estimateMzResolution: Estimate the m/z resolution of a spectrum

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

Estimate the m/z resolution of a spectrum

Description

estimateMzResolution estimates the m/z resolution of a profile-mode Spectrum (or of all spectra in an MSnExp or OnDiskMSnExp object. The m/z resolution is defined as the most frequent difference between a spectrum's m/z values.

Usage

## S4 method for signature 'MSnExp'
estimateMzResolution(object, ...)

## S4 method for signature 'Spectrum'
estimateMzResolution(object, ...)

Arguments

object	either a Spectrum, MSnExp or OnDiskMSnExp object.
...	currently not used.

Value

numeric(1) with the m/z resolution. If called on a MSnExp or OnDiskMSnExp a list of m/z resolutions are returned (one for each spectrum).

Note

This assumes the data to be in profile mode and does not return meaningful results for centroided data.

The estimated m/z resolution depends on the number of ions detected in a spectrum, as some instrument don't measure (or report) signal if below a certain threshold.

Author(s)

Johannes Rainer

Examples

## Load a profile mode example file
library(BiocParallel)
register(SerialParam())
library(msdata)
f <- proteomics(full.names = TRUE,
    pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")

od <- readMSData(f, mode = "onDisk")

## Estimate the m/z resolution on the 3rd spectrum.
estimateMzResolution(od[[3]])

## Estimate the m/z resolution for each spectrum
mzr <- estimateMzResolution(od)

## plot the distribution of estimated m/z resolutions. The bimodal
## distribution represents the m/z resolution of the MS1 (first peak) and
## MS2 spectra (second peak).
plot(density(unlist(mzr)))

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