PXD055085 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-08-22 10:23:11 | ID requested | |
⏵ 1 | 2025-02-19 06:00:34 | announced | |
Publication List
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] |
Keyword List
submitter keyword: antibody,Cross-linking, mass spectrometry, molecular docking, paratope mapping, SUMO |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD055085
- Label: PRIDE project
- Name: Epitope and paratope mapping of a SUMO-remnant antibody using cross-linking mass spectrometry and molecular docking