PXD023817

PXD023817 is an original dataset announced via ProteomeXchange.

Title	Reverse-phase liquid chromatography (RPLC) in Combination with Tip-Based Strong Cation Exchange (SCX-Tip) Fractionation, ReST, an Alternative Approach for Cross-linked Peptides analysis
Description	Chemical cross-linking in combination with mass spectrometry (XL-MS) has emerged as a useful method for structural elucidation of proteins and protein complexes. Efficient enrichment procedures are necessary to analyze cross-linked products due to their relatively low abundance. Currently, strong cation exchange chromatography (SCX), size exclusion chromatography (SEC), and affinity tag-based enrichment are among the widely used enrichment strategies. Herein, we present a two-dimensional enrichment strategy combining basic RPLC (bRPLC) fractionation and tip-based SCX (SCX-Tip) enrichment, termed ReST method, for the characterization of cross-linked peptides. We revealed the unbiased separation effects of the bRPLC in the cross-linked peptide fractionation. We optimized the enrichment conditions of SCX-Tip for cross-linked peptides using well-designed cross-linked peptides. Taking advantage of the high resolution of bRPLC fractionation and the high enrichment efficiency of SCX-Tip, we were able to identify 43.6% more cross-links than the conventional SCX approach. The presented ReST approach is an effective fractionation method for XL-MS analysis, and could be beneficial for protoeme-scale protein-protein interaction studies. Moreover, more stringent data filtering was proposed in order to achieve the high confidence of cross-linked peptide identification.
HostingRepository	PRIDE
AnnounceDate	2022-06-21
AnnouncementXML	Submission_2022-06-21_06:25:56.171.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhen Wu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-26 01:41:19	ID requested
⏵ 1	2022-06-21 06:25:56	announced

Wu Z, Li J, Huang L, Zhang X, Basic pH reversed-phase liquid chromatography (bRPLC) in combination with tip-based strong cation exchange (SCX-Tip), ReST, an efficient approach for large-scale cross-linked peptide analysis. Anal Chim Acta, 1179():338838(2021) [pubmed]

submitter keyword: SCX-Tip, Chemical cross-linking, Mass spectrometry, Fractionation

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. PXD023817
     1. Label: PRIDE project
     2. Name: Reverse-phase liquid chromatography (RPLC) in Combination with Tip-Based Strong Cation Exchange (SCX-Tip) Fractionation, ReST, an Alternative Approach for Cross-linked Peptides analysis