Xiaonan Liu, Lawrence Abad, Lopamudra Chatterjee, Ileana M Cristea, Markku Varjosalo
{"title":"Mapping protein-protein interactions by mass spectrometry.","authors":"Xiaonan Liu, Lawrence Abad, Lopamudra Chatterjee, Ileana M Cristea, Markku Varjosalo","doi":"10.1002/mas.21887","DOIUrl":"10.1002/mas.21887","url":null,"abstract":"<p><p>Protein-protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization and function of the proteome, and their perturbation is associated with various diseases, such as cancer, neurodegeneration, and infectious diseases. Recent advances in mass spectrometry (MS)-based protein interactomics have significantly expanded our understanding of the PPIs in cells, with techniques that continue to improve in terms of sensitivity, and specificity providing new opportunities for the study of PPIs in diverse biological systems. These techniques differ depending on the type of interaction being studied, with each approach having its set of advantages, disadvantages, and applicability. This review highlights recent advances in enrichment methodologies for interactomes before MS analysis and compares their unique features and specifications. It emphasizes prospects for further improvement and their potential applications in advancing our knowledge of PPIs in various biological contexts.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561166/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140920110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Anatoly A. Sorokin, Stanislav I. Pekov, Denis S. Zavorotnyuk, Mariya M. Shamraeva, Denis S. Bormotov, Igor A. Popov
{"title":"Modern machine-learning applications in ambient ionization mass spectrometry","authors":"Anatoly A. Sorokin, Stanislav I. Pekov, Denis S. Zavorotnyuk, Mariya M. Shamraeva, Denis S. Bormotov, Igor A. Popov","doi":"10.1002/mas.21886","DOIUrl":"10.1002/mas.21886","url":null,"abstract":"<p>This article provides a comprehensive overview of the applications of methods of machine learning (ML) and artificial intelligence (AI) in ambient ionization mass spectrometry (AIMS). AIMS has emerged as a powerful analytical tool in recent years, allowing for rapid and sensitive analysis of various samples without the need for extensive sample preparation. The integration of ML/AI algorithms with AIMS has further expanded its capabilities, enabling enhanced data analysis. This review discusses ML/AI algorithms applicable to the AIMS data and highlights the key advancements and potential benefits of utilizing ML/AI in the field of mass spectrometry, with a focus on the AIMS community.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"44 1","pages":"74-88"},"PeriodicalIF":6.6,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140809412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Photoaffinity labeling coupled to MS to identify peptide biological partners: Secondary reactions, for better or for worse?","authors":"Astrid Walrant, Emmanuelle Sachon","doi":"10.1002/mas.21880","DOIUrl":"10.1002/mas.21880","url":null,"abstract":"<p>Affinity photolabeling is a smart method to study noncovalent and transient interactions and provide a submolecular picture of the contacts between interacting partners. In this review, we will focus on the identification of peptide partners using photoaffinity labeling coupled to mass spectrometry in different contexts such as in vitro with a purified potential partner, in model systems such as model membranes, and with live cells using both targeted and nontargeted proteomics studies. Different biological partners will be described, among which glycoconjugates, oligonucleotides, peptides, proteins, and lipids, with the photoreactive label inserted either on the peptide of interest or on the potential partner. Particular attention will be paid to the observation and characterization of specific rearrangements following the photolabeling reaction, which can help characterize photoadducts and provide a better understanding of the interacting systems and environment.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"44 5","pages":"715-756"},"PeriodicalIF":6.6,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mas.21880","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140584392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Protein glycosylation in lung cancer from a mass spectrometry perspective","authors":"Mirjam Balbisi, Simon Sugár, Lilla Turiák","doi":"10.1002/mas.21882","DOIUrl":"https://doi.org/10.1002/mas.21882","url":null,"abstract":"Lung cancer is a severe disease for which better diagnostic and therapeutic approaches are urgently needed. Increasing evidence implies that aberrant protein glycosylation plays a crucial role in the pathogenesis and progression of lung cancer. Differences in glycosylation patterns have been previously observed between healthy and cancerous samples as well as between different lung cancer subtypes, which suggests untapped diagnostic potential. In addition, understanding the changes mediated by glycosylation may shed light on possible novel therapeutic targets and personalized treatment strategies for lung cancer patients. Mass spectrometry based glycomics and glycoproteomics have emerged as powerful tools for in‐depth characterization of changes in protein glycosylation, providing valuable insights into the molecular basis of lung cancer. This paper reviews the literature on the analysis of protein glycosylation in lung cancer using mass spectrometry, which is dominated by manuscripts published over the past 5 years. Studies analyzing <jats:italic>N</jats:italic>‐glycosylation, <jats:italic>O</jats:italic>‐glycosylation, and glycosaminoglycan patterns in tissue, serum, plasma, and rare biological samples of lung cancer patients are highlighted. The current knowledge on the potential utility of glycan and glycoprotein biomarkers is also discussed.","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"43 1","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140584383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Stanislav I. Pekov, Denis S. Bormotov, Svetlana I. Bocharova, Anatoly A. Sorokin, Maria M. Derkach, Igor A. Popov
{"title":"Mass spectrometry for neurosurgery: Intraoperative support in decision-making","authors":"Stanislav I. Pekov, Denis S. Bormotov, Svetlana I. Bocharova, Anatoly A. Sorokin, Maria M. Derkach, Igor A. Popov","doi":"10.1002/mas.21883","DOIUrl":"10.1002/mas.21883","url":null,"abstract":"<p>Ambient ionization mass spectrometry was proved to be a powerful tool for oncological surgery. Still, it remains a translational technique on the way from laboratory to clinic. Brain surgery is the most sensitive to resection accuracy field since the balance between completeness of resection and minimization of nerve fiber damage determines patient outcome and quality of life. In this review, we summarize efforts made to develop various intraoperative support techniques for oncological neurosurgery and discuss difficulties arising on the way to clinical implementation of mass spectrometry-guided brain surgery.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"44 1","pages":"62-73"},"PeriodicalIF":6.6,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140584061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Young mass spectrometrists special issue","authors":"","doi":"10.1002/mas.21884","DOIUrl":"10.1002/mas.21884","url":null,"abstract":"","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"43 4","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140583900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Understanding zwitterionic ring-expansion polymerization through mass spectrometry.","authors":"Mahi Ahmad, Scott M Grayson","doi":"10.1002/mas.21877","DOIUrl":"https://doi.org/10.1002/mas.21877","url":null,"abstract":"<p><p>Zwitterionic ring-expansion polymerization (ZREP) is a polymerization method in which a cyclic monomer is converted into a cyclic polymer through a zwitterionic intermediate. In this review, we explored the ZREP of various cyclic polymers and how mass spectrometry assists in identifying the product architectures and understanding their intricate reaction mechanism. For the majority of polymers (from a few thousand to a few million Da) matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is the most effective mass spectrometry technique to determine the true molecular weight (MW) of the resultant product, but only when the dispersity is low (approximately below 1.2). The key topics covered in this study were the ZREP of cyclic polyesters, cyclic polyamides, and cyclic ethers. In addition, this study also addresses a number of other preliminary topics, including the ZREP of cyclic polycarbonates, cyclic polysiloxanes, and cyclic poly(alkylene phosphates). The purity and efficiency of those syntheses largely depend on the catalyst. Among several catalysts, N-heterocyclic carbenes have exhibited high efficiency in the synthesis of cyclic polyesters and polyamides, whereas tris(pentafluorophenyl)borane [B(C<sub>6</sub>F<sub>5</sub>)<sub>3</sub>] is the most optimal catalyst for cyclic polyether synthesis.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140331346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"My journey in life and chemistry","authors":"Veronica M. Bierbaum","doi":"10.1002/mas.21879","DOIUrl":"10.1002/mas.21879","url":null,"abstract":"","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"44 2","pages":"93-100"},"PeriodicalIF":6.6,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140292304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Special issue of Dr. Veronica Bierbaum for her contributions to fundamental chemistry in mass spectrometry","authors":"","doi":"10.1002/mas.21878","DOIUrl":"10.1002/mas.21878","url":null,"abstract":"","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"44 2","pages":"91-92"},"PeriodicalIF":6.6,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140178766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}