Protein Quantification

Label-Free Quantification (LFQ)

Intensity-Based (MaxLFQ Algorithm)

import pandas as pd
import numpy as np

def maxlfq_normalize(intensities):
    '''Simplified MaxLFQ normalization'''
    log_int = np.log2(intensities.replace(0, np.nan))

    # Median centering per sample
    sample_medians = log_int.median(axis=0)
    global_median = sample_medians.median()
    normalized = log_int - sample_medians + global_median