The foundation of all biological processes is the network of diverse and dynamic protein interactions with other molecules in cells known as the interactome. Understanding the interactome is crucial for elucidating molecular mechanisms but has been a longstanding challenge. Recent developments in mass spectrometry (MS)-based techniques, including affinity purification, proximity labeling, cross-linking, and co-fractionation mass spectrometry (MS), have significantly enhanced our abilities to study the interactome. They do so by identifying and quantifying protein interactions, yielding profound insights into protein organizations and functions. This review summarizes recent advances in MS-based interactomics, focusing on the development of techniques that capture protein-protein, protein-metabolite, and protein-nucleic acid interactions. Additionally, we discuss how integrated MS-based approaches have been applied to diverse biological samples, focusing on significant discoveries that have leveraged our understanding of cellular functions. Finally, we highlight state-of-the-art bioinformatic approaches for predictions of interactome and complex modeling, as well as strategies for combining experimental interactome data with computation methods, thereby enhancing the ability of MS-based techniques to identify protein interactomes. Indeed, advances in MS technologies and their integrations with computational biology provide new directions and avenues for interactome research, leveraging new insights into mechanisms that govern the molecular architecture of living cells and, thereby, our comprehension of biological processes.

Shaowen Wu

Sheng Zhang

Chun-Ming Liu

Alisdair R Fernie

Shijuan Yan

Molecular & Cellular Proteomics

The mission of MCP is to foster the development and applications of proteomics in both basic and translational research. MCP will publish manuscripts that report significant new biological or clinical discoveries underpinned by proteomic observations across all kingdoms of life. Manuscripts must define the biological roles played by the proteins investigated or their mechanisms of action.

The journal also emphasizes articles that describe innovative new computational methods and technological advancements that will enable future discoveries. Manuscripts describing such approaches do not have to include a solution to a biological problem, but must demonstrate that the technology works as described, is reproducible and is appropriate to uncover yet unknown protein/proteome function or properties using relevant model systems or publicly available data.
Scope:
-Fundamental studies in biology, including integrative "omics" studies, that provide mechanistic insights
-Novel experimental and computational technologies
-Proteogenomic data integration and analysis that enable greater understanding of physiology and disease processes
-Pathway and network analyses of signaling that focus on the roles of post-translational modifications
-Studies of proteome dynamics and quality controls, and their roles in disease
-Studies of evolutionary processes effecting proteome dynamics, quality and regulation
-Chemical proteomics, including mechanisms of drug action
-Proteomics of the immune system and antigen presentation/recognition
-Microbiome proteomics, host-microbe and host-pathogen interactions, and their roles in health and disease
-Clinical and translational studies of human diseases
-Metabolomics to understand functional connections between genes, proteins and phenotypes

The mission of Molecular and Cellular Proteomics (MCP) is to promote the development and application of proteomics in both basic and translational research. MCP publishes manuscripts that report significant new biological or clinical discoveries supported by proteomic observations across all kingdoms of life. Manuscripts must clearly define the biological roles of the proteins investigated or their mechanisms of action.\n\nThe journal also emphasizes articles that describe innovative computational methods and technological advancements that will enable future discoveries. Manuscripts describing such approaches do not need to provide a solution to a biological problem but must demonstrate that the technology works as described, is reproducible, and is suitable for uncovering previously unknown protein/proteome functions or properties using relevant model systems or publicly available data.\n\nScope: \n- Fundamental studies in biology, including integrative "omics" studies that provide mechanistic insights\n- Novel experimental and computational technologies\n- Proteogenomic data integration and analysis that enhance understanding of physiology and disease processes\n- Pathway and network analyses of signaling that focus on the roles of post-translational modifications\n- Studies of proteome dynamics and quality controls, and their roles in disease\n- Studies of evolutionary processes affecting proteome dynamics, quality, and regulation\n- Chemical proteomics, including mechanisms of drug action\n- Proteomics of the immune system and antigen presentation/recognition\n- Microbiome proteomics, host-microbe and host-pathogen interactions, and their roles in health and disease\n- Clinical and translational studies of human diseases\n- Metabolomics to understand functional connections between genes, proteins, and phenotypes.

《Molecular and Cellular Proteomics》的使命是促进蛋白质组学在基础和转化研究中的发展与应用。该期刊将发表报告基于蛋白质组观察的新生物或临床发现的重要手稿，涵盖所有生命王国。手稿必须明确所研究蛋白质的生物学角色或其作用机制。\n\n该期刊还强调描述创新计算方法和技术进步的文章，这些方法和技术将促进未来的发现。描述此类方法的手稿不必包含生物问题的解决方案，但必须证明所述技术有效、可重复，并适合使用相关模型系统或公开数据揭示尚未知的蛋白质/蛋白组功能或特性。\n\n范围：\n- 生物学中的基础研究，包括提供机制性见解的综合“组学”研究\n- 新颖的实验和计算技术\n- 蛋白质组基因组数据整合与分析，以便更好地理解生理和疾病过程\n- 关注后转译修饰作用的信号通路和网络分析\n- 蛋白质组动态和质量控制的研究及其在疾病中的作用\n- 影响蛋白质组动态、质量和调控的进化过程研究\n- 化学蛋白质组学，包括药物作用机制\n- 免疫系统的蛋白质组学及抗原呈递/识别\n- 微生物组蛋白质组学、宿主-微生物和宿主-病原体相互作用及其在健康和疾病中的作用\n- 人类疾病的临床和转化研究\n- 代谢组学以理解基因、蛋白质和表型之间的功能联系

Category	Quartile
生物学	2
生物学, 生化研究方法	1

Recent Advances in Mass Spectrometry-based Protein Interactome Studies

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Journal Info

Category	Quartile
BIOCHEMICAL RESEARCH METHODS	1