Nina Stremmel, Oliver Lemke, Kathrin Textoris-Taube, Daniela Ludwig, Michael Mülleder, Julia Muenzner, Markus Ralser
Pancreatic beta cells secrete insulin in response to rising glucose levels, a process known as glucose-stimulated insulin secretion (GSIS). Here, we acquire proteomes of rat pancreatic INS-1 832/13 beta cells that were short-term stimulated with 11 different glucose concentrations from 0 to 20 mM, quantifying the response of 3703 proteins. Ensemble clustering of proteome profiles revealed unique response patterns of proteins expressed by INS-1 832/13 cells. Three hundred and fourteen proteins, amongst them proteins associated with vesicular SNARE interactions, protein export, and pancreatic secretion, increased in abundance upon glucose stimulation. In contrast, many proteins implicated in metabolic glucose sensing processes such as glycolysis, the TCA cycle, and the respiratory chain, did not respond. Interestingly, we observe that enzymes participating in fatty acid metabolism showed a “switch-on” response upon release of complete glucose starvation with no further changes in abundance upon increasing glucose levels. We speculate that increased activity of fatty acid metabolic activity might either be part of GSIS by replenishing membrane lipids required for vesicle-mediated exocytosis and/or by providing an electron sink to compensate for the increase in glucose catabolism. These findings offer new insights into beta cell function and may inform future strategies for targeting metabolic pathways in diabetes treatment.
Summary
We used high-throughput proteomics to capture comprehensive proteome changes 30 min post stimulation in the INS-1 832/13 beta cell line, a commonly used cell model in studying glucose-induced insulin secretion.
Our results show that specific parts of the proteome respond promptly upon glucose exposure in this cell line. Furthermore, while many proteins canonically associated with GSIS did not change in abundance in the time frame and cell line investigated, our results attribute a specific role to fatty acid biosynthesis in the early steps of insulin secretion.
By documenting protein abundance alterations in the initial phase of GSIS in the INS-1 832/13 beta cell line, our study highlights the necessity of sampling early time points, well-controlled study design and biological replicates in the study of beta cell function.
{"title":"An INS-1 832/13 𝛽-Cell Proteome Highlights the Rapid Regulation of Fatty Acid Biosynthesis in Glucose-Stimulated Insulin Secretion","authors":"Nina Stremmel, Oliver Lemke, Kathrin Textoris-Taube, Daniela Ludwig, Michael Mülleder, Julia Muenzner, Markus Ralser","doi":"10.1002/pmic.70005","DOIUrl":"10.1002/pmic.70005","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <p>Pancreatic beta cells secrete insulin in response to rising glucose levels, a process known as glucose-stimulated insulin secretion (GSIS). Here, we acquire proteomes of rat pancreatic INS-1 832/13 beta cells that were short-term stimulated with 11 different glucose concentrations from 0 to 20 mM, quantifying the response of 3703 proteins. Ensemble clustering of proteome profiles revealed unique response patterns of proteins expressed by INS-1 832/13 cells. Three hundred and fourteen proteins, amongst them proteins associated with vesicular SNARE interactions, protein export, and pancreatic secretion, increased in abundance upon glucose stimulation. In contrast, many proteins implicated in metabolic glucose sensing processes such as glycolysis, the TCA cycle, and the respiratory chain, did not respond. Interestingly, we observe that enzymes participating in fatty acid metabolism showed a “switch-on” response upon release of complete glucose starvation with no further changes in abundance upon increasing glucose levels. We speculate that increased activity of fatty acid metabolic activity might either be part of GSIS by replenishing membrane lipids required for vesicle-mediated exocytosis and/or by providing an electron sink to compensate for the increase in glucose catabolism. These findings offer new insights into beta cell function and may inform future strategies for targeting metabolic pathways in diabetes treatment.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Summary</h3>\u0000 \u0000 <div>\u0000 <ul>\u0000 \u0000 <li>We used high-throughput proteomics to capture comprehensive proteome changes 30 min post stimulation in the INS-1 832/13 beta cell line, a commonly used cell model in studying glucose-induced insulin secretion.</li>\u0000 \u0000 <li>Our results show that specific parts of the proteome respond promptly upon glucose exposure in this cell line. Furthermore, while many proteins canonically associated with GSIS did not change in abundance in the time frame and cell line investigated, our results attribute a specific role to fatty acid biosynthesis in the early steps of insulin secretion.</li>\u0000 \u0000 <li>By documenting protein abundance alterations in the initial phase of GSIS in the INS-1 832/13 beta cell line, our study highlights the necessity of sampling early time points, well-controlled study design and biological replicates in the study of beta cell function.</li>\u0000 </ul>\u0000 </div>\u0000 </section>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 15","pages":"13-26"},"PeriodicalIF":3.9,"publicationDate":"2025-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12332333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Olivia Martínez, Darielys Santana-Medero, Satomy Pousa, Jean Pierre Soubal, Arielis Rodríguez-Ulloa, Pablo E. Ramos-Bermúdez, Vladimir Besada, Raine Garrido, Paulo Carvalho, Michel Batista, Katharina Zetl, Jacek R. Wiśniewski, Tamy Boggiano, Yury Valdés-Balbín, Dagmar García-Rivera, Daniel G. Rivera, Vicente Verez-Bencomo, Luis Javier González
SOBERANA 02 is a safe and effective anti-SARS-CoV-2 conjugate vaccine, produced using the maleimide-thiol chemistry. In this vaccine, Cys538 in the recombinant receptor binding domain (RBD) of SARS-CoV-2 is linked through a N-thiosuccinimidopropionyl linker to lysine residues of tetanus toxoid (TT) preparation. LC-MS/MS analysis revealed the complex protein composition of TT. The fifteen most abundant proteins account for approximately 78% of the total protein mass. The detoxified tetanus neurotoxin (d-TeNT) was the most abundant protein (30%–56%) regardless of the quantification method used. LC-MS/MS analysis of d-TeNT activation reaction with BMPS (3-maleimidopropionic acid N-hydroxysuccinimide ester) showed that 102 (95%) of the 107 lysine residues incorporated a maleimide group. Of them, only 22 Lys residues (20%) were cross-linked to the RBD C-terminal tryptic peptide (538CVNF541-HHHHHH), probably due to steric hindrance. Affinity chromatography prior to LC-MS/MS analysis was critical to identify the conjugation sites. Linear peptides carrying a conjugated lysine residue and type 2 peptides with stabilized linker forms (hydrolyzed and transcyclized), allowed the identification of twelve and eighteen conjugation sites, respectively. The RBD was also conjugated, but to a lesser extent, to ten other low-abundance carrier proteins. This study represents the first report of a conjugation site assignment in a TT-based conjugate vaccine.
{"title":"LC-MS/MS Characterization of SOBERANA 02, a Receptor Binding Domain-Tetanus Toxoid Conjugate Vaccine Against SARS-CoV-2","authors":"Olivia Martínez, Darielys Santana-Medero, Satomy Pousa, Jean Pierre Soubal, Arielis Rodríguez-Ulloa, Pablo E. Ramos-Bermúdez, Vladimir Besada, Raine Garrido, Paulo Carvalho, Michel Batista, Katharina Zetl, Jacek R. Wiśniewski, Tamy Boggiano, Yury Valdés-Balbín, Dagmar García-Rivera, Daniel G. Rivera, Vicente Verez-Bencomo, Luis Javier González","doi":"10.1002/pmic.13978","DOIUrl":"10.1002/pmic.13978","url":null,"abstract":"<div>\u0000 \u0000 <p>SOBERANA 02 is a safe and effective anti-SARS-CoV-2 conjugate vaccine, produced using the maleimide-thiol chemistry. In this vaccine, Cys<sup>538</sup> in the recombinant receptor binding domain (RBD) of SARS-CoV-2 is linked through a <i>N</i>-thiosuccinimidopropionyl linker to lysine residues of tetanus toxoid (TT) preparation. LC-MS/MS analysis revealed the complex protein composition of TT. The fifteen most abundant proteins account for approximately 78% of the total protein mass. The detoxified tetanus neurotoxin (d-TeNT) was the most abundant protein (30%–56%) regardless of the quantification method used. LC-MS/MS analysis of d-TeNT activation reaction with BMPS (3-maleimidopropionic acid <i>N</i>-hydroxysuccinimide ester) showed that 102 (95%) of the 107 lysine residues incorporated a maleimide group. Of them, only 22 Lys residues (20%) were cross-linked to the RBD <i>C</i>-terminal tryptic peptide (<sup>538</sup>CVNF<sup>541</sup>-HHHHHH), probably due to steric hindrance. Affinity chromatography prior to LC-MS/MS analysis was critical to identify the conjugation sites. Linear peptides carrying a conjugated lysine residue and type 2 peptides with stabilized linker forms (hydrolyzed and transcyclized), allowed the identification of twelve and eighteen conjugation sites, respectively. The RBD was also conjugated, but to a lesser extent, to ten other low-abundance carrier proteins. This study represents the first report of a conjugation site assignment in a TT-based conjugate vaccine.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 14","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144657985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Md Abdul Hakim, Akeem Sanni, Shams T. Osman, Noha A. Hamdy, Waziha Tasnim Purba, Md Mostofa Al Amin Bhuiyan, Sherifdeen Onigbinde, Labiba K. El-Khordagui, Ahmed El-Yazbi, Yehia Mechref
Type 2 diabetes (T2D) is a complex metabolic disorder with rising global prevalence, leading to major complications such as cognitive decline, cardiovascular disease, and systemic inflammation. Although advances in T2D pharmacotherapy have shown promise in addressing these complications, the underlying protective mechanisms remain unclear, especially as they appear to be independent of glycemic control. In this study, we performed a comprehensive proteomic analysis using LC-MS/MS to explore the molecular effects of newer antidiabetic drugs, specifically dipeptidyl peptidase 4 (DPP4) and sodium-glucose cotransporter 2 (SGLT2) inhibitors (SGLT2is), when combined with metformin, the first-line treatment for T2D. Serum samples from 76 individuals were analyzed, including 16 healthy subjects, 32 T2D patients on metformin monotherapy, and 28 T2D patients receiving combination therapy. We identified and quantified 505 low-abundance proteins, followed by statistical analysis and ingenuity pathway analysis. Our findings revealed significant changes in key biological pathways related to synaptogenesis, insulin-like growth factor transport, and neurovascular coupling signaling. These results were further validated using parallel reaction monitoring. Notably, pathways associated with cognitive function and cardiovascular health were adversely affected in T2D patients on metformin monotherapy but showed improvement with combination therapy. These results suggest that the combination of DPP4 and SGLT2is offers a therapeutic advantage, underscoring the importance of personalized treatment strategies in managing T2D complications.
Summary: Type 2 diabetes (T2D) is a chronic metabolic disorder that contributes to the progression of cognitive impairment, cardiovascular diseases, and renal dysfunction. Cognitive decline in T2D patients can also increase the risk of developing neurological conditions like Alzheimer's disease.
Recently developed antidiabetic drugs have shown promising cardiovascular and renal health effects, such as dipeptidyl peptidase 4 (DPP4) inhibitors and sodium-glucose cotransporter 2 (SGLT2) inhibitors (SGLT2is). However, the precise mechanisms by which these drugs influence biological pathways related to cognitive function and central nervous system (CNS) development remain unclear.
In this study, we explored the impact of these newer antidiabetic drugs in combination with metformin, compared to metformin monotherapy and healthy controls, by investigating differentially expressed proteins and their role in cognitive processes.
Our findings reveal that DPP4 and SGLT2is activate key biological pathways—such as synaptogenesis, insulin-like growth factor regulation, and neurovascular coupling—that are either suppressed or not enriched in the metformin-only group. These pathways are critical for maintaining and regulating CNS function and cognitive h
{"title":"Serum Proteome Profiling of Diabetic Patients Treated With DPP4 and SGLT2 Inhibitors Shows Improved Cognitive and Cardiovascular Functions","authors":"Md Abdul Hakim, Akeem Sanni, Shams T. Osman, Noha A. Hamdy, Waziha Tasnim Purba, Md Mostofa Al Amin Bhuiyan, Sherifdeen Onigbinde, Labiba K. El-Khordagui, Ahmed El-Yazbi, Yehia Mechref","doi":"10.1002/pmic.70000","DOIUrl":"10.1002/pmic.70000","url":null,"abstract":"<div>\u0000 \u0000 <p>Type 2 diabetes (T2D) is a complex metabolic disorder with rising global prevalence, leading to major complications such as cognitive decline, cardiovascular disease, and systemic inflammation. Although advances in T2D pharmacotherapy have shown promise in addressing these complications, the underlying protective mechanisms remain unclear, especially as they appear to be independent of glycemic control. In this study, we performed a comprehensive proteomic analysis using LC-MS/MS to explore the molecular effects of newer antidiabetic drugs, specifically dipeptidyl peptidase 4 (DPP4) and sodium-glucose cotransporter 2 (SGLT2) inhibitors (SGLT2is), when combined with metformin, the first-line treatment for T2D. Serum samples from 76 individuals were analyzed, including 16 healthy subjects, 32 T2D patients on metformin monotherapy, and 28 T2D patients receiving combination therapy. We identified and quantified 505 low-abundance proteins, followed by statistical analysis and ingenuity pathway analysis. Our findings revealed significant changes in key biological pathways related to synaptogenesis, insulin-like growth factor transport, and neurovascular coupling signaling. These results were further validated using parallel reaction monitoring. Notably, pathways associated with cognitive function and cardiovascular health were adversely affected in T2D patients on metformin monotherapy but showed improvement with combination therapy. These results suggest that the combination of DPP4 and SGLT2is offers a therapeutic advantage, underscoring the importance of personalized treatment strategies in managing T2D complications.</p>\u0000 <p><b>Summary</b>: Type 2 diabetes (T2D) is a chronic metabolic disorder that contributes to the progression of cognitive impairment, cardiovascular diseases, and renal dysfunction. Cognitive decline in T2D patients can also increase the risk of developing neurological conditions like Alzheimer's disease.</p>\u0000 <p>Recently developed antidiabetic drugs have shown promising cardiovascular and renal health effects, such as dipeptidyl peptidase 4 (DPP4) inhibitors and sodium-glucose cotransporter 2 (SGLT2) inhibitors (SGLT2is). However, the precise mechanisms by which these drugs influence biological pathways related to cognitive function and central nervous system (CNS) development remain unclear.</p>\u0000 <p>In this study, we explored the impact of these newer antidiabetic drugs in combination with metformin, compared to metformin monotherapy and healthy controls, by investigating differentially expressed proteins and their role in cognitive processes.</p>\u0000 <p>Our findings reveal that DPP4 and SGLT2is activate key biological pathways—such as synaptogenesis, insulin-like growth factor regulation, and neurovascular coupling—that are either suppressed or not enriched in the metformin-only group. These pathways are critical for maintaining and regulating CNS function and cognitive h","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 14","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144657986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Julia Kitaygorodsky, Brendon Seale, Vesal Kasmaeifar, Reuben Samson, Zhen-Yuan Lin, Martina Tersigni, Saya Sedighi, Cassandra J. Wong, Anne-Claude Gingras
<div> <section> <p>Proximity-dependent biotinylation (BioID) is a powerful means of exploring the cellular environments in which proteins reside. Expressing a protein of interest (bait) fused to a biotin ligase and adding biotin induces the covalent biotinylation of proximal partners (preys), which are recovered on streptavidin beads and identified by MS. However, a major technical limitation of BioID is peptide carryover into subsequent MS runs. This is typically mitigated via lengthy intersample wash cycles, which lowers throughput considerably. The aim of this study was to optimize BioID sample acquisition using an EvoSep LC system coupled to a timsTOF mass spectrometer, which has higher throughput and sensitivity than our current system, with less carryover. Our efforts resulted in an ∼15-fold increase in throughput using the 60 samples-per-day gradient with better sensitivity, and identifying nearly double the proteins found by our previously standardized workflow. Significance scoring also revealed more sensitive detection of high-confidence proximal interactions (∼1.5-fold) for five well-characterized baits, validating the new experimental workflow. Importantly, carryover was extremely limited, even without intersample washing, and limited to abundant proteins that are easily filtered during data analyses. Without washing, the newly optimized method can process 60 samples per day, using half of the sample amount previously required.</p> </section> <section> <h3> Summary</h3> <div> <ul> <li>Proximity-dependent biotinylation (PDB) coupled with MS is a powerful approach to characterize subcellular protein localization.</li> <li>However, the carry-over of peptides from the abundant proteins into subsequent MS runs is problematic. While this was previously mitigated by lengthy wash cycles of the chromatography column, this ultimately lowered throughput.</li> <li>The introduction of the EvoSep chromatography system and more sensitive MS instrumentation has enabled robust and fast analysis with lower sample amounts and minimal carry-over.</li> <li>To date, there has been no systematic evaluation of this EvoSep-timsTOF instrumentation for PDB, nor a direct comparison to a previously standardized workflow.</li> <li>This study compares the identifications between these acquisition setups, recommends sample loading and gradient settings for the EvoSep-timsTOF, and investigates the high-confidence proximal interactors identified.</li> <li>The results highlight the necessity of optimization of scoring approaches f
{"title":"Optimizing Proximity Proteomics on the EvoSep-timsTOF LC–MS System","authors":"Julia Kitaygorodsky, Brendon Seale, Vesal Kasmaeifar, Reuben Samson, Zhen-Yuan Lin, Martina Tersigni, Saya Sedighi, Cassandra J. Wong, Anne-Claude Gingras","doi":"10.1002/pmic.70010","DOIUrl":"10.1002/pmic.70010","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <p>Proximity-dependent biotinylation (BioID) is a powerful means of exploring the cellular environments in which proteins reside. Expressing a protein of interest (bait) fused to a biotin ligase and adding biotin induces the covalent biotinylation of proximal partners (preys), which are recovered on streptavidin beads and identified by MS. However, a major technical limitation of BioID is peptide carryover into subsequent MS runs. This is typically mitigated via lengthy intersample wash cycles, which lowers throughput considerably. The aim of this study was to optimize BioID sample acquisition using an EvoSep LC system coupled to a timsTOF mass spectrometer, which has higher throughput and sensitivity than our current system, with less carryover. Our efforts resulted in an ∼15-fold increase in throughput using the 60 samples-per-day gradient with better sensitivity, and identifying nearly double the proteins found by our previously standardized workflow. Significance scoring also revealed more sensitive detection of high-confidence proximal interactions (∼1.5-fold) for five well-characterized baits, validating the new experimental workflow. Importantly, carryover was extremely limited, even without intersample washing, and limited to abundant proteins that are easily filtered during data analyses. Without washing, the newly optimized method can process 60 samples per day, using half of the sample amount previously required.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Summary</h3>\u0000 \u0000 <div>\u0000 <ul>\u0000 \u0000 <li>Proximity-dependent biotinylation (PDB) coupled with MS is a powerful approach to characterize subcellular protein localization.</li>\u0000 \u0000 <li>However, the carry-over of peptides from the abundant proteins into subsequent MS runs is problematic. While this was previously mitigated by lengthy wash cycles of the chromatography column, this ultimately lowered throughput.</li>\u0000 \u0000 <li>The introduction of the EvoSep chromatography system and more sensitive MS instrumentation has enabled robust and fast analysis with lower sample amounts and minimal carry-over.</li>\u0000 \u0000 <li>To date, there has been no systematic evaluation of this EvoSep-timsTOF instrumentation for PDB, nor a direct comparison to a previously standardized workflow.</li>\u0000 \u0000 <li>This study compares the identifications between these acquisition setups, recommends sample loading and gradient settings for the EvoSep-timsTOF, and investigates the high-confidence proximal interactors identified.</li>\u0000 \u0000 <li>The results highlight the necessity of optimization of scoring approaches f","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 15","pages":"58-71"},"PeriodicalIF":3.9,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329395/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144606961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ivo Fabrik, Rudolf Kupcik, Daniela Fabrikova, Marketa Chvojkova, Kristina Holubova, Kristina Hakenova, Martin Horak, Jiri Soukup, Monika Manethova, Robert Rusina, Radoslav Matej, Ales Ryska, Ondrej Soukup
One of the traditional treatments in Alzheimer's disease (AD) is administration of memantine, the NMDA receptor antagonist. However, the molecular mechanism of the complex memantine action and the impact on the hippocampal proteome in humans is unknown. In this study, hippocampal proteins extracted from formalin-fixed paraffin-embedded post mortem tissues obtained from healthy donors (n = 15), AD patients not treated with memantine (n = 11), and AD patients treated with memantine (n = 8) were investigated using tandem mass tag (TMT)-based quantitative proteomics. Memantine medication induced subtle but distinct changes in the hippocampal proteome in AD patients. Although it did not prevent the metabolic and physiologic decline associated with AD pathology, memantine administration upregulated several mitochondrially encoded proteins and mitigated the proteomic pattern of activated phagocytes. Furthermore, memantine specifically enhanced the expression of postsynaptic glutamatergic and GABAergic receptors and components of the respective pathways without affecting presynaptic proteome. This suggests that memantine treatment in AD patients not only alleviates excitotoxic stress by inhibiting NMDA receptor activity, but also triggers broader adaptations in the synaptic signaling and plasticity.
阿尔茨海默病（AD）的传统治疗方法之一是使用NMDA受体拮抗剂美金刚。然而，复杂美金刚作用的分子机制及其对人类海马蛋白质组的影响尚不清楚。在这项研究中，从健康供体（n = 15）、未接受美金刚治疗的AD患者（n = 11）和接受美金刚治疗的AD患者（n = 8）的死后组织中提取的福尔马林固定石蜡提取的海马蛋白，采用基于tandem mass tag （TMT）的定量蛋白质组学方法进行研究。美金刚药物诱导AD患者海马蛋白组发生细微但明显的变化。虽然它不能阻止与AD病理相关的代谢和生理衰退，但美金刚给药上调了一些线粒体编码的蛋白质，并减轻了活化吞噬细胞的蛋白质组模式。此外，美金刚特异性地增强了突触后谷氨酸能和gaba能受体及其各自通路组分的表达，而不影响突触前蛋白质组。这表明，AD患者的美金刚治疗不仅可以通过抑制NMDA受体活性来缓解兴奋性毒性应激，还可以在突触信号传导和可塑性方面引发更广泛的适应。
{"title":"Memantine Administration Enhances Glutamatergic and GABAergic Pathways in the Human Hippocampus of Alzheimer's Disease Patients","authors":"Ivo Fabrik, Rudolf Kupcik, Daniela Fabrikova, Marketa Chvojkova, Kristina Holubova, Kristina Hakenova, Martin Horak, Jiri Soukup, Monika Manethova, Robert Rusina, Radoslav Matej, Ales Ryska, Ondrej Soukup","doi":"10.1002/pmic.70006","DOIUrl":"10.1002/pmic.70006","url":null,"abstract":"<p>One of the traditional treatments in Alzheimer's disease (AD) is administration of memantine, the NMDA receptor antagonist. However, the molecular mechanism of the complex memantine action and the impact on the hippocampal proteome in humans is unknown. In this study, hippocampal proteins extracted from formalin-fixed paraffin-embedded post mortem tissues obtained from healthy donors (<i>n</i> = 15), AD patients not treated with memantine (<i>n</i> = 11), and AD patients treated with memantine (<i>n</i> = 8) were investigated using tandem mass tag (TMT)-based quantitative proteomics. Memantine medication induced subtle but distinct changes in the hippocampal proteome in AD patients. Although it did not prevent the metabolic and physiologic decline associated with AD pathology, memantine administration upregulated several mitochondrially encoded proteins and mitigated the proteomic pattern of activated phagocytes. Furthermore, memantine specifically enhanced the expression of postsynaptic glutamatergic and GABAergic receptors and components of the respective pathways without affecting presynaptic proteome. This suggests that memantine treatment in AD patients not only alleviates excitotoxic stress by inhibiting NMDA receptor activity, but also triggers broader adaptations in the synaptic signaling and plasticity.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 15","pages":"42-49"},"PeriodicalIF":3.9,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329391/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ayako Takemori, Philipp T. Kaulich, Andreas Tholey, Nobuaki Takemori
Top-down proteomics (TDP) is a powerful analytical approach for the highly sensitive measurement of intact proteoforms by mass spectrometry. However, its application to high molecular weight proteoforms remains challenging. Middle-down proteomics (MDP) offers a practical solution but requires pre-fractionation of the complex peptide mixture generated by limited digestion to successfully achieve trace-level peptide detection. Here, we present 2D-GeLC-FAIMS-MS, an innovative gel-based sample pre-fractionation workflow for in-depth MDP. This workflow integrates limited Glu-C digestion with a two-dimensional sample fractionation strategy that combines a BAC (N,N′-bis(acryloyl)cystamine)-cross-linked dissolvable polyacrylamide gel electrophoresis (BAC-PAGE) with PEPPI-MS, a highly efficient passive protein extraction method. Samples are first size-fractionated by BAC-PAGE and subsequently subjected to in-gel Glu-C digestion. The resulting middle-down peptides (< 50 kDa) undergo a second fractionation via SDS-PAGE, followed by peptide recovery using PEPPI-MS and LC-FAIMS-MS analysis. The dissolution properties of BAC gels enable efficient sample transfer between the two PAGE steps with minimal loss, ensuring high-resolution pre-fractionation. This novel workflow provides a robust and efficient strategy for the comprehensive characterization of middle-down peptides, facilitating improved sensitivity and depth in proteome analysis.
{"title":"Dissolvable Polyacrylamide Gel Electrophoresis-Enabled High-Resolution Sample Fractionation for Middle-Down Proteomics","authors":"Ayako Takemori, Philipp T. Kaulich, Andreas Tholey, Nobuaki Takemori","doi":"10.1002/pmic.70007","DOIUrl":"10.1002/pmic.70007","url":null,"abstract":"<div>\u0000 \u0000 <p>Top-down proteomics (TDP) is a powerful analytical approach for the highly sensitive measurement of intact proteoforms by mass spectrometry. However, its application to high molecular weight proteoforms remains challenging. Middle-down proteomics (MDP) offers a practical solution but requires pre-fractionation of the complex peptide mixture generated by limited digestion to successfully achieve trace-level peptide detection. Here, we present 2D-GeLC-FAIMS-MS, an innovative gel-based sample pre-fractionation workflow for in-depth MDP. This workflow integrates limited Glu-C digestion with a two-dimensional sample fractionation strategy that combines a BAC (<i>N,N′</i>-bis(acryloyl)cystamine)-cross-linked dissolvable polyacrylamide gel electrophoresis (BAC-PAGE) with PEPPI-MS, a highly efficient passive protein extraction method. Samples are first size-fractionated by BAC-PAGE and subsequently subjected to in-gel Glu-C digestion. The resulting middle-down peptides (< 50 kDa) undergo a second fractionation via SDS-PAGE, followed by peptide recovery using PEPPI-MS and LC-FAIMS-MS analysis. The dissolution properties of BAC gels enable efficient sample transfer between the two PAGE steps with minimal loss, ensuring high-resolution pre-fractionation. This novel workflow provides a robust and efficient strategy for the comprehensive characterization of middle-down peptides, facilitating improved sensitivity and depth in proteome analysis.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 15","pages":"50-57"},"PeriodicalIF":3.9,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144937461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EXPRESSION OF CONCERN: A, Roy, S, Gupta, D, Hess, K, P, Das, and S, Das, “Binding of Insecticidal Lectin Colocasia esculenta Tuber Agglutinin (CEA) to Midgut Receptors of Bemisia tabaci and Lipaphis erysimi Provides Clues to its Insecticidal Potential,” Proteomics 14, no. 13–14 (2014): 1646–1659, https://doi.org/10.1002/pmic.201300408.
This Expression of Concern is for the above article, published online on 17 April 2014 in Wiley Online Library (wileyonlinelibrary.com), and has been issued by agreement between the journal Editor-in-Chief, Lucie Kalvodova, and Wiley-VCH GmbH. A third party reported concerns that the image in Figure 1D as well as the marker lanes used in Figures 2D,E in this paper had been reused from another article by some of the same authors (Mondal et al. 2012 [http://doi.org/10.4236/ajps.2012.36094]). The authors responded to an inquiry by the publisher and stated that Figure 1D had been reused from the previous publication unintentionally and that the marker lanes in Figures 2D,E had been re-used across all their publications on mannose binding lectins during 2010 and through 2015. The authors supplied a new image for the CEA western blot in Figure 1D and the associated original data, but the parties could not confirm that the supplied data corresponded to the correct samples. The authors additionally confirmed that the original data for the CEA purification experiments were no longer available. The authors provided additional data which were related to the experiment in Figure 1D. However, the publisher could not verify its authenticity because the full set of data related to the experiment was not available. The Expression of Concern has been agreed to because, while the re-use of marker lanes is not viewed as a major concern, the parties have not been able to validate the data presented in Figure 1D. Therefore, the journal has decided to issue an expression of concern to inform and alert the readers. The authors disagree with the expression of concern.
{"title":"EXPRESSION OF CONCERN: Binding of Insecticidal Lectin Colocasia esculenta Tuber Agglutinin (CEA) to Midgut Receptors of Bemisia tabaci and Lipaphis erysimi Provides Clues to its Insecticidal Potential","authors":"Sampa Das","doi":"10.1002/pmic.70008","DOIUrl":"10.1002/pmic.70008","url":null,"abstract":"<p><b>EXPRESSION OF CONCERN</b>: A, Roy, S, Gupta, D, Hess, K, P, Das, and S, Das, “Binding of Insecticidal Lectin <i>Colocasia esculenta</i> Tuber Agglutinin (CEA) to Midgut Receptors of <i>Bemisia tabaci</i> and <i>Lipaphis erysimi</i> Provides Clues to its Insecticidal Potential,” <i>Proteomics</i> 14, no. 13–14 (2014): 1646–1659, https://doi.org/10.1002/pmic.201300408.</p><p>This Expression of Concern is for the above article, published online on 17 April 2014 in Wiley Online Library (wileyonlinelibrary.com), and has been issued by agreement between the journal Editor-in-Chief, Lucie Kalvodova, and Wiley-VCH GmbH. A third party reported concerns that the image in Figure 1D as well as the marker lanes used in Figures 2D,E in this paper had been reused from another article by some of the same authors (Mondal et al. 2012 [http://doi.org/10.4236/ajps.2012.36094]). The authors responded to an inquiry by the publisher and stated that Figure 1D had been reused from the previous publication unintentionally and that the marker lanes in Figures 2D,E had been re-used across all their publications on mannose binding lectins during 2010 and through 2015. The authors supplied a new image for the CEA western blot in Figure 1D and the associated original data, but the parties could not confirm that the supplied data corresponded to the correct samples. The authors additionally confirmed that the original data for the CEA purification experiments were no longer available. The authors provided additional data which were related to the experiment in Figure 1D. However, the publisher could not verify its authenticity because the full set of data related to the experiment was not available. The Expression of Concern has been agreed to because, while the re-use of marker lanes is not viewed as a major concern, the parties have not been able to validate the data presented in Figure 1D. Therefore, the journal has decided to issue an expression of concern to inform and alert the readers. The authors disagree with the expression of concern.</p><p>The authors declare no conflicts of interest.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 19","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.70008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144574570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Liang Xue, Shivani Tiwary, Mykola Bordyuh, Robert Stanton
In mass spectrometry-based proteomics, the use of deep learning algorithms can help improve the identification rates of peptides and proteins through the generation of high-fidelity theoretical spectrum which can be used as the basis of a more complete spectral library than those presently available, especially for unobserved protein/genetic variants. Here we focus on providing an end-to-end user-friendly machine learning workflow, which we call Complete Spectrum Predictor (CoSpred). Using CoSpred users can create their own machine learning compatible training dataset and then train a machine learning model to predict both backbone and non-backbone ions. For the model a transformer encoder architecture is used to predict the complete MS/MS spectrum from a given peptide sequence. In addition to the transformer model provided in the package, the code is built modularly to allow for alternate ML models to be easily “plugged in,” allowing for spectrum prediction optimization given different experimental conditions. The CoSpred workflow (preprocessing→training→inference) provides a path for state-of-art ML capabilities to be more accessible to proteomics scientists.
{"title":"CoSpred: Machine Learning Workflow to Predict Tandem Mass Spectrum in Proteomics","authors":"Liang Xue, Shivani Tiwary, Mykola Bordyuh, Robert Stanton","doi":"10.1002/pmic.70004","DOIUrl":"10.1002/pmic.70004","url":null,"abstract":"<div>\u0000 \u0000 <p>In mass spectrometry-based proteomics, the use of deep learning algorithms can help improve the identification rates of peptides and proteins through the generation of high-fidelity theoretical spectrum which can be used as the basis of a more complete spectral library than those presently available, especially for unobserved protein/genetic variants. Here we focus on providing an end-to-end user-friendly machine learning workflow, which we call <b>Co</b>mplete <b>S</b>pectrum <b>Pred</b>ictor (CoSpred). Using CoSpred users can create their own machine learning compatible training dataset and then train a machine learning model to predict both backbone and non-backbone ions. For the model a transformer encoder architecture is used to predict the complete MS/MS spectrum from a given peptide sequence. In addition to the transformer model provided in the package, the code is built modularly to allow for alternate ML models to be easily “plugged in,” allowing for spectrum prediction optimization given different experimental conditions. The CoSpred workflow (preprocessing→training→inference) provides a path for state-of-art ML capabilities to be more accessible to proteomics scientists.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 15","pages":"27-41"},"PeriodicalIF":3.9,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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