README.md

SUMOylation

This repository contains scripts for the data analysis of the results from the study for developing MaxSBM. The work presents MaxSBM, a module in MaxQuant, developed for improved site-specific identification of SUMOylation sites, using mass-spectrometry-based proteomics.

Documentation of the module can be found here: https://cox-labs.github.io/coxdocs/MaxSBM.html

The work is presented in;

• Lennartsson C, Kyriakidou P, Nielsen ML, Olsen JV, Cox J, Hendriks IA
  Improved peptide search for identification of SUMO and sequence-based modifications, in MaxSBM.
  bioRxiv (2025).
  https://www.biorxiv.org/content/10.1101/2025.08.27.672604v1.abstract

Datasets

SUMO-HEK (human cell lines)

• Hendriks IA, Lyon D, Su D, Skotte NH, Daniel JA, Jensen LJ, Nielsen ML (2018)
  Site-specific characterization of endogenous SUMOylation across species and organs.
  Nature Communications, 9(1), 2456.
  https://doi.org/10.1038/s41467-018-04957-4

SUMO-MEC (mouse embryonic cells)

• Theurillat I, Hendriks IA, Cossec J-C, Andrieux A, Nielsen ML, Dejean A (2020)
  Extensive SUMO modification of repressive chromatin factors distinguishes pluripotent from somatic cells.
  Cell Reports, 32(11), 108146.
  https://doi.org/10.1016/j.celrep.2020.108146

SUMO-Adip (mouse adipocytes)

• Zhao X, Hendriks IA, Le Gras S, Ye T, Ramos-Alonso L, Nguéa PA, et al. (2022)
  Waves of SUMOylation support transcription dynamics during adipocyte differentiation.
  Nucleic Acids Research, 50(3), 1351–1369.
  https://doi.org/10.1093/nar/gkac027

Ub-LysC (human cell lines)

• Akimov V, Barrio-Hernandez I, Hansen SVF, Hallenborg P, Pedersen AK, et al. (2018)
  UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites.
  Nature Structural & Molecular Biology, 25, 631–640.
  https://doi.org/10.1038/s41594-018-0084-y

Notebooks and scripts

This repository contains the following notebooks and scripts:

Method development and ion characterization

• Diagnostic ion mining
  Identification and characterization of diagnostic fragment ions associated with SUMO.

• d-ion series in search
  Assessment of the impact of including d-ion series during peptide database searching.

• p-ion optimisations (SUMO)
  Assessment of the impact of including p-ion series during peptide database searching.

• Which p-SUMO ions
  Evaluation of p-ion inlcusions and their contribution to peptide identification.

Spectral inspection and visualization

• Spectral viewer
  Interactive visualization of MS/MS spectra for inspection of fragment ion series and modification-specific peaks.

• Theoretical spectra
  Generation and analysis of theoretical spectra of peptides and their fragment ion compositions for SUMoylated peptides. Used for problem formulation and theory.

Dataset-specific analyses of SUMOylatated peptides

• Main SUMO-HEK analysis
  Primary analysis and summary of SUMOylation results in human HEK cell lines.

• Mouse embryonic cells (MEC) analysis
  Analysis of SUMOylation data from mouse embryonic cells (MEC).

• Mouse adipocytes analysis
  Analysis of SUMOylation data from mouse adipocytes.

Protein-level analysis

• Protein groups (SUMO)
  Protein-level summarization and grouping of SUMO-modified peptides.

• Protein groups (adipocytes)
  Protein group analysis for adipocyte datasets.

• Protein groups (MEC)
  Protein group analysis for mouse embryonic fibroblast datasets.

• Protein inference
  Python script implementing protein inference from uniprot metadata.

Data processing and utilities

• Percolator converter
  Conversion of MaxQuant search results into Percolator-compatible input formats.