Journal of Proteome Research最新文献_第6页

Enhancing Tandem MS Sensitivity and Peptide Identification via Ion Preaccumulation in an Orbitrap Mass Spectrometer. 轨道阱质谱仪离子预积累法提高串联质谱灵敏度及多肽鉴定。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-06-30 DOI: 10.1021/acs.jproteome.5c00186

Florian Harking, Ulises H Guzman, Julia Kraegenbring, Hamish Stewart, Konstantin Aizikov, Heiner Koch, Kyle L Fort, Alexander Harder, Jesper V Olsen

{"title":"Enhancing Tandem MS Sensitivity and Peptide Identification via Ion Preaccumulation in an Orbitrap Mass Spectrometer.","authors":"Florian Harking, Ulises H Guzman, Julia Kraegenbring, Hamish Stewart, Konstantin Aizikov, Heiner Koch, Kyle L Fort, Alexander Harder, Jesper V Olsen","doi":"10.1021/acs.jproteome.5c00186","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00186","url":null,"abstract":"High-throughput mass spectrometry-based proteomics has gained increasing interest for both academic and industrial applications. As implementation of faster gradients has facilitated higher sample throughput, mass spectrometers must adapt to shorter analysis times by enhancing the scanning speed and sensitivity. For Orbitrap mass spectrometers, faster scan rates are constrained by the need for sufficient ion accumulation time, particularly given the limitations on the duty cycle at high repetition rates, and transient length, which determines analyzer sensitivity and resolving power. In this context, implementing alternative ion scheduling and better ion signal-processing strategies is needed to unleash the speed of these instruments. Here, we introduce a new scanning strategy termed preaccumulation, which enables the storage of ions in the bent flatapole in parallel to the operation of the C-trap/IRM, leading to a significant improvement in ion beam utilization and enabling for the first time scanning speeds of ∼70 Hz on hybrid Orbitrap instruments. The combination of preaccumulation and increased scan speeds notably enhances peptide and protein group identifications for short LC gradients and improves sensitivity for high-throughput applications. These benefits were further amplified when coupled with the full mass range phase-constrained spectrum deconvolution method (ΦSDM), especially for fast, lower-resolution Orbitrap measurements with short LC gradients. Overall, we demonstrate that preaccumulation of ions in the bent flatapole offers distinct advantages, particularly for conditions with reduced signal input. Since no hardware changes are required, this approach is highly attractive for Orbitrap mass spectrometers operated with fast MS/MS acquisition methods.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteomic Analysis of FFPE Tissue Samples Identifies Potential Molecular Mechanisms Mediating Resistance to Radiotherapy in Rectal Cancer. FFPE组织样本的蛋白质组学分析确定了直肠癌放射治疗耐药的潜在分子机制。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-06-26 DOI: 10.1021/acs.jproteome.5c00114

Tobias Zott, Michael Wolf, Günter Plessl-Walder, Heinz Regele, Michael Bergmann, Samuel M Meier-Menches, Christopher Gerner, Gerd R Silberhumer, Andrea Bileck

{"title":"Proteomic Analysis of FFPE Tissue Samples Identifies Potential Molecular Mechanisms Mediating Resistance to Radiotherapy in Rectal Cancer.","authors":"Tobias Zott, Michael Wolf, Günter Plessl-Walder, Heinz Regele, Michael Bergmann, Samuel M Meier-Menches, Christopher Gerner, Gerd R Silberhumer, Andrea Bileck","doi":"10.1021/acs.jproteome.5c00114","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00114","url":null,"abstract":"Chemoradiation prior to surgery in locally advanced rectal cancer is the current standard therapy but is not effective in all rectal cancer patients. Prognostic markers supporting patient stratification with respect to clinical response would therefore be desirable. The aim of this study was to investigate pathophysiological mechanisms underlying radioresistance and to identify potential prognostic markers by comparative proteome profiling. Therefore, formalin fixed paraffin-embedded tissue (FFPE) samples from rectal tumors (n = 50) and normal control tissue (n = 39) of nonresponders and responders to neoadjuvant chemoradiation were analyzed. As a result, 1685 robustly identified proteins were further evaluated. Comparing tumor with corresponding control samples revealed 221 differentially expressed proteins (FDR < 0.05) with FTL, PCOLCE, and RCN3 being most striking in tumor tissue. CEACAM 1, 5, and 6, as well as MCM protein complex components, were significantly up-regulated in tumor tissue of nonresponders. The autophagic activity-related and DNA damage repair proteins TOM1, CAPNS1, TP53BP1, HS1BP3, as well as COTL1 and DCPS, discriminated non- and nearly complete from complete responders. In the tumor-surrounding tissue of nonresponders, the innate immune response-suppressing protein CD55 was found specifically up-regulated. These proteins may serve as prognostic markers and potential therapeutic targets, requiring further validation in prospective studies.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantitative Proteomic Analysis Reveals JMJD6 and DNAJB11 as Endogenous Substrates of E3 Ligase RFFL. 定量蛋白质组学分析显示JMJD6和DNAJB11是E3连接酶RFFL的内源性底物。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-06-26 DOI: 10.1021/acs.jproteome.5c00086

Nikhil Dev Narendradev, Soumitra Marathe, Sabyasachi Baboo, Daniel B McClatchy, Jolene K Diedrich, Parul Jain, Rahul Purwar, John R Yates, Srinivasa Murty Srinivasula

{"title":"Quantitative Proteomic Analysis Reveals JMJD6 and DNAJB11 as Endogenous Substrates of E3 Ligase RFFL.","authors":"Nikhil Dev Narendradev, Soumitra Marathe, Sabyasachi Baboo, Daniel B McClatchy, Jolene K Diedrich, Parul Jain, Rahul Purwar, John R Yates, Srinivasa Murty Srinivasula","doi":"10.1021/acs.jproteome.5c00086","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00086","url":null,"abstract":"The ubiquitin-proteasome system contributes to protein quality control, involving E3 ligases that ubiquitinate proteins and leading to their degradation. The dysregulation of protein degradation results in the abnormal accumulation of proteins and is implicated in the pathology of diverse diseases, making targeted protein degradation a promising therapeutic strategy. Here, we focus on RFFL, an endosome-associated RING E3 ligase involved in mitochondrial homeostasis and the clearance of misfolded cystic fibrosis transmembrane conductance regulator proteins. Using label-free quantitative mass spectrometry based proteomics for interactome and differential expression analyses, we systematically investigated and identified putative substrates of RFFL. For more confident identification, we performed these analyses on three cell lines that we generated: an RFFL knockout cell line generated using CRISPR/Cas9, another cell line rescuing RFFL expression when complemented with KO cells with stably expressing RFFL cDNA, and wild-type cells. We validated JMJD6 and DNAJB11 as substrates of endogenous RFFL, providing orthogonal validation and confidence in our screening approach. We demonstrated that RFFL ubiquitinates and degrades JMJD6 and DNAJB11 via the proteasomal pathway using in vivo assays. Interestingly, we also discovered a hitherto unknown role of RFFL in lipid metabolism. Collectively, this study provides the first comprehensive and unbiased analysis of RFFL substrates employing multiple complementary approaches.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144493171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

New Application of Histological Staining for Visualization of Endogenous Proteins in Fossil Material. 组织学染色在化石材料内源蛋白可视化中的新应用。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-06-25 DOI: 10.1021/acs.jproteome.5c00078

Hayato Inaba, Kentaro Chiba, Mototaka Saneyoshi, Takaaki Miyaji, Asako Kawakami, Noriyuki Nagaoka, Yasushi Takechi, Kiyofumi Takabatake, Kirstin S Brink, Miu Tanaka, Masaki Eda, Yoshitsugu Kobayashi, Hidetsugu Tsujigiwa

{"title":"New Application of Histological Staining for Visualization of Endogenous Proteins in Fossil Material.","authors":"Hayato Inaba, Kentaro Chiba, Mototaka Saneyoshi, Takaaki Miyaji, Asako Kawakami, Noriyuki Nagaoka, Yasushi Takechi, Kiyofumi Takabatake, Kirstin S Brink, Miu Tanaka, Masaki Eda, Yoshitsugu Kobayashi, Hidetsugu Tsujigiwa","doi":"10.1021/acs.jproteome.5c00078","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00078","url":null,"abstract":"Biochemical applications are increasingly utilized in paleontological studies, especially for detecting ancient proteins in fossil samples. Histopathological staining techniques have been applied, but they have yet to specifically target type I collagen, the primary bone matrix protein and the most significant protein of interest in paleoproteomic research. Moreover, these staining methods are often applied to demineralized fossils, which remove the original microstructure of the bone matrix and increase the risk of contamination. To address these limitations, this study aimed to test the effectiveness of special staining methods for detecting collagen using Pleistocene-aged fossil specimens. Trials on demineralized and nondemineralized modern bone samples, as well as nondemineralized fossil samples, demonstrated Van Gieson's staining method as the most suitable for visualizing collagen distribution in hard tissue matrices. Colorimetric analysis, electrophoresis, and subsequent mass spectrometry of extracts further confirmed the endogenous nature of the collagen in the fossil samples. Future studies may benefit from employing Van Gieson's staining on nondemineralized bone samples to detect collagen in fossils, advancing our understanding of ancient protein preservation.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144482566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Novel Strategy to Rapidly Profile and Quantify High-Risk Host Cell Proteins Using Integrated DDA-PRM-dMRM Mode. 利用DDA-PRM-dMRM集成模式快速分析和量化高危宿主细胞蛋白的新策略。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-06-25 DOI: 10.1021/acs.jproteome.5c00369

Xuan Xu, Lan Wang, Gang Wu, Shengyuan Xu, Yang Li, Ning Sheng, Jinlan Zhang

{"title":"A Novel Strategy to Rapidly Profile and Quantify High-Risk Host Cell Proteins Using Integrated DDA-PRM-dMRM Mode.","authors":"Xuan Xu, Lan Wang, Gang Wu, Shengyuan Xu, Yang Li, Ning Sheng, Jinlan Zhang","doi":"10.1021/acs.jproteome.5c00369","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00369","url":null,"abstract":"Host cell proteins (HCPs) are critical process-related impurities in biotherapeutics that threaten drug stability and safety. The substantial dynamic range (>5 orders of magnitude) between therapeutic proteins and residual HCPs often leads to difficulty in detecting high-risk species. Herein, we developed a novel strategy integrating data-dependent acquisition (DDA), parallel reaction monitoring (PRM), and multiple reaction monitoring (MRM) techniques to comprehensively profile and accurately quantify high-risk HCPs. We constructed a Chinese hamster ovary (CHO) cell spectral library by DDA that covers all potential HCPs present in downstream purification processes. Based on the constructed library, 38 reported high-risk HCPs were focused and their unique peptides and transitions were predicted. PRM and MRM were performed to cross-validate the existing high-risk HCPs in CHO cell samples, and 28 high-risk HCPs with 47 peptides and 141 transitions were validated. A new dynamic MRM (dMRM) method was established and validated to simultaneously quantify 28 high-risk HCPs. We applied this strategy to analyze five purified monoclonal antibody process samples, using the DDA method for comprehensive profiling of unknown HCPs and the dMRM method for rapid quantification of 28 known high-risk HCPs. Overall, this strategy enables thorough analysis of known and unknown HCPs, optimizing biopharmaceutical process development.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144493170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrated Physical and Proteomic Approaches Dissect the Effect of Leather Degradation by Bacteria. 综合物理和蛋白质组学方法剖析了细菌对皮革降解的影响。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-06-25 DOI: 10.1021/acs.jproteome.5c00090

Qingyu Lu, Nan Jiang, Lei Cai, Yu Wang, Hailiang Yang, Jiao Pan, Yanan Wang, Yang Zhou, Huabing Wang

{"title":"Integrated Physical and Proteomic Approaches Dissect the Effect of Leather Degradation by Bacteria.","authors":"Qingyu Lu, Nan Jiang, Lei Cai, Yu Wang, Hailiang Yang, Jiao Pan, Yanan Wang, Yang Zhou, Huabing Wang","doi":"10.1021/acs.jproteome.5c00090","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00090","url":null,"abstract":"Landfills and incineration of leather wastes cause serious environmental pollution. In contrast, leather biodegradation by microbes is an environmentally friendly option for the disposal of leather. However, the microbial degradation mechanism is not fully understood. In this study, Bacillus licheniformis (Gram-positive bacterium) and Pseudomonas putida (Gram-negative bacterium) were isolated from leather artifacts. The effects of leather degradation by these two bacteria were systematically investigated. P. putida and B. licheniformis destroyed the morphology of the leather and caused obvious color aberration by darkening, greening, and bluing the leather. The tensile strength of sheep leather was significantly damaged by B. licheniformis. P. putida and B. licheniformis altered the elemental contents and disrupted the collagen structure of cow and sheep leathers to varying degrees. Proteomic profiling revealed a significant depletion of structural proteins in cow and sheep leather substrates mediated by B. licheniformis, including collagen alpha-1(II) chain, collagen type VI, and fibrillar collagen. In contrast, many proteases and peptidases of B. licheniformis were increased, such as acylaminoacyl peptidase, aminopeptidase, and carboxypeptidase, suggesting that these enzymes contribute to the degradation of leather proteins. These findings highlighted that B. licheniformis can effectively degrade leather by secreting proteases and peptidases. This study provided new insights into the conservation and biodegradation of leather, which will contribute to green development of the leather industry.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144482565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Lipidomic Network Analysis Reveals Amyloid-β-Induced Lysosomal Lipid Accumulation in the Cortex and Hippocampus of 5xFAD Mice. 脂质组学网络分析揭示淀粉样蛋白β在5xFAD小鼠皮层和海马中诱导溶酶体脂质积累。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-06-24 DOI: 10.1021/acs.jproteome.4c01133

Yun Jae Cha, Young-Kwang Kim, Yun Ji Lim, Chan Ho Kim, Se Eun Park, Yun Pyo Kang, Min-Kyoo Shin

{"title":"Lipidomic Network Analysis Reveals Amyloid-β-Induced Lysosomal Lipid Accumulation in the Cortex and Hippocampus of 5xFAD Mice.","authors":"Yun Jae Cha, Young-Kwang Kim, Yun Ji Lim, Chan Ho Kim, Se Eun Park, Yun Pyo Kang, Min-Kyoo Shin","doi":"10.1021/acs.jproteome.4c01133","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01133","url":null,"abstract":"The 5xFAD mouse model serves as a valuable experimental system for investigating Alzheimer's disease (AD), specifically amyloid-beta (Aβ)-induced AD pathology. In this study, we explored temporal, regional, and sex-specific alternations in the lipidome within the cortex and hippocampus of 5xFAD mice. Our results revealed that lipid alternations become more pronounced with the progression of Aβ pathology in the cerebral cortex and hippocampus. These lipid changes were also more significant in the female mice, which exhibited more severe Aβ pathology than male mice. Through lipid network analysis, we identified AD-specific lipid coexpression network modules in both brain regions, marked by enriched lysosomal lipids such as BMP and GM3. Notably, this lipid profile was also observed in microglia cells overexpressing the Swedish mutant form of Aβ precursor protein (APPswe). Given the critical role of BMP in lysosomal lipid and membrane degradation, and the observed enhancement of GM3 accumulation under lysosomal inhibition in APPswe-transfected microglial cells, these findings suggest that Aβ-mediated microglial lysosomal dysfunction may contribute to AD progression. Overall, we discovered a previously unrecognized role of Aβ in dysregulating lysosomal lipid metabolism and highlighted the utility of lipidomics and network analysis as complementary approaches for elucidating disease mechanisms.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantitative Proteomic and Metabolomic Profiling Reveals Altered Purine Metabolism in Acute Kidney Injury after On-Pump Coronary Artery Bypass Graft. 定量蛋白质组学和代谢组学分析揭示无泵冠状动脉搭桥术后急性肾损伤中嘌呤代谢的改变。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-06-23 DOI: 10.1021/acs.jproteome.5c00113

Mindi Zhao, Xiaoyan Liu, Huawei Gao, Quaner Wang, Zhengguang Guo, Yan Yang, Meice Tian, Xianqiang Wang, Liqing Wang, Wei Sun, Chuanbao Li

{"title":"Quantitative Proteomic and Metabolomic Profiling Reveals Altered Purine Metabolism in Acute Kidney Injury after On-Pump Coronary Artery Bypass Graft.","authors":"Mindi Zhao, Xiaoyan Liu, Huawei Gao, Quaner Wang, Zhengguang Guo, Yan Yang, Meice Tian, Xianqiang Wang, Liqing Wang, Wei Sun, Chuanbao Li","doi":"10.1021/acs.jproteome.5c00113","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00113","url":null,"abstract":"Acute kidney injury (AKI) is a frequent complication following on-pump coronary artery bypass graft surgery (CABG). To better investigate the effect of CABG on kidney function and the pathological process of AKI during the operation, the urine metabolic and protein signatures of four time points in 55 postoperative AKI and 104 non-AKI patients after CABG were analyzed by using high-resolution tandem mass spectrometry combined with pattern recognition and functional annotation. In the longitudinal urinary metabolomics study, the protein catabolism pathway is prominent in AKI patients throughout the surgery and recovery process. The integration of metabolomic and proteomic data revealed that alterations in purine metabolism exhibited significant differences preoperatively between the AKI and the non-AKI cohorts. A panel of two proteins (ARFIP1 and SOD2) and two metabolites (tyrosyl-γ-glutamate and l-methionine) was discovered to have a good predicting performance (area under the curve, 0.92) in the preoperative urine. Our research suggests that the panel could play a significant role in distinguishing AKIs from non-AKIs prior to surgery. We propose targeting purine metabolism pathways that may help to identify potential renal protective approaches in acute kidney injury. This study helps to reveal changes in urinary metabolomics and proteomics after CABG and may provide diagnostic clues for patients with postoperative renal injury.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Comparative Proteomics Study of Autopsy and Fresh-Frozen Coronary Artery Samples. 解剖和新鲜冷冻冠状动脉样本的蛋白质组学比较研究。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-06-23 DOI: 10.1021/acs.jproteome.5c00152

Xiaoke Yin PhD, Alicia Beele MSc, Konstantinos Theofilatos PhD, Ferheen Baig PhD, Maria Hasman PhD, Lukas E Schmidt MSc, Joseph J Boyle PhD, Adam W Turner PhD, Clint L Miller PhD, Gerard Pasterkamp Md, Stefan Stojkovic Md PhD, Johann Wojta PhD, Michael Joner Md, Manuel Mayr Md PhD

{"title":"A Comparative Proteomics Study of Autopsy and Fresh-Frozen Coronary Artery Samples.","authors":"Xiaoke Yin PhD, Alicia Beele MSc, Konstantinos Theofilatos PhD, Ferheen Baig PhD, Maria Hasman PhD, Lukas E Schmidt MSc, Joseph J Boyle PhD, Adam W Turner PhD, Clint L Miller PhD, Gerard Pasterkamp Md, Stefan Stojkovic Md PhD, Johann Wojta PhD, Michael Joner Md, Manuel Mayr Md PhD","doi":"10.1021/acs.jproteome.5c00152","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00152","url":null,"abstract":"Proteomic analyses of human tissues are often conducted on autopsy samples. However, no detailed comparative analysis between proteomic changes derived from autopsy samples and fresh-frozen samples has been undertaken. In this study, human left anterior descending (LAD) coronary artery samples (n = 94) from deceased patients were analyzed using nanoflow LC-MS/MS. Among consistently quantified proteins, 37% of the protein abundances exhibited significant correlations with the post-mortem interval (PMI), most of which are inverse. Notably, smooth muscle cell markers displayed substantial reduction with prolonged PMI. Conversely, positive correlations were observed for immunoglobulins, coagulation factors, and complement factors, including coagulation factor XII, plasminogen, and lactotransferrin. Comparative analyses of sex-specific protein changes in autopsy LAD samples versus fresh-frozen LAD samples (n = 65) showed no concordance. However, a robust correlation was observed between 2 different cohorts of fresh-frozen carotid endarterectomies (n = 120 and n = 200). This study represents the first large-scale proteomics investigation into the influence of PMI on the protein composition of the human vasculature, showing significant correlations with PMI for 37% of the quantified proteins. Our findings underscore potential discrepancies in the quantitative accuracy of proteomics data derived from autopsy samples. Consequently, results obtained from post-mortem specimens may not be reproducible in fresh-frozen samples.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrated Single-Tip IMAC-HILIC Enables Simultaneous Analysis of Plant Phosphoproteomics and N-Glycoproteomics. 集成的单端IMAC-HILIC可以同时分析植物磷蛋白质组学和n -糖蛋白质组学。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-06-23 DOI: 10.1021/acs.jproteome.5c00185

Chin-Wen Chen, Ting-An Chen, Pei-Yi Lin, Shu-Yu Lin, Chuan-Chih Hsu

{"title":"Integrated Single-Tip IMAC-HILIC Enables Simultaneous Analysis of Plant Phosphoproteomics and N-Glycoproteomics.","authors":"Chin-Wen Chen, Ting-An Chen, Pei-Yi Lin, Shu-Yu Lin, Chuan-Chih Hsu","doi":"10.1021/acs.jproteome.5c00185","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00185","url":null,"abstract":"Protein phosphorylation and N-glycosylation are key post-translational modifications (PTMs) in plants that regulate critical signaling processes. However, coanalysis of these PTMs is often complicated by their relatively low abundance and divergent enrichment requirements. Here, we present a single-tip IMAC-HILIC approach that integrates immobilized metal affinity chromatography (IMAC) and hydrophilic interaction chromatography (HILIC) materials within one pipet tip, enabling concurrent enrichment and sequential elution of phosphopeptides and N-glycopeptides. This integrated workflow effectively reduces phosphopeptide coelution during N-glycopeptide elution and streamlines sample processing. In direct comparison with the tandem-tip TIMAHAC method, our single-tip strategy achieves a comparable identification depth and offers superior quantitative accuracy for N-glycopeptides. We further demonstrate its applicability by examining the impact of calcium deprivation in Arabidopsis, revealing distinct global changes in both the phosphoproteome and N-glycoproteome. Our optimized protocol thus provides a straightforward and high-throughput platform for dual PTM profiling in complex plant samples, paving the way for broader investigations of PTM crosstalk in diverse physiological and stress responses.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0