Deconvolute a Mass Spectrum from a list of raw data files.

DeconvoluteSpectrum will evaluate a list of `xcmsRaw` or `xcmsRawLike` objects at a given time (rt) and potential mass (mz1). The main purpose is to deconvolute the mass spectrum at rt including mz1.

Usage

DeconvoluteSpectrum(
  dat = NULL,
  rt = NULL,
  rt_dev = 3,
  mz1 = NULL,
  mz_dev = 0.003,
  use.mz.adjust = FALSE,
  ionization = c("APCI", "ESI")[1],
  smooth = 0
)

Arguments

dat

A list of `xcmsRaw` or `xcmsRawLike` objects.

rt

Retention time of the expected peak.

rt_dev

Allowed retention time deviation.

mz1

If specified, ensure that this mass is included in the spectrum (assumed base peak). Can be NULL otherwise in which case the most intense peak at rt will be selected as mz1.

mz_dev

Allowed mz deviation [Da].

use.mz.adjust

Will adjust mz on an experiment wide basis.

ionization

Either APCI or ESI. Choice will modify some internal parameters and checks performed.

smooth

Smoothing parameter passed on to getMultipleBPC.

Value

A pseudo spectrum at rt (containing mz1 if specified). Effectively a 2-column matrix (mz, int) with rt as attribute.

Details

The specific advantage of DeconvoluteSpectrum is, that it does not deconvolute signals within a single measurement file but uses correlation tests over a set of measurements to improve statistical power. It will test all mz around a specified rt to co-apex with some mz1, have a low rt difference and consistent intensity ratio over all samples.

Examples

# The example measurement data provided with HiResTEC contain a peak at 1026s
raw <- HiResTEC::raw
HiResTEC::DeconvoluteSpectrum(raw, rt = 1026)
#>             mz     int
#>  [1,] 540.2308   75861
#>  [2,] 541.2324   34783
#>  [3,] 542.2299   15238
#>  [4,] 554.2459    3975
#>  [5,] 555.2539   75198
#>  [6,] 556.2631 3312706
#>  [7,] 557.2637 1512582
#>  [8,] 558.2617  764573
#>  [9,] 559.2617  216982
#> [10,] 560.2605   53666
#> [11,] 570.2410  128202
#> [12,] 571.2431   61616
#> [13,] 572.2223  101369
#> [14,] 573.2235   42071
#> [15,] 574.2206   18551
#> [16,] 587.2433   51016
#> [17,] 588.2453   23189
#> [18,] 589.2433   11594
#> attr(,"rt")
#> [1] 1026.535