R/fragments-calculate2.R
calculateFragments2.RdCalculate ions produced by fragmentation with variable modifications
calculateFragments2(
sequence,
type = c("b", "y"),
z = 1,
fixed_modifications = c(C = 57.02146),
variable_modifications = numeric(),
max_mods = Inf,
neutralLoss = defaultNeutralLoss(),
verbose = TRUE,
modifications = NULL
)character() providing a peptide sequence.
character vector of target ions; possible values: c("a", "b", "c", "x", "y", "z"). Default is type = c("b", "y").
numeric with a desired charge state; default is 1.
A named numeric vector of used fixed modifications. The name must correspond to the one-letter-code of the modified amino acid and the numeric value must represent the mass that should be added to the original amino accid mass, default: Carbamidomethyl modifications = c(C = 57.02146). Use Nterm or Cterm as names for modifications that should be added to the amino respectively carboxyl-terminus.
A named numeric vector of variable modifications.
Depending on the maximum number of modifications (max_mods), all possible
combinations are returned.
A numeric indicating the maximum number of variable modifications allowed on the sequence at once. Does not include fixed modifications. Default value is positive infinity.
list, it has to have two named elments, namely water and ammonia that contain a character vector which type of neutral loss should be calculated. Currently neutral loss on the C terminal "Cterm", at the amino acids c("D", "E", "S", "T") for "water" (shown with an _) an d c("K", "N", "Q", "R") for "ammonia" (shown with an *) are supported.
logical(1). If TRUE (default) the used modifications are printed.
Named numeric(). Deprecated modifications parameter.
Will override fixed_modifications but is set to NULL by default. Please
refrain from using it, opt for fixed_modifications instead.
A dataframe showing all the ions produced by fragmentation with all possible combinations of modifications. The used variable modifications are displayed in the peptide column through the use of amino acids within brackets. Fixed modifications are not displayed.
calculateFragments2(sequence = "ARGSHKATC", type = c("b", "y"), z = 1,
fixed_modifications = c(C = 57), variable_modifications = c(S = 79, Y = 79, T = 79),
max_mods = 2)
#> Fixed modifications used: C=57
#> Variable modifications used: S=79, Y=79, T=79
#> mz ion type pos z seq peptide
#> 1 72.04439 b1 b 1 1 A ARGSHKATC
#> 2 228.14550 b2 b 2 1 AR ARGSHKATC
#> 3 285.16696 b3 b 3 1 ARG ARGSHKATC
#> 4 372.19899 b4 b 4 1 ARGS ARGSHKATC
#> 5 509.25790 b5 b 5 1 ARGSH ARGSHKATC
#> 6 637.35286 b6 b 6 1 ARGSHK ARGSHKATC
#> 7 708.38997 b7 b 7 1 ARGSHKA ARGSHKATC
#> 8 809.43765 b8 b 8 1 ARGSHKAT ARGSHKATC
#> 9 179.02703 y1 y 1 1 C ARGSHKATC
#> 10 280.07471 y2 y 2 1 TC ARGSHKATC
#> 11 351.11182 y3 y 3 1 ATC ARGSHKATC
#> 12 479.20678 y4 y 4 1 KATC ARGSHKATC
#> 13 616.26569 y5 y 5 1 HKATC ARGSHKATC
#> 14 703.29772 y6 y 6 1 SHKATC ARGSHKATC
#> 15 760.31918 y7 y 7 1 GSHKATC ARGSHKATC
#> 16 916.42029 y8 y 8 1 RGSHKATC ARGSHKATC
#> 17 491.24733 b5_ b_ 5 1 ARGSH ARGSHKATC
#> 18 619.34229 b6_ b_ 6 1 ARGSHK ARGSHKATC
#> 19 690.37940 b7_ b_ 7 1 ARGSHKA ARGSHKATC
#> 20 791.42708 b8_ b_ 8 1 ARGSHKAT ARGSHKATC
#> 21 333.10126 y3_ y_ 3 1 ATC ARGSHKATC
#> 22 461.19622 y4_ y_ 4 1 KATC ARGSHKATC
#> 23 598.25513 y5_ y_ 5 1 HKATC ARGSHKATC
#> 24 685.28716 y6_ y_ 6 1 SHKATC ARGSHKATC
#> 25 742.30862 y7_ y_ 7 1 GSHKATC ARGSHKATC
#> 26 898.40973 y8_ y_ 8 1 RGSHKATC ARGSHKATC
#> 27 161.01647 y1_ y_ 1 1 C ARGSHKATC
#> 28 262.06415 y2_ y_ 2 1 TC ARGSHKATC
#> 29 268.14041 b3* b* 3 1 ARG ARGSHKATC
#> 30 355.17244 b4* b* 4 1 ARGS ARGSHKATC
#> 31 492.23135 b5* b* 5 1 ARGSH ARGSHKATC
#> 32 620.32631 b6* b* 6 1 ARGSHK ARGSHKATC
#> 33 691.36342 b7* b* 7 1 ARGSHKA ARGSHKATC
#> 34 792.41110 b8* b* 8 1 ARGSHKAT ARGSHKATC
#> 35 462.18023 y4* y* 4 1 KATC ARGSHKATC
#> 36 599.23914 y5* y* 5 1 HKATC ARGSHKATC
#> 37 686.27117 y6* y* 6 1 SHKATC ARGSHKATC
#> 38 743.29263 y7* y* 7 1 GSHKATC ARGSHKATC
#> 39 899.39374 y8* y* 8 1 RGSHKATC ARGSHKATC
#> 40 72.04439 b1 b 1 1 A ARGS[79]HKATC
#> 41 228.14550 b2 b 2 1 AR ARGS[79]HKATC
#> 42 285.16696 b3 b 3 1 ARG ARGS[79]HKATC
#> 43 451.19899 b4 b 4 1 ARGS ARGS[79]HKATC
#> 44 588.25790 b5 b 5 1 ARGSH ARGS[79]HKATC
#> 45 716.35286 b6 b 6 1 ARGSHK ARGS[79]HKATC
#> 46 787.38997 b7 b 7 1 ARGSHKA ARGS[79]HKATC
#> 47 888.43765 b8 b 8 1 ARGSHKAT ARGS[79]HKATC
#> 48 179.02703 y1 y 1 1 C ARGS[79]HKATC
#> 49 280.07471 y2 y 2 1 TC ARGS[79]HKATC
#> 50 351.11182 y3 y 3 1 ATC ARGS[79]HKATC
#> 51 479.20678 y4 y 4 1 KATC ARGS[79]HKATC
#> 52 616.26569 y5 y 5 1 HKATC ARGS[79]HKATC
#> 53 782.29772 y6 y 6 1 SHKATC ARGS[79]HKATC
#> 54 839.31918 y7 y 7 1 GSHKATC ARGS[79]HKATC
#> 55 995.42029 y8 y 8 1 RGSHKATC ARGS[79]HKATC
#> 56 570.24733 b5_ b_ 5 1 ARGSH ARGS[79]HKATC
#> 57 698.34229 b6_ b_ 6 1 ARGSHK ARGS[79]HKATC
#> 58 769.37940 b7_ b_ 7 1 ARGSHKA ARGS[79]HKATC
#> 59 870.42708 b8_ b_ 8 1 ARGSHKAT ARGS[79]HKATC
#> 60 333.10126 y3_ y_ 3 1 ATC ARGS[79]HKATC
#> 61 461.19622 y4_ y_ 4 1 KATC ARGS[79]HKATC
#> 62 598.25513 y5_ y_ 5 1 HKATC ARGS[79]HKATC
#> 63 764.28716 y6_ y_ 6 1 SHKATC ARGS[79]HKATC
#> 64 821.30862 y7_ y_ 7 1 GSHKATC ARGS[79]HKATC
#> 65 977.40973 y8_ y_ 8 1 RGSHKATC ARGS[79]HKATC
#> 66 161.01647 y1_ y_ 1 1 C ARGS[79]HKATC
#> 67 262.06415 y2_ y_ 2 1 TC ARGS[79]HKATC
#> 68 268.14041 b3* b* 3 1 ARG ARGS[79]HKATC
#> 69 434.17244 b4* b* 4 1 ARGS ARGS[79]HKATC
#> 70 571.23135 b5* b* 5 1 ARGSH ARGS[79]HKATC
#> 71 699.32631 b6* b* 6 1 ARGSHK ARGS[79]HKATC
#> 72 770.36342 b7* b* 7 1 ARGSHKA ARGS[79]HKATC
#> 73 871.41110 b8* b* 8 1 ARGSHKAT ARGS[79]HKATC
#> 74 462.18023 y4* y* 4 1 KATC ARGS[79]HKATC
#> 75 599.23914 y5* y* 5 1 HKATC ARGS[79]HKATC
#> 76 765.27117 y6* y* 6 1 SHKATC ARGS[79]HKATC
#> 77 822.29263 y7* y* 7 1 GSHKATC ARGS[79]HKATC
#> 78 978.39374 y8* y* 8 1 RGSHKATC ARGS[79]HKATC
#> 79 72.04439 b1 b 1 1 A ARGSHKAT[79]C
#> 80 228.14550 b2 b 2 1 AR ARGSHKAT[79]C
#> 81 285.16696 b3 b 3 1 ARG ARGSHKAT[79]C
#> 82 372.19899 b4 b 4 1 ARGS ARGSHKAT[79]C
#> 83 509.25790 b5 b 5 1 ARGSH ARGSHKAT[79]C
#> 84 637.35286 b6 b 6 1 ARGSHK ARGSHKAT[79]C
#> 85 708.38997 b7 b 7 1 ARGSHKA ARGSHKAT[79]C
#> 86 888.43765 b8 b 8 1 ARGSHKAT ARGSHKAT[79]C
#> 87 179.02703 y1 y 1 1 C ARGSHKAT[79]C
#> 88 359.07471 y2 y 2 1 TC ARGSHKAT[79]C
#> 89 430.11182 y3 y 3 1 ATC ARGSHKAT[79]C
#> 90 558.20678 y4 y 4 1 KATC ARGSHKAT[79]C
#> 91 695.26569 y5 y 5 1 HKATC ARGSHKAT[79]C
#> 92 782.29772 y6 y 6 1 SHKATC ARGSHKAT[79]C
#> 93 839.31918 y7 y 7 1 GSHKATC ARGSHKAT[79]C
#> 94 995.42029 y8 y 8 1 RGSHKATC ARGSHKAT[79]C
#> 95 491.24733 b5_ b_ 5 1 ARGSH ARGSHKAT[79]C
#> 96 619.34229 b6_ b_ 6 1 ARGSHK ARGSHKAT[79]C
#> 97 690.37940 b7_ b_ 7 1 ARGSHKA ARGSHKAT[79]C
#> 98 870.42708 b8_ b_ 8 1 ARGSHKAT ARGSHKAT[79]C
#> 99 412.10126 y3_ y_ 3 1 ATC ARGSHKAT[79]C
#> 100 540.19622 y4_ y_ 4 1 KATC ARGSHKAT[79]C
#> 101 677.25513 y5_ y_ 5 1 HKATC ARGSHKAT[79]C
#> 102 764.28716 y6_ y_ 6 1 SHKATC ARGSHKAT[79]C
#> 103 821.30862 y7_ y_ 7 1 GSHKATC ARGSHKAT[79]C
#> 104 977.40973 y8_ y_ 8 1 RGSHKATC ARGSHKAT[79]C
#> 105 161.01647 y1_ y_ 1 1 C ARGSHKAT[79]C
#> 106 341.06415 y2_ y_ 2 1 TC ARGSHKAT[79]C
#> 107 268.14041 b3* b* 3 1 ARG ARGSHKAT[79]C
#> 108 355.17244 b4* b* 4 1 ARGS ARGSHKAT[79]C
#> 109 492.23135 b5* b* 5 1 ARGSH ARGSHKAT[79]C
#> 110 620.32631 b6* b* 6 1 ARGSHK ARGSHKAT[79]C
#> 111 691.36342 b7* b* 7 1 ARGSHKA ARGSHKAT[79]C
#> 112 871.41110 b8* b* 8 1 ARGSHKAT ARGSHKAT[79]C
#> 113 541.18023 y4* y* 4 1 KATC ARGSHKAT[79]C
#> 114 678.23914 y5* y* 5 1 HKATC ARGSHKAT[79]C
#> 115 765.27117 y6* y* 6 1 SHKATC ARGSHKAT[79]C
#> 116 822.29263 y7* y* 7 1 GSHKATC ARGSHKAT[79]C
#> 117 978.39374 y8* y* 8 1 RGSHKATC ARGSHKAT[79]C
#> 118 72.04439 b1 b 1 1 A ARGS[79]HKAT[79]C
#> 119 228.14550 b2 b 2 1 AR ARGS[79]HKAT[79]C
#> 120 285.16696 b3 b 3 1 ARG ARGS[79]HKAT[79]C
#> 121 451.19899 b4 b 4 1 ARGS ARGS[79]HKAT[79]C
#> 122 588.25790 b5 b 5 1 ARGSH ARGS[79]HKAT[79]C
#> 123 716.35286 b6 b 6 1 ARGSHK ARGS[79]HKAT[79]C
#> 124 787.38997 b7 b 7 1 ARGSHKA ARGS[79]HKAT[79]C
#> 125 967.43765 b8 b 8 1 ARGSHKAT ARGS[79]HKAT[79]C
#> 126 179.02703 y1 y 1 1 C ARGS[79]HKAT[79]C
#> 127 359.07471 y2 y 2 1 TC ARGS[79]HKAT[79]C
#> 128 430.11182 y3 y 3 1 ATC ARGS[79]HKAT[79]C
#> 129 558.20678 y4 y 4 1 KATC ARGS[79]HKAT[79]C
#> 130 695.26569 y5 y 5 1 HKATC ARGS[79]HKAT[79]C
#> 131 861.29772 y6 y 6 1 SHKATC ARGS[79]HKAT[79]C
#> 132 918.31918 y7 y 7 1 GSHKATC ARGS[79]HKAT[79]C
#> 133 1074.42029 y8 y 8 1 RGSHKATC ARGS[79]HKAT[79]C
#> 134 570.24733 b5_ b_ 5 1 ARGSH ARGS[79]HKAT[79]C
#> 135 698.34229 b6_ b_ 6 1 ARGSHK ARGS[79]HKAT[79]C
#> 136 769.37940 b7_ b_ 7 1 ARGSHKA ARGS[79]HKAT[79]C
#> 137 949.42708 b8_ b_ 8 1 ARGSHKAT ARGS[79]HKAT[79]C
#> 138 412.10126 y3_ y_ 3 1 ATC ARGS[79]HKAT[79]C
#> 139 540.19622 y4_ y_ 4 1 KATC ARGS[79]HKAT[79]C
#> 140 677.25513 y5_ y_ 5 1 HKATC ARGS[79]HKAT[79]C
#> 141 843.28716 y6_ y_ 6 1 SHKATC ARGS[79]HKAT[79]C
#> 142 900.30862 y7_ y_ 7 1 GSHKATC ARGS[79]HKAT[79]C
#> 143 1056.40973 y8_ y_ 8 1 RGSHKATC ARGS[79]HKAT[79]C
#> 144 161.01647 y1_ y_ 1 1 C ARGS[79]HKAT[79]C
#> 145 341.06415 y2_ y_ 2 1 TC ARGS[79]HKAT[79]C
#> 146 268.14041 b3* b* 3 1 ARG ARGS[79]HKAT[79]C
#> 147 434.17244 b4* b* 4 1 ARGS ARGS[79]HKAT[79]C
#> 148 571.23135 b5* b* 5 1 ARGSH ARGS[79]HKAT[79]C
#> 149 699.32631 b6* b* 6 1 ARGSHK ARGS[79]HKAT[79]C
#> 150 770.36342 b7* b* 7 1 ARGSHKA ARGS[79]HKAT[79]C
#> 151 950.41110 b8* b* 8 1 ARGSHKAT ARGS[79]HKAT[79]C
#> 152 541.18023 y4* y* 4 1 KATC ARGS[79]HKAT[79]C
#> 153 678.23914 y5* y* 5 1 HKATC ARGS[79]HKAT[79]C
#> 154 844.27117 y6* y* 6 1 SHKATC ARGS[79]HKAT[79]C
#> 155 901.29263 y7* y* 7 1 GSHKATC ARGS[79]HKAT[79]C
#> 156 1057.39374 y8* y* 8 1 RGSHKATC ARGS[79]HKAT[79]C