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Biochemistry and Biophysics Tools for Peptide and Protein Research

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

Deadline for manuscript submissions: 30 June 2026 | Viewed by 450

Special Issue Editor

Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
Interests: bio-molecular preparation and characterization

Special Issue Information

Dear Colleagues,

We are pleased to invite you to contribute to this Special Issue entitled "Biochemistry and Biophysics Tools for Peptide and Protein Research." Peptides and proteins are fundamental to virtually every biological process, serving as key drivers of cellular function, signaling, and structural integrity. Understanding their structure, dynamics, interactions, and function is essential for advancing fields ranging from basic molecular biology to drug discovery and biotechnology. Recent years have witnessed remarkable progress in the development of cutting-edge biochemical and biophysical tools—spanning spectroscopic, computational, single-molecule, and high-throughput methodologies—that are transforming our ability to probe and manipulate peptides and proteins with unprecedented precision. This Special Issue seeks to highlight these innovative approaches, fostering interdisciplinary dialogue and accelerating discoveries in this dynamically evolving area.

This Special Issue aims to focus on cutting-edge technologies and methodological advancements in peptide and protein research, providing a platform for scholars to showcase innovative tools, technological applications, and interdisciplinary research.

In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following:

  • Application of biophysical tools in peptides and protein characterization;
  • Emerging techniques for protein structure and function analysis;
  • Dynamics and folding mechanisms of peptides and proteins;
  • Integrated computational and experimental methods for protein design;
  • High-throughput screening and single-molecule techniques in peptide research;
  • Advances in biomarker discovery and proteomics tools;
  • Interdisciplinary approaches in peptide-based drug development.

We look forward to receiving your contributions.

Dr. Wenqi Li
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 250 words) can be sent to the Editorial Office for assessment.

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.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • protein–protein interactions
  • peptide therapeutics development
  • biosensor and labeling technologies
  • high-throughput screening
  • mass spectrometry proteomics
  • protein dynamics and folding
  • single-molecule biophysics
  • analytical ultra-centrifugation
  • computational protein design
  • structural biology techniques

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Published Papers (1 paper)

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Review

29 pages, 2051 KB  
Review
Navigating the Landscape of Cytometry-Based Single-Cell Proteomics: Quantification, Annotation, and Resources
by Yangbo Dai, Ziqiang Liu, Bing Liu, Li Guo, Huaicheng Sun and Qingxia Yang
Int. J. Mol. Sci. 2026, 27(8), 3620; https://doi.org/10.3390/ijms27083620 - 18 Apr 2026
Viewed by 187
Abstract
Cytometry-based single-cell proteomics (CySCP) has emerged as a powerful tool for analyzing cellular heterogeneity at the protein level because of its ability to reveal dynamic cell states and response patterns through high-dimensional protein expression profiling in thousands of individual cells. However, detailed summaries [...] Read more.
Cytometry-based single-cell proteomics (CySCP) has emerged as a powerful tool for analyzing cellular heterogeneity at the protein level because of its ability to reveal dynamic cell states and response patterns through high-dimensional protein expression profiling in thousands of individual cells. However, detailed summaries of quantification, processing and analysis of CySCP data remain limited. This review provides comprehensive perspectives on CySCP, including quantification technologies, analysis pipelines, annotation strategies, and resource platforms. Specifically, first, the strengths and limitations of the detection platforms are discussed. Second, comprehensive data processing steps, including compensation, transformation, normalization, batch effect correction, signal cleaning, and doublets, debris or dead cells removal, are described in detail. Third, various strategies for cell type annotation, including manual gating, unsupervised clustering, supervised/semi-supervised classification, and fully automated approaches, are illustrated. Fourth, emerging CySCP databases, as critical resources for facilitating antibody validation, panel optimization, and open-access data sharing, are summarized. In summary, this review provides a comprehensive guide for the use of CySCP to obtain novel biological insights at the single-cell protein level. Full article
(This article belongs to the Special Issue Biochemistry and Biophysics Tools for Peptide and Protein Research)
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