PXD020042

PXD020042 is an original dataset announced via ProteomeXchange.

Title	An Undesirable Side Effect of EDC-catalyzed Carboxyl Labeling Approach
Description	Carbodiimide catalyzed carboxyl and amine conjugation (amidation) has been widely used to protect carboxyl groups. N-(3-dimethylaminopropyl)-N’-ethylcarbodiimide (EDC) is the most commonly used carbodiimide reagent in protein chemis-try due to its high efficiency and high solubility in aqueous media. It has also been applied in different proteomics studies including protein terminomics, protein glycosylation and crosslinking. Herein, we report that the EDC catalyzed amidation could cause a +155 Da side-modification at the tyrosine residue and severely hamper the identification of Tyr-containing peptides. We discovered the extremely low identification rate of Tyr-containing peptides in different published studies that employed EDC-catalyzed amidation. We carried out a systematic study and discovered a +155 Da side-modification occur-ring specifically on Tyr as the addition of EDC. Consideration of the side-modification in database search enabled the identification of 13 times more Tyr-containing peptides. Furthermore, we demonstrated that the treatment with carbonate-containing buffer could effectively reduce the side-product. Our study also implies that chemical reactions in proteomic studies should be carefully evaluated prior to their wide applications.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:16:31.937.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Qingqing Li
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidoethyl-L-cysteine; amidated residue; monohydroxylated residue; acetylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-26 03:17:17	ID requested
1	2020-12-10 01:21:23	announced
⏵ 2	2024-10-22 05:16:32	announced	2024-10-22: Updated project metadata.

10.1021/acs.analchem.0c03487;

Li Q, Zhang Y, Wu Z, Huang J, Yue N, Huang L, Zhang X, Tyrosine-EDC Conjugation, an Undesirable Side Effect of the EDC-Catalyzed Carboxyl Labeling Approach. Anal Chem, 93(2):697-703(2021) [pubmed]

submitter keyword: Tyrosine,Carboxyl protection, C-TAILS, EDC

Xumin Zhang
contact affiliation	State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
contact email	Xumin_zhang@fudan.edu.cn
lab head
Qingqing Li
contact affiliation	Fudan University
contact email	liqqmail@126.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/2020/12/PXD020042

PRIDE project URI

• PRIDE
  1. PXD020042
     1. Label: PRIDE project
     2. Name: An Undesirable Side Effect of EDC-catalyzed Carboxyl Labeling Approach