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Read 'Varian' SMS

Source: R/read_varian_sms.R
read_varian_sms.Rd

Parser for reading 'Varian Workstation' SMS file.

Usage

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

Arguments

path

Path to .SMS files.

what

Whether to extract chromatograms (chroms) and/or MS1 data. Accepts multiple arguments.

format_out

R format. Either matrix or data.frame.

data_format

Whether to return data in wide or long format.

read_metadata

Whether to read metadata from file. (This is just a placeholder for now as there is not yet support for parsing metadata).

collapse

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

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.

Details

Varian SMS files begin with a "DIRECTORY" with offsets for each section. The first section (in all the files I've been able to inspect) is "MSData" generally beginning at byte 3238. This MSdata section is in turn divided into two sections. The first section (after a short header) contains chromatogram data. Some of the information found in this section includes scan numbers, retention times, (as 64-bit floats), the total ion chromatogram (TIC), the base peak chromatogram (BPC), ion time (µsec), as well as some other unidentified information. The scan numbers and intensities for the TIC and BPC are stored at 4-byte little-endian integers. Following this section, there is a series of null bytes, followed by a series of segments containing the mass spectra.

The encoding scheme for the mass spectra is somewhat more complicated. Each scan is represented by a series of values of variable length separated from the next scan by two null bytes. Within these segments, values are paired. The first value in each pair represents the delta-encoded mass-to-charge ratio, while the second value represents the intensity of the signal. Values in this section are variable-length, big-endian integers that are encoded using a selective bit masking based on the leading digit (d) of each value. The length of each integer seems to be determined as 1 + (d %/% 4). Integers beginning with digits 0-3 are simple 2-byte integers. If d >= 4, values are determined by masking to preserve the lowest n bits 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 (?)

Note

There is still only limited support for the extraction of metadata from this file format. Also, the timestamp conversions aren't quite right.

Author

Ethan Bass