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Read 'Shimadzu' QGD files

Source: R/read_shimadzu_qgd.R
read_shimadzu_qgd.Rd

Reads 'Shimadzu GCMSsolution' .qgd GC-MS data files.

Usage

read_shimadzu_qgd(
  path,
  what = c("MS1", "TIC"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE
)

Arguments

path

Path to 'Shimadzu' .qgd file.

what

What stream to get: current options are MS1 and/or TIC. If a stream is not specified, the function will return both streams.

format_out

Class of output. Either matrix, data.frame, or data.table.

data_format

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

read_metadata

Logical. Whether to attach metadata. Defaults to TRUE.

metadata_format

Format to output metadata. Either chromconverter (standardized field names) or raw (vendor field names, unmapped).

collapse

Logical. Whether to collapse lists that only contain a single element. Defaults to TRUE.

Value

A list holding the MS1 spectra and the TIC, or the one requested where collapse is TRUE. The TIC is returned in the format specified by data_format and format_out. If data_format is wide, it is returned with retention times as rows and a single column for the intensity. If long format is requested, two columns are returned: one for the retention time and one for the intensity. The format_out argument determines whether it is returned as a matrix, data.frame, or data.table. The spectra are always long, with columns scan, rt, mz and intensity, and a matrix resolves to a data.table. Metadata are attached as attributes if read_metadata is TRUE.

Details

The MS data is stored in the GCMS Raw Data storage, which contains an MS Raw Data stream with MS scans, a TIC Data stream containing the total ion chromatogram, and a Retention Time stream containing the retention times. All known values are little-endian. The retention time stream is an array of 4-byte integers giving the time of each scan in milliseconds, and the TIC stream an array of 8-byte integers, one per retention time.

The MS Raw Data stream holds one block per scan, located through the Spectrum Index stream. Each block begins with a 32-byte header:

  • scan number (4-byte integer)

  • retention time in milliseconds (4-byte integer)

  • unknown (12 bytes)

  • number of bytes in each intensity value (2-byte integer)

  • number of m/z values in the block (2-byte integer)

  • unknown (8 bytes)

After the header, each m/z value is followed by its intensity. The m/z values are 2-byte integers holding m/z times 20. Intensities are unsigned integers of the width given in the header, except that the top bit of a 4-byte intensity is dropped.

See also

Other 'Shimadzu' parsers: read_shimadzu(), read_shimadzu_gcd(), read_shimadzu_lcd(), read_shimadzu_method(), read_sz_lcd_2d(), read_sz_lcd_3d(), read_sz_tables()

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
read_shimadzu_qgd("path/to/file.qgd")
} # }