protViz (version 0.7.9)

deisotoper: find isotop pattern in a given mass spectrum

Description

deisotoper returns the indices and scores of the isotop pattern. The score is computed by considering the isotop L2 norm of a given iostop model. protViz contains the averagine data.

Usage

deisotoper(data, Z=1:4, isotopPatternDF=averagine, massError=0.005, plot=FALSE)

Arguments

data

A mass spectrometric measurement containing a list.

Z

Charge states to be considered. The default is Z=1:4

isotopPatternDF

a data frame containing isotope envelopes of peptide averagine.

massError

mass error in Dalton. default is 0.005.

plot

boolean if the isotops should be plotted. The default is false.

Author

Witold Eryk Wolski, Christian Trachsel, and Christian Panse 2013

Details

The output of the deisotoper function is a list data structure containing for each input MS data set a result, score, and group lists.

result is a list which contains for each charge state a list of isotop groups. Analoge to result a score is provide in the score list.

group provides information about the charge states of each isotop cluster.

The algorithm for finding the isotop chains as implemented in protViz is based on the idea of 'Features-Based Deisotoping Method for Tandem Mass Spectra'. Each peak represents one node of a graph G=(V,E) with V = {1, ..., n}. The edges are defined by (v, node_array_G[v]) iff node_array_G[v] > -1. In other words an edge is defined between two peaks if the mZ difference is below the given massError. The isotop chains are determined by a DFS run. The time complexity is O(n log (n)) where n is the number of peaks.

References

isotopic-cluster graphs:

Features-Based Deisotoping Method for Tandem Mass Spectra, Zheng Yuan Jinhong Shi Wenjun Lin Bolin Chen and Fang-Xiang Wu Advances in Bioinformatics Volume 2011 (2011), Article ID 210805, 12 pages tools:::Rd_expr_doi("10.1155/2011/210805")

Examples

    # example1 - tandem ms
    x <- list(mZ = c(726.068, 726.337, 726.589, 726.842, 727.343, 727.846, 728.346, 
        728.846, 729.348, 730.248, 730.336, 730.581, 730.836),
        intensity = c(6.77850e+03, 2.81688e+04, 6.66884e+04, 1.22032e+07, 
            9.90405e+06, 4.61409e+06, 1.50973e+06, 3.33996e+05, 5.09421e+04, 
            1.15869e+03, 2.14788e+03, 5.37853e+03, 5.79094e+02))

    # the plain C interface function
    out1 <- .Call("deisotoper_main", x$mZ, x$intensity, Z=1:4, averagine, 
        massError=0.01, PACKAGE="protViz")

    out<-deisotoper(data=list(x), Z=2:4, isotopPatternDF=averagine)

    # example2 - a ms from heavy labeld peptide in water background    
    x <- list(mZ=c(642.572, 643.054, 643.569, 644.062, 644.557),
        intensity=c(17000, 25000, 12000, 9000,4000))

    diff(x$mZ)
    diff(x$mZ,lag=2)
    diff(x$mZ, difference=2)

    out2<-deisotoper(data=list(x), Z=1:2, isotopPatternDF=averagine, 
        massError=0.02, plot=TRUE)