I am analyzing mass spectrometry data from circulating nucleosomes in blood samples of non-small cell lung cancer (NSCLC) patients. The samples were processed with immunoprecipitation and analyzed using MaxQuant to detect post-translational modifications (PTMs) in histones.

Using the modificationSpecificPeptides.txt file from MaxQuant, I aim to determine the exact positions of PTMs (e.g., acetylation, methylation, phosphorylation) on specific residues within histones. This has proven challenging, especially when the same peptide contains multiple potential modification sites. I plan to use Perseus for downstream analysis but need guidance on how to accurately map PTMs to their positions in the full histone sequences.

Key questions:

Any suggestions on best practices, tools, or workflows for this type of analysis would be highly appreciated. Thank you in advance for your insights!