MSnbase: meanMzInts – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

meanMzInts

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

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")

MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release