PXD042549-3

PXD042549 is an original dataset announced via ProteomeXchange.

Title	Denaturing mass photometry for rapid optimization of chemical protein-protein cross-linking reactions
Description	Chemical cross-linking reactions (XL) are an important strategy for studying protein-protein interactions (PPIs), including low abundant sub-complexes, in structural biology. However, choosing XL reagents and conditions is laborious and mostly limited to analysis of protein assemblies that can be resolved using SDS-PAGE. To overcome these limitations, we develop here a denaturing mass photometry (dMP) method for fast, reliable and user-friendly optimization and monitoring of chemical XL reactions. The dMP is a robust 2-step protocol that ensures 95 % of irreversible denaturation within only 5 min. We show that dMP provides accurate mass identification across a broad mass range (30 kDa-5 MDa) along with direct label-free relative quantification of all coexisting XL species (sub-complexes and aggregates). We compare dMP with SDS-PAGE and observe that, unlike the benchmark, dMP is time-efficient (3 min/triplicate), requires significantly less material (20-100x) and affords single molecule sensitivity. To illustrate its utility for routine structural biology applications, we show that dMP affords screening of 20 XL conditions in 1 h, accurately identifying and quantifying all coexisting species. Taken together, we anticipate that dMP will have an impact on ability to structurally characterize more PPIs and macromolecular assemblies, expected final complexes but also sub-complexes that form en route.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:33:33.016.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD042549
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Hugo Gizardin-Fredon
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-30 12:44:58	ID requested
1	2024-03-15 02:19:19	announced
2	2024-07-30 05:13:48	announced	2024-07-30: Updated project metadata.
⏵ 3	2024-10-22 06:33:33	announced	2024-10-22: Updated project metadata.

10.1038/s41467-024-47732-4;

Gizardin-Fredon H, Santo PE, Chagot ME, Charpentier B, Bandeiras TM, Manival X, Hernandez-Alba O, Cianf, é, rani S, Denaturing mass photometry for rapid optimization of chemical protein-protein cross-linking reactions. Nat Commun, 15(1):3516(2024) [pubmed]

10.6019/PXD042549;

submitter keyword: Mass Photometry, Cross-linking mass spectrometry

Sarah Cianférani
contact affiliation	1. Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67000 Strasbourg, France 2. Infrastructure Nationale de Protéomique ProFI – FR2048, 67087 Strasbourg, France
contact email	sarah.cianferani@unistra.fr
lab head
Hugo Gizardin-Fredon
contact affiliation	IPHC LSMBO, CNRS/Université de Strasbourg
contact email	hugo.gizardin-fredon@etu.unistra.fr
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/2024/03/PXD042549

PRIDE project URI

• PRIDE
  1. PXD042549
     1. Label: PRIDE project
     2. Name: Denaturing mass photometry for rapid optimization of chemical protein-protein cross-linking reactions