bio-proteomics-data-import

Loading mzML/mzXML Files with pyOpenMS

Goal: Parse raw mass spectrometry data files into memory for programmatic access.

Approach: Load mzML/mzXML into an MSExperiment object, then iterate spectra by MS level to access peaks and precursor info.

Loading MaxQuant Output

Goal: Import MaxQuant proteinGroups.txt with contaminant and decoy filtering.

Approach: Read the TSV file, remove reverse hits, contaminants, and site-only identifications, then extract intensity columns.

import pandas as pd

protein_groups = pd.read_csv('proteinGroups.txt', sep='\t', low_memory=False)

## Extract intensity columns (LFQ or iBAQ)

intensity_cols = [c for c in protein_groups.columns if c.startswith('LFQ intensity') or c.startswith('iBAQ ')]
if not intensity_cols:
    intensity_cols = [c for c in protein_groups.columns if c.startswith('Intensity ') and 'Intensity L' not in c]
intensities = protein_groups[['Protein IDs', 'Gene names'] + intensity_cols]