labels MS2 Fragments — labelFragments • PSMatch

Creates a list of annotations based on calculateFragments results.

labelFragments(x, tolerance = 0, ppm = 20, what = c("ion", "mz"), ...)

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).
what: character(1), one of "ion" (default) or "mz", defining whether labels should be fragment ions, , or their m/z values. If the latter, then the m/z values are named with the ion labels.
...: additional parameters (except verbose) passed to calculateFragments() to calculate fragment m/z values to be added to the spectra in x.

Value

Return a list() of character() with fragment ion labels. The elements are named after the peptide they belong to (variable modifications included).

Details

addFragments is deprecated and will be made defunct; use labelFragments instead.

Author

Johannes Rainer, Guillaume Deflandre, Sebastian Gibb, Laurent Gatto

Examples

library("Spectra")
#> Loading required package: BiocParallel

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)

## The fragment ion labels
labelFragments(sp)
#> $SIGFEGDSIGR
#>  [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   
#> 
#> attr(,"group")
#> [1] 1

## The fragment mz labels
labelFragments(sp, what = "mz")
#> $SIGFEGDSIGR
#>  [1]        NA        NA        NA        NA        NA        NA  175.1190
#>  [8]        NA  214.1298  232.1404        NA        NA        NA        NA
#> [15]        NA        NA        NA        NA        NA        NA        NA
#> [22]        NA        NA  529.2729        NA        NA        NA        NA
#> [29]        NA        NA        NA        NA        NA        NA        NA
#> [36]        NA        NA        NA        NA  880.4159        NA        NA
#> [43]        NA        NA 1050.5214        NA        NA        NA        NA
#> [50]        NA
#> 
#> attr(,"group")
#> [1] 1

## Call additional parameters sur as variable modifications to calculateFragments
labelFragments(sp, type = c("a", "b", "x", "y"), variable_modifications = c(R = 5))
#> $SIGFEGDSIGR
#>  [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   
#> 
#> $`SIGFEGDSIGR[5]`
#>  [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 
#> attr(,"group")
#> [1] 1 1

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


## By default used in `plotSpectraPTM()`.
plotSpectraPTM(sp)