PXD055085

PXD055085 is an original dataset announced via ProteomeXchange.

Title	Epitope and paratope mapping of a SUMO-remnant antibody using cross-linking mass spectrometry and molecular docking
Description	The small ubiquitin-like modifier (SUMO) is an important post-translational modification that regulates the function of various proteins essential for DNA damage repair, genome integrity and cell homeostasis. To identify protein SUMOylation effectively, an enrichment step is necessary, often requires exogenous gene expression in cells and immunoaffinity purification of SUMO-remnant peptides following tryptic digestion. Previously, an antibody was developed to enrich tryptic peptides containing the remnant NQTGG on the receptor lysine, though the specifics of the structural interaction motif remained unclear. Here, we conducted de novo sequencing by mass spectrometry to analyze the SUMO-remnant antibody and performed paratope mapping using cross-linking experiments to identify key interacting residues within the complementarity-determining regions (CDRs). Additional cross-linking experiments were performed using SUMOylated peptides and high-field asymmetric waveform ion mobility spectrometry (FAIMS) to enhance sensitivity and confirm interactions at the paratope interface. Our comprehensive analyses have provided a detailed understanding of the structural interaction motifs of the SUMO-remnant antibody, offering valuable insights into the antibody’s specificity and binding mechanisms. This enhanced understanding paves the way for improved methodologies in studying protein SUMOylation and its regulatory roles in cellular processes.
HostingRepository	PRIDE
AnnounceDate	2025-02-19
AnnouncementXML	Submission_2025-02-19_06:00:33.273.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Simon Comtois-Marotte
SpeciesList	scientific name: Oryctolagus sp. 'Rabbit_OD'; NCBI TaxID: 2665958;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF; Orbitrap Exploris 480; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-22 10:23:11	ID requested
⏵ 1	2025-02-19 06:00:34	announced

10.1021/acs.jproteome.4c00717;

Comtois-Marotte S, Bonneil É, Li C, Smith MJ, Thibault P, Epitope and Paratope Mapping of a SUMO-Remnant Antibody Using Cross-Linking Mass Spectrometry and Molecular Docking. J Proteome Res, 24(3):1092-1101(2025) [pubmed]

submitter keyword: antibody,Cross-linking, mass spectrometry, molecular docking, paratope mapping, SUMO

Pierre Thibault
contact affiliation	Institute for Research in Immunology and Cancer (IRIC) Université de Montréal, Department of Chemistry, Université de Montréal, MIL campus, Montréal, H2V 0B3, Canada
contact email	pierre.thibault@umontreal.ca
lab head
Simon Comtois-Marotte
contact affiliation	Institute for Research in Immunology and Cancer (IRIC) Université de Montréal
contact email	simon.comtois-marotte@umontreal.ca
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/02/PXD055085

PRIDE project URI

• PRIDE
  1. PXD055085
     1. Label: PRIDE project
     2. Name: Epitope and paratope mapping of a SUMO-remnant antibody using cross-linking mass spectrometry and molecular docking