PXD020042 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2020-12-10 |
AnnouncementXML | Submission_2020-12-10_01:21:22.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; acetylated residue; monohydroxylated residue |
Instrument | LTQ Orbitrap Elite |
Dataset History
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. |
Publication List
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] |
Keyword List
submitter keyword: Carboxyl protection, EDC, Tyrosine, C-TAILS |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD020042
- Label: PRIDE project
- Name: An Undesirable Side Effect of EDC-catalyzed Carboxyl Labeling Approach