CorrectOverloadedPeaks {CorrectOverloadedPeaks}

Correct Overloaded Peaks from GC-MS data.

Description

CorrectOverloadedPeaks will take an xcmsRaw data structure (or any imported mzXML) and search for overloaded peaks within the mass traces. It will correct overloaded peaks automatically using an Gaussian or IsotopicRatio approach, generate QC plots and write the corrected data back into the original xcmsRaw.

Usage

CorrectOverloadedPeaks(
  data = NULL,
  method = c("Isoratio", "Gauss", "EMG"),
  detection_limit = 1,
  ds = NULL,
  silent = TRUE,
  testing = FALSE,
  attotwm = FALSE,
  region = NULL,
  peak = NULL
)

Arguments

data

An xcmsRaw-object or an mzXML-object as imported by read.mzXML.

method

Either Gauss or EMG (usually better results) or Isoratio (more robust for non-Gaussian peak shapes).

detection_limit

If=1 only peaks hitting detector saturation (ds) will be corrected, can be lowered to 0.95 to catch also peaks going into saturation.

ds

Detector saturation. Will be determined based on data if not specified explicitly.

silent

QC-plots will be generated if silent=FALSE and additional Warnings() will be generated.

testing

Will automatically set silent=FALSE and store all extracted regions with overloaded peaks in the working directory as cor_df_all.RData.

attotwm

All-the-Time-of-the-World-Mode. If calculation time doesn't matter try this out. :)

region

From an initial QC-Plot file you may reprocess a specific overloaded region. Don't forget to specify the ds parameter explicitly.

peak

You may further restrict the reprocessing to a specific peak within the region.

Details

This is a high level function to batch pre-process metabolomics data which are partially overloaded before continuing with the standard workflow of peak identification etc.. It relies internally on FitGaussPeak and FitPeakByIsotopicRatio to modify data of individual intensity signal. Basically the function aims to identify automatically overloaded regions and extracts base peak chromatograms for all overloaded m/z traces within these regions, which are corrected and put back into the original data structure. For simplicity some potentially interesting parameters are hidden at the top of the function definition. They have been set to values determined empirically to be working for a Bruker impact II MS (high-res QTOF) coupled to GC and LC via APCI and ESI respectively. For more details please see doi:10.1021/acs.analchem.6b02515.

Value

An corrected xcmsRaw- or mzXML-object which can be exported to file. Additionally a QC-plot pdf-file if silent=FALSE.

References

doi:10.1021/acs.analchem.6b02515

See Also

ModelGaussPeak

FitGaussPeak

FitPeakByIsotopicRatio

read.mzXML

write.mzXML

Examples

## Not run: 
  # load mzXML test data
  data(mzXML_data)
  CorrectOverloadedPeaks(data = mzXML_data, method = "EMG", silent = FALSE)

## End(Not run)