Adds MS2 Fragments

addFragments(x, tolerance = 0, ppm = 20, ...)

Arguments

x: An instance of class Spectra of length 1, containing a spectra variable "sequence" with a character(1) representing a valid peptide sequence.
tolerance: absolute acceptable difference of m/z values for peaks to be considered matching (see MsCoreUtils::common() for more details).
ppm: m/z relative acceptable difference (in ppm) for peaks to be considered matching (see MsCoreUtils::common() for more #' details).
...: additional parameters (except verbose) passed to calculateFragments() to calculate fragment m/z values to be added to the spectra in x.

Value

Return a character() with fragment ion labels.

Author

Johannes Rainer, Sebastian Gibb, Laurent Gatto

Examples


library("Spectra")
#> Loading required package: BiocParallel
#> Loading required package: ProtGenerics
#> 
#> Attaching package: ‘ProtGenerics’
#> The following object is masked from ‘package:stats’:
#> 
#>     smooth

sp <- DataFrame(msLevel = 2L, rtime = 2345, sequence = "SIGFEGDSIGR")
sp$mz <- list(c(100.048614501953, 110.069030761719, 112.085876464844,
                117.112571716309, 158.089569091797, 163.114898681641,
                175.117172241211, 177.098587036133, 214.127075195312,
                232.137542724609, 233.140335083008, 259.938415527344,
                260.084167480469, 277.111572265625, 282.680786132812,
                284.079437255859, 291.208282470703, 315.422576904297,
                317.22509765625, 327.2060546875, 362.211944580078,
                402.235290527344, 433.255004882812, 529.265991210938,
                549.305236816406, 593.217041015625, 594.595092773438,
                609.848327636719, 631.819702148438, 632.324035644531,
                632.804931640625, 640.8193359375, 641.309936523438,
                641.82568359375, 678.357238769531, 679.346252441406,
                688.291259765625, 735.358947753906, 851.384033203125,
                880.414001464844, 881.40185546875, 919.406433105469,
                938.445861816406, 1022.56658935547, 1050.50415039062,
                1059.82800292969, 1107.52734375, 1138.521484375,
                1147.51538085938, 1226.056640625))
sp$intensity <- list(c(83143.03, 65473.8, 192735.53, 3649178.5,
                       379537.81, 89117.58, 922802.69, 61190.44,
                       281353.22, 2984798.75, 111935.03, 42512.57,
                       117443.59, 60773.67, 39108.15, 55350.43,
                       209952.97, 37001.18, 439515.53, 139584.47,
                       46842.71, 1015457.44, 419382.31, 63378.77,
                       444406.66, 58426.91, 46007.71, 58711.72,
                       80675.59, 312799.97, 134451.72, 151969.72,
                       3215457.75, 1961975, 395735.62, 71002.98,
                       69405.73, 136619.47, 166158.69, 682329.75,
                       239964.69, 242025.44, 1338597.62, 50118.02,
                       1708093.12, 43119.03, 97048.02, 2668231.75,
                       83310.2, 40705.72))
sp <- Spectra(sp)
#> Warning: Direct call of 'as.data.frame.integer()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead

## The fragment ion labels
addFragments(sp)
#>  [1] NA    NA    NA    NA    NA    NA    "y1"  NA    "y2_" "y2"  NA    NA   
#> [13] NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    "y5_"
#> [25] NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA   
#> [37] NA    NA    NA    "y8"  NA    NA    NA    NA    "y10" NA    NA    NA   
#> [49] NA    NA   

## Annotate the spectum with the fragment labels
plotSpectra(sp, labels = addFragments, labelPos = 3)