PXD038761-2

PXD038761 is an original dataset announced via ProteomeXchange.

Title	Optimizing High-Throughput Shotgun Immunoproteomics for Antigen Identification
Description	Identification of individual proteins (i.e., antigens) which initiate and/or perpetuate adaptive immune responses has potential to greatly impact pre-clinical and clinical work across numerous fields. To date, however, the methodologies available to identify antigens responsible for driving adaptive immune responses have been plagued by numerous issues which have drastically limited their widespread adoption. Therefore, in this study, we sought to optimize a shotgun immunoproteomics approach to alleviate these persistent issues and create a high-throughput, quantitative methodology for antigen identification. Three individual components of a previously published approach, namely the protein extraction, antigen elution, and LC-MS/MS analysis steps, were optimized in a systematic manner. These studies determined that preparation of protein extracts using a one-step tissue disruption method in immunoprecipitation (IP) buffer, eluting antigens from affinity chromatography columns with 1% trifluoroacetic acid (TFA), and TMT-labeling & multiplexing equal volumes of eluted samples for LC-MS/MS analysis, resulted in quantitative longitudinal antigen identification, with reduced variability between replicates and increased total number of antigens identified. This optimized pipeline provides a multiplexed, highly reproducible, and fully quantitative approach to antigen identification which is broadly applicable to determine the role of antigenic proteins in inciting (i.e. primary antigens) and perpetuating (i.e., secondary antigens) a wide range of diseases.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:44:52.666.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-12 22:27:19	ID requested
1	2023-04-18 09:03:12	announced
⏵ 2	2023-11-14 08:45:02	announced	2023-11-14: Updated project metadata.

Shortreed NA, Panicker AJ, Mangalaparthi KK, Zhong J, Pandey A, Griffiths LG, Optimization of a high-throughput shotgun immunoproteomics pipeline for antigen identification. J Proteomics, 281():104906(2023) [pubmed]

submitter keyword: Tandem-Mass Tag labeling,Antigen identification, Xenogeneic biomaterials, Affinity chromatography, Humoral immune response, Proteomics

Akhilesh Pandey
contact affiliation	Professor Department of Laboratory Medicine and Pathology Mayo Clinic 200 First St SW, Rochester, MN – 55905, USA
contact email	pandey.akhilesh@mayo.edu
lab head
Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
contact email	pandey.akhilesh@mayo.edu
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/2023/04/PXD038761

PRIDE project URI

• PRIDE
  1. PXD038761
     1. Label: PRIDE project
     2. Name: Optimizing High-Throughput Shotgun Immunoproteomics for Antigen Identification