correct_peak_selection {MSnID} | R Documentation

## Corrects wrong selection of monoisotopic peak

### Description

In a typical setting instruments select ions for fragmentation primarily based on ion intensity. For low molecular weight peptides the most intense peak usually corresponds to monoisotopic peak (that is only C12 carbon isotopes). With increase of molecular weight, instensity of monoisotopic peak becomes smaller relatively to heavier peptide isotopes (that is containing one or a few C13 isotopes).

The function subtracts or adds the mass difference between C13 and C12 isotopes (1.0033548378 Da) if that reduces the mass error. Such a mass error arises from the fact that instrument may peak non-monoisotopic peak for fragmentation and thus report the mass that is different by ~ 1 Da.

### Usage

        correct_peak_selection(object)

### Arguments

`object` | An instance of class "MSnID".

### Value

Returns an instance of "MSnID" class with updated `experimentalMassToCharge` value.

### Author(s)

Vladislav A Petyuk vladislav.petyuk@pnnl.gov

### See Also

`MSnID` `recalibrate` `mass_measurement_error`

### Examples

    data(c_elegans)
    # plot original mass error
    massErr <- (msnidObj$experimentalMassToCharge -
                msnidObj$calculatedMassToCharge) *
                msnidObj$chargeState
    hist(massErr,xlim=c(-1,+1), breaks=seq(-1.5,+1.5,0.01))
    # fixing the problem of picking wrong monoisotopic peak
    msnidObj <- correct_peak_selection(msnidObj)
    # plot fixed mass error
    massErr <- (msnidObj$experimentalMassToCharge -
                msnidObj$calculatedMassToCharge) *
                msnidObj$chargeState
    hist(massErr,xlim=c(-1,+1), breaks=seq(-1.5,+1.5,0.01))

[Package MSnID version 1.28.0 Index]