Read 'Shimadzu' TLM stream

Read the TLM Raw Data mass spectrometry stream from 'Shimadzu LabSolutions' .lcd files.

Usage

read_sz_tlm(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = "long",
  levels = c("MS1", "MS2"),
  sparse = 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. Both are decoded either way, since the level of a scan is recorded inside its own compressed record.

sparse

Logical. Whether to return spectra in sparse format (excluding zeros), as call_rainbow() does. Defaults to TRUE, since a profile scan is mostly empty and keeping its zeros costs roughly an order of magnitude more memory.

read_metadata

Logical. Whether to attach metadata.

metadata_format

Format to output metadata.

Value

A named list holding whichever of MS1 and MS2 the file has, each a long table with columns scan, rt (minutes), mz and intensity, preceded by precursor_mz where the scans carry one. A per-scan summary (retention time, event, MS level, polarity, precursor m/z, point count) is attached to each as a scan_info attribute.

Details

Spectra live in the MS Raw Data stream and are located through Spectrum Index, which holds one 24-byte entry per spectrum:

Offset	Type	Field
0–3	uint32	Record size in bytes
4–7	uint32	Event number
8–11	uint32	Offset into MS Raw Data
12–15	uint32	Padding
16–19	uint32	Cycle number
20–23	uint32	Scan number

Each record begins with a 12-byte wrapper (0xFFFFFFFF, uncompressed size, compressed size) followed by a zlib stream. The decompressed block opens with a 44-byte header shared by every scan type:

Offset	Type	Field
0–3	uint32	Retention time (milliseconds)
4–7	uint32	Retention time of the first scan in the cycle
8–11	uint32	Event number
12–15	uint32	Scan counter within the event
16–19	uint32	Scan index (0-based)
20–21	uint16	Scan type: 10 = MS1 profile, 14 = MS2 profile, 15 = MRM/SIM
22–23	uint16	MS level + 1 (0 in a truncated final scan)
24–27	uint32	Constant (0x00010000)
28–31	uint32	Last precursor m/z x 100 (stale outside MS2 scans)
32–35	uint32	Instrument state bit field; bit 0 follows polarity
36–39	uint32	Polarity (0 = positive, 1 = negative)
40–43	uint32	Number of data points (profile) or transitions (MRM)

Profile scans (type 10 and 14) follow the header with two m/z pairs stored as m/z x 100 — the isolation window (equal low and high values for MS2; the scan range for MS1), then the scan range — and then n unsigned 32-bit intensities. Bit 31 of an intensity marks detector saturation and is not part of the value. Intensities are already in the units LabSolutions reports, so no scaling is applied.

Points lie on an evenly spaced m/z grid running from the low end of the scan range, with a bin width of (high - low) / (100 * n) (0.1 in the files seen so far). The grid overhangs the acquired range by 10 bins at the bottom and 9 at the top; those are dropped, which is what makes the summed intensity match the TIC Data stream exactly.

MRM and SIM scans (type 15) instead follow the header with n 12-byte transitions: Q1 m/z x 100, Q3 m/z x 100, and intensity.

Author

Ethan Bass