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New Research in Spatial Proteomics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: 20 September 2025 | Viewed by 1228

Special Issue Editor


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Guest Editor
Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
Interests: mass spectrometry imaging; spatial omics; molecular pathology; kidney; oncology; proteomics; lipidomics; metabolomics
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Special Issue Information

Dear Colleagues,

Our ability to dig ever deeper into the cellular proteome is providing a more detailed understanding of the biology that governs human health. In particular, the realm of spatial proteomics is a rapidly evolving branch of this field which is garnering heightened interest given its potential to shed further light on how structured communities of individual cells function and interact within the context of their networked environment. This potential is further enhanced by the development of computational approaches, primarily based upon machine learning algorithms, capable of deciphering the most relevant proteomic findings within highly dimensional datasets.

We therefore invite academic and industrial investigators working in spatial proteomics to submit original research articles or reviews describing and discussing the most recent advancements and developments in this field.

Potential topics include, but are not limited to, the following:

  • Instrumental developments;
  • Untargeted spatial proteomics;
  • Targeted spatial proteomics;
  • Sub-cellular protein imaging;
  • Clinical applications of spatial proteomics;
  • Biocomputational approaches for the management of spatial proteomic datasets;
  • Integration with data derived from complementary molecular levels (multi-omics).

Dr. Andrew Smith
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • spatial proteomics
  • mass spectrometry imaging
  • mass cytometry
  • biomarker
  • machine learning
  • spatial biology
  • molecular pathology
  • cancer

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Published Papers (1 paper)

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Research

22 pages, 4754 KiB  
Article
Identification of MCM2-Interacting Proteins Associated with Replication Initiation Using APEX2-Based Proximity Labeling Technology
by Sitong Yao, Zhen Yue, Shaotang Ye, Xiaohuan Liang, Yugu Li, Haiyun Gan and Jiaqi Zhou
Int. J. Mol. Sci. 2025, 26(3), 1020; https://doi.org/10.3390/ijms26031020 - 25 Jan 2025
Viewed by 1006
Abstract
DNA replication is a crucial biological process that ensures the accurate transmission of genetic information, underpinning the growth, development, and reproduction of organisms. Abnormalities in DNA replication are a primary source of genomic instability and tumorigenesis. During DNA replication, the assembly of the [...] Read more.
DNA replication is a crucial biological process that ensures the accurate transmission of genetic information, underpinning the growth, development, and reproduction of organisms. Abnormalities in DNA replication are a primary source of genomic instability and tumorigenesis. During DNA replication, the assembly of the pre-RC at the G1-G1/S transition is a crucial licensing step that ensures the successful initiation of replication. Although many pre-replication complex (pre-RC) proteins have been identified, technical limitations hinder the detection of transiently interacting proteins. The APEX system employs peroxidase-mediated rapid labeling with high catalytic efficiency, enabling protein labeling within one minute and detection of transient protein interactions. MCM2 is a key component of the eukaryotic replication initiation complex, which is essential for DNA replication. In this study, we fused MCM2 with enhanced APEX2 to perform in situ biotinylation. By combining this approach with mass spectrometry, we identified proteins proximal to the replication initiation complex in synchronized mouse ESCs and NIH/3T3. Through a comparison of the results from both cell types, we identified some candidate proteins. Interactions between MCM2 and the candidate proteins CD2BP2, VRK1, and GTSE1 were confirmed by bimolecular fluorescence complementation. This research establishes a basis for further study of the component proteins of the conserved DNA replication initiation complex and the transient regulatory network involving its proximal proteins. Full article
(This article belongs to the Special Issue New Research in Spatial Proteomics)
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