findIsotopesWithValidation-methods: Deconvolute/Annotate LC/ESI-MS data

In sneumann/CAMERA: Collection of annotation related methods for mass spectrometry data

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 <[e-mail]>

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

sneumann/CAMERA documentation built on April 5, 2024, 2:33 a.m.