Proteomics最新文献

{"title":"Metaproteomics Reveals Community Coalescence Outcomes in Co-Cultured Human Gut Microbiota.","authors":"Boyan Sun, Jinhui Yuan, Xin Zhang, Xiaoyu Ma, Zikai Hao, Luman Wang, Yutong Li, Lingqiang Zhang, Leyuan Li","doi":"10.1002/pmic.70009","DOIUrl":"https://doi.org/10.1002/pmic.70009","url":null,"abstract":"<p><p>The human gut microbiome exhibits characteristics of complex ecosystems, including the ability to resist and compete with exogenous species or communities. Understanding the microbiome response that emerges from such competitive interactions is crucial, particularly for applications like fecal microbiota transplantation (FMT), where the success of treatment largely depends on the outcome of these microbial competitions. During these processes, microbial communities undergo coalescence, a phenomenon where distinct microbial communities combine and interact, leading to complex ecological outcomes that are still being uncovered. In this study, we examined the coalescent dynamics of 10 different pairs of human gut microbiota by co-culturing the plateau-phase communities of individual samples in vitro, and highlighted the critical role of metaproteomics in elucidating the competitive dynamics of co-cultured human fecal samples. Results showed that microbiome changes observed after coalescent co-culture were not straightforwardly an approximate average of the initial taxonomic or functional compositions of the two samples. Instead, both coalescent microbiotas behaved as cohesive structures, influencing the competitive outcome toward one of them. Although co-cultured communities usually exhibited high degrees of taxonomic similarities to one of its parental samples, we found that 23% of the observed proteins still showed differential expression or abundance at the metaproteomic level. Interestingly, and somewhat counterintuitively, no specific microbial ecological characteristic could linearly determine which of the two initial microbiotas would act as the driving microbiota. Instead, we observed that the outcomes of the microbial co-cultures resembled a \"rock-paper-scissors\"-like dynamic. Through an analysis of co-colonizing species in such \"rock-paper-scissors\"-like triangle, we discovered that co-colonizing species that contributed to winning each between-community competition differed from one community pair to another. This suggests that no single species or function consistently dominates across all situations; instead, this involves more complex mechanisms, which require further in-depth investigation in future studies. Our findings demonstrate that the complex competitive interactions between microbial communities make predicting success through a single parameter challenging, whereas pre-co-culturing shows promise as an effective method for predicting outcomes in ecological therapies such as FMT. SUMMARY: This study underscores the critical importance of integrating metaproteomics with microbial systems ecology to gain a functional understanding of microbial coalescence. By addressing the ecological question of how two communities compete when they are brought into contact, we investigated the metaproteomic responses of pairs of coalescent co-cultured human gut microbiotas. Our results revealed significant insights: post-co-culture microb","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70009"},"PeriodicalIF":3.4,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717125","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}

{"title":"Psidium Defenses Against Meloidogyne enterolobii: Proteomic and Microscopic Analysis of this Plant-Predator Association.","authors":"Sara Nállia de Oliveira Costa, Roberta Pena da Paschoa, Camilla Ribeiro Alexandrino, Pamela Maciel Cremonez, Juliana Martins Ribeiro, José Mauro da Cunha E Castro, Maura Da Cunha, Vanildo Silveira, Antônia Elenir Amâncio Oliveira, Kátia Valevski Sales Fernandes","doi":"10.1002/pmic.70015","DOIUrl":"https://doi.org/10.1002/pmic.70015","url":null,"abstract":"<p><p>Guava (Psidium guajava), referred to as the \"tropical apple,\" is esteemed for its sweet flavor, nutritional density, and medicinal attributes, being rich in ascorbic acid, phenolics, carotenoids, fibers, and minerals. Despite its agricultural significance, guava cultivation faces considerable challenges from plant-parasitic nematodes, particularly root-knot nematodes from the Meloidogyne spp. In South America, Meloidogyne enterolobii causes severe root damage and economic losses to this crop. Plants fight nematodes through complex immune mechanisms involving pattern recognition receptors and signaling pathways, such as pattern-triggered immunity. The present research employed comparative shotgun proteomic analysis complemented by microscopic imaging and histochemical assays of roots from susceptible P. guajava and resistant P. guineense, inoculated or not with M. enterolobii. Psidium-M. enterolobii interactions revealed intricate plant cellular responses such as giant cells formation, hypersensitivity reactions, and biochemical pathway adjustments in sucrose transport and antioxidant enzyme activities. Synthesis and accumulation of secondary metabolites like terpenes, alkaloids, and phenolics in inoculated and resistant plants were positively correlated to plant resilience. Heat shock proteins and protein disulfide isomerases also emerged as pivotal in plant response, being upregulated during nematode infection. SUMMARY: The work addresses and unravels some of the puzzle pieces in the net of processes triggered in a plant prey (Psidium spp.), of either susceptible (P. guajava) or resistant (P. guineense) phenotypes, when confronted by its nematode predator (Meloidogyne enterolobii). The main alterations detected in the roots of these plants ranged from giant cells formation, hypersensitivity reactions, biochemical adjustments in sucrose transport pathways and in antioxidant enzyme activities, to increases in secondary metabolites (terpenes, alkaloids, and phenolics) and in heat shock proteins and protein disulfide isomerases. All these defensive mechanisms were triggered by the nematode attack on both species and were more prominent in P. guineense, which positively correlates them to the plant resistance against M. enterolobii.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70015"},"PeriodicalIF":3.4,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717126","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}

{"title":"Enhanced Separation of Intact Proteins and Proteoforms by CZE-MS Using Sulfobetaine-Modified Poly(α-L-lysine)-Based Multilayer Coatings for EOF Adjustment.","authors":"Alisa Höchsmann, Henry Frick, Laura Dhellemmes, Laurent Leclercq, Philipp T Kaulich, Andreas Tholey, Hervé Cottet, Norbert Schaschke, Christian Neusüß","doi":"10.1002/pmic.70012","DOIUrl":"https://doi.org/10.1002/pmic.70012","url":null,"abstract":"<p><p>Mass spectrometry-based top-down protein analysis requires efficient separation. In the context of proteoform analysis, capillary zone electrophoresis (CZE) is very valuable. The resolution of two peaks in CZE can be increased when the absolute mobility of the counter-directed electroosmotic flow (EOF) is close to the effective mobility of the analytes, resulting in a low apparent mobility of the analytes. The mobility of the EOF of highly efficient sulfobetaine-modified poly(α-L-lysine) (α-PLL) coatings changes depending on the number of modified side chains. Here, such coatings are used to selectively increase the peak resolution of proteoforms of model proteins and analytes in a complex protein sample (intact yeast protein extract). Whereas a high EOF system allows for the separation of proteins of a wide mobility range (complete proteome), lower EOF systems allow for a much better separation of proteins and proteoforms of low mobility, including those containing acidic post-translation modifications (PTMs). This leads to the identification of 2.5 times more proteoforms by MS/MS experiments in the lower mobility range of the yeast proteome. The sulfobetaine-modified α-PLL coatings presented here exhibit a toolbox for highly resolved separation of proteins and proteoforms in targeted or untargeted top-down protein analysis. SUMMARY: Sample complexity is one of the main challenges when analyzing a proteome on the proteoform level. In the course of this, capillary electrophoresis-mass spectrometry turned out to be an excellent tool because of its high-performing separation, particularly for large molecules. Here, we present a method enabling the best possible separation due to efficient and EOF-tunable coatings, allowing for flexible and dedicated selection of a range of proteins and proteoforms to be analyzed under ideal separation conditions. The high performance is demonstrated by the separation of proteoforms of common PTM-rich model proteins as well as complex proteome samples.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70012"},"PeriodicalIF":3.4,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144705904","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}

{"title":"Extracellular Origins of Cognition: Lessons from Primate Neocortical ECM","authors":"Shani Stern","doi":"10.1002/pmic.13979","DOIUrl":"https://doi.org/10.1002/pmic.13979","url":null,"abstract":"<p>The brain's extracellular matrix (ECM) is an intricate and dynamic network that plays essential roles in neurodevelopment, synaptic plasticity, and circuit stability. Despite its importance, the molecular composition and spatial organization of the developing brain ECM remain poorly characterized. In this commentary, we highlight the recent study by Vilicich et al., which employs a multi-modal approach, integrating single-cell transcriptomics, proteomics, and immunohistofluorescence, to construct a map of the ECM in the developing neocortex of humans and non-human primates. By curating a comprehensive list of extracellular proteins termed the “Exomatrix” and analyzing their distribution across cortical layers and developmental stages, the authors reveal layer-specific and evolutionarily conserved ECM features. These findings not only expand our understanding of ECM's role in shaping the brain during early development but also emphasize its potential involvement in the pathogenesis of neurodevelopmental disorders, urging further research into ECM biology as a frontier in neuroscience.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 14","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.13979","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144681213","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}

{"title":"Issue Information: Proteomics 14'25","authors":"","doi":"10.1002/pmic.70021","DOIUrl":"https://doi.org/10.1002/pmic.70021","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 14","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.70021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144681000","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}

{"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":"https://doi.org/10.1002/pmic.70005","url":null,"abstract":"<p><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. 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.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70005"},"PeriodicalIF":3.4,"publicationDate":"2025-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LC-MS/MS Characterization of SOBERANA 02, a Receptor Binding Domain-Tetanus Toxoid Conjugate Vaccine Against SARS-CoV-2","authors":"Olivia Martínez,&nbsp;Darielys Santana-Medero,&nbsp;Satomy Pousa,&nbsp;Jean Pierre Soubal,&nbsp;Arielis Rodríguez-Ulloa,&nbsp;Pablo E. Ramos-Bermúdez,&nbsp;Vladimir Besada,&nbsp;Raine Garrido,&nbsp;Paulo Carvalho,&nbsp;Michel Batista,&nbsp;Katharina Zetl,&nbsp;Jacek R. Wiśniewski,&nbsp;Tamy Boggiano,&nbsp;Yury Valdés-Balbín,&nbsp;Dagmar García-Rivera,&nbsp;Daniel G. Rivera,&nbsp;Vicente Verez-Bencomo,&nbsp;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, Cys⁵³⁸ 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 (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.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 14","pages":""},"PeriodicalIF":3.4,"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}

{"title":"Serum Proteome Profiling of Diabetic Patients Treated With DPP4 and SGLT2 Inhibitors Shows Improved Cognitive and Cardiovascular Functions","authors":"Md Abdul Hakim,&nbsp;Akeem Sanni,&nbsp;Shams T. Osman,&nbsp;Noha A. Hamdy,&nbsp;Waziha Tasnim Purba,&nbsp;Md Mostofa Al Amin Bhuiyan,&nbsp;Sherifdeen Onigbinde,&nbsp;Labiba K. El-Khordagui,&nbsp;Ahmed El-Yazbi,&nbsp;Yehia Mechref","doi":"10.1002/pmic.70000","DOIUrl":"10.1002/pmic.70000","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 &lt;p&gt;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.&lt;/p&gt;\u0000 &lt;p&gt;&lt;b&gt;Summary&lt;/b&gt;: 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.&lt;/p&gt;\u0000 &lt;p&gt;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.&lt;/p&gt;\u0000 &lt;p&gt;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.&lt;/p&gt;\u0000 &lt;p&gt;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":3.4,"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}

{"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":"https://doi.org/10.1002/pmic.70010","url":null,"abstract":"<p><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. SUMMARY: Proximity-dependent biotinylation (PDB) coupled with MS is a powerful approach to characterize subcellular protein localization. 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. 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. To date, there has been no systematic evaluation of this EvoSep-timsTOF instrumentation for PDB, nor a direct comparison to a previously standardized workflow. 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. The results highlight the necessity of optimization of scoring approaches for PDB alongside faster MS methods to maximize recovery of known high-confidence proximal interactors. Importantly, the EvoSep-timsTOF system substantially increases the effective throughput of MS acquisition, as washing between samples could be eliminated without compromising the recovery of bona fide proximal interactors, likely due to both carry-over reduction from both the EvoSep chromatography system and the decreased sample load.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70010"},"PeriodicalIF":3.4,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Issue Information: Proteomics 13ė25","authors":"","doi":"10.1002/pmic.70011","DOIUrl":"https://doi.org/10.1002/pmic.70011","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 13","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.70011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144598518","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}