bio-proteomics-ptm-analysis

Processing MaxQuant PTM Output

Goal: Extract high-confidence phosphorylation sites from MaxQuant output with proper filtering and site annotation.

Approach: Load the Phospho(STY)Sites table, remove reverse hits and contaminants, filter by localization probability, and construct gene-level site identifiers.

import pandas as pd
import numpy as np

## Filter valid sites

phospho = phospho[
    (phospho['Reverse'] != '+') &
    (phospho['Potential contaminant'] != '+')
]

## Filter by localization probability

phospho_confident = phospho[phospho['Localization prob'] >= 0.75]
print(f'Confident sites (prob >= 0.75): {len(phospho_confident)}')