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https://github.com/yufongpeng/peptideseq.jl

Predict and match digested peptides sequences, their mass m/z and MS/MS spectra with chemical derivatization or post-translational modification.
https://github.com/yufongpeng/peptideseq.jl

lc-msms peptide-identification peptide-sequences proteomics

Last synced: about 6 hours ago
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Predict and match digested peptides sequences, their mass m/z and MS/MS spectra with chemical derivatization or post-translational modification.

Host: GitHub
URL: https://github.com/yufongpeng/peptideseq.jl
Owner: yufongpeng
License: mit
Created: 2022-06-30T09:07:08.000Z (over 2 years ago)
Default Branch: main
Last Pushed: 2023-06-17T10:59:34.000Z (over 1 year ago)
Last Synced: 2023-06-17T11:27:25.094Z (over 1 year ago)
Topics: lc-msms, peptide-identification, peptide-sequences, proteomics
Language: Julia
Homepage:
Size: 2.98 MB
Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

# PeptideSeq

[![Build Status](https://github.com/yufongpeng/PeptideSeq.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/yufongpeng/PeptideSeq.jl/actions/workflows/CI.yml?query=branch%3Amain)
[![Coverage](https://codecov.io/gh/yufongpeng/PeptideSeq.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/yufongpeng/PeptideSeq.jl)

*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.

## Installation
This package is not registered yet. Insall it through github:
```julia
julia> using Pkg; Pkg.add("https://github.com/yufongpeng/PeptideSeq.jl")
```

## Example
```julia
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,
Protein: DPCHKPKRRKP
Modification: 3NPH
Enzyme: Trypsin
Peptides:
┌───────
│ Peptide_sequence
├───────
│ DPCHKPK │
│ DPCHKPK │
│ R │
│ R │
│ R │
│ R │
│
│
│ DPCHKPKR │
│ DPCHKPKR │
│ RR │
│ RR │
│ RKP │
│ RKP │
│ DPCHKPKRR │
│ DPCHKPKRR │
│ RRKP │
│ RRKP │
└─────── "[M+H]+", "[M+2H]2+") ───────────┬──────────┬─────────┬──────────┬───────────────┬───────────────┐ │ Position │ Mass │ Adduct │ Miss_cleavage │ Modification │ ───────────┼──────────┼─────────┼──────────┼───────────────┼───────────────┤ 1:7 │ 1094.5 │ [M+H]⁺ │ 0 │ 3NPH (@ 1, 7) │ 1:7 │ 547.752 │ [M+2H]²⁺ │ 0 │ 3NPH (@ 1, 7) │ 8:8 │ 310.163 │ [M+H]⁺ │ 0 │ 3NPH (@ 8) │ 8:8 │ 155.585 │ [M+2H]²⁺ │ 0 │ 3NPH (@ 8) │ 9:9 │ 310.163 │ [M+H]⁺ │ 0 │ 3NPH (@ 9) │ 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) │ 1:8 │ 1250.6 │ [M+H]⁺ │ 1 │ 3NPH (@ 1, 8) │ 1:8 │ 625.802 │ [M+2H]²⁺ │ 1 │ 3NPH (@ 1, 8) │ 8:9 │ 466.264 │ [M+H]⁺ │ 1 │ 3NPH (@ 9) │ 8:9 │ 233.636 │ [M+2H]²⁺ │ 1 │ 3NPH (@ 9) │ 9:11 │ 535.31 │ [M+H]⁺ │ 1 │ 3NPH (@ 11) │ 9:11 │ 268.159 │ [M+2H]²⁺ │ 1 │ 3NPH (@ 11) │ 1:9 │ 1406.7 │ [M+H]⁺ │ 2 │ 3NPH (@ 1, 9) │ 1:9 │ 703.853 │ [M+2H]²⁺ │ 2 │ 3NPH (@ 1, 9) │ 8:11 │ 691.412 │ [M+H]⁺ │ 2 │ 3NPH (@ 11) │ 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 │
└──────┴─────────┘

```