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Read 'Shimadzu' single quadrupole stream

Source: R/read_shimadzu_sq.R
read_sz_sq.Rd

Read the Mass Raw Data mass spectrometry stream written by 'Shimadzu' single quadrupole instruments, such as the LCMS-2020, to .lcd files.

Usage

read_sz_sq(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = "long",
  levels = c("MS1", "MS2"),
  centroided = TRUE,
  read_metadata = TRUE,
  metadata_format = "shimadzu_lcd"
)

Arguments

path

Path to .lcd file.

format_out

Class of output. Either data.table or data.frame. Spectra are long and mixed-type, so matrix resolves to data.table.

data_format

Ignored: spectra have no wide representation and are always returned in long format.

levels

Which MS levels to return, spelled MS1 and MS2. A single quadrupole records only MS1.

centroided

Logical. Whether to return the centroided scans (TRUE) or the profile scans (FALSE).

read_metadata

Logical. Whether to attach metadata.

metadata_format

Format to output metadata.

Value

A named list holding MS1 if it was requested, a long table with columns scan, rt (minutes), mz and intensity. A per-scan summary (retention time, event, MS level, polarity, point count) is attached as a scan_info attribute.

Details

Spectra are centroided and returned as stored, except that each spectrum is sorted by m/z, as ProteoWizard's msconvert also does, because the stored m/z values do not always increase within a scan. The intensities of a scan sum to its value in TIC Data, so no scaling is applied.

Some methods record profile scans as a separate event. With centroided = FALSE these are returned instead of the centroids, so events recorded only as centroids, such as the negative scans of the one file checked, are absent. The stored values are multiplied by 2/3, which puts their sum in the units of TIC Data in the one file checked. The vendor's export applies a 9-point Savitzky-Golay filter to them, which is not applied here.

The file stores no m/z values for profile points, and it's unknown how the vendor's library computes them. Profile points are instead spread evenly over the method's m/z range, from lo to hi, so that point j (0-based) of n lies at lo + (j - 12) * (hi - lo)/(n - 27). Against a msconvert export of the one file checked (150-2000 at 15 points per m/z), these m/z values are up to 0.012 low, about a fifth of the point spacing. The offsets 12 and 27 come from that file alone. Profile scans with any other number of points than 15 per m/z of the range plus 26 give an error.

Polarity is read from bit 2 of the event flags. In the one method seen, which alternates positive and negative scans, the method's event table stores the same flags beside a signed interface voltage, and bit 2 is set on the event with the negative voltage. msconvert, which reads the file through the vendor's library, reports the same polarity as this reader for every scan.

No file with SIM events has been seen, and no header field is known to give the scan type. A SIM event whose records match the layout below would be returned in MS1 as its own event, with nothing marking it as SIM.

File format

Values are little-endian unsigned integers.

  • Mass Raw Data/Spectrum Index: the byte offset of each scan in MS Raw Data (uint32).

  • Mass Raw Data/TIC Data: the total ion current of each scan (uint64).

  • Mass Raw Data/MS Raw Data: one block per scan, a 64-byte header followed by one record per centroid. Header:

    • 0: scan index, 0-based (uint32).

    • 4: retention time in milliseconds, as in Retention Time (uint32).

    • 8: acquisition event, 0-based (uint16).

    • 44: event flags; bit 2 is the polarity, 0 positive and 1 negative (uint16).

    • 52: intensity width code, w: the width in bytes, 2 or 3, or 1 for 4 bytes (uint16).

    • 54: number of centroids, n (uint16).

    • 60: number of profile points, 0 in centroid scans (uint32).

    Each of the n records is the m/z times 20 (uint16) followed by the intensity. Bit 31 of a 4-byte intensity is a flag and is masked off. Scans with bit 4 of the event flags set hold profile data instead: n is 0 and the block holds the profile points (uint16) with no m/z values. A point with bit 15 set holds its lower 15 bits times 32. Bytes not listed are not read.

  • Mass Raw Data/Status: the m/z range of the method (uint16 at bytes 14 and 16).

Author

Ethan Bass