Read mzML files

Extracts data from mzML files using parsers from either RaMS or mzR.

Usage

read_mzml(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  parser = c("RaMS", "mzR"),
  what = c("MS1", "MS2", "BPC", "TIC", "DAD", "chroms", "metadata", "everything"),
  verbose = FALSE,
  ...
)

Arguments

path

Path to .mzml file.

format_out

Class of output. Either matrix, data.frame, or data.table. Applies only to the TIC, BPC, DAD and chroms in wide format.

data_format

Whether to return data in wide (default) or long format.

parser

What parser to use. Either RaMS or mzR.

what

What types of data to return (argument to RaMS::grabMSdata). Options include MS1, MS2, BPC, TIC, DAD, chroms, metadata, or everything. Defaults to all of them. EIC and EIC_MS2 return extracted ion chromatograms from the MS1 or MS2 data for the masses given by the mz and ppm arguments of RaMS::grabMSdata, passed through ....

verbose

Argument to grabMSdata controlling verbosity. Ignored by mzR.

...

Additional arguments to grabMSdata. Ignored by mzR.

Value

A named list of the streams in what.

Details

Both parsers return a list with one element per stream in what. Mass spectra and EICs are always long. With data_format = "wide" (the default), TIC and BPC are returned as 2D chromatograms of class format_out, and DAD as a wide chromatogram of class format_out; with "long", every stream is a long data.table.

The chroms stream holds the chromatograms stored in the file, such as the SIM and SRM traces of a triple quadrupole run. In wide format it is a list of 2D chromatograms named by their ID in the file (or Chromatogram 1, Chromatogram 2 and so on where it has none), each with the precursor_mz and product_mz it monitors as attributes. If any trace repeats a retention time, as in some malformed files, the whole stream is returned as the long data.table instead, with a warning.

The mzR parser reads files that RaMS cannot, such as those compressed with MS-Numpress. It returns only MS1, MS2, BPC, TIC and DAD, and no file metadata. Its TIC and BPC are the per-scan values recorded in the MS1 spectra.

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
read_mzml("path/to/file.mzML")
} # }