pyteomics

library5.0pypypiunverified

Pyteomics is a Python framework for proteomics data analysis, providing parsers and tools for common mass spectrometry formats (mzML, mzXML, MGF, etc.) and sequence database handling. Current version 4.7.5 is stable with monthly releases.

data ai-ml

pip install pyteomics

github ↗package ↗homepage ↗docs ↗

INSTALL

IMPORT

SIG · PYTEOMICS

pyteomics

datapythonv5.0

Install

1.8s avg

Import

—

Disk

18MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v5.0 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

installs and imports cleanly · install 0.0s · import 0.000s · 19.8MB

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 1.8s · import 0.000s · 20MB

18MB installed

● package 18MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

mzml

✓ import pyteomics.mzml

✗ from pyteomics import mzml

Read an mzML file and print first 5 m/z values of each spectrum.

from pyteomics import mzml with mzml.MzML('example.mzML') as reader: for spectrum in reader: print(spectrum['m/z array'][:5])

Debug

Known issues

breakingIn version 4.x, the API for mzML reader changed from pyteomics.mzml.MzML to context manager with 'with' statement. Old code using mzml.MzML('file') may break if not wrapped in 'with'.

fix

Use 'with mzml.MzML('file') as reader:' pattern.

affects: >=4.0

deprecatedThe 'pyteomics.mzml.MzML' class is deprecated in favor of 'pyteomics.mzml.read' for iteration.

fix

Use 'from pyteomics import mzml; for spec in mzml.read('file'):' instead.

affects: >=4.5

gotchaIndexing spectra by scan number is not always sequential; use 'by_id' method rather than list index.

fix

Use 'reader[('scan', scan_number)]' or 'reader.by_id(scan_number)' to access by scan ID.

affects: all

Upgrade

Version history

5.0latest on PyPI · released May 28, 2026

Audit

Dependencies

No dependency data recorded yet.

Agent activity

14 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/levitsky/pyteomics ↗

packagehttps://pypi.org/project/pyteomics/ ↗

homepagehttp://pyteomics.readthedocs.io ↗

docshttp://pyteomics.readthedocs.io ↗