PXD048204

PXD048204 is an original dataset announced via ProteomeXchange.

Title	Exploration of nitrotyrosine-containing proteins and peptides by antibody-based enrichment strategies
Description	Nitrotyrosine is a modification in proteins caused by oxidative reactions with reactive nitrogen species. It's commonly associated with oxidative stress and linked to various health conditions like inflammation, neurodegeneration, cardiovascular disease, and cancer. However, detecting nitrotyrosine-modified proteins is challenging due to their low levels in biological samples. To make this detection more comprehensive, we optimized an immunoprecipitation-based method for both proteins and peptides using a cell line model. We tested the efficiency of four different commercially available monoclonal antibodies for enriching nitrotyrosine-modified proteins and peptides. Through LC-MS/MS analysis, we identified 1,377 nitrotyrosine-containing peptides from protein-based enrichment and 1,624 from peptide-based enrichment. However, we noticed a bias in the peptides enriched; a significant portion (37-65%) had nitrotyrosine at the beginning of the peptide when using the peptide-based approach, whereas this bias was minimal (<9%) with the protein-based immunoprecipitation. In total, we found 2,605 nitrotyrosine-containing peptides, with over 2,000 of them not previously reported. To validate our findings, we synthesized 110 of these peptides and analyzed them with LC-MS/MS. Additionally, we confirmed the presence of nitrotyrosine modifications in PKM and EF2 proteins in peroxynitrite-treated samples through immunoblot analysis. This extensive dataset and workflow will aid further exploration of nitrotyrosine as an oxidative modification in various contexts.
HostingRepository	PRIDE
AnnounceDate	2024-03-12
AnnouncementXML	Submission_2024-03-12_15:13:49.617.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	3'-nitro-L-tyrosine
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-02 16:02:21	ID requested
⏵ 1	2024-03-12 15:13:50	announced

10.1016/j.mcpro.2024.100733;

Bhat FA, Mangalaparthi KK, Ding H, Jain A, Hsu JS, Peterson JA, Zenka RM, Mun DG, Kandasamy RK, Pandey A, Exploration of Nitrotyrosine-Containing Proteins and Peptides by Antibody-Based Enrichment Strategies. Mol Cell Proteomics, 23(3):100733(2024) [pubmed]

submitter keyword: Protein kinase,Post-translational modifications, Immunoaffinity, Peroxynitrite, Nitrotyrosine, Oxidative stress

Akhilesh Pandey
contact affiliation	Professor Laboratory Medicine and Pathology Mayo Clinic, Rochester, MN, 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

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PRIDE project URI

• PRIDE
  1. PXD048204
     1. Label: PRIDE project
     2. Name: Exploration of nitrotyrosine-containing proteins and peptides by antibody-based enrichment strategies