PXD056617

PXD056617 is an original dataset announced via ProteomeXchange.

Title	IP-to-MS: an unbiased workflow for antigen profiling
Description	Immunoprecipitation is among the most widely utilized methods in biomedical research, with applications that include the identification of antibody targets and associated proteins. The path to identifying these targets is not straightforward, however, and often requires the use of chemical crosslinking and/or gel electrophoresis to separate targets from an overabundance of immunoglobulin protein. Such experiments are labor intensive and often yield long lists of candidate antibody targets. Here, we describe an unbiased immunoprecipitation-to-mass spectrometry (IP-to-MS) method that relies on a novel protein tag to separate low abundance immunoprecipitated proteins from overwhelmingly abundant immunoglobulins. We demonstrate that the IP-to-MS serotyping workflow is highly reproducible and can be used for the identification of novel, patient-specific antigen targets in multiple disease states. Furthermore, we show that IP-to-MS may outperform conventional methods of antibody detection, including ELISA, while also enabling patient stratification beyond what is possible with traditional approaches.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_03:43:01.424.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Stephanie Biedka
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480; timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-08 07:21:56	ID requested
⏵ 1	2025-05-07 03:43:02	announced

10.1021/acs.jproteome.4c00837;

Biedka S, Yablonska S, Peng X, Alkam D, Hartoyo M, VanEvery H, Kass DJ, Byrum SD, Xiao K, Zhang Y, Domsic RT, Lafyatis R, Ascherman DP, Minden JS, IP-to-MS: An Unbiased Workflow for Antigen Profiling. J Proteome Res, 24(2):795-812(2025) [pubmed]

submitter keyword: autoimmune disease, mass spectrometry,unbiased antigen identification, immunoprecipitation

Jonathan Minden
contact affiliation	Impact Proteomics
contact email	jonathan.minden@impactproteomics.com
lab head
Stephanie Biedka
contact affiliation	Impact Proteomics
contact email	stephanie.biedka@impactproteomics.com
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/2025/05/PXD056617

PRIDE project URI

• PRIDE
  1. PXD056617
     1. Label: PRIDE project
     2. Name: IP-to-MS: an unbiased workflow for antigen profiling