psm: Compute a matching between a peptide sequence and a MS2...

In protViz/protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Compute a matching between a peptide sequence and a MS2 spectrum

Description

The function computes a matching between a given peptide sequence and a given tandem mass spectrum (MS2). psm determines for each fragment ion mass peak the smallest mass error to a peak in the theretical spectrum from the peptide sequence. If the mass error is below the given fragmentIonError the match is considered a hit. psm returns a list of computed fragment ions and a vector of the mass error (Da and ppm). psm uses a generic ANSI-C function to determines the nearest mass peak of array of double values. If the plot is set to TRUE an error plot is drawn.

The function psm reqires the arguments sequence and spec. All other arguments are optional.

Usage

    psm(sequence, 
        spec, 
        FUN=defaultIon,
        plot=TRUE, 
        fi=fragmentIon(sequence, FUN=FUN)[[1]],
        fragmentIonError)

 

Arguments

sequence	peptide sequence encoded as character sequence using the 20 amino acid letters.
spec	MS2 which is a R list having a sorted mZ vector and an intensity vector of the same size.
FUN	this function is passed to the fragmentIon function. the function to be applied to compute further ions. If no function is assigned fragmentIon will use defaultIon.
plot	boolean if the error plot function is to be called.
fi	fragment ion table, if not specified fragmentIon(sequence, FUN=FUN)[[1]] is called.
fragmentIonError	fragment ion error cut-off. default is 0.6 Da.

Details

This function can be very useful to make assignements to spectra. Moreover it is used for validation or clairifying ambiguities between different sequences assigned to the same spectrum. Additinally it can be used to generate spectral libraries.

Value

returns a psm match.

Author(s)

Christian Panse 2007, 2008, 2009, 2010, 2012, 2017

See Also

peakplot and fragmentIon

Examples

spec <- list(scans=1138,
    title="178: (rt=22.3807) [20080816_23_fetuin_160.RAW]",
    rtinseconds=1342.8402,
    charge=2,
    mZ=c(195.139940, 221.211970, 239.251780, 290.221750, 
    316.300770, 333.300050, 352.258420, 448.384360, 466.348830, 
    496.207570, 509.565910, 538.458310, 547.253380, 556.173940, 
    560.358050, 569.122080, 594.435500, 689.536940, 707.624790, 
    803.509240, 804.528220, 822.528020, 891.631250, 909.544400, 
    916.631600, 973.702160, 990.594520, 999.430580, 1008.583600, 
    1017.692500, 1027.605900),
    intensity=c(931.8, 322.5, 5045, 733.9, 588.8, 9186, 604.6,
    1593, 531.8, 520.4, 976.4, 410.5, 2756, 2279, 5819, 2.679e+05,
    1267, 1542, 979.2, 9577, 3283, 9441, 1520, 1310, 1.8e+04,
    587.5, 2685, 671.7, 3734, 8266, 3309)
    )

m <- psm('HTLNQIDSVK', spec,plot=TRUE)
hist(m$mZ.Da.error)
hist(m$mZ.ppm.error)

protViz/protViz documentation built on Jan. 19, 2024, 8:10 a.m.