Calculate ions produced by fragmentation.
calculateFragments-methods.RdThese method calculates a-, b-, c-, x-, y- and z-ions produced by fragmentation.
Arguments
- sequence
character, peptide sequence.- object
Object of class
"Spectrum2"or"missing".- tolerance
numerictolerance between the theoretical and measured MZ values (only available ifobjectis notmissing).- method
methodused for for duplicated matches. Choose"highest"or"closest"to select the peak with the highest intensity respectively the closest MZ in the tolerance range. If"all"is given all possible matches in the tolerance range are reported (only available ifobjectis notmissing).- type
charactervector of target ions; possible values:c("a", "b", "c", "x", "y", "z"); default:type=c("b", "y").- z
numericdesired charge state; defaultz=1.- modifications
named
numericvector of used modifications. The name must correspond to the one-letter-code of the modified amino acid and thenumericvalue must represent the mass that should be added to the original amino accid mass, default: Carbamidomethylmodifications=c(C=57.02146). UseNtermorCtermas names for modifications that should be added to the amino respectively carboxyl-terminus.- neutralLoss
list, it has to have two named elments, namelywaterandammoniathat contain acharactervector which type of neutral loss should be calculated. Currently neutral loss on the C terminal"Cterm", at the amino acidsc("D", "E", "S", "T")for"water"(shown with an_) andc("K", "N", "Q", "R")for"ammonia"(shown with an*) are supported.
There is a helper functiondefaultNeutralLossthat returns the correct list. It has two argumentsdisableWaterLossanddisableAmmoniaLossto remove single neutral loss options. See the example section for use cases.- verbose
logicalifTRUE(default) the used modifications are printed.
Methods
signature(sequence = "character", object = "missing", ...)Calculates the theoretical fragments for a peptide
sequence. Returns adata.framewith the columnsc("mz", "ion", "type", "pos", "z", "seq").signature(sequence = "character", object = "Spectrum2", ...)Calculates and matches the theoretical fragments for a peptide
sequenceand a"Spectrum2"object. The...arguments are passed to the internal functions. Currentlytolerance,methodandrelativeare supported.You could change the
tolerance(default0.1) and decide whether this tolerance should be applied relative to the target m/z (relative = TRUE) or absolute (defaultrelative = FALSE) to match the theoretical fragment MZ with the MZ of the spectrum. When (relative = TRUE) the mass tolerance window is set totarget mz +/- (target mz * tolerance)andtarget mz +/- toleranceotherwise. In cases of multiple matches usemethodto select the peak with the highest intensity (method = "highest", default) respectively closest MZ (method = "closes"). Ifmethod = "all"is set all possible matches in the current tolerance range are reported. Returns the samedata.frameas above but themzcolumn represents the matched MZ values of the spectrum. Additionally there is a columnerrorthat contains the difference between the observed MZ (from the spectrum) to the theoretical fragment MZ.
Examples
## find path to a mzXML file
file <- dir(system.file(package = "MSnbase", dir = "extdata"),
full.name = TRUE, pattern = "mzXML$")
## create basic MSnExp
msexp <- readMSData(file, centroided = FALSE)
## centroid them
msexp <- pickPeaks(msexp)
## calculate fragments for ACE with default modification
calculateFragments("ACE", modifications=c(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))
#> 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)
#> 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)
#> 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
calculateFragments("VESITARHGEVLQLRPK", msexp[[1]])
#> mz intensity ion type pos z seq error
#> 1 429.2563 1972344.0 b4 b 4 1 VESI -0.02189010
#> 2 512.3044 684918.0 b5_ b_ 5 1 VESIT -0.03290132
#> 3 513.3047 2574137.0 y4 y 4 1 LRPK 0.04598246
#> 4 583.3300 1440833.8 b6_ b_ 6 1 VESITA -0.02142609
#> 5 754.4504 537234.8 y6 y 6 1 LQLRPK 0.04293155
#> 6 982.5354 500159.1 y8 y 8 1 EVLQLRPK 0.06897061
#> 7 1080.5867 209363.7 b10 b 10 1 VESITARHGE -0.04344392
#> 8 1688.0375 136748.8 y15* y* 15 1 SITARHGEVLQLRPK -0.07729359
## neutral loss
PSMatch::defaultNeutralLoss()
#> $water
#> [1] "Cterm" "D" "E" "S" "T"
#>
#> $ammonia
#> [1] "K" "N" "Q" "R"
#>
## disable water loss on the C terminal
PSMatch::defaultNeutralLoss(disableWaterLoss="Cterm")
#> $water
#> [1] "D" "E" "S" "T"
#>
#> $ammonia
#> [1] "K" "N" "Q" "R"
#>
## real example
calculateFragments("PQR")
#> 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=PSMatch::defaultNeutralLoss(disableWaterLoss="Cterm"))
#> 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=PSMatch::defaultNeutralLoss(disableAmmoniaLoss="Q"))
#> 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)
#> 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