PreprocessMassSpectra {mssearchr}

Pre-process mass spectra

Description

Pre-process mass spectra. Pre-processing includes rounding/binning, sorting, and normalization.

Usage

PreprocessMassSpectra(msp_objs, bin_boundary = 0.649, remove_zeros = TRUE)

Arguments

msp_objs

A list of nested lists. Each nested list is a mass spectrum. Each nested list must contain at least three elements: (1) the name element (a string) - compound name (or short description); (2) the mz element (a numeric/integer vector) - m/z values of mass spectral peaks; (3) the intst (a numeric/integer vector) - intensities of mass spectral peaks.

bin_boundary

A numeric value. The position of a bin boundary (it can be considered as a 'rounding point'). The bin_boundary argument must be in the following range: 0.01 <= bin_boundary <= 0.99. The default value is 0.649. This value is used in the AMDIS software and it is close to the optimal rounding rule proposed in our research (Khrisanfov, M.; Samokhin, A. A General Procedure for Rounding m/z Values in Low‐resolution Mass Spectra. Rapid Comm Mass Spectrometry 2022, 36 (11), e9294. https://doi.org/10.1002/rcm.9294).

remove_zeros

An integer value. If TRUE, all m/z values with zero intensity are excluded from mass spectra. It should be taken into account that all zero-intensity peaks presented in a mass spectrum are considered as 'trace peaks' in the case of MS Search software. As a result, the presence/absence of such peaks can influence the value of the match factor.

Details

Pre-processing includes the following steps:

• Calculating a nominal mass spectrum. All floating point m/z values are rounded to the nearest integer using the value of the bin_boundary argument. Intensities of peaks with identical m/z values are summed.

• Intensities of mass spectral peaks are normalized to 999 (as it is done in the MS Search software).

• Intensities of mass spectral peaks are rounded to the nearest integer.

• If the remove_zeros argument is TRUE, all zero-intensity peaks are removed from the mass spectrum.

• The preprocessed attribute is added and set to TRUE for the respective mass spectrum.

Value

A list of nested lists. Each nested list is a mass spectrum. Only the mz and intst elements of each nested list are modified during the pre-processing step.

Examples

# Original mass spectra of chlorine and methane
msp_objs <- list(
  list(name = "Chlorine",
       mz = c(34.96885, 36.96590, 69.93771, 71.93476, 73.93181),
       intst = c(0.83 * c(100, 32), c(100, 63.99, 10.24))),
  list(name = "Methane",
       mz = c(10, 11, 12, 13, 14, 15, 16, 17, 18, 19),
       intst = c(0, 0, 25, 75, 155, 830, 999, 10, 0, 0))
)
matrix(c(msp_objs[[1]]$mz, msp_objs[[1]]$intst), ncol = 2) # Chlorine
matrix(c(msp_objs[[2]]$mz, msp_objs[[2]]$intst), ncol = 2) # Methane

# Pre-processed mass spectra of chlorine and methane
pp_msp_objs <- PreprocessMassSpectra(msp_objs, remove_zeros = TRUE)
matrix(c(pp_msp_objs[[1]]$mz, pp_msp_objs[[1]]$intst), ncol = 2) # Chlorine
matrix(c(pp_msp_objs[[2]]$mz, pp_msp_objs[[2]]$intst), ncol = 2) # Methane