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Read a 'Shimadzu' method

Source: R/read_shimadzu_method.R
read_shimadzu_method.Rd

Reads the instrument settings stored with a 'Shimadzu' GC run (.gcd), LC run (.lcd) or GC-MS run (.qgd), such as the oven program, gradient, flows and column.

Usage

read_shimadzu_method(
  path,
  what = NULL,
  format_out = c("data.frame", "tibble", "data.table")
)

Arguments

path

Path to a .gcd, .lcd or .qgd file.

what

One or more modules to read. For GC runs, any of "oven", "injector", "detector", "autosampler" and "column"; for GC-MS runs, "oven", "injector", "autosampler", "column" and "ms"; for LC runs, "pump", "column" and, with a PDA detector, "dad", and with a single or triple quadrupole mass spectrometer, "ms". Defaults to all the modules the run has.

format_out

Class of the tables returned: "data.frame", "tibble" or "data.table".

Value

A named list with one element per module.

For GC runs:

oven: a list with scalar elements equilibration_time_min, initial_temperature_C and initial_hold_min, plus program, a table of the temperature ramps with columns rate_C_min, temperature_C and hold_min.

injector: a list with scalar elements name, temperature_C, split_ratio, column_flow_mL_min, linear_velocity_cm_s, pressure_kPa, total_flow_mL_min and purge_flow_mL_min.

detector: a list with scalar elements name, temperature_C, h2_flow_mL_min, air_flow_mL_min, makeup_flow_mL_min and sampling_rate_ms.

autosampler: a list with scalar element injection_volume_uL.

column: a list with scalar elements name, length_m, diameter_mm, film_thickness_um, max_temperature_C and serial_number.

For GC-MS runs, oven, injector, autosampler and column as for GC runs, and ms, a list with scalar elements start_time_min and end_time_min (the window in which the mass spectrometer acquires), ion_source_temperature_C, interface_temperature_C and event_time_s. Files without the labeled method (e.g. from a GC-2010) record no equilibration_time_min, injector name or pressure_kPa, injection_volume_uL, column diameter_mm or film_thickness_um, or interface_temperature_C, which are then NA. A split ratio of -1 appears to mean the split is off. The injector settings are the values at the start of the run; a method may program the pressure or purge flow to change later, so a purge flow of 0 can be the start of a purge program.

For LC runs:

pump: a list with scalar elements mode, the abbreviation 'LabSolutions' stores for the pump mode (e.g. ISO, BGE or LPGE), flow_mL_min and stop_time_min, plus gradient, a table with columns time_min and pct_B, and solvents, a table of the mobile phase names entered in the method, with columns pump, line and solvent, or NULL if none were entered. The gradient starts from the pump's initial concentration of B at time 0 and changes linearly between the times listed. It is NULL for an isocratic run whose time program sets no concentration. flow_mL_min is NA if the method sets no flow.

column: a list with scalar element temperature_C, the temperature of the column oven, which is NA if the oven is not in use.

ms: the ion source interface of a single or triple quadrupole mass spectrometer, a list with scalar elements dl_temperature_C, the temperature of the desolvation line (CDL on single quadrupole instruments), and heat_block_temperature_C. It is attached to the chromatograms as ms_params.

dad: the PDA detector, a list with scalar elements start_wavelength_nm, end_wavelength_nm, sampling_interval_ms, end_time_min and cell_temperature_C (NA if the cell is not thermostatted), plus channels, a table of the channels the acquisition method extracts, with columns channel, wavelength_nm and bandwidth_nm. Data processing can change these channels; the wavelengths of the peak tables are those of the processed channels.

Details

Method parameters are attached automatically to every chromatogram and peak table read from these files, in the method_params metadata field. This includes all scalar values but leaves out the oven program, gradient and other tables, which are only returned by this function. The ms module of a GC-MS or LC-MS run is attached as ms_params.

File format

.gcd and .lcd files store the method and instrument configuration as labeled XML, in the GUC.1.METHOD and GUC.1.CONFIG streams, and the PDA settings in PDA.1.METHOD. The settings of a single or triple quadrupole mass spectrometer are records stored as hex in the same XML, in the LCMS unit of its own GUC.1.METHOD or GUM.METHOD stream; of these, only the interface record (Ifs) is read, whose DL and heat block temperatures are uint16 in hundredths of a degree at bytes 70 and 74. They were checked against a method printout for an 'LCMS-2020' and the published method of an 'LCMS-8040'.

.qgd files from a GC-2030 (e.g. with a 'GCMS-QP2020 NX') also hold the GC method and configuration as labeled XML, in GCMS Configuration/GUC_GC2, and their oven, injector, autosampler and column settings are read from it as for .gcd files. Every .qgd file stores the method as unlabeled binary records, one stream per module, at fixed byte offsets, which are read for the other settings and for files without the XML. Values are little-endian float32 unless marked otherwise, and bytes not listed are not read. The same streams are found in files from 'GCMS-QP2010' and 'QP2020 NX' instruments:

  • GC-2010 Instrument Parameters/Column Oven Parameter, 260 bytes:

    • 8: the number of ramps, n (int32).

    • 12, 16: the initial temperature and hold.

    • 20, 100, 180: the rates, target temperatures and holds, each an array of 20 slots, of which those past n are zero.

  • GC-2010 Instrument Parameters/Injection Parameter-1, 512 bytes:

    • 12, 16, 20: the column flow, linear velocity and split ratio.

    • 24, 120, 216, 312: the temperature, total flow, pressure and purge flow programs, 96 bytes each: the number of ramps (int32), the initial value and hold, then arrays of 7 rates, targets and holds.

  • GCMS Configuration/Column-1, 832 bytes:

    • 0, 64: the column name and serial number, null-terminated strings of up to 64 bytes.

    • 132: the length in tenths of a metre (int32).

    • 140: the maximum temperature (int32).

  • QP5K Instrument Parameters/MS Parameter, 600 or 664 bytes:

    • 20: the ion source temperature in tenths of a degree (int32).

    • 44, 48: the start and end of acquisition in milliseconds (int32).

    • 52: the event time in milliseconds (int32).

The interface temperature is only read from the XML, as the additional heater the configuration names MS. Method heaters are numbered by their position in the configuration's list of heaters, which starts at 2, so the MS heater is method heater 4 in every file seen.

The settings were checked against the 'GCMSsolution' method printouts published with three 'QP2020 NX' runs.

See also

read_chemstation_method and read_agilent_amx for 'Agilent' methods.

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

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
method <- read_shimadzu_method("path/to/file.gcd")
method$oven$program
} # }