findIsotopesWithValidation {CAMERA} | R Documentation

## Deconvolute/Annotate LC/ESI-MS data

### Description

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`.

### Usage

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

### Arguments

`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()`.

### Details

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.

### Author(s)

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

### References

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".

### See Also

`findIsotopes`

### Examples

     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)

[Package CAMERA version 1.42.0 Index]