Digest: Predict Peptides Resulting from Enzymatic Digest
In OrgMassSpecR: Organic Mass Spectrometry
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
Description
Cleave an amino acid sequence (a protein or peptide) according to enzyme specific rules and calculate the precursor ion m/z values.
Usage
1
2
Arguments
sequence
a character string representing the amino acid sequence to be cleaved by the enzyme.
enzyme
a character string specifying the rules for cleavage. Options are "trypsin" (default), "trypsin.strict" (see details), or "pepsin".
missed
the maximum number of missed cleavages. Must be an integer of 0 (default) or greater. An error will result if the specified number of missed cleavages is greater than the maximum possible number of missed cleavages.
IAA
logical. TRUE specifies iodoacetylated cysteine and FALSE specifies unmodified cystine.
N15
logical indicating if the nitrogen-15 isotope should be used in place of the default nitrogen-14 isotope.
custom
a list specifying user defined residues as custom = list(code, mass), where code is a vector of one letter characters and mass is a vector of the respective monoisotopic masses. See Details and Examples.
Details
The amino acid residues must be specified by one letter codes. The predefined residues are:
A = alanine L = leucine
R = arginine K = lysine
N = asparagine M = methionine
D = aspartic acid F = phenylalanine
C = cysteine P = proline
E = glutamic acid S = serine
Q = glutamine T = threonine
G = glycine W = tryptophan
H = histidine Y = tyrosine
I = isoleucine V = valine
If "trypsin" is specified, the sequence is cleaved on the c-terminal side of K and R residues, except if K or R is followed by P. If "trypsin.strict" is specified, the sequence is cleaved on the c-terminal side of K and R residues. If "pepsin" is specified, the sequence is cleaved on the c-terminal side of F, L, W, Y, A, E, and Q residues. This rule is specific to pepsin at pH > 2, as used in hydrogen-deuterium exchange experiments.
When "trypsin" is specified, KP and RP are not considered missed cleavages when missed is > 0.
The argument IAA specifies treatment of the protein with iodoacetamide. This treatment produces iodoacetylated cysteine residues (elemental formula C5H8N2O2S).
If TRUE, the argument N15 specifies 100% nitrogen-15 incorporation. It is intended for proteins grown with a nitrogen-15 labeled food source. (Although the experiment itself may grow a protein with less than 100% nitrogen-15 incorporation). Setting N15 = TRUE does not modify the mass of a custom residue, or the mass of the nitrogen(s) added if IAA = TRUE.
If a custom residue code is identical to a predefined residue code, the custom residue mass will be used in place of the predefined mass.
The error message “object "mass" not found” indicates the input sequence contains an undefined residue(s).
Value
A data frame with the following column names.
peptide
resulting peptides.
start
beginning residue positions in the the original sequence.
end
ending residue positions in the the original sequence.
mc
number of missed cleavages.
mz1
monoisotopic m/z values for the [M + H]1+ ions (where M is the precursor mass).
mz2
monoisotopic m/z values for the [M + 2H]2+ ions.
mz3
monoisotopic m/z values for the [M + 3H]3+ ions.
Author(s)
Nathan G. Dodder
References
The relative atomic masses of the isotopes are from the NIST Physical Reference Data Website http://physics.nist.gov/PhysRefData/Compositions/. The molar mass of a proton (H+) is from the NIST CODATA Website http://physics.nist.gov/cuu/Constants/index.html.
See Also
MonoisotopicMass, FragmentPeptide
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
## digest human serum albumin with 0 and 1 missed cleavages
Digest(example.sequence, missed = 1)
## digest human serum albumin with a phosphoserine at position 58
## and all methionines oxidized
modifiedHsaSequence <- strsplit(example.sequence, split = "")[[1]]
modifiedHsaSequence[58] <- "s" # insert code for phosphoserine
modifiedHsaSequence <- paste(modifiedHsaSequence, collapse = "")
Digest(modifiedHsaSequence, custom = list(code = c("s","M"),
mass = c(MonoisotopicMass(list(C=3, H=6, N=1, O=5, P=1)),
MonoisotopicMass(list(C=5, H=9, N=1, O=2, S=1)))))
## digest human serum albumin with strict rules
Digest(example.sequence, enzyme = "trypsin.strict")
Example output
Loading required package: grid
peptide start stop mc mz1 mz2
1 DAHK 1 4 0 470.236 235.622
2 SEVAHR 5 10 0 698.358 349.683
3 FK 11 12 0 294.181 147.594
4 DLGEENFK 13 20 0 951.442 476.225
5 ALVLIAFAQYLQQCPFEDHVK 21 41 0 2490.285 1245.646
6 LVNEVTEFAK 42 51 0 1149.615 575.311
7 TCVADESAENCDK 52 64 0 1498.578 749.793
8 SLHTLFGDK 65 73 0 1017.536 509.272
9 LCTVATLR 74 81 0 933.519 467.263
10 ETYGEMADCCAK 82 93 0 1434.533 717.770
11 QEPER 94 98 0 658.315 329.661
12 NECFLQHK 99 106 0 1075.499 538.253
13 DDNPNLPR 107 114 0 940.448 470.728
14 LVRPEVDVMCTAFHDNEETFLK 115 136 0 2650.264 1325.636
15 K 137 137 0 147.113 74.060
16 YLYEIAR 138 144 0 927.493 464.250
17 R 145 145 0 175.119 88.063
18 HPYFYAPELLFFAK 146 159 0 1742.894 871.951
19 R 160 160 0 175.119 88.063
20 YK 161 162 0 310.176 155.592
21 AAFTECCQAADK 163 174 0 1371.567 686.287
22 AACLLPK 175 181 0 772.439 386.723
23 LDELR 182 186 0 645.357 323.182
24 DEGK 187 190 0 448.204 224.606
25 ASSAK 191 195 0 463.251 232.129
26 QR 196 197 0 303.178 152.092
27 LK 198 199 0 260.197 130.602
28 CASLQK 200 205 0 706.355 353.681
29 FGER 206 209 0 508.251 254.629
30 AFK 210 212 0 365.218 183.113
31 AWAVAR 213 218 0 673.378 337.193
32 LSQR 219 222 0 503.294 252.150
33 FPK 223 225 0 391.234 196.121
34 AEFAEVSK 226 233 0 880.441 440.724
35 LVTDLTK 234 240 0 789.472 395.239
36 VHTECCHGDLLECADDR 241 257 0 2086.838 1043.922
37 ADLAK 258 262 0 517.298 259.153
38 YICENQDSISSK 263 274 0 1443.642 722.325
39 LK 275 276 0 260.197 130.602
40 ECCEKPLLEK 277 286 0 1305.618 653.313
41 SHCIAEVENDEMPADLPSLAADFVESK 287 313 0 2974.344 1487.676
42 DVCK 314 317 0 521.239 261.123
43 NYAEAK 318 323 0 695.336 348.172
44 DVFLGMFLYEYAR 324 336 0 1623.788 812.397
45 R 337 337 0 175.119 88.063
46 HPDYSVVLLLR 338 348 0 1311.742 656.375
47 LAK 349 351 0 331.234 166.121
48 TYETTLEK 352 359 0 984.488 492.748
49 CCAAADPHECYAK 360 372 0 1552.598 776.803
50 VFDEFKPLVEEPQNLIK 373 389 0 2045.095 1023.051
51 QNCELFEQLGEYK 390 402 0 1657.753 829.380
52 FQNALLVR 403 410 0 960.563 480.785
53 YTK 411 413 0 411.224 206.116
54 K 414 414 0 147.113 74.060
55 VPQVSTPTLVEVSR 415 428 0 1511.843 756.425
56 NLGK 429 432 0 431.261 216.134
57 VGSK 433 436 0 390.235 195.621
58 CCK 437 439 0 467.174 234.091
59 HPEAK 440 444 0 581.304 291.156
60 R 445 445 0 175.119 88.063
61 MPCAEDYLSVVLNQLCVLHEK 446 466 0 2518.214 1259.611
62 TPVSDR 467 472 0 674.347 337.677
63 VTK 473 475 0 347.229 174.118
64 CCTESLVNR 476 484 0 1138.498 569.753
65 RPCFSALEVDETYVPK 485 500 0 1910.932 955.969
66 EFNAETFTFHADICTLSEK 501 519 0 2260.023 1130.515
67 ER 520 521 0 304.162 152.584
68 QIK 522 524 0 388.255 194.631
69 K 525 525 0 147.113 74.060
70 QTALVELVK 526 534 0 1000.604 500.805
71 HKPK 535 538 0 509.319 255.163
72 ATK 539 541 0 319.198 160.102
73 EQLK 542 545 0 517.298 259.153
74 AVMDDFAAFVEK 546 557 0 1342.635 671.821
75 CCK 558 560 0 467.174 234.091
76 ADDK 561 564 0 448.204 224.606
77 ETCFAEEGK 565 573 0 1070.446 535.727
78 K 574 574 0 147.113 74.060
79 LVAASQAALGL 575 585 0 1013.599 507.303
80 DAHKSEVAHR 1 10 1 1149.576 575.292
81 SEVAHRFK 5 12 1 973.521 487.264
82 FKDLGEENFK 11 20 1 1226.605 613.806
83 DLGEENFKALVLIAFAQYLQQCPFEDHVK 13 41 1 3422.709 1711.858
84 ALVLIAFAQYLQQCPFEDHVKLVNEVTEFAK 21 51 1 3620.882 1810.945
85 LVNEVTEFAKTCVADESAENCDK 42 64 1 2629.176 1315.091
86 TCVADESAENCDKSLHTLFGDK 52 73 1 2497.097 1249.052
87 SLHTLFGDKLCTVATLR 65 81 1 1932.037 966.522
88 LCTVATLRETYGEMADCCAK 74 93 1 2349.034 1175.021
89 ETYGEMADCCAKQEPER 82 98 1 2073.831 1037.419
90 QEPERNECFLQHK 94 106 1 1714.797 857.902
91 NECFLQHKDDNPNLPR 99 114 1 1996.929 998.968
92 DDNPNLPRLVRPEVDVMCTAFHDNEETFLK 107 136 1 3571.694 1786.351
93 LVRPEVDVMCTAFHDNEETFLKK 115 137 1 2778.359 1389.683
94 KYLYEIAR 137 144 1 1055.588 528.298
95 YLYEIARR 138 145 1 1083.595 542.301
96 RHPYFYAPELLFFAK 145 159 1 1898.995 950.001
97 HPYFYAPELLFFAKR 146 160 1 1898.995 950.001
98 RYK 160 162 1 466.277 233.642
99 YKAAFTECCQAADK 161 174 1 1662.725 831.866
100 AAFTECCQAADKAACLLPK 163 181 1 2124.987 1062.997
101 AACLLPKLDELR 175 186 1 1398.777 699.892
102 LDELRDEGK 182 190 1 1074.543 537.775
103 DEGKASSAK 187 195 1 892.437 446.722
104 ASSAKQR 191 197 1 747.411 374.209
105 QRLK 196 199 1 544.357 272.682
106 LKCASLQK 198 205 1 947.534 474.271
107 CASLQKFGER 200 209 1 1195.589 598.298
108 FGERAFK 206 212 1 854.452 427.730
109 AFKAWAVAR 210 218 1 1019.579 510.293
110 AWAVARLSQR 213 222 1 1157.654 579.331
111 LSQRFPK 219 225 1 875.510 438.259
112 FPKAEFAEVSK 223 233 1 1252.657 626.832
113 AEFAEVSKLVTDLTK 226 240 1 1650.895 825.951
114 LVTDLTKVHTECCHGDLLECADDR 234 257 1 2857.291 1429.149
115 VHTECCHGDLLECADDRADLAK 241 262 1 2585.118 1293.063
116 ADLAKYICENQDSISSK 258 274 1 1941.922 971.465
117 YICENQDSISSKLK 263 276 1 1684.821 842.914
118 LKECCEKPLLEK 275 286 1 1546.797 773.902
119 ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESK 277 313 1 4260.944 2130.976
120 SHCIAEVENDEMPADLPSLAADFVESKDVCK 287 317 1 3476.565 1738.786
121 DVCKNYAEAK 314 323 1 1197.557 599.282
122 NYAEAKDVFLGMFLYEYAR 318 336 1 2300.106 1150.556
123 DVFLGMFLYEYARR 324 337 1 1779.889 890.448
124 RHPDYSVVLLLR 337 348 1 1467.843 734.425
125 HPDYSVVLLLRLAK 338 351 1 1623.958 812.483
126 LAKTYETTLEK 349 359 1 1296.705 648.856
127 TYETTLEKCCAAADPHECYAK 352 372 1 2518.068 1259.538
128 CCAAADPHECYAKVFDEFKPLVEEPQNLIK 360 389 1 3578.675 1789.841
129 VFDEFKPLVEEPQNLIKQNCELFEQLGEYK 373 402 1 3683.830 1842.419
130 QNCELFEQLGEYKFQNALLVR 390 410 1 2599.297 1300.152
131 FQNALLVRYTK 403 413 1 1352.768 676.888
132 YTKK 411 414 1 539.319 270.163
133 KVPQVSTPTLVEVSR 414 428 1 1639.938 820.473
134 VPQVSTPTLVEVSRNLGK 415 432 1 1924.086 962.547
135 NLGKVGSK 429 436 1 802.478 401.743
136 VGSKCCK 433 439 1 838.391 419.699
137 CCKHPEAK 437 444 1 1029.460 515.234
138 HPEAKR 440 445 1 737.405 369.206
139 RMPCAEDYLSVVLNQLCVLHEK 445 466 1 2674.315 1337.661
140 MPCAEDYLSVVLNQLCVLHEKTPVSDR 446 472 1 3173.543 1587.275
141 TPVSDRVTK 467 475 1 1002.558 501.783
142 VTKCCTESLVNR 473 484 1 1466.709 733.858
143 CCTESLVNRRPCFSALEVDETYVPK 476 500 1 3030.412 1515.710
144 RPCFSALEVDETYVPKEFNAETFTFHADICTLSEK 485 519 1 4151.937 2076.472
145 EFNAETFTFHADICTLSEKER 501 521 1 2545.166 1273.087
146 ERQIK 520 524 1 673.399 337.203
147 QIKK 522 525 1 516.350 258.679
148 KQTALVELVK 525 534 1 1128.699 564.853
149 QTALVELVKHKPK 526 538 1 1490.905 745.956
150 HKPKATK 535 541 1 809.499 405.253
151 ATKEQLK 539 545 1 817.478 409.243
152 EQLKAVMDDFAAFVEK 542 557 1 1840.915 920.961
153 AVMDDFAAFVEKCCK 546 560 1 1790.791 895.899
154 CCKADDK 558 564 1 896.360 448.684
155 ADDKETCFAEEGK 561 573 1 1499.632 750.320
156 ETCFAEEGKK 565 574 1 1198.541 599.774
157 KLVAASQAALGL 574 585 1 1141.694 571.351
mz3
1 157.417
2 233.458
3 98.732
4 317.819
5 830.767
6 383.877
7 500.198
8 339.850
9 311.844
10 478.849
11 220.110
12 359.171
13 314.154
14 884.093
15 49.709
16 309.836
17 59.045
18 581.636
19 59.045
20 104.064
21 457.860
22 258.151
23 215.790
24 150.073
25 155.089
26 101.731
27 87.404
28 236.123
29 170.089
30 122.411
31 225.131
32 168.436
33 131.083
34 294.152
35 263.829
36 696.284
37 173.104
38 481.886
39 87.404
40 435.877
41 992.120
42 174.418
43 232.450
44 541.934
45 59.045
46 437.919
47 111.083
48 328.834
49 518.204
50 682.370
51 553.256
52 320.859
53 137.746
54 49.709
55 504.619
56 144.425
57 130.750
58 156.396
59 194.440
60 59.045
61 840.076
62 225.454
63 116.414
64 380.171
65 637.649
66 754.012
67 102.059
68 130.090
69 49.709
70 334.206
71 170.445
72 107.071
73 173.104
74 448.216
75 156.396
76 150.073
77 357.487
78 49.709
79 338.538
80 383.863
81 325.179
82 409.540
83 1141.574
84 1207.632
85 877.063
86 833.037
87 644.684
88 783.683
89 691.949
90 572.270
91 666.315
92 1191.236
93 926.791
94 352.534
95 361.870
96 633.670
97 633.670
98 156.097
99 554.913
100 709.001
101 466.931
102 358.852
103 298.151
104 249.808
105 182.124
106 316.516
107 399.201
108 285.489
109 340.531
110 386.556
111 292.508
112 418.224
113 550.970
114 953.102
115 862.377
116 647.979
117 562.279
118 516.270
119 1420.986
120 1159.527
121 399.857
122 767.373
123 593.968
124 489.953
125 541.991
126 432.906
127 840.028
128 1193.563
129 1228.615
130 867.104
131 451.594
132 180.444
133 547.317
134 642.034
135 268.164
136 280.135
137 343.825
138 246.473
139 892.110
140 1058.519
141 334.857
142 489.575
143 1010.809
144 1384.650
145 849.060
146 225.138
147 172.788
148 376.904
149 497.640
150 270.505
151 273.164
152 614.310
153 597.602
154 299.458
155 500.549
156 400.185
157 381.236
peptide start stop mc mz1 mz2 mz3
1 DAHK 1 4 0 470.236 235.622 157.417
2 SEVAHR 5 10 0 698.358 349.683 233.458
3 FK 11 12 0 294.181 147.594 98.732
4 DLGEENFK 13 20 0 951.442 476.225 317.819
5 ALVLIAFAQYLQQCPFEDHVK 21 41 0 2490.285 1245.646 830.767
6 LVNEVTEFAK 42 51 0 1149.615 575.311 383.877
7 TCVADEsAENCDK 52 64 0 1578.545 789.776 526.853
8 SLHTLFGDK 65 73 0 1017.536 509.272 339.850
9 LCTVATLR 74 81 0 933.519 467.263 311.844
10 ETYGEMADCCAK 82 93 0 1450.528 725.768 484.181
11 QEPER 94 98 0 658.315 329.661 220.110
12 NECFLQHK 99 106 0 1075.499 538.253 359.171
13 DDNPNLPR 107 114 0 940.448 470.728 314.154
14 LVRPEVDVMCTAFHDNEETFLK 115 136 0 2666.259 1333.633 889.424
15 K 137 137 0 147.113 74.060 49.709
16 YLYEIAR 138 144 0 927.493 464.250 309.836
17 R 145 145 0 175.119 88.063 59.045
18 HPYFYAPELLFFAK 146 159 0 1742.894 871.951 581.636
19 R 160 160 0 175.119 88.063 59.045
20 YK 161 162 0 310.176 155.592 104.064
21 AAFTECCQAADK 163 174 0 1371.567 686.287 457.860
22 AACLLPK 175 181 0 772.439 386.723 258.151
23 LDELR 182 186 0 645.357 323.182 215.790
24 DEGK 187 190 0 448.204 224.606 150.073
25 ASSAK 191 195 0 463.251 232.129 155.089
26 QR 196 197 0 303.178 152.092 101.731
27 LK 198 199 0 260.197 130.602 87.404
28 CASLQK 200 205 0 706.355 353.681 236.123
29 FGER 206 209 0 508.251 254.629 170.089
30 AFK 210 212 0 365.218 183.113 122.411
31 AWAVAR 213 218 0 673.378 337.193 225.131
32 LSQR 219 222 0 503.294 252.150 168.436
33 FPK 223 225 0 391.234 196.121 131.083
34 AEFAEVSK 226 233 0 880.441 440.724 294.152
35 LVTDLTK 234 240 0 789.472 395.239 263.829
36 VHTECCHGDLLECADDR 241 257 0 2086.838 1043.922 696.284
37 ADLAK 258 262 0 517.298 259.153 173.104
38 YICENQDSISSK 263 274 0 1443.642 722.325 481.886
39 LK 275 276 0 260.197 130.602 87.404
40 ECCEKPLLEK 277 286 0 1305.618 653.313 435.877
41 SHCIAEVENDEMPADLPSLAADFVESK 287 313 0 2990.339 1495.673 997.451
42 DVCK 314 317 0 521.239 261.123 174.418
43 NYAEAK 318 323 0 695.336 348.172 232.450
44 DVFLGMFLYEYAR 324 336 0 1639.782 820.395 547.266
45 R 337 337 0 175.119 88.063 59.045
46 HPDYSVVLLLR 338 348 0 1311.742 656.375 437.919
47 LAK 349 351 0 331.234 166.121 111.083
48 TYETTLEK 352 359 0 984.488 492.748 328.834
49 CCAAADPHECYAK 360 372 0 1552.598 776.803 518.204
50 VFDEFKPLVEEPQNLIK 373 389 0 2045.095 1023.051 682.370
51 QNCELFEQLGEYK 390 402 0 1657.753 829.380 553.256
52 FQNALLVR 403 410 0 960.563 480.785 320.859
53 YTK 411 413 0 411.224 206.116 137.746
54 K 414 414 0 147.113 74.060 49.709
55 VPQVSTPTLVEVSR 415 428 0 1511.843 756.425 504.619
56 NLGK 429 432 0 431.261 216.134 144.425
57 VGSK 433 436 0 390.235 195.621 130.750
58 CCK 437 439 0 467.174 234.091 156.396
59 HPEAK 440 444 0 581.304 291.156 194.440
60 R 445 445 0 175.119 88.063 59.045
61 MPCAEDYLSVVLNQLCVLHEK 446 466 0 2534.209 1267.608 845.408
62 TPVSDR 467 472 0 674.347 337.677 225.454
63 VTK 473 475 0 347.229 174.118 116.414
64 CCTESLVNR 476 484 0 1138.498 569.753 380.171
65 RPCFSALEVDETYVPK 485 500 0 1910.932 955.969 637.649
66 EFNAETFTFHADICTLSEK 501 519 0 2260.023 1130.515 754.012
67 ER 520 521 0 304.162 152.584 102.059
68 QIK 522 524 0 388.255 194.631 130.090
69 K 525 525 0 147.113 74.060 49.709
70 QTALVELVK 526 534 0 1000.604 500.805 334.206
71 HKPK 535 538 0 509.319 255.163 170.445
72 ATK 539 541 0 319.198 160.102 107.071
73 EQLK 542 545 0 517.298 259.153 173.104
74 AVMDDFAAFVEK 546 557 0 1358.630 679.818 453.548
75 CCK 558 560 0 467.174 234.091 156.396
76 ADDK 561 564 0 448.204 224.606 150.073
77 ETCFAEEGK 565 573 0 1070.446 535.727 357.487
78 K 574 574 0 147.113 74.060 49.709
79 LVAASQAALGL 575 585 0 1013.599 507.303 338.538
peptide start stop mc mz1 mz2 mz3
1 DAHK 1 4 0 470.236 235.622 157.417
2 SEVAHR 5 10 0 698.358 349.683 233.458
3 FK 11 12 0 294.181 147.594 98.732
4 DLGEENFK 13 20 0 951.442 476.225 317.819
5 ALVLIAFAQYLQQCPFEDHVK 21 41 0 2490.285 1245.646 830.767
6 LVNEVTEFAK 42 51 0 1149.615 575.311 383.877
7 TCVADESAENCDK 52 64 0 1498.578 749.793 500.198
8 SLHTLFGDK 65 73 0 1017.536 509.272 339.850
9 LCTVATLR 74 81 0 933.519 467.263 311.844
10 ETYGEMADCCAK 82 93 0 1434.533 717.770 478.849
11 QEPER 94 98 0 658.315 329.661 220.110
12 NECFLQHK 99 106 0 1075.499 538.253 359.171
13 DDNPNLPR 107 114 0 940.448 470.728 314.154
14 LVR 115 117 0 387.271 194.139 129.762
15 PEVDVMCTAFHDNEETFLK 118 136 0 2282.010 1141.509 761.342
16 K 137 137 0 147.113 74.060 49.709
17 YLYEIAR 138 144 0 927.493 464.250 309.836
18 R 145 145 0 175.119 88.063 59.045
19 HPYFYAPELLFFAK 146 159 0 1742.894 871.951 581.636
20 R 160 160 0 175.119 88.063 59.045
21 YK 161 162 0 310.176 155.592 104.064
22 AAFTECCQAADK 163 174 0 1371.567 686.287 457.860
23 AACLLPK 175 181 0 772.439 386.723 258.151
24 LDELR 182 186 0 645.357 323.182 215.790
25 DEGK 187 190 0 448.204 224.606 150.073
26 ASSAK 191 195 0 463.251 232.129 155.089
27 QR 196 197 0 303.178 152.092 101.731
28 LK 198 199 0 260.197 130.602 87.404
29 CASLQK 200 205 0 706.355 353.681 236.123
30 FGER 206 209 0 508.251 254.629 170.089
31 AFK 210 212 0 365.218 183.113 122.411
32 AWAVAR 213 218 0 673.378 337.193 225.131
33 LSQR 219 222 0 503.294 252.150 168.436
34 FPK 223 225 0 391.234 196.121 131.083
35 AEFAEVSK 226 233 0 880.441 440.724 294.152
36 LVTDLTK 234 240 0 789.472 395.239 263.829
37 VHTECCHGDLLECADDR 241 257 0 2086.838 1043.922 696.284
38 ADLAK 258 262 0 517.298 259.153 173.104
39 YICENQDSISSK 263 274 0 1443.642 722.325 481.886
40 LK 275 276 0 260.197 130.602 87.404
41 ECCEK 277 281 0 725.259 363.133 242.425
42 PLLEK 282 286 0 599.376 300.192 200.464
43 SHCIAEVENDEMPADLPSLAADFVESK 287 313 0 2974.344 1487.676 992.120
44 DVCK 314 317 0 521.239 261.123 174.418
45 NYAEAK 318 323 0 695.336 348.172 232.450
46 DVFLGMFLYEYAR 324 336 0 1623.788 812.397 541.934
47 R 337 337 0 175.119 88.063 59.045
48 HPDYSVVLLLR 338 348 0 1311.742 656.375 437.919
49 LAK 349 351 0 331.234 166.121 111.083
50 TYETTLEK 352 359 0 984.488 492.748 328.834
51 CCAAADPHECYAK 360 372 0 1552.598 776.803 518.204
52 VFDEFK 373 378 0 784.388 392.697 262.134
53 PLVEEPQNLIK 379 389 0 1279.726 640.366 427.247
54 QNCELFEQLGEYK 390 402 0 1657.753 829.380 553.256
55 FQNALLVR 403 410 0 960.563 480.785 320.859
56 YTK 411 413 0 411.224 206.116 137.746
57 K 414 414 0 147.113 74.060 49.709
58 VPQVSTPTLVEVSR 415 428 0 1511.843 756.425 504.619
59 NLGK 429 432 0 431.261 216.134 144.425
60 VGSK 433 436 0 390.235 195.621 130.750
61 CCK 437 439 0 467.174 234.091 156.396
62 HPEAK 440 444 0 581.304 291.156 194.440
63 R 445 445 0 175.119 88.063 59.045
64 MPCAEDYLSVVLNQLCVLHEK 446 466 0 2518.214 1259.611 840.076
65 TPVSDR 467 472 0 674.347 337.677 225.454
66 VTK 473 475 0 347.229 174.118 116.414
67 CCTESLVNR 476 484 0 1138.498 569.753 380.171
68 R 485 485 0 175.119 88.063 59.045
69 PCFSALEVDETYVPK 486 500 0 1754.831 877.919 585.615
70 EFNAETFTFHADICTLSEK 501 519 0 2260.023 1130.515 754.012
71 ER 520 521 0 304.162 152.584 102.059
72 QIK 522 524 0 388.255 194.631 130.090
73 K 525 525 0 147.113 74.060 49.709
74 QTALVELVK 526 534 0 1000.604 500.805 334.206
75 HK 535 536 0 284.172 142.589 95.395
76 PK 537 538 0 244.166 122.586 82.060
77 ATK 539 541 0 319.198 160.102 107.071
78 EQLK 542 545 0 517.298 259.153 173.104
79 AVMDDFAAFVEK 546 557 0 1342.635 671.821 448.216
80 CCK 558 560 0 467.174 234.091 156.396
81 ADDK 561 564 0 448.204 224.606 150.073
82 ETCFAEEGK 565 573 0 1070.446 535.727 357.487
83 K 574 574 0 147.113 74.060 49.709
84 LVAASQAALGL 575 585 0 1013.599 507.303 338.538
OrgMassSpecR documentation built on May 2, 2019, 11:04 a.m.
R Package Documentation
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Description Usage Arguments Details Value Author(s) References See Also Examples
Description
Cleave an amino acid sequence (a protein or peptide) according to enzyme specific rules and calculate the precursor ion m/z values.
Usage
1 2 |
Arguments
sequence |
a character string representing the amino acid sequence to be cleaved by the enzyme. |
enzyme |
a character string specifying the rules for cleavage. Options are |
missed |
the maximum number of missed cleavages. Must be an integer of 0 (default) or greater. An error will result if the specified number of missed cleavages is greater than the maximum possible number of missed cleavages. |
IAA |
logical. |
N15 |
logical indicating if the nitrogen-15 isotope should be used in place of the default nitrogen-14 isotope. |
custom |
a list specifying user defined residues as |
Details
The amino acid residues must be specified by one letter codes. The predefined residues are:
| A = alanine | L = leucine |
| R = arginine | K = lysine |
| N = asparagine | M = methionine |
| D = aspartic acid | F = phenylalanine |
| C = cysteine | P = proline |
| E = glutamic acid | S = serine |
| Q = glutamine | T = threonine |
| G = glycine | W = tryptophan |
| H = histidine | Y = tyrosine |
| I = isoleucine | V = valine |
If "trypsin" is specified, the sequence is cleaved on the c-terminal side of K and R residues, except if K or R is followed by P. If "trypsin.strict" is specified, the sequence is cleaved on the c-terminal side of K and R residues. If "pepsin" is specified, the sequence is cleaved on the c-terminal side of F, L, W, Y, A, E, and Q residues. This rule is specific to pepsin at pH > 2, as used in hydrogen-deuterium exchange experiments.
When "trypsin" is specified, KP and RP are not considered missed cleavages when missed is > 0.
The argument IAA specifies treatment of the protein with iodoacetamide. This treatment produces iodoacetylated cysteine residues (elemental formula C5H8N2O2S).
If TRUE, the argument N15 specifies 100% nitrogen-15 incorporation. It is intended for proteins grown with a nitrogen-15 labeled food source. (Although the experiment itself may grow a protein with less than 100% nitrogen-15 incorporation). Setting N15 = TRUE does not modify the mass of a custom residue, or the mass of the nitrogen(s) added if IAA = TRUE.
If a custom residue code is identical to a predefined residue code, the custom residue mass will be used in place of the predefined mass.
The error message “object "mass" not found” indicates the input sequence contains an undefined residue(s).
Value
A data frame with the following column names.
peptide |
resulting peptides. |
start |
beginning residue positions in the the original sequence. |
end |
ending residue positions in the the original sequence. |
mc |
number of missed cleavages. |
mz1 |
monoisotopic m/z values for the [M + H]1+ ions (where M is the precursor mass). |
mz2 |
monoisotopic m/z values for the [M + 2H]2+ ions. |
mz3 |
monoisotopic m/z values for the [M + 3H]3+ ions. |
Author(s)
Nathan G. Dodder
References
The relative atomic masses of the isotopes are from the NIST Physical Reference Data Website http://physics.nist.gov/PhysRefData/Compositions/. The molar mass of a proton (H+) is from the NIST CODATA Website http://physics.nist.gov/cuu/Constants/index.html.
See Also
MonoisotopicMass, FragmentPeptide
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## digest human serum albumin with 0 and 1 missed cleavages
Digest(example.sequence, missed = 1)
## digest human serum albumin with a phosphoserine at position 58
## and all methionines oxidized
modifiedHsaSequence <- strsplit(example.sequence, split = "")[[1]]
modifiedHsaSequence[58] <- "s" # insert code for phosphoserine
modifiedHsaSequence <- paste(modifiedHsaSequence, collapse = "")
Digest(modifiedHsaSequence, custom = list(code = c("s","M"),
mass = c(MonoisotopicMass(list(C=3, H=6, N=1, O=5, P=1)),
MonoisotopicMass(list(C=5, H=9, N=1, O=2, S=1)))))
## digest human serum albumin with strict rules
Digest(example.sequence, enzyme = "trypsin.strict")
|
Example output
Loading required package: grid
peptide start stop mc mz1 mz2
1 DAHK 1 4 0 470.236 235.622
2 SEVAHR 5 10 0 698.358 349.683
3 FK 11 12 0 294.181 147.594
4 DLGEENFK 13 20 0 951.442 476.225
5 ALVLIAFAQYLQQCPFEDHVK 21 41 0 2490.285 1245.646
6 LVNEVTEFAK 42 51 0 1149.615 575.311
7 TCVADESAENCDK 52 64 0 1498.578 749.793
8 SLHTLFGDK 65 73 0 1017.536 509.272
9 LCTVATLR 74 81 0 933.519 467.263
10 ETYGEMADCCAK 82 93 0 1434.533 717.770
11 QEPER 94 98 0 658.315 329.661
12 NECFLQHK 99 106 0 1075.499 538.253
13 DDNPNLPR 107 114 0 940.448 470.728
14 LVRPEVDVMCTAFHDNEETFLK 115 136 0 2650.264 1325.636
15 K 137 137 0 147.113 74.060
16 YLYEIAR 138 144 0 927.493 464.250
17 R 145 145 0 175.119 88.063
18 HPYFYAPELLFFAK 146 159 0 1742.894 871.951
19 R 160 160 0 175.119 88.063
20 YK 161 162 0 310.176 155.592
21 AAFTECCQAADK 163 174 0 1371.567 686.287
22 AACLLPK 175 181 0 772.439 386.723
23 LDELR 182 186 0 645.357 323.182
24 DEGK 187 190 0 448.204 224.606
25 ASSAK 191 195 0 463.251 232.129
26 QR 196 197 0 303.178 152.092
27 LK 198 199 0 260.197 130.602
28 CASLQK 200 205 0 706.355 353.681
29 FGER 206 209 0 508.251 254.629
30 AFK 210 212 0 365.218 183.113
31 AWAVAR 213 218 0 673.378 337.193
32 LSQR 219 222 0 503.294 252.150
33 FPK 223 225 0 391.234 196.121
34 AEFAEVSK 226 233 0 880.441 440.724
35 LVTDLTK 234 240 0 789.472 395.239
36 VHTECCHGDLLECADDR 241 257 0 2086.838 1043.922
37 ADLAK 258 262 0 517.298 259.153
38 YICENQDSISSK 263 274 0 1443.642 722.325
39 LK 275 276 0 260.197 130.602
40 ECCEKPLLEK 277 286 0 1305.618 653.313
41 SHCIAEVENDEMPADLPSLAADFVESK 287 313 0 2974.344 1487.676
42 DVCK 314 317 0 521.239 261.123
43 NYAEAK 318 323 0 695.336 348.172
44 DVFLGMFLYEYAR 324 336 0 1623.788 812.397
45 R 337 337 0 175.119 88.063
46 HPDYSVVLLLR 338 348 0 1311.742 656.375
47 LAK 349 351 0 331.234 166.121
48 TYETTLEK 352 359 0 984.488 492.748
49 CCAAADPHECYAK 360 372 0 1552.598 776.803
50 VFDEFKPLVEEPQNLIK 373 389 0 2045.095 1023.051
51 QNCELFEQLGEYK 390 402 0 1657.753 829.380
52 FQNALLVR 403 410 0 960.563 480.785
53 YTK 411 413 0 411.224 206.116
54 K 414 414 0 147.113 74.060
55 VPQVSTPTLVEVSR 415 428 0 1511.843 756.425
56 NLGK 429 432 0 431.261 216.134
57 VGSK 433 436 0 390.235 195.621
58 CCK 437 439 0 467.174 234.091
59 HPEAK 440 444 0 581.304 291.156
60 R 445 445 0 175.119 88.063
61 MPCAEDYLSVVLNQLCVLHEK 446 466 0 2518.214 1259.611
62 TPVSDR 467 472 0 674.347 337.677
63 VTK 473 475 0 347.229 174.118
64 CCTESLVNR 476 484 0 1138.498 569.753
65 RPCFSALEVDETYVPK 485 500 0 1910.932 955.969
66 EFNAETFTFHADICTLSEK 501 519 0 2260.023 1130.515
67 ER 520 521 0 304.162 152.584
68 QIK 522 524 0 388.255 194.631
69 K 525 525 0 147.113 74.060
70 QTALVELVK 526 534 0 1000.604 500.805
71 HKPK 535 538 0 509.319 255.163
72 ATK 539 541 0 319.198 160.102
73 EQLK 542 545 0 517.298 259.153
74 AVMDDFAAFVEK 546 557 0 1342.635 671.821
75 CCK 558 560 0 467.174 234.091
76 ADDK 561 564 0 448.204 224.606
77 ETCFAEEGK 565 573 0 1070.446 535.727
78 K 574 574 0 147.113 74.060
79 LVAASQAALGL 575 585 0 1013.599 507.303
80 DAHKSEVAHR 1 10 1 1149.576 575.292
81 SEVAHRFK 5 12 1 973.521 487.264
82 FKDLGEENFK 11 20 1 1226.605 613.806
83 DLGEENFKALVLIAFAQYLQQCPFEDHVK 13 41 1 3422.709 1711.858
84 ALVLIAFAQYLQQCPFEDHVKLVNEVTEFAK 21 51 1 3620.882 1810.945
85 LVNEVTEFAKTCVADESAENCDK 42 64 1 2629.176 1315.091
86 TCVADESAENCDKSLHTLFGDK 52 73 1 2497.097 1249.052
87 SLHTLFGDKLCTVATLR 65 81 1 1932.037 966.522
88 LCTVATLRETYGEMADCCAK 74 93 1 2349.034 1175.021
89 ETYGEMADCCAKQEPER 82 98 1 2073.831 1037.419
90 QEPERNECFLQHK 94 106 1 1714.797 857.902
91 NECFLQHKDDNPNLPR 99 114 1 1996.929 998.968
92 DDNPNLPRLVRPEVDVMCTAFHDNEETFLK 107 136 1 3571.694 1786.351
93 LVRPEVDVMCTAFHDNEETFLKK 115 137 1 2778.359 1389.683
94 KYLYEIAR 137 144 1 1055.588 528.298
95 YLYEIARR 138 145 1 1083.595 542.301
96 RHPYFYAPELLFFAK 145 159 1 1898.995 950.001
97 HPYFYAPELLFFAKR 146 160 1 1898.995 950.001
98 RYK 160 162 1 466.277 233.642
99 YKAAFTECCQAADK 161 174 1 1662.725 831.866
100 AAFTECCQAADKAACLLPK 163 181 1 2124.987 1062.997
101 AACLLPKLDELR 175 186 1 1398.777 699.892
102 LDELRDEGK 182 190 1 1074.543 537.775
103 DEGKASSAK 187 195 1 892.437 446.722
104 ASSAKQR 191 197 1 747.411 374.209
105 QRLK 196 199 1 544.357 272.682
106 LKCASLQK 198 205 1 947.534 474.271
107 CASLQKFGER 200 209 1 1195.589 598.298
108 FGERAFK 206 212 1 854.452 427.730
109 AFKAWAVAR 210 218 1 1019.579 510.293
110 AWAVARLSQR 213 222 1 1157.654 579.331
111 LSQRFPK 219 225 1 875.510 438.259
112 FPKAEFAEVSK 223 233 1 1252.657 626.832
113 AEFAEVSKLVTDLTK 226 240 1 1650.895 825.951
114 LVTDLTKVHTECCHGDLLECADDR 234 257 1 2857.291 1429.149
115 VHTECCHGDLLECADDRADLAK 241 262 1 2585.118 1293.063
116 ADLAKYICENQDSISSK 258 274 1 1941.922 971.465
117 YICENQDSISSKLK 263 276 1 1684.821 842.914
118 LKECCEKPLLEK 275 286 1 1546.797 773.902
119 ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESK 277 313 1 4260.944 2130.976
120 SHCIAEVENDEMPADLPSLAADFVESKDVCK 287 317 1 3476.565 1738.786
121 DVCKNYAEAK 314 323 1 1197.557 599.282
122 NYAEAKDVFLGMFLYEYAR 318 336 1 2300.106 1150.556
123 DVFLGMFLYEYARR 324 337 1 1779.889 890.448
124 RHPDYSVVLLLR 337 348 1 1467.843 734.425
125 HPDYSVVLLLRLAK 338 351 1 1623.958 812.483
126 LAKTYETTLEK 349 359 1 1296.705 648.856
127 TYETTLEKCCAAADPHECYAK 352 372 1 2518.068 1259.538
128 CCAAADPHECYAKVFDEFKPLVEEPQNLIK 360 389 1 3578.675 1789.841
129 VFDEFKPLVEEPQNLIKQNCELFEQLGEYK 373 402 1 3683.830 1842.419
130 QNCELFEQLGEYKFQNALLVR 390 410 1 2599.297 1300.152
131 FQNALLVRYTK 403 413 1 1352.768 676.888
132 YTKK 411 414 1 539.319 270.163
133 KVPQVSTPTLVEVSR 414 428 1 1639.938 820.473
134 VPQVSTPTLVEVSRNLGK 415 432 1 1924.086 962.547
135 NLGKVGSK 429 436 1 802.478 401.743
136 VGSKCCK 433 439 1 838.391 419.699
137 CCKHPEAK 437 444 1 1029.460 515.234
138 HPEAKR 440 445 1 737.405 369.206
139 RMPCAEDYLSVVLNQLCVLHEK 445 466 1 2674.315 1337.661
140 MPCAEDYLSVVLNQLCVLHEKTPVSDR 446 472 1 3173.543 1587.275
141 TPVSDRVTK 467 475 1 1002.558 501.783
142 VTKCCTESLVNR 473 484 1 1466.709 733.858
143 CCTESLVNRRPCFSALEVDETYVPK 476 500 1 3030.412 1515.710
144 RPCFSALEVDETYVPKEFNAETFTFHADICTLSEK 485 519 1 4151.937 2076.472
145 EFNAETFTFHADICTLSEKER 501 521 1 2545.166 1273.087
146 ERQIK 520 524 1 673.399 337.203
147 QIKK 522 525 1 516.350 258.679
148 KQTALVELVK 525 534 1 1128.699 564.853
149 QTALVELVKHKPK 526 538 1 1490.905 745.956
150 HKPKATK 535 541 1 809.499 405.253
151 ATKEQLK 539 545 1 817.478 409.243
152 EQLKAVMDDFAAFVEK 542 557 1 1840.915 920.961
153 AVMDDFAAFVEKCCK 546 560 1 1790.791 895.899
154 CCKADDK 558 564 1 896.360 448.684
155 ADDKETCFAEEGK 561 573 1 1499.632 750.320
156 ETCFAEEGKK 565 574 1 1198.541 599.774
157 KLVAASQAALGL 574 585 1 1141.694 571.351
mz3
1 157.417
2 233.458
3 98.732
4 317.819
5 830.767
6 383.877
7 500.198
8 339.850
9 311.844
10 478.849
11 220.110
12 359.171
13 314.154
14 884.093
15 49.709
16 309.836
17 59.045
18 581.636
19 59.045
20 104.064
21 457.860
22 258.151
23 215.790
24 150.073
25 155.089
26 101.731
27 87.404
28 236.123
29 170.089
30 122.411
31 225.131
32 168.436
33 131.083
34 294.152
35 263.829
36 696.284
37 173.104
38 481.886
39 87.404
40 435.877
41 992.120
42 174.418
43 232.450
44 541.934
45 59.045
46 437.919
47 111.083
48 328.834
49 518.204
50 682.370
51 553.256
52 320.859
53 137.746
54 49.709
55 504.619
56 144.425
57 130.750
58 156.396
59 194.440
60 59.045
61 840.076
62 225.454
63 116.414
64 380.171
65 637.649
66 754.012
67 102.059
68 130.090
69 49.709
70 334.206
71 170.445
72 107.071
73 173.104
74 448.216
75 156.396
76 150.073
77 357.487
78 49.709
79 338.538
80 383.863
81 325.179
82 409.540
83 1141.574
84 1207.632
85 877.063
86 833.037
87 644.684
88 783.683
89 691.949
90 572.270
91 666.315
92 1191.236
93 926.791
94 352.534
95 361.870
96 633.670
97 633.670
98 156.097
99 554.913
100 709.001
101 466.931
102 358.852
103 298.151
104 249.808
105 182.124
106 316.516
107 399.201
108 285.489
109 340.531
110 386.556
111 292.508
112 418.224
113 550.970
114 953.102
115 862.377
116 647.979
117 562.279
118 516.270
119 1420.986
120 1159.527
121 399.857
122 767.373
123 593.968
124 489.953
125 541.991
126 432.906
127 840.028
128 1193.563
129 1228.615
130 867.104
131 451.594
132 180.444
133 547.317
134 642.034
135 268.164
136 280.135
137 343.825
138 246.473
139 892.110
140 1058.519
141 334.857
142 489.575
143 1010.809
144 1384.650
145 849.060
146 225.138
147 172.788
148 376.904
149 497.640
150 270.505
151 273.164
152 614.310
153 597.602
154 299.458
155 500.549
156 400.185
157 381.236
peptide start stop mc mz1 mz2 mz3
1 DAHK 1 4 0 470.236 235.622 157.417
2 SEVAHR 5 10 0 698.358 349.683 233.458
3 FK 11 12 0 294.181 147.594 98.732
4 DLGEENFK 13 20 0 951.442 476.225 317.819
5 ALVLIAFAQYLQQCPFEDHVK 21 41 0 2490.285 1245.646 830.767
6 LVNEVTEFAK 42 51 0 1149.615 575.311 383.877
7 TCVADEsAENCDK 52 64 0 1578.545 789.776 526.853
8 SLHTLFGDK 65 73 0 1017.536 509.272 339.850
9 LCTVATLR 74 81 0 933.519 467.263 311.844
10 ETYGEMADCCAK 82 93 0 1450.528 725.768 484.181
11 QEPER 94 98 0 658.315 329.661 220.110
12 NECFLQHK 99 106 0 1075.499 538.253 359.171
13 DDNPNLPR 107 114 0 940.448 470.728 314.154
14 LVRPEVDVMCTAFHDNEETFLK 115 136 0 2666.259 1333.633 889.424
15 K 137 137 0 147.113 74.060 49.709
16 YLYEIAR 138 144 0 927.493 464.250 309.836
17 R 145 145 0 175.119 88.063 59.045
18 HPYFYAPELLFFAK 146 159 0 1742.894 871.951 581.636
19 R 160 160 0 175.119 88.063 59.045
20 YK 161 162 0 310.176 155.592 104.064
21 AAFTECCQAADK 163 174 0 1371.567 686.287 457.860
22 AACLLPK 175 181 0 772.439 386.723 258.151
23 LDELR 182 186 0 645.357 323.182 215.790
24 DEGK 187 190 0 448.204 224.606 150.073
25 ASSAK 191 195 0 463.251 232.129 155.089
26 QR 196 197 0 303.178 152.092 101.731
27 LK 198 199 0 260.197 130.602 87.404
28 CASLQK 200 205 0 706.355 353.681 236.123
29 FGER 206 209 0 508.251 254.629 170.089
30 AFK 210 212 0 365.218 183.113 122.411
31 AWAVAR 213 218 0 673.378 337.193 225.131
32 LSQR 219 222 0 503.294 252.150 168.436
33 FPK 223 225 0 391.234 196.121 131.083
34 AEFAEVSK 226 233 0 880.441 440.724 294.152
35 LVTDLTK 234 240 0 789.472 395.239 263.829
36 VHTECCHGDLLECADDR 241 257 0 2086.838 1043.922 696.284
37 ADLAK 258 262 0 517.298 259.153 173.104
38 YICENQDSISSK 263 274 0 1443.642 722.325 481.886
39 LK 275 276 0 260.197 130.602 87.404
40 ECCEKPLLEK 277 286 0 1305.618 653.313 435.877
41 SHCIAEVENDEMPADLPSLAADFVESK 287 313 0 2990.339 1495.673 997.451
42 DVCK 314 317 0 521.239 261.123 174.418
43 NYAEAK 318 323 0 695.336 348.172 232.450
44 DVFLGMFLYEYAR 324 336 0 1639.782 820.395 547.266
45 R 337 337 0 175.119 88.063 59.045
46 HPDYSVVLLLR 338 348 0 1311.742 656.375 437.919
47 LAK 349 351 0 331.234 166.121 111.083
48 TYETTLEK 352 359 0 984.488 492.748 328.834
49 CCAAADPHECYAK 360 372 0 1552.598 776.803 518.204
50 VFDEFKPLVEEPQNLIK 373 389 0 2045.095 1023.051 682.370
51 QNCELFEQLGEYK 390 402 0 1657.753 829.380 553.256
52 FQNALLVR 403 410 0 960.563 480.785 320.859
53 YTK 411 413 0 411.224 206.116 137.746
54 K 414 414 0 147.113 74.060 49.709
55 VPQVSTPTLVEVSR 415 428 0 1511.843 756.425 504.619
56 NLGK 429 432 0 431.261 216.134 144.425
57 VGSK 433 436 0 390.235 195.621 130.750
58 CCK 437 439 0 467.174 234.091 156.396
59 HPEAK 440 444 0 581.304 291.156 194.440
60 R 445 445 0 175.119 88.063 59.045
61 MPCAEDYLSVVLNQLCVLHEK 446 466 0 2534.209 1267.608 845.408
62 TPVSDR 467 472 0 674.347 337.677 225.454
63 VTK 473 475 0 347.229 174.118 116.414
64 CCTESLVNR 476 484 0 1138.498 569.753 380.171
65 RPCFSALEVDETYVPK 485 500 0 1910.932 955.969 637.649
66 EFNAETFTFHADICTLSEK 501 519 0 2260.023 1130.515 754.012
67 ER 520 521 0 304.162 152.584 102.059
68 QIK 522 524 0 388.255 194.631 130.090
69 K 525 525 0 147.113 74.060 49.709
70 QTALVELVK 526 534 0 1000.604 500.805 334.206
71 HKPK 535 538 0 509.319 255.163 170.445
72 ATK 539 541 0 319.198 160.102 107.071
73 EQLK 542 545 0 517.298 259.153 173.104
74 AVMDDFAAFVEK 546 557 0 1358.630 679.818 453.548
75 CCK 558 560 0 467.174 234.091 156.396
76 ADDK 561 564 0 448.204 224.606 150.073
77 ETCFAEEGK 565 573 0 1070.446 535.727 357.487
78 K 574 574 0 147.113 74.060 49.709
79 LVAASQAALGL 575 585 0 1013.599 507.303 338.538
peptide start stop mc mz1 mz2 mz3
1 DAHK 1 4 0 470.236 235.622 157.417
2 SEVAHR 5 10 0 698.358 349.683 233.458
3 FK 11 12 0 294.181 147.594 98.732
4 DLGEENFK 13 20 0 951.442 476.225 317.819
5 ALVLIAFAQYLQQCPFEDHVK 21 41 0 2490.285 1245.646 830.767
6 LVNEVTEFAK 42 51 0 1149.615 575.311 383.877
7 TCVADESAENCDK 52 64 0 1498.578 749.793 500.198
8 SLHTLFGDK 65 73 0 1017.536 509.272 339.850
9 LCTVATLR 74 81 0 933.519 467.263 311.844
10 ETYGEMADCCAK 82 93 0 1434.533 717.770 478.849
11 QEPER 94 98 0 658.315 329.661 220.110
12 NECFLQHK 99 106 0 1075.499 538.253 359.171
13 DDNPNLPR 107 114 0 940.448 470.728 314.154
14 LVR 115 117 0 387.271 194.139 129.762
15 PEVDVMCTAFHDNEETFLK 118 136 0 2282.010 1141.509 761.342
16 K 137 137 0 147.113 74.060 49.709
17 YLYEIAR 138 144 0 927.493 464.250 309.836
18 R 145 145 0 175.119 88.063 59.045
19 HPYFYAPELLFFAK 146 159 0 1742.894 871.951 581.636
20 R 160 160 0 175.119 88.063 59.045
21 YK 161 162 0 310.176 155.592 104.064
22 AAFTECCQAADK 163 174 0 1371.567 686.287 457.860
23 AACLLPK 175 181 0 772.439 386.723 258.151
24 LDELR 182 186 0 645.357 323.182 215.790
25 DEGK 187 190 0 448.204 224.606 150.073
26 ASSAK 191 195 0 463.251 232.129 155.089
27 QR 196 197 0 303.178 152.092 101.731
28 LK 198 199 0 260.197 130.602 87.404
29 CASLQK 200 205 0 706.355 353.681 236.123
30 FGER 206 209 0 508.251 254.629 170.089
31 AFK 210 212 0 365.218 183.113 122.411
32 AWAVAR 213 218 0 673.378 337.193 225.131
33 LSQR 219 222 0 503.294 252.150 168.436
34 FPK 223 225 0 391.234 196.121 131.083
35 AEFAEVSK 226 233 0 880.441 440.724 294.152
36 LVTDLTK 234 240 0 789.472 395.239 263.829
37 VHTECCHGDLLECADDR 241 257 0 2086.838 1043.922 696.284
38 ADLAK 258 262 0 517.298 259.153 173.104
39 YICENQDSISSK 263 274 0 1443.642 722.325 481.886
40 LK 275 276 0 260.197 130.602 87.404
41 ECCEK 277 281 0 725.259 363.133 242.425
42 PLLEK 282 286 0 599.376 300.192 200.464
43 SHCIAEVENDEMPADLPSLAADFVESK 287 313 0 2974.344 1487.676 992.120
44 DVCK 314 317 0 521.239 261.123 174.418
45 NYAEAK 318 323 0 695.336 348.172 232.450
46 DVFLGMFLYEYAR 324 336 0 1623.788 812.397 541.934
47 R 337 337 0 175.119 88.063 59.045
48 HPDYSVVLLLR 338 348 0 1311.742 656.375 437.919
49 LAK 349 351 0 331.234 166.121 111.083
50 TYETTLEK 352 359 0 984.488 492.748 328.834
51 CCAAADPHECYAK 360 372 0 1552.598 776.803 518.204
52 VFDEFK 373 378 0 784.388 392.697 262.134
53 PLVEEPQNLIK 379 389 0 1279.726 640.366 427.247
54 QNCELFEQLGEYK 390 402 0 1657.753 829.380 553.256
55 FQNALLVR 403 410 0 960.563 480.785 320.859
56 YTK 411 413 0 411.224 206.116 137.746
57 K 414 414 0 147.113 74.060 49.709
58 VPQVSTPTLVEVSR 415 428 0 1511.843 756.425 504.619
59 NLGK 429 432 0 431.261 216.134 144.425
60 VGSK 433 436 0 390.235 195.621 130.750
61 CCK 437 439 0 467.174 234.091 156.396
62 HPEAK 440 444 0 581.304 291.156 194.440
63 R 445 445 0 175.119 88.063 59.045
64 MPCAEDYLSVVLNQLCVLHEK 446 466 0 2518.214 1259.611 840.076
65 TPVSDR 467 472 0 674.347 337.677 225.454
66 VTK 473 475 0 347.229 174.118 116.414
67 CCTESLVNR 476 484 0 1138.498 569.753 380.171
68 R 485 485 0 175.119 88.063 59.045
69 PCFSALEVDETYVPK 486 500 0 1754.831 877.919 585.615
70 EFNAETFTFHADICTLSEK 501 519 0 2260.023 1130.515 754.012
71 ER 520 521 0 304.162 152.584 102.059
72 QIK 522 524 0 388.255 194.631 130.090
73 K 525 525 0 147.113 74.060 49.709
74 QTALVELVK 526 534 0 1000.604 500.805 334.206
75 HK 535 536 0 284.172 142.589 95.395
76 PK 537 538 0 244.166 122.586 82.060
77 ATK 539 541 0 319.198 160.102 107.071
78 EQLK 542 545 0 517.298 259.153 173.104
79 AVMDDFAAFVEK 546 557 0 1342.635 671.821 448.216
80 CCK 558 560 0 467.174 234.091 156.396
81 ADDK 561 564 0 448.204 224.606 150.073
82 ETCFAEEGK 565 573 0 1070.446 535.727 357.487
83 K 574 574 0 147.113 74.060 49.709
84 LVAASQAALGL 575 585 0 1013.599 507.303 338.538
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