Pyteomics

4.7.5 verified Mon Apr 27 auth: no python

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.

pip install pyteomics

Common errors

error ModuleNotFoundError: No module named 'pyteomics.mzml' ↓

cause Wrong import path; pyteomics modules are lowercase with no leading underscore.

fix

Use 'from pyteomics import mzml' (not 'pyteomics.MzML' or 'pyteomics.mzML').

error TypeError: 'MzML' object is not callable ↓

cause Using 'mzml.MzML()' as a function instead of as a context manager.

fix

Wrap in 'with mzml.MzML('file') as reader:'

Warnings

breaking In 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.

deprecated The '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.

gotcha Indexing 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.

Imports

MzML
wrong
```
from pyteomics.mzml import MzML
```
correct
```
from pyteomics import mzml
```
MzML is not a class; use the mzml module functions (e.g., read, MzML as a reader context).
MS1
wrong
```
from pyteomics.ms1 import MS1
```
correct
```
from pyteomics import mass
```
There is no ms1 module; use pyteomics.mass for mass calculations.

Quickstart

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])