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Read 'Varian' SMS

Source: R/read_varian_sms.R
read_varian_sms.Rd

Reads 'Varian Workstation' SMS files.

Usage

read_varian_sms(
  path,
  what = c("MS1", "TIC", "BPC"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = "long",
  read_metadata = TRUE,
  collapse = TRUE
)

Arguments

path

Path to a 'Varian' .SMS file.

what

Which streams to get: mass spectra (MS1), the total ion chromatogram (TIC) and/or the base peak chromatogram (BPC). Accepts multiple arguments. Defaults to all three.

format_out

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

data_format

Whether to return data in long (default) or wide format. Mass spectra are always returned in long format.

read_metadata

Logical. Whether to attach metadata. Defaults to TRUE.

collapse

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

Value

A chromatogram or list of chromatograms from the specified file, according to the value of what. Chromatograms are returned in the format specified by format_out, except that mass spectra are returned as a data.table when format_out is matrix.

Details

Varian SMS files begin with a DIRECTORY holding the offsets of each section. The first section is MSData, which begins at byte 3238 in every file seen so far, and is itself divided in two. The first part, after a short header, holds chromatogram data, one record per scan: the scan number, the retention time (as a 64-bit float), the ion time (µsec, as a 2-byte unsigned integer), the total ion chromatogram (TIC), the base peak chromatogram (BPC), and further unidentified fields. The scan numbers and the TIC and BPC intensities are stored as 4-byte little-endian integers. A run of null bytes then separates this part from the segments holding the mass spectra.

The mass spectra are encoded differently. Each scan is a series of variable-length values, separated from the next scan by two null bytes. Within a scan the values are paired: the first of each pair is the delta-encoded mass-to-charge ratio and the second is the intensity. Each value is a big-endian integer whose length, 1 + (d %/% 4) bytes, and bit width are set by its leading hexadecimal digit (d). Values beginning with 0-3 are single bytes. For d >= 4, the lowest n bits are preserved according to the following scheme:

  • d = 4-5 -> preserve lowest 13 bits

  • d = 6-7 -> preserve lowest 14 bits

  • d = 8-9 -> preserve lowest 21 bits

  • d = 10-11 (A-B) -> preserve lowest 22 bits

  • d = 12-13 (C-D) -> preserve lowest 27 bits

  • d = 14-15 (E-F) -> preserve lowest 28 bits

No file seen so far carries a leading digit above C, so the rules for D and for E-F are extrapolated from the others rather than observed.

Note

There is still only limited support for the extraction of metadata from this file format.

See also

Other 'Varian' parsers: read_varian_peaklist()

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
read_varian_sms(path)
} # }