PXD007994

PXD007994 is an original dataset announced via ProteomeXchange.

Title	Reversible Lysine Derivatization Enables High Specificity of Arg-C Digestion Using Trypsin
Description	Bottom-up proteomics approach has become an important strategy in diverse areas of biological research, and the enzymatic digestion is essential for this technology. Endopeptidase Arg-C catalyzing the hydrolytic cleavage of peptide bonds C-terminal to arginine could be an important protease in bottom-up proteomics. However, it has been seldom applied due to its low specificity and high cost. Reversible chemical derivatization of amine allows a real Arg-C digestion using trypsin. In this paper, a reversible amine derivatization method, citraconylation and decitraconylation were optimized and evaluated for large-scale proteomics studies. Combination of the reversible derivatization and trypsin digestion (termed Arg-C* digestion to distinguish from the conventional Arg-C digestion) resulted in 64.2% more peptide identification (11,925 ± 199 vs 7,262 ± 59) and significantly higher cleavage specificity (95.6% vs 73.6%) than the conventional Arg-C digestion. Comparison of Arg-C* digestion with the widely used trypsin and Lys-C digestion revealed that Arg-C* performed equally or slightly better than Lys-C although not comparable to trypsin. Therefore, the well-established Arg-C* digestion method is a promising approach for proteomics studies and could be used as the prior alternative digestion method to trypsin digestion in order to achieve higher proteome coverage.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:16:25.350.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhen Wu
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidoethyl-L-cysteine; monohydroxylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2017-10-18 07:03:56	ID requested
1	2018-01-04 03:02:50	announced
⏵ 2	2024-10-22 04:16:26	announced	2024-10-22: Updated project metadata.

10.1021/acs.analchem.7b04410;

curator keyword: Technical

submitter keyword: proteomics, Arg-C, trypsin, Lys-C,citraconylation, LC-MS/MS

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
Zhen Wu
contact affiliation	State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University
contact email	wuz16@fudan.edu.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD007994
     1. Label: PRIDE project
     2. Name: Reversible Lysine Derivatization Enables High Specificity of Arg-C Digestion Using Trypsin