MS data conversion

Conversion of MS analysis files between several open and closed data formats.

getMSConversionTypes(algorithm, direction)

getMSConversionFormats(algorithm, direction, type = NULL)

convertMSFilesPWiz(
  inFiles,
  outFiles,
  formatTo = "mzML",
  centroid = TRUE,
  IMS = FALSE,
  minIntensity = 0,
  filters = NULL,
  extraOpts = NULL,
  PWizBatchSize = 1
)

convertMSFilesOpenMS(inFiles, outFiles, formatTo = "mzML", extraOpts = NULL)

convertMSFilesBruker(inFiles, outFiles, formatTo = "mzML", centroid = TRUE)

convertMSFilesIMSCollapse(
  inFiles,
  outFiles,
  typeFrom,
  formatTo = "mzML",
  mzRange = NULL,
  mobilityRange = NULL,
  smoothWindow = 0,
  halfWindow = 2,
  maxGap = 0.005,
  clusterMethod = "distance_mean",
  mzWindow = defaultLim("mz", "medium"),
  minIntensityIMS = 0,
  includeMSMS = FALSE,
  ...
)

convertMSFilesTIMSCONVERT(
  inFiles,
  outFiles,
  formatTo = "mzML",
  centroid = TRUE,
  centroidRaw = FALSE,
  IMS = FALSE,
  extraOpts = NULL,
  virtualenv = "patRoon-TIMSCONVERT"
)

convertMSFilesPaths(
  files,
  formatFrom,
  formatTo = "mzML",
  outPath = NULL,
  dirs = TRUE,
  overwrite = FALSE,
  algorithm = "pwiz",
  ...
)

convertMSFiles(
  anaInfo,
  typeFrom = "raw",
  typeTo = "centroid",
  formatFrom,
  formatTo = "mzML",
  overwrite = FALSE,
  algorithm = "pwiz",
  centroidVendor = TRUE,
  ...
)

Arguments

algorithm

Either "pwiz" (ProteoWizard), "openms", "bruker" (Bruker DataAnalysis) , "imscollapse" or "timsconvert".

direction

A character specifying the direction of conversion. Either "input" or "output".

type, typeFrom, typeTo

The type of the input or output files. See getMSConversionTypes for the supported types.

inFiles, outFiles

A character vector with input and output files, respectively. Lengths and order should be the same.

centroid

Set to TRUE to perform centroiding.

For convertMSFilesPWiz: the value may be "vendor" to perform centroiding with the vendor algorithm or "cwt" to use ProteoWizard's wavelet algorithm.

IMS

How to handle IMS data.

For convertMSFilesPWiz: if TRUE then IMS data is exported and spectra for each IMS frame are combined into a single spectrum (using the –combineIonMobilitySpectra option), which is the format supported by patRoon. Set to NA to collapse the IMS data by scan summing, which mimics 'regular' HRMS data. Set to FALSE for non-IMS data. NOTE: do not set IMS=FALSE if the data has IMS data. This will result in very large files where MS spectra are not combined by frame, which cannot be properly read by patRoon.

For convertMSFilesTIMSCONVERT: set to TRUE to keep IMS data or FALSE to exclude IMS data to mimic 'regular' LC-MS data.

minIntensity

The minimum intensity of the mass peaks to be kept. Applying an intensity threshold is especially beneficial to reduce export file size when there are a lot of zero or very low intensity mass peaks. NOTE this currently does not work well with IMS data.

filters

A character vector specifying one or more filters to msconvert. The elements of the specified vector are directly passed to the --filter option (see here)

extraOpts

A character vector specifying any extra command line parameters passed to msconvert or FileConverter. Set to NULL to ignore. For options: see FileConverter and msconvert.

PWizBatchSize

The number of analyses to process by a single call to msconvert. Usually a value of one is most efficient. Set to zero to run all analyses all at once from a single call.

mzRange, mobilityRange

A two sized vector specifying the m/z and mobility range to be exported, respectively. Set to NULL to export the full range.

smoothWindow, halfWindow, maxGap

Centroiding parameters: see getDefAvgPListParams for details. NOTE: As described there, maxGap may need to be increased for Agilent instruments (e.g. 0.01).

clusterMethod, mzWindow

The clustering method and window (see clustering parameters) used to find and combine MS/MS spectra of precursors with close m/z.

minIntensityIMS

The minimum intensity for MS peaks in raw data.

includeMSMS

Set to TRUE to include MS/MS spectra in the output. For IMS workflows where IMS data is only collapsed to produce compatible data files for feature detection, MS/MS data are not needed and can be excluded to reduce computational times and file sizes. Setting includeMSMS=TRUE is primarily intended to perform 'classical LC-MS workflows' with IMS data.

...

For convertMSFilesIMSCollapse: further arguments passed to mzR::writeMSData.

For convertMSFilesPaths and convertMSFiles: further arguments passed to algorithm specific conversion functions.

centroidRaw

Only applicable if IMS=FALSE. Sets the mode parameter of TIMSCONVERT: raw if centroidRaw=TRUE or centroid if centroidRaw=FALSE. See https://gtluu.github.io/timsconvert/local.html#notes-on-mode-parameter for more details.

virtualenv

The virtual Python environment in which TIMSCONVERT is installed. This is passed to reticulate::use_virtualenv, which will ensure that the TIMSCONVERT command line utility can be found by patRoon. Set to NULL to skip this step.

files, dirs

The files argument should be a character vector with input files. If files contains directories and dirs=TRUE then files from these directories are also considered.

formatFrom, formatTo

The input or output format. See getMSConversionFormats for the supported formats.

outPath

A character vector specifying directories that should be used for the output. Will be re-cycled if necessary. If NULL, output directories will be kept the same as the input directories.

overwrite

Should existing destination file be overwritten (TRUE) or not (FALSE)?

anaInfo

An analysis info table that is used to retrieve the input files. The paths set by path_centroid, path_profile and path_ims are used to determine the output directories. This function automatically determines if and how centroiding and IMS conversions should be applied.

centroidVendor

Only for algorithm="pwiz": whether centroiding should be performed with vendor algorithms.

Details

getMSConversionTypes returns a character with all supported input or output conversion types for an algorithm.

getMSConversionFormats returns a character with all supported input or output conversion formats for an algorithm, optionally filtered by the given type.

convertMSFilesPWiz converts and pre-treats HRMS data with the msconvert tool from ProteoWizard.

convertMSFilesOpenMS converts HRMS data with the FileConvert tool of OpenMS.

convertMSFilesBruker converts and pre-treats Bruker HRMS data with Bruker DataAnalysis. Note that TIMS data currently is not supported.

convertMSFilesIMSCollapse is used to convert IMS data to data that mimics 'regular' HRMS data by collapsing the IMS dimension. The raw data interface of patRoon first sums up all spectra within each IMS frame, performs centroiding and finally exports the resulting data with the mzR::writeMSData function. Several thresholds can be set to speed up the conversion process and reduce noise, but care should be taken that no mass peaks of interest are lost.

convertMSFilesTIMSCONVERT converts and pre-treats TIMS data with TIMSCONVERT. The installTIMSCONVERT function can be used to automatically install TIMSCONVERT.

convertMSFilesPaths is a wrapper function that simplifies the use of algorithm specific MS conversion functions, such as convertMSFilesPWiz, and convertMSFilesTIMSCONVERT.

convertMSFiles is a wrapper function that simplifies the use of convertMSFilesPaths.

Parallelization

convertMSFilesPWiz, convertMSFilesOpenMS and convertMSFilesTIMSCONVERT uses multiprocessing to parallelize computations. Please see the parallelization section in the handbook for more details and patRoon options for configuration options.

Use of raw HRMS data

The raw data interface of patRoon is used by convertMSFilesIMSCollapse to process HRMS (or IMS-HRMS) data. Please see its documentation for more information on the supported formats and available configuration options.

References

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