meanMzInts: Combine a list of spectra to a single spectrum

In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Combine a list of spectra to a single spectrum

Description

Combine peaks from several spectra into a single spectrum. Intensity and m/z values from the input spectra are aggregated into a single peak if the difference between their m/z values is smaller than mzd or smaller than ppm of their m/z. While mzd can be used to group mass peaks with a single fixed value, ppm allows a m/z dependent mass peak grouping. Intensity values of grouped mass peaks are aggregated with the intensityFun, m/z values by the mean, or intensity weighted mean if weighted = TRUE.

Usage

meanMzInts(
  x,
  ...,
  intensityFun = base::mean,
  weighted = FALSE,
  main = 1L,
  mzd,
  ppm = 0,
  timeDomain = FALSE,
  unionPeaks = TRUE
)

Arguments

x	list of Spectrum objects.
...	additional parameters that are passed to intensityFun.
intensityFun	function to aggregate the intensity values per m/z group. Should be a function or the name of a function. The function is expected to return a numeric(1).
weighted	logical(1) whether m/z values per m/z group should be aggregated with an intensity-weighted mean. The default is to report the mean m/z.
main	integer(1) defining the main spectrum, i.e. the spectrum which m/z and intensity values get replaced and is returned. By default the first spectrum in x is used.
mzd	numeric(1) defining the maximal m/z difference below which mass peaks are considered to represent the same ion/mass peak. Intensity values for such grouped mass peaks are aggregated. If not specified this value is estimated from the distribution of differences of m/z values from the provided spectra (see details).
ppm	numeric(1) allowing to perform a m/z dependent grouping of mass peaks. See details for more information.
timeDomain	logical(1) whether definition of the m/z values to be combined into one m/z is performed on m/z values (timeDomain = FALSE) or on sqrt(mz) (timeDomain = TRUE). Profile data from TOF MS instruments should be aggregated based on the time domain (see details). Note that a pre-defined mzd should also be estimated on the square root of m/z values if timeDomain = TRUE.
unionPeaks	logical(1) whether the union of all peaks (peak groups) from all spectra are reported or only peak groups that contain peaks that are present in the main spectrum (defined by main). The default is to report the union of peaks from all spectra.

Details

For general merging of spectra, the mzd and/or ppm should be manually specified based on the precision of the MS instrument. Peaks from spectra with a difference in their m/z being smaller than mzd or smaller than ppm of their m/z are grouped into the same final peak.

Some details for the combination of consecutive spectra of an LCMS run:

The m/z values of the same ion in consecutive scans (spectra) of a LCMS run will not be identical. Assuming that this random variation is much smaller than the resolution of the MS instrument (i.e. the difference between m/z values within each single spectrum), m/z value groups are defined across the spectra and those containing m/z values of the main spectrum are retained. The maximum allowed difference between m/z values for the same ion is estimated as in estimateMzScattering(). Alternatively it is possible to define this maximal m/z difference with the mzd parameter. All m/z values with a difference smaller than this value are combined to a m/z group. Intensities and m/z values falling within each of these m/z groups are aggregated using the intensity_fun and mz_fun, respectively. It is highly likely that all QTOF profile data is collected with a timing circuit that collects data points with regular intervals of time that are then later converted into m/z values based on the relationship t = k * sqrt(m/z). The m/z scale is thus non-linear and the m/z scattering (which is in fact caused by small variations in the time circuit) will thus be different in the lower and upper m/z scale. m/z-intensity pairs from consecutive scans to be combined are therefore defined by default on the square root of the m/z values. With timeDomain = FALSE, the actual m/z values will be used.

Value

Spectrum with m/z and intensity values representing the aggregated values across the provided spectra. The returned spectrum contains the union of all peaks from all spectra (if unionPeaks = TRUE), or the same number of m/z and intensity pairs than the spectrum with index main in x (if unionPeaks = FALSE. All other spectrum data (such as retention time etc) is taken from the main spectrum.

Note

This allows e.g. to combine profile-mode spectra of consecutive scans into the values for the main spectrum. This can improve centroiding of profile-mode data by increasing the signal-to-noise ratio and is used in the combineSpectraMovingWindow() function.

Author(s)

Johannes Rainer, Sigurdur Smarason

See Also

estimateMzScattering() for a function to estimate m/z scattering in consecutive scans.

estimateMzResolution() for a function estimating the m/z resolution of a spectrum.

combineSpectraMovingWindow() for the function to combine consecutive spectra of an MSnExp object using a moving window approach.

Other spectra combination functions: consensusSpectrum()

Examples

library(MSnbase)
## Create 3 example profile-mode spectra with a resolution of 0.1 and small
## random variations on these m/z values on consecutive scans.
set.seed(123)
mzs <- seq(1, 20, 0.1)
ints1 <- abs(rnorm(length(mzs), 10))
ints1[11:20] <- c(15, 30, 90, 200, 500, 300, 100, 70, 40, 20) # add peak
ints2 <- abs(rnorm(length(mzs), 10))
ints2[11:20] <- c(15, 30, 60, 120, 300, 200, 90, 60, 30, 23)
ints3 <- abs(rnorm(length(mzs), 10))
ints3[11:20] <- c(13, 20, 50, 100, 200, 100, 80, 40, 30, 20)

## Create the spectra.
sp1 <- new("Spectrum1", mz = mzs + rnorm(length(mzs), sd = 0.01),
    intensity = ints1)
sp2 <- new("Spectrum1", mz = mzs + rnorm(length(mzs), sd = 0.01),
    intensity = ints2)
sp3 <- new("Spectrum1", mz = mzs + rnorm(length(mzs), sd = 0.009),
    intensity = ints3)

## Combine the spectra
sp_agg <- meanMzInts(list(sp1, sp2, sp3))

## Plot the spectra before and after combining
par(mfrow = c(2, 1), mar = c(4.3, 4, 1, 1))
plot(mz(sp1), intensity(sp1), xlim = range(mzs[5:25]), type = "h", col = "red")
points(mz(sp2), intensity(sp2), type = "h", col = "green")
points(mz(sp3), intensity(sp3), type = "h", col = "blue")
plot(mz(sp_agg), intensity(sp_agg), xlim = range(mzs[5:25]), type = "h",
    col = "black")

lgatto/MSnbase documentation built on Nov. 12, 2024, 10:58 a.m.