Evidence map›Paper›PMID 40665372›Full record

ArticleGenome biology2025

Enrichable cross-linkers for mapping direct protein interactions.

Ting Wu, Hang-Xu Zhou, Jing Tian, Rong Zhou, Shangwei Huangfu, Bi-Kun Jin, Anna Sablina, Fangfang Zhou, Hongli Chen, Shibing Tang and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Ting Wu *Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang, China.
Hang-Xu Zhou *Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
Jing Tian *State Key Laboratory of Respiratory Disease, Institute of Drug Discovery, Guangzhou, Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
Rong Zhou *The State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
Shangwei HuangfuShanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
Bi-Kun JinLife Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
Anna SablinaVIB-KU Leuven Center for Cancer Biology, VIB, 3000, Louvain, Belgium.
Fangfang ZhouKey Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang, China.
Hongli ChenShanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China. chenhl@shanghaitech.edu.cn.
Shibing TangState Key Laboratory of Respiratory Disease, Institute of Drug Discovery, Guangzhou, Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. tang_shibing@gibh.ac.cn.
Long ZhangKey Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang, China. l_zhang@zju.edu.cn.
Bing YangLife Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China. bingyang@zju.edu.cn.

Funding

Basic and Applied Basic Research Foundation of Guangdong Province 2023B0303000023Basic Research Project of Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences GIBHBRP23-02Chinese National Natural Science Funds 22374128National Key Research and Development Program of China 2019YFA0904500National Key Research and Development Program of China 2022YFF0608402Open Project Program of the State Key Laboratory of Proteomics SKLPO201806STI2030-Major Projects 2023ZD0404702The special COVID-19 program of the Sino-German Center for Research Promotion C-0023Zhejiang Provincial Outstanding Youth Science Foundation LR20B050001
6 · The paper itself

Abstract

backgroundIt is crucial to investigate protein functions in specific subcellular environments. Cross-linking mass spectrometry is a powerful tool to map the direct interactome of proteins by identifying inter-protein cross-links. However, it is challenging to identify inter-protein cross-linked peptides due to their low abundance.

resultsWe chemically synthesize the cross-linkers ePDES1 and ePDES2 with an alkyne group and a compound with azide linked to a phosphate group to enrich for cross-linked peptides.

conclusionBased on the high-quality cross-linking spectra of ePDES1 and ePDES2, our methods achieve the identification of hundreds of directly interacting proteins or substrates of thioredoxins in the nucleus and mitochondria.

Indexed as

Cross-Linking ReagentsProtein Interaction MappingHumansMass SpectrometryPeptidesCross-Linking ReagentsPeptidesCross-linking mass spectrometryDirect protein interactionIMACSubcellular organellesThioredoxin

Identifiers

PMID40665372
PMCPMC12261600

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