R/fragments-calculate.R
calculateFragments.RdThis 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, seq and peptide.
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.
# S4 method for class 'character,missing'
calculateFragments(
sequence,
type = c("b", "y"),
z = 1,
fixed_modifications = NULL,
variable_modifications = NULL,
addCarbamidomethyl = TRUE,
max_mods = Inf,
neutralLoss = defaultNeutralLoss(),
verbose = TRUE
)character() providing a peptide sequence. If positional
modifications are included in the sequence, variable modifications may not be
used. See examples below for more detail.
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.
Deprecated parameter. Please use
PTMods::addFixedModifications() to generate sequences with positional
modifications instead. Named numeric or character. If a character is
given, values must be in UniMod name or UniMod ID format
(e.g. "Phospho", "UNIMOD:21"). The annotation style of
the values is preserved in the output. Specifies which fixed
modifications are applied to which amino acids.
Deprecated parameter. Please use
PTMods::addVariableModifications() to generate sequences with positional
modifications instead. Named numeric or character. If a character
is given, values must be in UniMod name or UniMod ID format
(e.g. "Phospho", "UNIMOD:21"). The annotation style of
the values is preserved in the output. Specifies which
variable modifications are used on which amino acids.
logical(1L) set to TRUE by default. Applies
carbamidomethylation as a fixed modification unless fixed_modifications is
not NULL or if a carbamidomethyl is already present in the given sequences.
It is strongly suggested to rely on PTMods::addFixedModifications()
instead.
Deprecated parameter. Please use in combination with PTMods::addVariableModifications() instead. 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 _) and
c("K", "N", "Q", "R") for "ammonia" (shown with an *) are
supported.
logical(1). Deprecated parameter.
If TRUE (default) the used modifications are printed.
A data.frame 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 followed by the modification within brackets.
Fixed modifications are not displayed.
## No modifications
calculateFragments("ACE")
#> Fixed modifications used: C=57.02146
#> Variable modifications used: None
#> mz ion type pos z seq peptide
#> 1 72.04439 b1 b 1 1 A AC[+57.02146]E
#> 2 232.07504 b2 b 2 1 AC AC[+57.02146]E
#> 3 148.06043 y1 y 1 1 E AC[+57.02146]E
#> 4 308.09108 y2 y 2 1 CE AC[+57.02146]E
#> 5 130.04987 y1_ y_ 1 1 E AC[+57.02146]E
#> 6 290.08052 y2_ y_ 2 1 CE AC[+57.02146]E
## Multiple ion types and charge states
calculateFragments("ACE",
type = c("a", "b", "c", "x", "y", "z"),
z = 1:2)
#> Fixed modifications used: C=57.02146
#> Variable modifications used: None
#> mz ion type pos z seq peptide
#> 1 44.04947 a1 a 1 1 A AC[+57.02146]E
#> 2 22.52837 a1 a 1 2 A AC[+57.02146]E
#> 3 204.08012 a2 a 2 1 AC AC[+57.02146]E
#> 4 102.54370 a2 a 2 2 AC AC[+57.02146]E
#> 5 72.04439 b1 b 1 1 A AC[+57.02146]E
#> 6 36.52583 b1 b 1 2 A AC[+57.02146]E
#> 7 232.07504 b2 b 2 1 AC AC[+57.02146]E
#> 8 116.54116 b2 b 2 2 AC AC[+57.02146]E
#> 9 89.07094 c1 c 1 1 A AC[+57.02146]E
#> 10 45.03911 c1 c 1 2 A AC[+57.02146]E
#> 11 249.10158 c2 c 2 1 AC AC[+57.02146]E
#> 12 125.05443 c2 c 2 2 AC AC[+57.02146]E
#> 13 174.03970 x1 x 1 1 E AC[+57.02146]E
#> 14 87.52349 x1 x 1 2 E AC[+57.02146]E
#> 15 334.07035 x2 x 2 1 CE AC[+57.02146]E
#> 16 167.53881 x2 x 2 2 CE AC[+57.02146]E
#> 17 148.06043 y1 y 1 1 E AC[+57.02146]E
#> 18 74.53385 y1 y 1 2 E AC[+57.02146]E
#> 19 308.09108 y2 y 2 1 CE AC[+57.02146]E
#> 20 154.54918 y2 y 2 2 CE AC[+57.02146]E
#> 21 131.03388 z1 z 1 1 E AC[+57.02146]E
#> 22 66.02058 z1 z 1 2 E AC[+57.02146]E
#> 23 291.06453 z2 z 2 1 CE AC[+57.02146]E
#> 24 146.03590 z2 z 2 2 CE AC[+57.02146]E
#> 25 156.02913 x1_ x_ 1 1 E AC[+57.02146]E
#> 26 78.51820 x1_ x_ 1 2 E AC[+57.02146]E
#> 27 316.05978 x2_ x_ 2 1 CE AC[+57.02146]E
#> 28 158.53353 x2_ x_ 2 2 CE AC[+57.02146]E
#> 29 130.04987 y1_ y_ 1 1 E AC[+57.02146]E
#> 30 65.52857 y1_ y_ 1 2 E AC[+57.02146]E
#> 31 290.08052 y2_ y_ 2 1 CE AC[+57.02146]E
#> 32 145.54390 y2_ y_ 2 2 CE AC[+57.02146]E
#> 33 113.02332 z1_ z_ 1 1 E AC[+57.02146]E
#> 34 57.01530 z1_ z_ 1 2 E AC[+57.02146]E
#> 35 273.05397 z2_ z_ 2 1 CE AC[+57.02146]E
#> 36 137.03062 z2_ z_ 2 2 CE AC[+57.02146]E
## Positional modification written directly in the sequence string
## The annotation style must be supported by PTMods::convertAnnotation
calculateFragments("T[+79.966]CE")
#> Fixed modifications used: C=57.02146
#> Variable modifications used: None
#> mz ion type pos z seq peptide
#> 1 182.0210 b1 b 1 1 T T[+79.966]C[+57.02146]E
#> 2 342.0516 b2 b 2 1 TC T[+79.966]C[+57.02146]E
#> 3 148.0604 y1 y 1 1 E T[+79.966]C[+57.02146]E
#> 4 308.0911 y2 y 2 1 CE T[+79.966]C[+57.02146]E
#> 5 130.0499 y1_ y_ 1 1 E T[+79.966]C[+57.02146]E
#> 6 290.0805 y2_ y_ 2 1 CE T[+79.966]C[+57.02146]E
calculateFragments("T[Phospho]CE")
#> Fixed modifications used: C=57.02146
#> Variable modifications used: None
#> mz ion type pos z seq peptide
#> 1 182.0213 b1 b 1 1 T T[Phospho]C[+57.02146]E
#> 2 342.0519 b2 b 2 1 TC T[Phospho]C[+57.02146]E
#> 3 148.0604 y1 y 1 1 E T[Phospho]C[+57.02146]E
#> 4 308.0911 y2 y 2 1 CE T[Phospho]C[+57.02146]E
#> 5 130.0499 y1_ y_ 1 1 E T[Phospho]C[+57.02146]E
#> 6 290.0805 y2_ y_ 2 1 CE T[Phospho]C[+57.02146]E
## Notice carbamidomethylation applied by default, but ignored if already
## present.
calculateFragments("T[UNIMOD:21]C[Carbamidomethyl]E")
#> mz ion type pos z seq peptide
#> 1 182.0213 b1 b 1 1 T T[UNIMOD:21]C[Carbamidomethyl]E
#> 2 342.0519 b2 b 2 1 TC T[UNIMOD:21]C[Carbamidomethyl]E
#> 3 148.0604 y1 y 1 1 E T[UNIMOD:21]C[Carbamidomethyl]E
#> 4 308.0911 y2 y 2 1 CE T[UNIMOD:21]C[Carbamidomethyl]E
#> 5 130.0499 y1_ y_ 1 1 E T[UNIMOD:21]C[Carbamidomethyl]E
#> 6 290.0805 y2_ y_ 2 1 CE T[UNIMOD:21]C[Carbamidomethyl]E
## 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")
#> Fixed modifications used: C=57.02146
#> Variable modifications used: None
#> mz ion type pos z seq peptide
#> 1 98.06004 b1 b 1 1 P PQR
#> 2 226.11862 b2 b 2 1 PQ PQR
#> 3 175.11895 y1 y 1 1 R PQR
#> 4 303.17753 y2 y 2 1 QR PQR
#> 5 157.10839 y1_ y_ 1 1 R PQR
#> 6 285.16697 y2_ y_ 2 1 QR PQR
#> 7 286.15098 y2* y* 2 1 QR PQR
calculateFragments("PQR",
neutralLoss=defaultNeutralLoss(disableWaterLoss="Cterm"))
#> Fixed modifications used: C=57.02146
#> Variable modifications used: None
#> mz ion type pos z seq peptide
#> 1 98.06004 b1 b 1 1 P PQR
#> 2 226.11862 b2 b 2 1 PQ PQR
#> 3 175.11895 y1 y 1 1 R PQR
#> 4 303.17753 y2 y 2 1 QR PQR
#> 5 286.15098 y2* y* 2 1 QR PQR
calculateFragments("PQR",
neutralLoss=defaultNeutralLoss(disableAmmoniaLoss="Q"))
#> Fixed modifications used: C=57.02146
#> Variable modifications used: None
#> mz ion type pos z seq peptide
#> 1 98.06004 b1 b 1 1 P PQR
#> 2 226.11862 b2 b 2 1 PQ PQR
#> 3 175.11895 y1 y 1 1 R PQR
#> 4 303.17753 y2 y 2 1 QR PQR
#> 5 157.10839 y1_ y_ 1 1 R PQR
#> 6 285.16697 y2_ y_ 2 1 QR PQR
## disable neutral loss completely
calculateFragments("PQR", neutralLoss=NULL)
#> Fixed modifications used: C=57.02146
#> Variable modifications used: None
#> mz ion type pos z seq peptide
#> 1 98.06004 b1 b 1 1 P PQR
#> 2 226.11862 b2 b 2 1 PQ PQR
#> 3 175.11895 y1 y 1 1 R PQR
#> 4 303.17753 y2 y 2 1 QR PQR
## Recommended workflow: use PTMods functions to produce positional sequences
## before calling calculateFragments.
## Fixed modification (Carbamidomethyl on C) using addFixedModifications
seq_fixed <- PTMods::addFixedModifications("ACE",
fixedModifications = c(C = 57.02))
calculateFragments(seq_fixed)
#> mz ion type pos z seq peptide
#> 1 72.04439 b1 b 1 1 A AC[+57.02]E
#> 2 232.07358 b2 b 2 1 AC AC[+57.02]E
#> 3 148.06043 y1 y 1 1 E AC[+57.02]E
#> 4 308.08962 y2 y 2 1 CE AC[+57.02]E
#> 5 130.04987 y1_ y_ 1 1 E AC[+57.02]E
#> 6 290.07906 y2_ y_ 2 1 CE AC[+57.02]E
## Fixed modification including N-terminus using addFixedModifications
seq_nterm <- PTMods::addFixedModifications(
"ACE",
fixedModifications = c(C = 57.02, Nterm = 229.16))
calculateFragments(seq_nterm)
#> mz ion type pos z seq peptide
#> 1 301.2044 b1 b 1 1 A [+229.16]-AC[+57.02]E
#> 2 461.2336 b2 b 2 1 AC [+229.16]-AC[+57.02]E
#> 3 148.0604 y1 y 1 1 E [+229.16]-AC[+57.02]E
#> 4 308.0896 y2 y 2 1 CE [+229.16]-AC[+57.02]E
#> 5 130.0499 y1_ y_ 1 1 E [+229.16]-AC[+57.02]E
#> 6 290.0791 y2_ y_ 2 1 CE [+229.16]-AC[+57.02]E
## Variable modification (delta mass on A) using addVariableModifications
seq_var <- PTMods::addVariableModifications("ACE",
variableModifications = c(A = 43.25))
calculateFragments(seq_var)
#> Warning: Could not find Unimod entry for modification +43.25, see `?modifications`
#> Fixed modifications used: C=57.02146
#> Variable modifications used: None
#> mz ion type pos z seq peptide
#> 1 72.04439 b1 b 1 1 A AC[+57.02146]E
#> 2 232.07504 b2 b 2 1 AC AC[+57.02146]E
#> 3 148.06043 y1 y 1 1 E AC[+57.02146]E
#> 4 308.09108 y2 y 2 1 CE AC[+57.02146]E
#> 5 130.04987 y1_ y_ 1 1 E AC[+57.02146]E
#> 6 290.08052 y2_ y_ 2 1 CE AC[+57.02146]E
#> 7 115.29439 b1 b 1 1 A A[+43.25]C[+57.02146]E
#> 8 275.32504 b2 b 2 1 AC A[+43.25]C[+57.02146]E
#> 9 148.06043 y1 y 1 1 E A[+43.25]C[+57.02146]E
#> 10 308.09108 y2 y 2 1 CE A[+43.25]C[+57.02146]E
#> 11 130.04987 y1_ y_ 1 1 E A[+43.25]C[+57.02146]E
#> 12 290.08052 y2_ y_ 2 1 CE A[+43.25]C[+57.02146]E
## Both fixed and variable modifications using addModifications
seq_mods <- PTMods::addModifications("ARGSHKATC",
fixedModifications = c(C = 57),
variableModifications = c(S = 79, T = 79),
maxMods = 2)
calculateFragments(seq_mods)
#> Warning: Could not find Unimod entry for modification +57, see `?modifications`
#> Warning: Could not find Unimod entry for modification +79, see `?modifications`
#> Warning: Could not find Unimod entry for modification +57, see `?modifications`
#> Warning: Could not find Unimod entry for modification +79, see `?modifications`
#> Warning: Could not find Unimod entry for modification +57, see `?modifications`
#> Warning: Could not find Unimod entry for modification +79, see `?modifications`
#> Warning: Could not find Unimod entry for modification +79, see `?modifications`
#> Warning: Could not find Unimod entry for modification +57, see `?modifications`
#> Fixed modifications used: C=57.02146
#> Variable modifications used: None
#> mz ion type pos z seq peptide
#> 1 72.04439 b1 b 1 1 A ARGSHKATC[+57][+57.02146]
#> 2 228.14550 b2 b 2 1 AR ARGSHKATC[+57][+57.02146]
#> 3 285.16696 b3 b 3 1 ARG ARGSHKATC[+57][+57.02146]
#> 4 372.19899 b4 b 4 1 ARGS ARGSHKATC[+57][+57.02146]
#> 5 509.25790 b5 b 5 1 ARGSH ARGSHKATC[+57][+57.02146]
#> 6 637.35286 b6 b 6 1 ARGSHK ARGSHKATC[+57][+57.02146]
#> 7 708.38997 b7 b 7 1 ARGSHKA ARGSHKATC[+57][+57.02146]
#> 8 809.43765 b8 b 8 1 ARGSHKAT ARGSHKATC[+57][+57.02146]
#> 9 236.04849 y1 y 1 1 C ARGSHKATC[+57][+57.02146]
#> 10 337.09617 y2 y 2 1 TC ARGSHKATC[+57][+57.02146]
#> 11 408.13328 y3 y 3 1 ATC ARGSHKATC[+57][+57.02146]
#> 12 536.22824 y4 y 4 1 KATC ARGSHKATC[+57][+57.02146]
#> 13 673.28715 y5 y 5 1 HKATC ARGSHKATC[+57][+57.02146]
#> 14 760.31918 y6 y 6 1 SHKATC ARGSHKATC[+57][+57.02146]
#> 15 817.34064 y7 y 7 1 GSHKATC ARGSHKATC[+57][+57.02146]
#> 16 973.44175 y8 y 8 1 RGSHKATC ARGSHKATC[+57][+57.02146]
#> 17 491.24733 b5_ b_ 5 1 ARGSH ARGSHKATC[+57][+57.02146]
#> 18 619.34229 b6_ b_ 6 1 ARGSHK ARGSHKATC[+57][+57.02146]
#> 19 690.37940 b7_ b_ 7 1 ARGSHKA ARGSHKATC[+57][+57.02146]
#> 20 791.42708 b8_ b_ 8 1 ARGSHKAT ARGSHKATC[+57][+57.02146]
#> 21 390.12272 y3_ y_ 3 1 ATC ARGSHKATC[+57][+57.02146]
#> 22 518.21768 y4_ y_ 4 1 KATC ARGSHKATC[+57][+57.02146]
#> 23 655.27659 y5_ y_ 5 1 HKATC ARGSHKATC[+57][+57.02146]
#> 24 742.30862 y6_ y_ 6 1 SHKATC ARGSHKATC[+57][+57.02146]
#> 25 799.33008 y7_ y_ 7 1 GSHKATC ARGSHKATC[+57][+57.02146]
#> 26 955.43119 y8_ y_ 8 1 RGSHKATC ARGSHKATC[+57][+57.02146]
#> 27 218.03793 y1_ y_ 1 1 C ARGSHKATC[+57][+57.02146]
#> 28 319.08561 y2_ y_ 2 1 TC ARGSHKATC[+57][+57.02146]
#> 29 268.14041 b3* b* 3 1 ARG ARGSHKATC[+57][+57.02146]
#> 30 355.17244 b4* b* 4 1 ARGS ARGSHKATC[+57][+57.02146]
#> 31 492.23135 b5* b* 5 1 ARGSH ARGSHKATC[+57][+57.02146]
#> 32 620.32631 b6* b* 6 1 ARGSHK ARGSHKATC[+57][+57.02146]
#> 33 691.36342 b7* b* 7 1 ARGSHKA ARGSHKATC[+57][+57.02146]
#> 34 792.41110 b8* b* 8 1 ARGSHKAT ARGSHKATC[+57][+57.02146]
#> 35 519.20169 y4* y* 4 1 KATC ARGSHKATC[+57][+57.02146]
#> 36 656.26060 y5* y* 5 1 HKATC ARGSHKATC[+57][+57.02146]
#> 37 743.29263 y6* y* 6 1 SHKATC ARGSHKATC[+57][+57.02146]
#> 38 800.31409 y7* y* 7 1 GSHKATC ARGSHKATC[+57][+57.02146]
#> 39 956.41520 y8* y* 8 1 RGSHKATC ARGSHKATC[+57][+57.02146]
#> 40 72.04439 b1 b 1 1 A ARGS[+79]HKATC[+57][+57.02146]
#> 41 228.14550 b2 b 2 1 AR ARGS[+79]HKATC[+57][+57.02146]
#> 42 285.16696 b3 b 3 1 ARG ARGS[+79]HKATC[+57][+57.02146]
#> 43 451.19899 b4 b 4 1 ARGS ARGS[+79]HKATC[+57][+57.02146]
#> 44 588.25790 b5 b 5 1 ARGSH ARGS[+79]HKATC[+57][+57.02146]
#> 45 716.35286 b6 b 6 1 ARGSHK ARGS[+79]HKATC[+57][+57.02146]
#> 46 787.38997 b7 b 7 1 ARGSHKA ARGS[+79]HKATC[+57][+57.02146]
#> 47 888.43765 b8 b 8 1 ARGSHKAT ARGS[+79]HKATC[+57][+57.02146]
#> 48 236.04849 y1 y 1 1 C ARGS[+79]HKATC[+57][+57.02146]
#> 49 337.09617 y2 y 2 1 TC ARGS[+79]HKATC[+57][+57.02146]
#> 50 408.13328 y3 y 3 1 ATC ARGS[+79]HKATC[+57][+57.02146]
#> 51 536.22824 y4 y 4 1 KATC ARGS[+79]HKATC[+57][+57.02146]
#> 52 673.28715 y5 y 5 1 HKATC ARGS[+79]HKATC[+57][+57.02146]
#> 53 839.31918 y6 y 6 1 SHKATC ARGS[+79]HKATC[+57][+57.02146]
#> 54 896.34064 y7 y 7 1 GSHKATC ARGS[+79]HKATC[+57][+57.02146]
#> 55 1052.44175 y8 y 8 1 RGSHKATC ARGS[+79]HKATC[+57][+57.02146]
#> 56 570.24733 b5_ b_ 5 1 ARGSH ARGS[+79]HKATC[+57][+57.02146]
#> 57 698.34229 b6_ b_ 6 1 ARGSHK ARGS[+79]HKATC[+57][+57.02146]
#> 58 769.37940 b7_ b_ 7 1 ARGSHKA ARGS[+79]HKATC[+57][+57.02146]
#> 59 870.42708 b8_ b_ 8 1 ARGSHKAT ARGS[+79]HKATC[+57][+57.02146]
#> 60 390.12272 y3_ y_ 3 1 ATC ARGS[+79]HKATC[+57][+57.02146]
#> 61 518.21768 y4_ y_ 4 1 KATC ARGS[+79]HKATC[+57][+57.02146]
#> 62 655.27659 y5_ y_ 5 1 HKATC ARGS[+79]HKATC[+57][+57.02146]
#> 63 821.30862 y6_ y_ 6 1 SHKATC ARGS[+79]HKATC[+57][+57.02146]
#> 64 878.33008 y7_ y_ 7 1 GSHKATC ARGS[+79]HKATC[+57][+57.02146]
#> 65 1034.43119 y8_ y_ 8 1 RGSHKATC ARGS[+79]HKATC[+57][+57.02146]
#> 66 218.03793 y1_ y_ 1 1 C ARGS[+79]HKATC[+57][+57.02146]
#> 67 319.08561 y2_ y_ 2 1 TC ARGS[+79]HKATC[+57][+57.02146]
#> 68 268.14041 b3* b* 3 1 ARG ARGS[+79]HKATC[+57][+57.02146]
#> 69 434.17244 b4* b* 4 1 ARGS ARGS[+79]HKATC[+57][+57.02146]
#> 70 571.23135 b5* b* 5 1 ARGSH ARGS[+79]HKATC[+57][+57.02146]
#> 71 699.32631 b6* b* 6 1 ARGSHK ARGS[+79]HKATC[+57][+57.02146]
#> 72 770.36342 b7* b* 7 1 ARGSHKA ARGS[+79]HKATC[+57][+57.02146]
#> 73 871.41110 b8* b* 8 1 ARGSHKAT ARGS[+79]HKATC[+57][+57.02146]
#> 74 519.20169 y4* y* 4 1 KATC ARGS[+79]HKATC[+57][+57.02146]
#> 75 656.26060 y5* y* 5 1 HKATC ARGS[+79]HKATC[+57][+57.02146]
#> 76 822.29263 y6* y* 6 1 SHKATC ARGS[+79]HKATC[+57][+57.02146]
#> 77 879.31409 y7* y* 7 1 GSHKATC ARGS[+79]HKATC[+57][+57.02146]
#> 78 1035.41520 y8* y* 8 1 RGSHKATC ARGS[+79]HKATC[+57][+57.02146]
#> 79 72.04439 b1 b 1 1 A ARGSHKAT[+79]C[+57][+57.02146]
#> 80 228.14550 b2 b 2 1 AR ARGSHKAT[+79]C[+57][+57.02146]
#> 81 285.16696 b3 b 3 1 ARG ARGSHKAT[+79]C[+57][+57.02146]
#> 82 372.19899 b4 b 4 1 ARGS ARGSHKAT[+79]C[+57][+57.02146]
#> 83 509.25790 b5 b 5 1 ARGSH ARGSHKAT[+79]C[+57][+57.02146]
#> 84 637.35286 b6 b 6 1 ARGSHK ARGSHKAT[+79]C[+57][+57.02146]
#> 85 708.38997 b7 b 7 1 ARGSHKA ARGSHKAT[+79]C[+57][+57.02146]
#> 86 888.43765 b8 b 8 1 ARGSHKAT ARGSHKAT[+79]C[+57][+57.02146]
#> 87 236.04849 y1 y 1 1 C ARGSHKAT[+79]C[+57][+57.02146]
#> 88 416.09617 y2 y 2 1 TC ARGSHKAT[+79]C[+57][+57.02146]
#> 89 487.13328 y3 y 3 1 ATC ARGSHKAT[+79]C[+57][+57.02146]
#> 90 615.22824 y4 y 4 1 KATC ARGSHKAT[+79]C[+57][+57.02146]
#> 91 752.28715 y5 y 5 1 HKATC ARGSHKAT[+79]C[+57][+57.02146]
#> 92 839.31918 y6 y 6 1 SHKATC ARGSHKAT[+79]C[+57][+57.02146]
#> 93 896.34064 y7 y 7 1 GSHKATC ARGSHKAT[+79]C[+57][+57.02146]
#> 94 1052.44175 y8 y 8 1 RGSHKATC ARGSHKAT[+79]C[+57][+57.02146]
#> 95 491.24733 b5_ b_ 5 1 ARGSH ARGSHKAT[+79]C[+57][+57.02146]
#> 96 619.34229 b6_ b_ 6 1 ARGSHK ARGSHKAT[+79]C[+57][+57.02146]
#> 97 690.37940 b7_ b_ 7 1 ARGSHKA ARGSHKAT[+79]C[+57][+57.02146]
#> 98 870.42708 b8_ b_ 8 1 ARGSHKAT ARGSHKAT[+79]C[+57][+57.02146]
#> 99 469.12272 y3_ y_ 3 1 ATC ARGSHKAT[+79]C[+57][+57.02146]
#> 100 597.21768 y4_ y_ 4 1 KATC ARGSHKAT[+79]C[+57][+57.02146]
#> 101 734.27659 y5_ y_ 5 1 HKATC ARGSHKAT[+79]C[+57][+57.02146]
#> 102 821.30862 y6_ y_ 6 1 SHKATC ARGSHKAT[+79]C[+57][+57.02146]
#> 103 878.33008 y7_ y_ 7 1 GSHKATC ARGSHKAT[+79]C[+57][+57.02146]
#> 104 1034.43119 y8_ y_ 8 1 RGSHKATC ARGSHKAT[+79]C[+57][+57.02146]
#> 105 218.03793 y1_ y_ 1 1 C ARGSHKAT[+79]C[+57][+57.02146]
#> 106 398.08561 y2_ y_ 2 1 TC ARGSHKAT[+79]C[+57][+57.02146]
#> 107 268.14041 b3* b* 3 1 ARG ARGSHKAT[+79]C[+57][+57.02146]
#> 108 355.17244 b4* b* 4 1 ARGS ARGSHKAT[+79]C[+57][+57.02146]
#> 109 492.23135 b5* b* 5 1 ARGSH ARGSHKAT[+79]C[+57][+57.02146]
#> 110 620.32631 b6* b* 6 1 ARGSHK ARGSHKAT[+79]C[+57][+57.02146]
#> 111 691.36342 b7* b* 7 1 ARGSHKA ARGSHKAT[+79]C[+57][+57.02146]
#> 112 871.41110 b8* b* 8 1 ARGSHKAT ARGSHKAT[+79]C[+57][+57.02146]
#> 113 598.20169 y4* y* 4 1 KATC ARGSHKAT[+79]C[+57][+57.02146]
#> 114 735.26060 y5* y* 5 1 HKATC ARGSHKAT[+79]C[+57][+57.02146]
#> 115 822.29263 y6* y* 6 1 SHKATC ARGSHKAT[+79]C[+57][+57.02146]
#> 116 879.31409 y7* y* 7 1 GSHKATC ARGSHKAT[+79]C[+57][+57.02146]
#> 117 1035.41520 y8* y* 8 1 RGSHKATC ARGSHKAT[+79]C[+57][+57.02146]
#> 118 72.04439 b1 b 1 1 A ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 119 228.14550 b2 b 2 1 AR ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 120 285.16696 b3 b 3 1 ARG ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 121 451.19899 b4 b 4 1 ARGS ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 122 588.25790 b5 b 5 1 ARGSH ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 123 716.35286 b6 b 6 1 ARGSHK ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 124 787.38997 b7 b 7 1 ARGSHKA ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 125 967.43765 b8 b 8 1 ARGSHKAT ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 126 236.04849 y1 y 1 1 C ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 127 416.09617 y2 y 2 1 TC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 128 487.13328 y3 y 3 1 ATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 129 615.22824 y4 y 4 1 KATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 130 752.28715 y5 y 5 1 HKATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 131 918.31918 y6 y 6 1 SHKATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 132 975.34064 y7 y 7 1 GSHKATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 133 1131.44175 y8 y 8 1 RGSHKATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 134 570.24733 b5_ b_ 5 1 ARGSH ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 135 698.34229 b6_ b_ 6 1 ARGSHK ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 136 769.37940 b7_ b_ 7 1 ARGSHKA ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 137 949.42708 b8_ b_ 8 1 ARGSHKAT ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 138 469.12272 y3_ y_ 3 1 ATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 139 597.21768 y4_ y_ 4 1 KATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 140 734.27659 y5_ y_ 5 1 HKATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 141 900.30862 y6_ y_ 6 1 SHKATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 142 957.33008 y7_ y_ 7 1 GSHKATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 143 1113.43119 y8_ y_ 8 1 RGSHKATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 144 218.03793 y1_ y_ 1 1 C ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 145 398.08561 y2_ y_ 2 1 TC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 146 268.14041 b3* b* 3 1 ARG ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 147 434.17244 b4* b* 4 1 ARGS ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 148 571.23135 b5* b* 5 1 ARGSH ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 149 699.32631 b6* b* 6 1 ARGSHK ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 150 770.36342 b7* b* 7 1 ARGSHKA ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 151 950.41110 b8* b* 8 1 ARGSHKAT ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 152 598.20169 y4* y* 4 1 KATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 153 735.26060 y5* y* 5 1 HKATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 154 901.29263 y6* y* 6 1 SHKATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 155 958.31409 y7* y* 7 1 GSHKATC ARGS[+79]HKAT[+79]C[+57][+57.02146]
#> 156 1114.41520 y8* y* 8 1 RGSHKATC ARGS[+79]HKAT[+79]C[+57][+57.02146]