Version Compatibility
Reference examples tested with: numpy 1.26+, pandas 2.2+, scipy 1.12+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package> then help(module.function) to check signatures
- R:
packageVersion('<pkg>') then ?function_name to verify parameters
If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.
Post-Translational Modification Analysis
"Analyze phosphorylation sites from my proteomics data" → Identify and quantify post-translational modifications including phosphorylation, acetylation, and ubiquitination with site localization and motif analysis.
- Python:
pyopenms for PTM-aware search, scipy for site-level statistics
- CLI: MaxQuant with variable modifications for enrichment-based PTM analysis
Common PTMs and Mass Shifts
PTM_MASSES = {
'Phosphorylation': 79.966331, # STY
'Oxidation': 15.994915, # M
'Acetylation': 42.010565, # K, N-term
'Methylation': 14.015650, # KR
'Dimethylation': 28.031300, # KR
'Trimethylation': 42.046950, # K
'Ubiquitination': 114.042927, # K (GlyGly remnant)
'Deamidation': 0.984016, # NQ
'Carbamidomethyl': 57.021464, # C (fixed mod from IAA)
}
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
# Phospho(STY)Sites.txt from MaxQuant
phospho = pd.read_csv('Phospho (STY)Sites.txt', sep='\t', low_memory=False)
# 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)}')
# Extract site information
phospho_confident['site'] = phospho_confident.apply(
lambda r: f"{r['Gene names']}_{r['Amino acid']}{r['Position']}", axis=1
)
Site Localization Scoring
def calculate_ascore_simple(peak_matches_with_ptm, peak_matches_without_ptm, total_peaks):
'''Simplified A-score calculation'''
if peak_matches_without_ptm >= peak_matches_with_ptm:
return 0
p = peak_matches_with_ptm / total_peaks if total_peaks > 0 else 0
if p <= 0 or p >= 1:
return 0
from scipy.stats import binom
p_value = 1 - binom.cdf(peak_matches_with_ptm - 1, total_peaks, 0.5)
return -10 * np.log10(p_value) if p_value > 0 else 100
Motif Analysis
from collections import Counter
def extract_motifs(sites_df, sequence_col, position_col, window=7):
'''Extract sequence windows around modification sites'''
motifs = []
for _, row in sites_df.iterrows():
seq = row[sequence_col]
pos = row[position_col] - 1 # 0-indexed
start = max(0, pos - window)
end = min(len(seq), pos + window + 1)
# Pad if at sequence boundary
motif = '_' * (window - (pos - start)) + seq[start:end] + '_' * (window - (end - pos - 1))
motifs.append(motif)
return motifs
def count_amino_acids_by_position(motifs, center=7):
'''Count amino acid frequencies by position'''
position_counts = {i: Counter() for i in range(-center, center + 1)}
for motif in motifs:
for i, aa in enumerate(motif):
position_counts[i - center][aa] += 1
return position_counts
R: Site-Level Quantification with MSstatsPTM
library(MSstatsPTM)
# Prepare input from MaxQuant
ptm_input <- MaxQtoMSstatsPTMFormat(
evidence = read.table('evidence.txt', sep = '\t', header = TRUE),
annotation = read.csv('annotation.csv'),
fasta = 'uniprot_human.fasta',
mod_type = 'Phospho'
)
# Process data
processed_ptm <- dataSummarizationPTM(ptm_input, method = 'msstats')
# Differential PTM analysis (adjusting for protein-level changes)
ptm_results <- groupComparisonPTM(processed_ptm, contrast.matrix = comparison_matrix)
Related Skills
- peptide-identification - Identify modified peptides
- quantification - Quantify PTM sites
- pathway-analysis/go-enrichment - Enrichment of modified proteins