These method calculates a-, b-, c-, x-, y- and z-ions produced by fragmentation.
Available methods
The default method with signature sequence = "character" and
object = "missing" calculates the theoretical fragments for a
peptide sequence. It returns a data.frame with the columns
mz, ion, type, pos, z and seq.
Additional method can be defined that will adapt their behaviour
based on spectra defined in object. See for example the MSnbase
package that implements a method for objects of class
Spectrum2.
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 desired charge state; default is 1.
A named numeric vector of used
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.
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 _) and
c("K", "N", "Q", "R") for "ammonia" (shown with an *) are
supported.
logical(1). If TRUE (default) the used
modifications are printed.
The methods with oject = "missing" returns a
data.frame.
## calculate fragments for ACE with default modification
calculateFragments("ACE", modifications = c(C = 57.02146))
#> Modifications used: C=57.02146
#> mz ion type pos z seq
#> 1 72.04439 b1 b 1 1 A
#> 2 232.07504 b2 b 2 1 AC
#> 3 148.06043 y1 y 1 1 E
#> 4 308.09108 y2 y 2 1 CE
#> 5 130.04987 y1_ y_ 1 1 E
#> 6 290.08052 y2_ y_ 2 1 CE
## calculate fragments for ACE with an addition N-terminal modification
calculateFragments("ACE", modifications = c(C = 57.02146, Nterm = 229.1629))
#> Modifications used: C=57.02146, Nterm=229.1629
#> mz ion type pos z seq
#> 1 301.2073 b1 b 1 1 A
#> 2 461.2379 b2 b 2 1 AC
#> 3 148.0604 y1 y 1 1 E
#> 4 308.0911 y2 y 2 1 CE
#> 5 130.0499 y1_ y_ 1 1 E
#> 6 290.0805 y2_ y_ 2 1 CE
## calculate fragments for ACE without any modifications
calculateFragments("ACE", modifications = NULL)
#> Modifications used: None
#> mz ion type pos z seq
#> 1 72.04439 b1 b 1 1 A
#> 2 175.05358 b2 b 2 1 AC
#> 3 148.06043 y1 y 1 1 E
#> 4 251.06962 y2 y 2 1 CE
#> 5 130.04987 y1_ y_ 1 1 E
#> 6 233.05906 y2_ y_ 2 1 CE
calculateFragments("VESITARHGEVLQLRPK",
type = c("a", "b", "c", "x", "y", "z"),
z = 1:2)
#> Modifications used: C=57.02146
#> mz ion type pos z seq
#> 1 72.08077 a1 a 1 1 V
#> 2 36.54402 a1 a 1 2 V
#> 3 201.12336 a2 a 2 1 VE
#> 4 101.06532 a2 a 2 2 VE
#> 5 288.15539 a3 a 3 1 VES
#> 6 144.58133 a3 a 3 2 VES
#> 7 401.23945 a4 a 4 1 VESI
#> 8 201.12336 a4 a 4 2 VESI
#> 9 502.28713 a5 a 5 1 VESIT
#> 10 251.64720 a5 a 5 2 VESIT
#> 11 573.32424 a6 a 6 1 VESITA
#> 12 287.16576 a6 a 6 2 VESITA
#> 13 729.42535 a7 a 7 1 VESITAR
#> 14 365.21631 a7 a 7 2 VESITAR
#> 15 866.48426 a8 a 8 1 VESITARH
#> 16 433.74577 a8 a 8 2 VESITARH
#> 17 923.50572 a9 a 9 1 VESITARHG
#> 18 462.25650 a9 a 9 2 VESITARHG
#> 19 1052.54831 a10 a 10 1 VESITARHGE
#> 20 526.77779 a10 a 10 2 VESITARHGE
#> 21 1151.61672 a11 a 11 1 VESITARHGEV
#> 22 576.31200 a11 a 11 2 VESITARHGEV
#> 23 1264.70078 a12 a 12 1 VESITARHGEVL
#> 24 632.85403 a12 a 12 2 VESITARHGEVL
#> 25 1392.75936 a13 a 13 1 VESITARHGEVLQ
#> 26 696.88332 a13 a 13 2 VESITARHGEVLQ
#> 27 1505.84342 a14 a 14 1 VESITARHGEVLQL
#> 28 753.42535 a14 a 14 2 VESITARHGEVLQL
#> 29 1661.94453 a15 a 15 1 VESITARHGEVLQLR
#> 30 831.47590 a15 a 15 2 VESITARHGEVLQLR
#> 31 1758.99729 a16 a 16 1 VESITARHGEVLQLRP
#> 32 880.00228 a16 a 16 2 VESITARHGEVLQLRP
#> 33 100.07569 b1 b 1 1 V
#> 34 50.54148 b1 b 1 2 V
#> 35 229.11828 b2 b 2 1 VE
#> 36 115.06278 b2 b 2 2 VE
#> 37 316.15031 b3 b 3 1 VES
#> 38 158.57879 b3 b 3 2 VES
#> 39 429.23437 b4 b 4 1 VESI
#> 40 215.12082 b4 b 4 2 VESI
#> 41 530.28205 b5 b 5 1 VESIT
#> 42 265.64466 b5 b 5 2 VESIT
#> 43 601.31916 b6 b 6 1 VESITA
#> 44 301.16322 b6 b 6 2 VESITA
#> 45 757.42027 b7 b 7 1 VESITAR
#> 46 379.21377 b7 b 7 2 VESITAR
#> 47 894.47918 b8 b 8 1 VESITARH
#> 48 447.74323 b8 b 8 2 VESITARH
#> 49 951.50064 b9 b 9 1 VESITARHG
#> 50 476.25396 b9 b 9 2 VESITARHG
#> 51 1080.54323 b10 b 10 1 VESITARHGE
#> 52 540.77525 b10 b 10 2 VESITARHGE
#> 53 1179.61164 b11 b 11 1 VESITARHGEV
#> 54 590.30946 b11 b 11 2 VESITARHGEV
#> 55 1292.69570 b12 b 12 1 VESITARHGEVL
#> 56 646.85149 b12 b 12 2 VESITARHGEVL
#> 57 1420.75428 b13 b 13 1 VESITARHGEVLQ
#> 58 710.88078 b13 b 13 2 VESITARHGEVLQ
#> 59 1533.83834 b14 b 14 1 VESITARHGEVLQL
#> 60 767.42281 b14 b 14 2 VESITARHGEVLQL
#> 61 1689.93945 b15 b 15 1 VESITARHGEVLQLR
#> 62 845.47336 b15 b 15 2 VESITARHGEVLQLR
#> 63 1786.99221 b16 b 16 1 VESITARHGEVLQLRP
#> 64 893.99974 b16 b 16 2 VESITARHGEVLQLRP
#> 65 117.10224 c1 c 1 1 V
#> 66 59.05476 c1 c 1 2 V
#> 67 246.14482 c2 c 2 1 VE
#> 68 123.57605 c2 c 2 2 VE
#> 69 333.17685 c3 c 3 1 VES
#> 70 167.09207 c3 c 3 2 VES
#> 71 446.26091 c4 c 4 1 VESI
#> 72 223.63410 c4 c 4 2 VESI
#> 73 547.30860 c5 c 5 1 VESIT
#> 74 274.15794 c5 c 5 2 VESIT
#> 75 618.34571 c6 c 6 1 VESITA
#> 76 309.67649 c6 c 6 2 VESITA
#> 77 774.44682 c7 c 7 1 VESITAR
#> 78 387.72705 c7 c 7 2 VESITAR
#> 79 911.50573 c8 c 8 1 VESITARH
#> 80 456.25650 c8 c 8 2 VESITARH
#> 81 968.52719 c9 c 9 1 VESITARHG
#> 82 484.76723 c9 c 9 2 VESITARHG
#> 83 1097.56977 c10 c 10 1 VESITARHGE
#> 84 549.28853 c10 c 10 2 VESITARHGE
#> 85 1196.63819 c11 c 11 1 VESITARHGEV
#> 86 598.82273 c11 c 11 2 VESITARHGEV
#> 87 1309.72224 c12 c 12 1 VESITARHGEVL
#> 88 655.36476 c12 c 12 2 VESITARHGEVL
#> 89 1437.78083 c13 c 13 1 VESITARHGEVLQ
#> 90 719.39405 c13 c 13 2 VESITARHGEVLQ
#> 91 1550.86488 c14 c 14 1 VESITARHGEVLQL
#> 92 775.93608 c14 c 14 2 VESITARHGEVLQL
#> 93 1706.96600 c15 c 15 1 VESITARHGEVLQLR
#> 94 853.98664 c15 c 15 2 VESITARHGEVLQLR
#> 95 1804.01876 c16 c 16 1 VESITARHGEVLQLRP
#> 96 902.51302 c16 c 16 2 VESITARHGEVLQLRP
#> 97 173.09207 x1 x 1 1 K
#> 98 87.04967 x1 x 1 2 K
#> 99 270.14483 x2 x 2 1 PK
#> 100 135.57605 x2 x 2 2 PK
#> 101 426.24594 x3 x 3 1 RPK
#> 102 213.62661 x3 x 3 2 RPK
#> 103 539.33000 x4 x 4 1 LRPK
#> 104 270.16864 x4 x 4 2 LRPK
#> 105 667.38858 x5 x 5 1 QLRPK
#> 106 334.19793 x5 x 5 2 QLRPK
#> 107 780.47264 x6 x 6 1 LQLRPK
#> 108 390.73996 x6 x 6 2 LQLRPK
#> 109 879.54105 x7 x 7 1 VLQLRPK
#> 110 440.27416 x7 x 7 2 VLQLRPK
#> 111 1008.58364 x8 x 8 1 EVLQLRPK
#> 112 504.79546 x8 x 8 2 EVLQLRPK
#> 113 1065.60510 x9 x 9 1 GEVLQLRPK
#> 114 533.30619 x9 x 9 2 GEVLQLRPK
#> 115 1202.66401 x10 x 10 1 HGEVLQLRPK
#> 116 601.83564 x10 x 10 2 HGEVLQLRPK
#> 117 1358.76512 x11 x 11 1 RHGEVLQLRPK
#> 118 679.88620 x11 x 11 2 RHGEVLQLRPK
#> 119 1429.80223 x12 x 12 1 ARHGEVLQLRPK
#> 120 715.40475 x12 x 12 2 ARHGEVLQLRPK
#> 121 1530.84991 x13 x 13 1 TARHGEVLQLRPK
#> 122 765.92859 x13 x 13 2 TARHGEVLQLRPK
#> 123 1643.93397 x14 x 14 1 ITARHGEVLQLRPK
#> 124 822.47062 x14 x 14 2 ITARHGEVLQLRPK
#> 125 1730.96600 x15 x 15 1 SITARHGEVLQLRPK
#> 126 865.98664 x15 x 15 2 SITARHGEVLQLRPK
#> 127 1860.00859 x16 x 16 1 ESITARHGEVLQLRPK
#> 128 930.50793 x16 x 16 2 ESITARHGEVLQLRPK
#> 129 147.11280 y1 y 1 1 K
#> 130 74.06004 y1 y 1 2 K
#> 131 244.16556 y2 y 2 1 PK
#> 132 122.58642 y2 y 2 2 PK
#> 133 400.26667 y3 y 3 1 RPK
#> 134 200.63697 y3 y 3 2 RPK
#> 135 513.35073 y4 y 4 1 LRPK
#> 136 257.17900 y4 y 4 2 LRPK
#> 137 641.40931 y5 y 5 1 QLRPK
#> 138 321.20829 y5 y 5 2 QLRPK
#> 139 754.49337 y6 y 6 1 LQLRPK
#> 140 377.75032 y6 y 6 2 LQLRPK
#> 141 853.56178 y7 y 7 1 VLQLRPK
#> 142 427.28453 y7 y 7 2 VLQLRPK
#> 143 982.60437 y8 y 8 1 EVLQLRPK
#> 144 491.80582 y8 y 8 2 EVLQLRPK
#> 145 1039.62583 y9 y 9 1 GEVLQLRPK
#> 146 520.31655 y9 y 9 2 GEVLQLRPK
#> 147 1176.68474 y10 y 10 1 HGEVLQLRPK
#> 148 588.84601 y10 y 10 2 HGEVLQLRPK
#> 149 1332.78585 y11 y 11 1 RHGEVLQLRPK
#> 150 666.89656 y11 y 11 2 RHGEVLQLRPK
#> 151 1403.82296 y12 y 12 1 ARHGEVLQLRPK
#> 152 702.41512 y12 y 12 2 ARHGEVLQLRPK
#> 153 1504.87064 y13 y 13 1 TARHGEVLQLRPK
#> 154 752.93896 y13 y 13 2 TARHGEVLQLRPK
#> 155 1617.95470 y14 y 14 1 ITARHGEVLQLRPK
#> 156 809.48099 y14 y 14 2 ITARHGEVLQLRPK
#> 157 1704.98673 y15 y 15 1 SITARHGEVLQLRPK
#> 158 852.99700 y15 y 15 2 SITARHGEVLQLRPK
#> 159 1834.02932 y16 y 16 1 ESITARHGEVLQLRPK
#> 160 917.51830 y16 y 16 2 ESITARHGEVLQLRPK
#> 161 130.08625 z1 z 1 1 K
#> 162 65.54676 z1 z 1 2 K
#> 163 227.13901 z2 z 2 1 PK
#> 164 114.07314 z2 z 2 2 PK
#> 165 383.24012 z3 z 3 1 RPK
#> 166 192.12370 z3 z 3 2 RPK
#> 167 496.32418 z4 z 4 1 LRPK
#> 168 248.66573 z4 z 4 2 LRPK
#> 169 624.38276 z5 z 5 1 QLRPK
#> 170 312.69502 z5 z 5 2 QLRPK
#> 171 737.46682 z6 z 6 1 LQLRPK
#> 172 369.23705 z6 z 6 2 LQLRPK
#> 173 836.53523 z7 z 7 1 VLQLRPK
#> 174 418.77125 z7 z 7 2 VLQLRPK
#> 175 965.57782 z8 z 8 1 EVLQLRPK
#> 176 483.29255 z8 z 8 2 EVLQLRPK
#> 177 1022.59928 z9 z 9 1 GEVLQLRPK
#> 178 511.80328 z9 z 9 2 GEVLQLRPK
#> 179 1159.65819 z10 z 10 1 HGEVLQLRPK
#> 180 580.33273 z10 z 10 2 HGEVLQLRPK
#> 181 1315.75930 z11 z 11 1 RHGEVLQLRPK
#> 182 658.38329 z11 z 11 2 RHGEVLQLRPK
#> 183 1386.79641 z12 z 12 1 ARHGEVLQLRPK
#> 184 693.90184 z12 z 12 2 ARHGEVLQLRPK
#> 185 1487.84409 z13 z 13 1 TARHGEVLQLRPK
#> 186 744.42568 z13 z 13 2 TARHGEVLQLRPK
#> 187 1600.92815 z14 z 14 1 ITARHGEVLQLRPK
#> 188 800.96771 z14 z 14 2 ITARHGEVLQLRPK
#> 189 1687.96018 z15 z 15 1 SITARHGEVLQLRPK
#> 190 844.48373 z15 z 15 2 SITARHGEVLQLRPK
#> 191 1817.00277 z16 z 16 1 ESITARHGEVLQLRPK
#> 192 909.00502 z16 z 16 2 ESITARHGEVLQLRPK
#> 193 383.22889 a4_ a_ 4 1 VESI
#> 194 192.11808 a4_ a_ 4 2 VESI
#> 195 484.27657 a5_ a_ 5 1 VESIT
#> 196 242.64192 a5_ a_ 5 2 VESIT
#> 197 555.31368 a6_ a_ 6 1 VESITA
#> 198 278.16048 a6_ a_ 6 2 VESITA
#> 199 711.41479 a7_ a_ 7 1 VESITAR
#> 200 356.21103 a7_ a_ 7 2 VESITAR
#> 201 848.47370 a8_ a_ 8 1 VESITARH
#> 202 424.74049 a8_ a_ 8 2 VESITARH
#> 203 905.49516 a9_ a_ 9 1 VESITARHG
#> 204 453.25122 a9_ a_ 9 2 VESITARHG
#> 205 1034.53775 a10_ a_ 10 1 VESITARHGE
#> 206 517.77251 a10_ a_ 10 2 VESITARHGE
#> 207 1133.60616 a11_ a_ 11 1 VESITARHGEV
#> 208 567.30672 a11_ a_ 11 2 VESITARHGEV
#> 209 1246.69022 a12_ a_ 12 1 VESITARHGEVL
#> 210 623.84875 a12_ a_ 12 2 VESITARHGEVL
#> 211 1374.74880 a13_ a_ 13 1 VESITARHGEVLQ
#> 212 687.87804 a13_ a_ 13 2 VESITARHGEVLQ
#> 213 1487.83286 a14_ a_ 14 1 VESITARHGEVLQL
#> 214 744.42007 a14_ a_ 14 2 VESITARHGEVLQL
#> 215 1643.93397 a15_ a_ 15 1 VESITARHGEVLQLR
#> 216 822.47062 a15_ a_ 15 2 VESITARHGEVLQLR
#> 217 1740.98673 a16_ a_ 16 1 VESITARHGEVLQLRP
#> 218 870.99700 a16_ a_ 16 2 VESITARHGEVLQLRP
#> 219 411.22380 b4_ b_ 4 1 VESI
#> 220 206.11554 b4_ b_ 4 2 VESI
#> 221 512.27148 b5_ b_ 5 1 VESIT
#> 222 256.63938 b5_ b_ 5 2 VESIT
#> 223 583.30859 b6_ b_ 6 1 VESITA
#> 224 292.15793 b6_ b_ 6 2 VESITA
#> 225 739.40970 b7_ b_ 7 1 VESITAR
#> 226 370.20849 b7_ b_ 7 2 VESITAR
#> 227 876.46861 b8_ b_ 8 1 VESITARH
#> 228 438.73794 b8_ b_ 8 2 VESITARH
#> 229 933.49007 b9_ b_ 9 1 VESITARHG
#> 230 467.24867 b9_ b_ 9 2 VESITARHG
#> 231 1062.53266 b10_ b_ 10 1 VESITARHGE
#> 232 531.76997 b10_ b_ 10 2 VESITARHGE
#> 233 1161.60107 b11_ b_ 11 1 VESITARHGEV
#> 234 581.30417 b11_ b_ 11 2 VESITARHGEV
#> 235 1274.68513 b12_ b_ 12 1 VESITARHGEVL
#> 236 637.84620 b12_ b_ 12 2 VESITARHGEVL
#> 237 1402.74371 b13_ b_ 13 1 VESITARHGEVLQ
#> 238 701.87549 b13_ b_ 13 2 VESITARHGEVLQ
#> 239 1515.82777 b14_ b_ 14 1 VESITARHGEVLQL
#> 240 758.41752 b14_ b_ 14 2 VESITARHGEVLQL
#> 241 1671.92888 b15_ b_ 15 1 VESITARHGEVLQLR
#> 242 836.46808 b15_ b_ 15 2 VESITARHGEVLQLR
#> 243 1768.98164 b16_ b_ 16 1 VESITARHGEVLQLRP
#> 244 884.99446 b16_ b_ 16 2 VESITARHGEVLQLRP
#> 245 428.25035 c4_ c_ 4 1 VESI
#> 246 214.62881 c4_ c_ 4 2 VESI
#> 247 529.29803 c5_ c_ 5 1 VESIT
#> 248 265.15265 c5_ c_ 5 2 VESIT
#> 249 600.33514 c6_ c_ 6 1 VESITA
#> 250 300.67121 c6_ c_ 6 2 VESITA
#> 251 756.43625 c7_ c_ 7 1 VESITAR
#> 252 378.72176 c7_ c_ 7 2 VESITAR
#> 253 893.49516 c8_ c_ 8 1 VESITARH
#> 254 447.25122 c8_ c_ 8 2 VESITARH
#> 255 950.51662 c9_ c_ 9 1 VESITARHG
#> 256 475.76195 c9_ c_ 9 2 VESITARHG
#> 257 1079.55921 c10_ c_ 10 1 VESITARHGE
#> 258 540.28324 c10_ c_ 10 2 VESITARHGE
#> 259 1178.62762 c11_ c_ 11 1 VESITARHGEV
#> 260 589.81745 c11_ c_ 11 2 VESITARHGEV
#> 261 1291.71168 c12_ c_ 12 1 VESITARHGEVL
#> 262 646.35948 c12_ c_ 12 2 VESITARHGEVL
#> 263 1419.77026 c13_ c_ 13 1 VESITARHGEVLQ
#> 264 710.38877 c13_ c_ 13 2 VESITARHGEVLQ
#> 265 1532.85432 c14_ c_ 14 1 VESITARHGEVLQL
#> 266 766.93080 c14_ c_ 14 2 VESITARHGEVLQL
#> 267 1688.95543 c15_ c_ 15 1 VESITARHGEVLQLR
#> 268 844.98135 c15_ c_ 15 2 VESITARHGEVLQLR
#> 269 1786.00819 c16_ c_ 16 1 VESITARHGEVLQLRP
#> 270 893.50773 c16_ c_ 16 2 VESITARHGEVLQLRP
#> 271 990.57307 x8_ x_ 8 1 EVLQLRPK
#> 272 495.79017 x8_ x_ 8 2 EVLQLRPK
#> 273 1625.92340 x14_ x_ 14 1 ITARHGEVLQLRPK
#> 274 813.46534 x14_ x_ 14 2 ITARHGEVLQLRPK
#> 275 1712.95543 x15_ x_ 15 1 SITARHGEVLQLRPK
#> 276 856.98135 x15_ x_ 15 2 SITARHGEVLQLRPK
#> 277 1841.99802 x16_ x_ 16 1 ESITARHGEVLQLRPK
#> 278 921.50265 x16_ x_ 16 2 ESITARHGEVLQLRPK
#> 279 964.59381 y8_ y_ 8 1 EVLQLRPK
#> 280 482.80054 y8_ y_ 8 2 EVLQLRPK
#> 281 1599.94414 y14_ y_ 14 1 ITARHGEVLQLRPK
#> 282 800.47571 y14_ y_ 14 2 ITARHGEVLQLRPK
#> 283 1686.97617 y15_ y_ 15 1 SITARHGEVLQLRPK
#> 284 843.99172 y15_ y_ 15 2 SITARHGEVLQLRPK
#> 285 1816.01876 y16_ y_ 16 1 ESITARHGEVLQLRPK
#> 286 908.51302 y16_ y_ 16 2 ESITARHGEVLQLRPK
#> 287 947.56726 z8_ z_ 8 1 EVLQLRPK
#> 288 474.28727 z8_ z_ 8 2 EVLQLRPK
#> 289 1582.91759 z14_ z_ 14 1 ITARHGEVLQLRPK
#> 290 791.96243 z14_ z_ 14 2 ITARHGEVLQLRPK
#> 291 1669.94962 z15_ z_ 15 1 SITARHGEVLQLRPK
#> 292 835.47845 z15_ z_ 15 2 SITARHGEVLQLRPK
#> 293 1798.99221 z16_ z_ 16 1 ESITARHGEVLQLRPK
#> 294 899.99974 z16_ z_ 16 2 ESITARHGEVLQLRPK
#> 295 155.08150 x1_ x_ 1 1 K
#> 296 78.04439 x1_ x_ 1 2 K
#> 297 252.13426 x2_ x_ 2 1 PK
#> 298 126.57077 x2_ x_ 2 2 PK
#> 299 408.23537 x3_ x_ 3 1 RPK
#> 300 204.62132 x3_ x_ 3 2 RPK
#> 301 521.31943 x4_ x_ 4 1 LRPK
#> 302 261.16335 x4_ x_ 4 2 LRPK
#> 303 649.37801 x5_ x_ 5 1 QLRPK
#> 304 325.19264 x5_ x_ 5 2 QLRPK
#> 305 762.46207 x6_ x_ 6 1 LQLRPK
#> 306 381.73467 x6_ x_ 6 2 LQLRPK
#> 307 861.53048 x7_ x_ 7 1 VLQLRPK
#> 308 431.26888 x7_ x_ 7 2 VLQLRPK
#> 309 1047.59453 x9_ x_ 9 1 GEVLQLRPK
#> 310 524.30090 x9_ x_ 9 2 GEVLQLRPK
#> 311 1184.65344 x10_ x_ 10 1 HGEVLQLRPK
#> 312 592.83036 x10_ x_ 10 2 HGEVLQLRPK
#> 313 1340.75455 x11_ x_ 11 1 RHGEVLQLRPK
#> 314 670.88091 x11_ x_ 11 2 RHGEVLQLRPK
#> 315 1411.79166 x12_ x_ 12 1 ARHGEVLQLRPK
#> 316 706.39947 x12_ x_ 12 2 ARHGEVLQLRPK
#> 317 1512.83934 x13_ x_ 13 1 TARHGEVLQLRPK
#> 318 756.92331 x13_ x_ 13 2 TARHGEVLQLRPK
#> 319 129.10224 y1_ y_ 1 1 K
#> 320 65.05476 y1_ y_ 1 2 K
#> 321 226.15500 y2_ y_ 2 1 PK
#> 322 113.58114 y2_ y_ 2 2 PK
#> 323 382.25611 y3_ y_ 3 1 RPK
#> 324 191.63169 y3_ y_ 3 2 RPK
#> 325 495.34017 y4_ y_ 4 1 LRPK
#> 326 248.17372 y4_ y_ 4 2 LRPK
#> 327 623.39875 y5_ y_ 5 1 QLRPK
#> 328 312.20301 y5_ y_ 5 2 QLRPK
#> 329 736.48281 y6_ y_ 6 1 LQLRPK
#> 330 368.74504 y6_ y_ 6 2 LQLRPK
#> 331 835.55122 y7_ y_ 7 1 VLQLRPK
#> 332 418.27925 y7_ y_ 7 2 VLQLRPK
#> 333 1021.61527 y9_ y_ 9 1 GEVLQLRPK
#> 334 511.31127 y9_ y_ 9 2 GEVLQLRPK
#> 335 1158.67418 y10_ y_ 10 1 HGEVLQLRPK
#> 336 579.84073 y10_ y_ 10 2 HGEVLQLRPK
#> 337 1314.77529 y11_ y_ 11 1 RHGEVLQLRPK
#> 338 657.89128 y11_ y_ 11 2 RHGEVLQLRPK
#> 339 1385.81240 y12_ y_ 12 1 ARHGEVLQLRPK
#> 340 693.40984 y12_ y_ 12 2 ARHGEVLQLRPK
#> 341 1486.86008 y13_ y_ 13 1 TARHGEVLQLRPK
#> 342 743.93368 y13_ y_ 13 2 TARHGEVLQLRPK
#> 343 112.07569 z1_ z_ 1 1 K
#> 344 56.54148 z1_ z_ 1 2 K
#> 345 209.12845 z2_ z_ 2 1 PK
#> 346 105.06786 z2_ z_ 2 2 PK
#> 347 365.22956 z3_ z_ 3 1 RPK
#> 348 183.11842 z3_ z_ 3 2 RPK
#> 349 478.31362 z4_ z_ 4 1 LRPK
#> 350 239.66045 z4_ z_ 4 2 LRPK
#> 351 606.37220 z5_ z_ 5 1 QLRPK
#> 352 303.68974 z5_ z_ 5 2 QLRPK
#> 353 719.45626 z6_ z_ 6 1 LQLRPK
#> 354 360.23177 z6_ z_ 6 2 LQLRPK
#> 355 818.52467 z7_ z_ 7 1 VLQLRPK
#> 356 409.76597 z7_ z_ 7 2 VLQLRPK
#> 357 1004.58872 z9_ z_ 9 1 GEVLQLRPK
#> 358 502.79800 z9_ z_ 9 2 GEVLQLRPK
#> 359 1141.64763 z10_ z_ 10 1 HGEVLQLRPK
#> 360 571.32745 z10_ z_ 10 2 HGEVLQLRPK
#> 361 1297.74874 z11_ z_ 11 1 RHGEVLQLRPK
#> 362 649.37801 z11_ z_ 11 2 RHGEVLQLRPK
#> 363 1368.78585 z12_ z_ 12 1 ARHGEVLQLRPK
#> 364 684.89656 z12_ z_ 12 2 ARHGEVLQLRPK
#> 365 1469.83353 z13_ z_ 13 1 TARHGEVLQLRPK
#> 366 735.42040 z13_ z_ 13 2 TARHGEVLQLRPK
#> 367 849.45771 a8* a* 8 1 VESITARH
#> 368 425.23249 a8* a* 8 2 VESITARH
#> 369 906.47917 a9* a* 9 1 VESITARHG
#> 370 453.74322 a9* a* 9 2 VESITARHG
#> 371 1035.52176 a10* a* 10 1 VESITARHGE
#> 372 518.26452 a10* a* 10 2 VESITARHGE
#> 373 1134.59017 a11* a* 11 1 VESITARHGEV
#> 374 567.79872 a11* a* 11 2 VESITARHGEV
#> 375 1247.67423 a12* a* 12 1 VESITARHGEVL
#> 376 624.34075 a12* a* 12 2 VESITARHGEVL
#> 377 1375.73281 a13* a* 13 1 VESITARHGEVLQ
#> 378 688.37004 a13* a* 13 2 VESITARHGEVLQ
#> 379 1488.81687 a14* a* 14 1 VESITARHGEVLQL
#> 380 744.91207 a14* a* 14 2 VESITARHGEVLQL
#> 381 1644.91798 a15* a* 15 1 VESITARHGEVLQLR
#> 382 822.96263 a15* a* 15 2 VESITARHGEVLQLR
#> 383 1741.97074 a16* a* 16 1 VESITARHGEVLQLRP
#> 384 871.48901 a16* a* 16 2 VESITARHGEVLQLRP
#> 385 877.45263 b8* b* 8 1 VESITARH
#> 386 439.22995 b8* b* 8 2 VESITARH
#> 387 934.47409 b9* b* 9 1 VESITARHG
#> 388 467.74068 b9* b* 9 2 VESITARHG
#> 389 1063.51668 b10* b* 10 1 VESITARHGE
#> 390 532.26198 b10* b* 10 2 VESITARHGE
#> 391 1162.58509 b11* b* 11 1 VESITARHGEV
#> 392 581.79618 b11* b* 11 2 VESITARHGEV
#> 393 1275.66915 b12* b* 12 1 VESITARHGEVL
#> 394 638.33821 b12* b* 12 2 VESITARHGEVL
#> 395 1403.72773 b13* b* 13 1 VESITARHGEVLQ
#> 396 702.36750 b13* b* 13 2 VESITARHGEVLQ
#> 397 1516.81179 b14* b* 14 1 VESITARHGEVLQL
#> 398 758.90953 b14* b* 14 2 VESITARHGEVLQL
#> 399 1672.91290 b15* b* 15 1 VESITARHGEVLQLR
#> 400 836.96009 b15* b* 15 2 VESITARHGEVLQLR
#> 401 1769.96566 b16* b* 16 1 VESITARHGEVLQLRP
#> 402 885.48647 b16* b* 16 2 VESITARHGEVLQLRP
#> 403 894.47918 c8* c* 8 1 VESITARH
#> 404 447.74323 c8* c* 8 2 VESITARH
#> 405 951.50064 c9* c* 9 1 VESITARHG
#> 406 476.25396 c9* c* 9 2 VESITARHG
#> 407 1080.54323 c10* c* 10 1 VESITARHGE
#> 408 540.77525 c10* c* 10 2 VESITARHGE
#> 409 1179.61164 c11* c* 11 1 VESITARHGEV
#> 410 590.30946 c11* c* 11 2 VESITARHGEV
#> 411 1292.69570 c12* c* 12 1 VESITARHGEVL
#> 412 646.85149 c12* c* 12 2 VESITARHGEVL
#> 413 1420.75428 c13* c* 13 1 VESITARHGEVLQ
#> 414 710.88078 c13* c* 13 2 VESITARHGEVLQ
#> 415 1533.83834 c14* c* 14 1 VESITARHGEVLQL
#> 416 767.42281 c14* c* 14 2 VESITARHGEVLQL
#> 417 1689.93945 c15* c* 15 1 VESITARHGEVLQLR
#> 418 845.47336 c15* c* 15 2 VESITARHGEVLQLR
#> 419 1786.99221 c16* c* 16 1 VESITARHGEVLQLRP
#> 420 893.99974 c16* c* 16 2 VESITARHGEVLQLRP
#> 421 522.30345 x4* x* 4 1 LRPK
#> 422 261.65536 x4* x* 4 2 LRPK
#> 423 650.36203 x5* x* 5 1 QLRPK
#> 424 325.68465 x5* x* 5 2 QLRPK
#> 425 763.44609 x6* x* 6 1 LQLRPK
#> 426 382.22668 x6* x* 6 2 LQLRPK
#> 427 862.51450 x7* x* 7 1 VLQLRPK
#> 428 431.76089 x7* x* 7 2 VLQLRPK
#> 429 991.55709 x8* x* 8 1 EVLQLRPK
#> 430 496.28218 x8* x* 8 2 EVLQLRPK
#> 431 1048.57855 x9* x* 9 1 GEVLQLRPK
#> 432 524.79291 x9* x* 9 2 GEVLQLRPK
#> 433 1185.63746 x10* x* 10 1 HGEVLQLRPK
#> 434 593.32237 x10* x* 10 2 HGEVLQLRPK
#> 435 1341.73857 x11* x* 11 1 RHGEVLQLRPK
#> 436 671.37292 x11* x* 11 2 RHGEVLQLRPK
#> 437 1412.77568 x12* x* 12 1 ARHGEVLQLRPK
#> 438 706.89148 x12* x* 12 2 ARHGEVLQLRPK
#> 439 1513.82336 x13* x* 13 1 TARHGEVLQLRPK
#> 440 757.41532 x13* x* 13 2 TARHGEVLQLRPK
#> 441 1626.90742 x14* x* 14 1 ITARHGEVLQLRPK
#> 442 813.95735 x14* x* 14 2 ITARHGEVLQLRPK
#> 443 1713.93945 x15* x* 15 1 SITARHGEVLQLRPK
#> 444 857.47336 x15* x* 15 2 SITARHGEVLQLRPK
#> 445 1842.98204 x16* x* 16 1 ESITARHGEVLQLRPK
#> 446 921.99466 x16* x* 16 2 ESITARHGEVLQLRPK
#> 447 496.32418 y4* y* 4 1 LRPK
#> 448 248.66573 y4* y* 4 2 LRPK
#> 449 624.38276 y5* y* 5 1 QLRPK
#> 450 312.69502 y5* y* 5 2 QLRPK
#> 451 737.46682 y6* y* 6 1 LQLRPK
#> 452 369.23705 y6* y* 6 2 LQLRPK
#> 453 836.53523 y7* y* 7 1 VLQLRPK
#> 454 418.77125 y7* y* 7 2 VLQLRPK
#> 455 965.57782 y8* y* 8 1 EVLQLRPK
#> 456 483.29255 y8* y* 8 2 EVLQLRPK
#> 457 1022.59928 y9* y* 9 1 GEVLQLRPK
#> 458 511.80328 y9* y* 9 2 GEVLQLRPK
#> 459 1159.65819 y10* y* 10 1 HGEVLQLRPK
#> 460 580.33273 y10* y* 10 2 HGEVLQLRPK
#> 461 1315.75930 y11* y* 11 1 RHGEVLQLRPK
#> 462 658.38329 y11* y* 11 2 RHGEVLQLRPK
#> 463 1386.79641 y12* y* 12 1 ARHGEVLQLRPK
#> 464 693.90184 y12* y* 12 2 ARHGEVLQLRPK
#> 465 1487.84409 y13* y* 13 1 TARHGEVLQLRPK
#> 466 744.42568 y13* y* 13 2 TARHGEVLQLRPK
#> 467 1600.92815 y14* y* 14 1 ITARHGEVLQLRPK
#> 468 800.96771 y14* y* 14 2 ITARHGEVLQLRPK
#> 469 1687.96018 y15* y* 15 1 SITARHGEVLQLRPK
#> 470 844.48373 y15* y* 15 2 SITARHGEVLQLRPK
#> 471 1817.00277 y16* y* 16 1 ESITARHGEVLQLRPK
#> 472 909.00502 y16* y* 16 2 ESITARHGEVLQLRPK
#> 473 479.29763 z4* z* 4 1 LRPK
#> 474 240.15245 z4* z* 4 2 LRPK
#> 475 607.35621 z5* z* 5 1 QLRPK
#> 476 304.18174 z5* z* 5 2 QLRPK
#> 477 720.44027 z6* z* 6 1 LQLRPK
#> 478 360.72377 z6* z* 6 2 LQLRPK
#> 479 819.50868 z7* z* 7 1 VLQLRPK
#> 480 410.25798 z7* z* 7 2 VLQLRPK
#> 481 948.55127 z8* z* 8 1 EVLQLRPK
#> 482 474.77927 z8* z* 8 2 EVLQLRPK
#> 483 1005.57273 z9* z* 9 1 GEVLQLRPK
#> 484 503.29000 z9* z* 9 2 GEVLQLRPK
#> 485 1142.63164 z10* z* 10 1 HGEVLQLRPK
#> 486 571.81946 z10* z* 10 2 HGEVLQLRPK
#> 487 1298.73275 z11* z* 11 1 RHGEVLQLRPK
#> 488 649.87001 z11* z* 11 2 RHGEVLQLRPK
#> 489 1369.76986 z12* z* 12 1 ARHGEVLQLRPK
#> 490 685.38857 z12* z* 12 2 ARHGEVLQLRPK
#> 491 1470.81754 z13* z* 13 1 TARHGEVLQLRPK
#> 492 735.91241 z13* z* 13 2 TARHGEVLQLRPK
#> 493 1583.90160 z14* z* 14 1 ITARHGEVLQLRPK
#> 494 792.45444 z14* z* 14 2 ITARHGEVLQLRPK
#> 495 1670.93363 z15* z* 15 1 SITARHGEVLQLRPK
#> 496 835.97045 z15* z* 15 2 SITARHGEVLQLRPK
#> 497 1799.97622 z16* z* 16 1 ESITARHGEVLQLRPK
#> 498 900.49175 z16* z* 16 2 ESITARHGEVLQLRPK
## neutral loss
defaultNeutralLoss()
#> $water
#> [1] "Cterm" "D" "E" "S" "T"
#>
#> $ammonia
#> [1] "K" "N" "Q" "R"
#>
## disable water loss on the C terminal
defaultNeutralLoss(disableWaterLoss="Cterm")
#> $water
#> [1] "D" "E" "S" "T"
#>
#> $ammonia
#> [1] "K" "N" "Q" "R"
#>
## real example
calculateFragments("PQR")
#> Modifications used: C=57.02146
#> mz ion type pos z seq
#> 1 98.06004 b1 b 1 1 P
#> 2 226.11862 b2 b 2 1 PQ
#> 3 175.11895 y1 y 1 1 R
#> 4 303.17753 y2 y 2 1 QR
#> 5 157.10839 y1_ y_ 1 1 R
#> 6 285.16697 y2_ y_ 2 1 QR
#> 7 286.15098 y2* y* 2 1 QR
calculateFragments("PQR",
neutralLoss=defaultNeutralLoss(disableWaterLoss="Cterm"))
#> Modifications used: C=57.02146
#> mz ion type pos z seq
#> 1 98.06004 b1 b 1 1 P
#> 2 226.11862 b2 b 2 1 PQ
#> 3 175.11895 y1 y 1 1 R
#> 4 303.17753 y2 y 2 1 QR
#> 5 286.15098 y2* y* 2 1 QR
calculateFragments("PQR",
neutralLoss=defaultNeutralLoss(disableAmmoniaLoss="Q"))
#> Modifications used: C=57.02146
#> mz ion type pos z seq
#> 1 98.06004 b1 b 1 1 P
#> 2 226.11862 b2 b 2 1 PQ
#> 3 175.11895 y1 y 1 1 R
#> 4 303.17753 y2 y 2 1 QR
#> 5 157.10839 y1_ y_ 1 1 R
#> 6 285.16697 y2_ y_ 2 1 QR
## disable neutral loss completely
calculateFragments("PQR", neutralLoss=NULL)
#> Modifications used: C=57.02146
#> mz ion type pos z seq
#> 1 98.06004 b1 b 1 1 P
#> 2 226.11862 b2 b 2 1 PQ
#> 3 175.11895 y1 y 1 1 R
#> 4 303.17753 y2 y 2 1 QR