Write mzML

Writes spectra and chromatograms to an mzML file.

Usage

write_mzml(
  data,
  path_out,
  sample_name = NULL,
  what = NULL,
  instrument_info = NULL,
  centroided = TRUE,
  compress = TRUE,
  indexed = TRUE,
  force = FALSE,
  show_progress = TRUE,
  verbose = getOption("verbose")
)

Arguments

data

A named list of data.frames or data.tables, keyed by stream (MS1, MS2, TIC, BPC, DAD), or a single chromatogram carrying a detector attribute that says which stream it is.

path_out

The path to write the file.

sample_name

The name of the file. If a name is not provided, the name will be derived from the sample_name attribute, and it is an error if there is no such attribute.

what

Which streams to write to mzML: "MS1", "MS2", "TIC", "BPC", and/or "DAD". Defaults to every element of data that holds any rows.

instrument_info

Controlled-vocabulary terms describing the instrument, as a list of lists with elements cvRef, accession, name and value, each written as one cvParam of the instrumentConfiguration. Defaults to NULL, in which case MS:1000031 ("instrument model") is written with the chromatogram's detector_model or instrument as its value, or bare where it records neither.

centroided

Logical. Whether the spectra are centroided, written as MS:1000127 or, when FALSE, MS:1000128 ("profile spectrum"). Defaults to TRUE. Set it to FALSE for the profile scan types of a triple quadrupole (a full scan or a product-ion scan, as opposed to SIM or MRM).

compress

Logical. Whether to use zlib compression. Defaults to TRUE.

indexed

Logical. Whether to write indexed mzML. Defaults to TRUE.

force

Logical. Whether to overwrite existing files at path_out. Defaults to FALSE.

show_progress

Logical. Whether to show progress bar. Defaults to TRUE.

verbose

Logical. Whether or not to print status messages.

Value

Invisibly returns the path to the written mzML file.

Details

Mass spectra and DAD spectra are written to the spectrumList, while the total ion current (TIC) and the base peak chromatogram (BPC) go to the chromatogramList, since the controlled vocabulary has terms for those two summaries. DAD spectra are written as electromagnetic radiation spectra (MS:1000804) using Thermo's naming convention, with controllerType=4 in the spectrum ID for compatibility with existing tools.

Asking for both MS1 and MS2 writes them into one spectrumList, interleaved in acquisition order: on the scan column they share, or on retention time where neither has one. Each spectrum is then named for its scan (scan=417) rather than for its position in the list, which keeps the names unique across the levels. An MS2 spectrum carries the precursor it came from as MS:1000744 ("selected ion m/z"), and a spectrumRef to the MS1 spectrum that precedes it. Collision energy, isolation window and precursor charge are not written, as no parser in the package reads them.

Retention times are written in minutes (UO:0000031), as chromConverter reports them, rather than converted to seconds as write_andi_ms does.

The streams to write come from the names of data, so a bare chromatogram has to say what it holds through its detector attribute: UV and DAD are written as a DAD stream, and MS as MS1, or as MS2 where the table also carries an ms_level attribute above 1. Any other detector, including a missing or NA one (which is how several parsers report an unknown detector), is an error: the function stops rather than guess, and asks for a named list instead.

A one-dimensional DAD stream (a single wavelength) is refused: mzML has no axis to write it along, so it would become one single-point spectrum per retention time. Use write_andi_chrom for a single trace. If it is the only stream requested this is an error; otherwise it is dropped with a warning and the rest is written.

The file's metadata are taken from the MS1 stream if it is written, and otherwise from the first stream requested. That stream's sample_name attribute names the file unless sample_name is supplied.

If indexed = TRUE, the function will generate an indexed mzML file, which allows faster random access to spectra. The file is assembled by writing XML strings straight to a connection rather than by building a document in memory.

See also

Other write functions: write_andi_chrom(), write_andi_ms(), write_chroms()

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
chrom <- read_chroms("path/to/file.qgd", progress_bar = FALSE)
write_mzml(chrom[[1]], path_out = "path/to/directory")
} # }