PeptideSeq.jl is a julia package for predicting peptide sequence after digestion, adding modification and generating expected fragments in mass spectrometry. Digestion enzyme and modification can be customized.
This package is not registered yet. Insall it through github:
julia> using Pkg; Pkg.add("https://github.com/yufongpeng/PeptideSeq.jl")julia> using PeptideSeq
julia> p = Protein("DPCHKPKRRKP")
Protein: DPCHKPKRRKP
Modification:
Enzyme:
julia> digest!(p, 2, "Trypsin") # Digest protein with Trypsin
Protein: DPCHKPKRRKP
Modification:
Enzyme: Trypsin
Peptides:
┌──────────────────┬──────────┬─────────┬────────┬───────────────┬──────────────┐
│ Peptide_sequence │ Position │ Mass │ Adduct │ Miss_cleavage │ Modification │
├──────────────────┼──────────┼─────────┼────────┼───────────────┼──────────────┤
│ DPCHKPK │ 1:7 │ 823.401 │ [M] │ 0 │ │
│ R │ 8:8 │ 174.112 │ [M] │ 0 │ │
│ R │ 9:9 │ 174.112 │ [M] │ 0 │ │
│ KP │ 10:11 │ 243.158 │ [M] │ 0 │ │
│ DPCHKPKR │ 1:8 │ 979.502 │ [M] │ 1 │ │
│ RR │ 8:9 │ 330.213 │ [M] │ 1 │ │
│ RKP │ 9:11 │ 399.259 │ [M] │ 1 │ │
│ DPCHKPKRR │ 1:9 │ 1135.6 │ [M] │ 2 │ │
│ RRKP │ 8:11 │ 555.361 │ [M] │ 2 │ │
└──────────────────┴──────────┴─────────┴────────┴───────────────┴──────────────┘
julia> modify!(p, "3NPH") # Derivatize peptides with 3NPH. It can be also modified first and then digested.
Protein: DPCHKPKRRKP
Modification: 3NPH
Enzyme: Trypsin
Peptides:
┌──────────────────┬──────────┬─────────┬────────┬───────────────┬───────────────┐
│ Peptide_sequence │ Position │ Mass │ Adduct │ Miss_cleavage │ Modification │
├──────────────────┼──────────┼─────────┼────────┼───────────────┼───────────────┤
│ DPCHKPK │ 1:7 │ 1093.49 │ [M] │ 0 │ 3NPH (@ 1, 7) │
│ R │ 8:8 │ 309.155 │ [M] │ 0 │ 3NPH (@ 8) │
│ R │ 9:9 │ 309.155 │ [M] │ 0 │ 3NPH (@ 9) │
│ KP │ 10:11 │ 378.202 │ [M] │ 0 │ 3NPH (@ 11) │
│ DPCHKPKR │ 1:8 │ 1249.59 │ [M] │ 1 │ 3NPH (@ 1, 8) │
│ RR │ 8:9 │ 465.256 │ [M] │ 1 │ 3NPH (@ 9) │
│ RKP │ 9:11 │ 534.303 │ [M] │ 1 │ 3NPH (@ 11) │
│ DPCHKPKRR │ 1:9 │ 1405.69 │ [M] │ 2 │ 3NPH (@ 1, 9) │
│ RRKP │ 8:11 │ 690.404 │ [M] │ 2 │ 3NPH (@ 11) │
└──────────────────┴──────────┴─────────┴────────┴───────────────┴───────────────┘
julia> ionize!(p, "[M+H]+", "[M+2H]2+")
Protein: DPCHKPKRRKP
Modification: 3NPH
Enzyme: Trypsin
Peptides:
┌──────────────────┬──────────┬─────────┬──────────┬───────────────┬───────────────┐
│ Peptide_sequence │ Position │ Mass │ Adduct │ Miss_cleavage │ Modification │
├──────────────────┼──────────┼─────────┼──────────┼───────────────┼───────────────┤
│ DPCHKPK │ 1:7 │ 1094.5 │ [M+H]⁺ │ 0 │ 3NPH (@ 1, 7) │
│ DPCHKPK │ 1:7 │ 547.752 │ [M+2H]²⁺ │ 0 │ 3NPH (@ 1, 7) │
│ R │ 8:8 │ 310.163 │ [M+H]⁺ │ 0 │ 3NPH (@ 8) │
│ R │ 8:8 │ 155.585 │ [M+2H]²⁺ │ 0 │ 3NPH (@ 8) │
│ R │ 9:9 │ 310.163 │ [M+H]⁺ │ 0 │ 3NPH (@ 9) │
│ R │ 9:9 │ 155.585 │ [M+2H]²⁺ │ 0 │ 3NPH (@ 9) │
│ KP │ 10:11 │ 379.209 │ [M+H]⁺ │ 0 │ 3NPH (@ 11) │
│ KP │ 10:11 │ 190.109 │ [M+2H]²⁺ │ 0 │ 3NPH (@ 11) │
│ DPCHKPKR │ 1:8 │ 1250.6 │ [M+H]⁺ │ 1 │ 3NPH (@ 1, 8) │
│ DPCHKPKR │ 1:8 │ 625.802 │ [M+2H]²⁺ │ 1 │ 3NPH (@ 1, 8) │
│ RR │ 8:9 │ 466.264 │ [M+H]⁺ │ 1 │ 3NPH (@ 9) │
│ RR │ 8:9 │ 233.636 │ [M+2H]²⁺ │ 1 │ 3NPH (@ 9) │
│ RKP │ 9:11 │ 535.31 │ [M+H]⁺ │ 1 │ 3NPH (@ 11) │
│ RKP │ 9:11 │ 268.159 │ [M+2H]²⁺ │ 1 │ 3NPH (@ 11) │
│ DPCHKPKRR │ 1:9 │ 1406.7 │ [M+H]⁺ │ 2 │ 3NPH (@ 1, 9) │
│ DPCHKPKRR │ 1:9 │ 703.853 │ [M+2H]²⁺ │ 2 │ 3NPH (@ 1, 9) │
│ RRKP │ 8:11 │ 691.412 │ [M+H]⁺ │ 2 │ 3NPH (@ 11) │
│ RRKP │ 8:11 │ 346.21 │ [M+2H]²⁺ │ 2 │ 3NPH (@ 11) │
└──────────────────┴──────────┴─────────┴──────────┴───────────────┴───────────────┘
julia> fragmentation(p.peptides[16]) # Fragmentation of 16th peptide
Peptide: DPCHKPKRR
Modification: 3NPH (@ 1, 9)
Precursor: 703.8527195000001
Adduct: [M+2H]²⁺
Fragment ions:
┌──────┬─────────┐
│ Type │ Mass │
├──────┼─────────┤
│ b₁⁺ │ 251.078 │
│ b₂⁺ │ 348.131 │
│ b₃⁺ │ 451.14 │
│ b₄⁺ │ 588.199 │
│ b₅⁺ │ 716.294 │
│ b₆⁺ │ 813.347 │
│ b₆²⁺ │ 407.177 │
│ b₇⁺ │ 941.442 │
│ b₇²⁺ │ 471.225 │
│ b₈⁺ │ 1097.54 │
│ b₈²⁺ │ 549.275 │
│ y₁⁺ │ 310.163 │
│ y₂⁺ │ 466.264 │
│ y₃⁺ │ 594.359 │
│ y₄⁺ │ 691.412 │
│ y₅⁺ │ 819.507 │
│ y₆⁺ │ 956.565 │
│ y₆²⁺ │ 478.787 │
│ y₇⁺ │ 1059.57 │
│ y₇²⁺ │ 530.291 │
│ y₈⁺ │ 1156.63 │
│ y₈²⁺ │ 578.818 │
└──────┴─────────┘
julia> data = read_msdial("test/data.txt") # MSDIAL data
Table with 6 columns and 411 rows:
Alignment ID Average Rt(min) Average Mz Metabolite name Adduct type MS/MS spectrum
┌────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ 0 0.691 100.077 Unknown [M+H-2H2O]+ [50.1298 0.0; 50.3013 0.0; 50.3086 0.0; 50.3209 0.0; 50.3…
2 │ 1 15.696 102.128 Unknown [M+H]+ [50.3038 0.0; 50.5715 1.0; 50.9706 1.0; 51.0595 0.0; 51.1…
3 │ 2 19.7 102.129 Unknown [M+H]+ [50.147 0.0; 50.2033 0.0; 50.2523 0.0; 50.3038 0.0; 50.38…
4 │ 3 16.241 102.129 Unknown [M+H]+ Float64[]
5 │ 4 17.278 102.129 Unknown [M+H]+ [50.1228 0.0; 50.2895 0.0; 50.4195 0.0; 50.5325 0.0; 50.5…
6 │ 5 4.481 118.085 Unknown [M+H]+ [50.3526 0.0; 50.4704 0.0; 50.5515 0.0; 50.5663 0.0; 50.6…
7 │ 6 11.167 118.086 Unknown [M+H]+ Float64[]
8 │ 7 0.682 132.103 NAE 4:0 [M+H]+ [50.064 0.0; 50.1986 0.0; 50.2673 0.0; 50.2746 0.0; 50.28…
9 │ 8 3.383 149.026 Unknown [M+H+2Na]+ [50.0222 0.0; 50.1054 0.0; 50.2719 0.0; 50.3332 0.0; 50.4…
10 │ 9 6.261 149.026 Unknown [M+H-H2O]+ [50.154 0.0; 50.3697 0.0; 50.4311 0.0; 50.4925 0.0; 50.68…
11 │ 10 0.605 152.02 Unknown [M+H]+ [50.227 0.0; 50.5264 0.0; 50.5363 0.0; 50.7774 0.0; 50.98…
⋮ │ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮
julia> result = find_peptides(data, db) # Find peptides in data
Table with 11 columns and 411 rows:
Alignment ID Average Rt(min) Average Mz Metabolite name Adduct type MS/MS spectrum Peptide Matched Peptide ⋯
┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ 0 0.691 100.077 Unknown [M+H-2H2O]+ [50.1298 0.0; 50.30… false nothing ⋯
2 │ 1 15.696 102.128 Unknown [M+H]+ [50.3038 0.0; 50.57… false nothing ⋯
3 │ 2 19.7 102.129 Unknown [M+H]+ [50.147 0.0; 50.203… false nothing ⋯
4 │ 3 16.241 102.129 Unknown [M+H]+ Float64[] false nothing ⋯
5 │ 4 17.278 102.129 Unknown [M+H]+ [50.1228 0.0; 50.28… false nothing ⋯
6 │ 5 4.481 118.085 Unknown [M+H]+ [50.3526 0.0; 50.47… false nothing ⋯
7 │ 6 11.167 118.086 Unknown [M+H]+ Float64[] false nothing ⋯
8 │ 7 0.682 132.103 NAE 4:0 [M+H]+ [50.064 0.0; 50.198… false nothing ⋯
9 │ 8 3.383 149.026 Unknown [M+H+2Na]+ [50.0222 0.0; 50.10… false nothing ⋯
10 │ 9 6.261 149.026 Unknown [M+H-H2O]+ [50.154 0.0; 50.369… false nothing ⋯
11 │ 10 0.605 152.02 Unknown [M+H]+ [50.227 0.0; 50.526… false nothing ⋯
⋮ │ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋱
julia> result.Peptide[121]
Peptide: DPCHKPKR
Modification: 3NPH (@ 1)
Precursor: 558.2805335
Adduct: [M+2H]²⁺
Fragment ions:
┌──────┬─────────┐
│ Type │ Mass │
├──────┼─────────┤
│ b₁⁺ │ 251.078 │
│ b₂⁺ │ 348.131 │
│ b₃⁺ │ 451.14 │
│ b₄⁺ │ 588.199 │
│ b₅⁺ │ 716.294 │
│ b₆⁺ │ 813.347 │
│ b₆²⁺ │ 407.177 │
│ b₇⁺ │ 941.442 │
│ b₇²⁺ │ 471.225 │
│ y₁⁺ │ 175.119 │
│ y₂⁺ │ 303.214 │
│ y₃⁺ │ 400.267 │
│ y₄⁺ │ 528.362 │
│ y₅⁺ │ 665.421 │
│ y₆⁺ │ 768.43 │
│ y₆²⁺ │ 384.719 │
│ y₇⁺ │ 865.483 │
│ y₇²⁺ │ 433.245 │
└──────┴─────────┘