Store xcms preprocessing results to a file in mzTab-M format

The saveMsObject() and readMsObject() methods with the mzTabParam option enable users to save/load XcmsExperiment objects in Mz-Tab-m file format. Mainly the metadata (MTD) and Small molecule feature (SMF) tables will represent the XcmsExperiment. More specifically, sampleData() of the object will be stored in the metadata section (MTD) along with the user-inputed studyId and polarity. The featureDefinitions() will be stored in the small molecule feature (SMF) section but by default only the mzmed, rtmed, rtmin and rtmax are exported. More info avaialble in featureDefinitions() can be exported by specifying the optionalFeatureColumns parameter. The featureValues() will also be stored in the small molecule feature (SMF) section.

The small molecule summary section (SML) will be filled with null values as no annotation and identification of compound is performed in xcms.

Writing data to a folder that contains already exported data will result in an error.

Usage

mzTabParam(
  studyId = character(),
  polarity = c("positive", "negative"),
  sampleDataColumn = character(),
  path = tempdir(),
  optionalFeatureColumns = character(),
  ...
)

# S4 method for class 'XcmsExperiment,mzTabParam'
saveMsObject(object, param)

Arguments

studyId: character(1) Will be both the filename of the object saved in mzTab-M format and the mzTab-ID in the file.
polarity: character(1) Describes the polarity of the experiment. Two inputs are possible, "positive" (default) or "negative".
sampleDataColumn: character with the column name(s) of the sampleData() of the XcmsExperiment object that should be exported to the mzTab-M file. Defaults to sampleDataColumn = character(). At least one column in sampleData() has to be specified.
path: character(1) Define where the file is going to be stored. The default is path = tempdir().
optionalFeatureColumns: character with optional column names from featureDefinitions() that should be exported. Defaults to optionalFeatureColumns = character(). Feature columns "mzmed", "rtmed", "rtmin" and "rtmax" are always exported.
...: additional optional arguments. See documentation of respective method for more information.
object: for saveMsObject(): the MS data object to save, for readMsObject(): the MS data object that should be returned
param: an object defining and (eventually configuring) the file format and file name or directory to/from which the data object should be exported/imported.

Slots

dots: Correspond to any optional parameters to be passed to the featureValues() function. (e.g. parameters method or value).

Note

This function was build so that the output fit the recommendation of mzTab-M file format version 2.0. These can be found here.

References

Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O, Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y, Vizcaino JA, Salek RM, Neumann S, Jones AR. mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics. Anal Chem. 2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310. Epub 2019 Feb 13. PMID: 30688441; PMCID: PMC6660005.

Author

Philippine Louail, Johannes Rainer

Examples

## Load a test data set with detected peaks, of class `XcmsExperiment`
library(xcms)
test_xcms <- loadXcmsData()

## Define param
param <- mzTabParam(studyId = "test",
                    polarity = "positive",
                    sampleDataColumn = "sample_type")

## Save as a mzTab-M file
saveMsObject(test_xcms, param)