Peptacular

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A Python package for peptide sequence analysis built around ProForma 2.1 notation. Calculate masses, generate fragments, predict isotopic patterns, and more. Peptacular uses type annotations extensively, so it is type safe.

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Features

• ProForma 2.1 Parsing
• Modifiable ProFormaAnnotation Objects (Factory Pattern)
• Mass/Mz/Composition Calculations
• Predicted Isotopic Distributions
• Enzymatic Protein Digestion
• Fragment Ion Generation
• Physiochemical Property Calculations
• Built-in Parallel Processing

Installation

pip install peptacular

Quick Start (Object Based)

See docs for more detail.

import peptacular as pt

# Parse a sequence into a ProFormaAnnotation
peptide: pt.ProFormaAnnotation = pt.parse("PEM[Oxidation]TIDE")

# Calculate mass and m/z
mass: float = peptide.mass() # 849.342
mz: float = peptide.mz(charge=2) # 425.678

# Factory pattern
print(peptide.set_charge(2).set_peptide_name("Peptacular").serialize())
# (>Peptacular)PEM[Oxidation]TIDE/2

Quick Start (Functional Based)

When more than one item is passed to the functional API methods, it is automatically parallelized.

import peptacular as pt

peptides = ['[Acetyl]-PEPTIDES', '<C13>ARE', 'SICK/2']

# Calculate mass and m/z for all peptides
masses: list[float] = pt.mass(peptides) # [928.4026, 374.1914, 451.2454]
mzs: list[float] = pt.mz(peptides, charge=2) # [465.2086, 188.103, 225.6227]

ProForma 2.1 Compliance

See PROFORMA_COMPLIANCE.md for detailed compliance status.

Contributing

Contributions welcome! See CONTRIBUTING.md for guidelines on setting up the development environment, code style, testing, and submitting pull requests.

License

MIT

Citation

Working on a JOSS submission, but in the meantime use:

https://doi.org/10.5281/zenodo.15054278