estimateMzResolution,MSnExp-method {MSnbase} | R Documentation

## 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)))

[Package MSnbase version 2.20.1 Index]