---
id: pyteomics
version: "5.0.1"
license: Apache-2.0
license_treatment: permissive
maintenance: active
---

# pyteomics — A framework for proteomics data analysis.

License: permissive · Maintenance: active · Downloads: 286.4K/mo

## What it is and what it does

Pyteomics is a collection of Python modules designed to handle proteomics data analysis tasks. It provides utilities for calculating physico-chemical properties of peptides and proteins (mass, isotopic distribution, charge, pI, retention time), accessing common proteomics data formats (MS/LC-MS data, FASTA databases, search engine outputs), and manipulating sequences of modified peptides and proteins. The library targets reproducible statistical analysis and rapid prototyping in proteomics research.

The package has no external runtime dependencies, making it lightweight and straightforward to integrate into existing Python workflows. It is actively maintained, with current Python version support (>=3.10), and has been in development since 2012, indicating a mature codebase for the proteomics community.

Use it for:

- Calculate molecular mass and isotopic distributions for peptide sequences in mass spectrometry workflows
- Parse and process FASTA database files for proteomics searches and sequence analysis
- Extract and analyze results from proteomics search engines (e.g., Mascot, SEQUEST output)
- Compute physicochemical properties (pI, charge, retention time) for peptide characterization
- Manipulate and annotate sequences containing post-translational modifications

## Worth the install?

AI-flagged interpretation of the facts above — verify before relying.

Pyteomics provides Python tools for proteomics data analysis, including mass calculation, sequence manipulation, and access to MS/LC-MS data, FASTA databases, and search engine outputs.

Yes. Pyteomics is a mature, actively maintained library with no security vulnerabilities, zero runtime dependencies, and straightforward installation. It directly addresses core proteomics data analysis tasks. Install it if you work with mass spectrometry data, peptide sequences, or proteomics search results in Python.

## Install

pip install pyteomics
uv add pyteomics
poetry add pyteomics

## Installing pyteomics

Before you install: Low friction installation with no runtime dependencies. Active maintenance: last commit 2026-07-22, released 23 days ago. Supported on current Python versions (requires Python >=3.10).

License in practice: Apache-2.0 is permissive; you can use, modify, and distribute this package freely in commercial or private projects with minimal restrictions.

Quickstart:

pip install pyteomics

from pyteomics import mass
mass_value = mass.calculate_mass(sequence='PEPTIDE')

Requires Python >=3.10

Verify before relying:

- Scope and completeness of supported MS data formats and search engine output types
- Performance characteristics for large-scale proteomics datasets
- Availability and quality of example workflows or tutorials beyond the documentation

## Package facts

- License: Apache-2.0 (permissive)
- Python support: supports_current
- Install friction: low
- Maintenance: active
- Downloads: 286.4K/month (top 15,000 on PyPI)
- Known vulnerabilities: none known

## Tags

proteomics data analysis, mass spectrometry python, peptide mass calculation, fasta database tools, protein sequence analysis, lcms data processing, search engine output parsing, mass-spectrometry, bioinformatics, proteomics

[View on SkillFed](https://skillfed.io/packages/pyteomics) · [View on PyPI](https://pypi.org/project/pyteomics/)