given rules (maxcharge, maxiso). The algorithm benefits from a earlier grouping of the data, with groupFWHM. Generates a list of all possible isotopes, which is stored in object@isotopes. Those isotope information will be used in the groupCorr funtion. The ratios between isotope peaks are checked against the mass–specific $99%$ confidence interval based on statistics of the KEGG database.

Hendrik Treutler <hendrik.treutler@ipb-halle.de>

Hendrik Treutler and Steffen Neumann. "Prediction, detection, and validation of isotope clusters in mass spectrometry data". Submitted to Metabolites 2016, Special Issue "Bioinformatics and Data Analysis".

findIsotopes

 library(CAMERA)
 file <- system.file('mzdata/MM14.mzdata', package = "CAMERA")
 xs   <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5,10))
 an   <- xsAnnotate(xs)
 an   <- groupFWHM(an)
 an   <- findIsotopesWithValidation(an)