IF 3.4 4区生物学

Proteomics Pub Date : 2024-11-18 DOI: 10.1002/pmic.202400072

Lucia Grenga, Magnus Øverlie Arntzen, Jean Armengaud

引用次数: 0

In-Depth Proteome Profiling of the Hippocampus of LDLR Knockout Mice Reveals Alternation in Synaptic Signaling Pathway. LDLR 基因敲除小鼠海马体的深度蛋白质组分析揭示了突触信号通路的交替。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-11-16 DOI: 10.1002/pmic.202400152

Hong-Beom Park, Hyeyoon Kim, Dohyun Han

{"title":"In-Depth Proteome Profiling of the Hippocampus of LDLR Knockout Mice Reveals Alternation in Synaptic Signaling Pathway.","authors":"Hong-Beom Park, Hyeyoon Kim, Dohyun Han","doi":"10.1002/pmic.202400152","DOIUrl":"https://doi.org/10.1002/pmic.202400152","url":null,"abstract":"The low-density lipoprotein receptor (LDLR) is a major apolipoprotein receptor that regulates cholesterol homeostasis. LDLR deficiency is associated with cognitive impairment by the induction of synaptopathy in the hippocampus. Despite the close relationship between LDLR and neurodegenerative disorders, proteomics research for protein profiling in the LDLR knockout (KO) model remains insufficient. Therefore, understanding LDLR KO-mediated differential protein expression within the hippocampus is crucial for elucidating a role of LDLR in neurodegenerative disorders. In this study, we conducted first-time proteomic profiling of hippocampus tissue from LDLR KO mice using tandem mass tag (TMT)-based MS analysis. LDLR deficiency induces changes in proteins associated with the transport of diverse molecules, and activity of kinase and catalyst within the hippocampus. Additionally, significant alterations in the expression of components in the major synaptic pathways were found. Furthermore, these synaptic effects were verified using a data-independent acquisition (DIA)-based proteomic method. Our data will serve as a valuable resource for further studies to discover the molecular function of LDLR in neurodegenerative disorders.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400152"},"PeriodicalIF":3.4,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643571","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}

引用次数: 0

Review and Practical Guide for Getting Started With Single-Cell Proteomics. 单细胞蛋白质组学入门回顾与实用指南》。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-11-16 DOI: 10.1002/pmic.202400021

Hsien-Jung L Lin, Kei G I Webber, Andikan J Nwosu, Ryan T Kelly

引用次数: 0

Parallel Analyses by Mass Spectrometry (MS) and Reverse Phase Protein Array (RPPA) Reveal Complementary Proteomic Profiles in Triple-Negative Breast Cancer (TNBC) Patient Tissues and Cell Cultures. 质谱法 (MS) 和反相蛋白质阵列 (RPPA) 的平行分析揭示了三阴性乳腺癌 (TNBC) 患者组织和细胞培养物中互补的蛋白质组图谱。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-11-16 DOI: 10.1002/pmic.202400107

Nan Wang, Yiying Zhu, Lianshui Wang, Wenshuang Dai, Taobo Hu, Zhentao Song, Xia Li, Qi Zhang, Jianfei Ma, Qianghua Xia, Jin Li, Yiqiang Liu, Mengping Long, Zhiyong Ding

{"title":"Parallel Analyses by Mass Spectrometry (MS) and Reverse Phase Protein Array (RPPA) Reveal Complementary Proteomic Profiles in Triple-Negative Breast Cancer (TNBC) Patient Tissues and Cell Cultures.","authors":"Nan Wang, Yiying Zhu, Lianshui Wang, Wenshuang Dai, Taobo Hu, Zhentao Song, Xia Li, Qi Zhang, Jianfei Ma, Qianghua Xia, Jin Li, Yiqiang Liu, Mengping Long, Zhiyong Ding","doi":"10.1002/pmic.202400107","DOIUrl":"https://doi.org/10.1002/pmic.202400107","url":null,"abstract":"High-plex proteomic technologies have made substantial contributions to mechanism studies and biomarker discovery in complex diseases, particularly cancer. Despite technological advancements, inherent limitations in individual proteomic approaches persist, impeding the achievement of comprehensive quantitative insights into the proteome. In this study, we employed two widely used proteomic technologies, mass spectrometry (MS) and reverse phase protein array (RPPA) to analyze identical samples, aiming to systematically assess the outcomes and performance of the different technologies. Additionally, we sought to establish an integrated workflow by combining these two proteomic approaches to augment the coverage of protein targets for discovery purposes. We used 14 fresh frozen tissue samples from triple-negative breast cancer (TNBC: seven tumors versus seven adjacent non-cancerous tissues) and cell line samples to evaluate both technologies and implement this dual-proteomic strategy. Using a single-step protein denaturation and extraction protocol, protein samples were subjected to reverse-phase liquid chromatography (LC) followed by electrospray ionization (ESI)-mediated MS/MS for proteomic profiling. Concurrently, identical sample aliquots were analyzed by RPPA for profiling of over 300 proteins and phosphoproteins that are in key signaling pathways or druggable targets in cancer. Both proteomic methods demonstrated the expected ability to differentiate samples by groups, revealing distinct proteomic patterns under various experimental conditions, albeit with minimal overlap in identified targets. Mechanism-based analysis uncovered divergent biological processes identified with the two proteomic technologies, capitalizing on their complementary exploratory potential.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400107"},"PeriodicalIF":3.4,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643572","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}

引用次数: 0

Omics Studies in CKD: Diagnostic Opportunities and Therapeutic Potential. 慢性肾脏病的分子生物学研究：诊断机会和治疗潜力。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-11-11 DOI: 10.1002/pmic.202400151

Merita Rroji, Goce Spasovski

引用次数: 0

Transforming peptide hormone prediction: The role of AI in modern proteomics. 转化肽类激素预测：人工智能在现代蛋白质组学中的作用。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-11-07 DOI: 10.1002/pmic.202400156

Nguyen Quoc Khanh Le

引用次数: 0

Proteome integral solubility alteration via label-free DIA approach (PISA-DIA), game changer in drug target deconvolution. 通过无标记 DIA 方法改变蛋白质组整体溶解度（PISA-DIA），改变药物靶点解旋的游戏规则。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-11-07 DOI: 10.1002/pmic.202400147

Zheng Ser, Radoslaw M Sobota

{"title":"Proteome integral solubility alteration via label-free DIA approach (PISA-DIA), game changer in drug target deconvolution.","authors":"Zheng Ser, Radoslaw M Sobota","doi":"10.1002/pmic.202400147","DOIUrl":"https://doi.org/10.1002/pmic.202400147","url":null,"abstract":"Drug protein-target identification in past decades required screening compound libraries against known proteins to determine drugs binding to specific protein. Protein targets used in drug-target screening were selected predominantly used laborious genetic manipulation assays. In 2013, a team led by Pär Nordlund from Karolinska Institutet (Stockholm, Sweden) developed Cellular Thermal Shift Assay (CETSA), a method which, for the first time, enabled the possibility of drug protein-target identification in the complex cellular proteome. High throughput, quantitative mass spectrometry (MS) proteomics appeared as a compatible analytical method of choice to complement CETSA, aka Thermal Protein Profiling assay (TPP). Since the seminal CETSA-MS/ TPP-MS publications, different protein-target deconvolution strategies emerged including Proteome Integral Solubility Alteration (PISA). The work of Emery-Corbin et al. (Proteomics 2024, 2300644), titled Proteome Integral Solubility Alteration via label-free DIA approach (PISA-DIA), introduces Data-Independent Acquisition (DIA) as a quantification method, opening new avenues in drug target-deconvolution field. Application of DIA for target deconvolution offers attractive alternative to widely used data dependent methodology.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e2400147"},"PeriodicalIF":3.4,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602743","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}

引用次数: 0

Integrative Proteomic and Phosphoproteomic Profiling Reveals the Salt-Responsive Mechanisms in Two Rice Varieties (Oryza Sativa subsp. Japonica and Indica). 综合蛋白质组和磷酸蛋白质组分析揭示了两个水稻品种（Oryza Sativa subsp.）

IF 3.4 4区生物学

Proteomics Pub Date : 2024-11-03 DOI: 10.1002/pmic.202400251

Cheol Woo Min, Ravi Gupta, Gi Hyun Lee, Jun-Hyeon Cho, Yu-Jin Kim, Yiming Wang, Ki-Hong Jung, Sun Tae Kim

{"title":"Integrative Proteomic and Phosphoproteomic Profiling Reveals the Salt-Responsive Mechanisms in Two Rice Varieties (Oryza Sativa subsp. Japonica and Indica).","authors":"Cheol Woo Min, Ravi Gupta, Gi Hyun Lee, Jun-Hyeon Cho, Yu-Jin Kim, Yiming Wang, Ki-Hong Jung, Sun Tae Kim","doi":"10.1002/pmic.202400251","DOIUrl":"https://doi.org/10.1002/pmic.202400251","url":null,"abstract":"Salinity stress induces ionic and osmotic imbalances in rice plants that in turn negatively affect the photosynthesis rate, resulting in growth retardation and yield penalty. Efforts have, therefore, been carried out to understand the mechanism of salt tolerance, however, the complexity of biological processes at proteome levels remains a major challenge. Here, we performed a comparative proteome and phosphoproteome profiling of microsome enriched fractions of salt-tolerant (cv. IR73; indica) and salt-susceptible (cv. Dongjin/DJ; japonica) rice varieties. This approach led to the identification of 5856 proteins, of which 473 and 484 proteins showed differential modulation between DJ and IR73 sample sets, respectively. The phosphoproteome analysis led to the identification of a total of 10,873 phosphopeptides of which 2929 and 3049 phosphopeptides showed significant differences in DJ and IR73 sample sets, respectively. The integration of proteome and phosphoproteome data showed activation of ABA and Ca2+ signaling components exclusively in the salt-tolerant variety IR73 in response to salinity stress. Taken together, our results highlight the changes at proteome and phosphoproteome levels and provide a mechanistic understanding of salinity stress tolerance in rice.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400251"},"PeriodicalIF":3.4,"publicationDate":"2024-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567149","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}

引用次数: 0

Filling the gaps in peptide maps with a platform assay for top-down characterization of purified protein samples. 利用自上而下表征纯化蛋白质样品的平台测定法填补肽图空白。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-11-01 Epub Date: 2024-07-14 DOI: 10.1002/pmic.202400036

Aaron O Bailey, Kenneth R Durbin, Matthew T Robey, Lee K Palmer, William K Russell

{"title":"Filling the gaps in peptide maps with a platform assay for top-down characterization of purified protein samples.","authors":"Aaron O Bailey, Kenneth R Durbin, Matthew T Robey, Lee K Palmer, William K Russell","doi":"10.1002/pmic.202400036","DOIUrl":"10.1002/pmic.202400036","url":null,"abstract":"Liquid chromatography-mass spectrometry (LC-MS) intact mass analysis and LC-MS/MS peptide mapping are decisional assays for developing biological drugs and other commercial protein products. Certain PTM types, such as truncation and oxidation, increase the difficulty of precise proteoform characterization owing to inherent limitations in peptide and intact protein analyses. Top-down MS (TDMS) can resolve this ambiguity via fragmentation of specific proteoforms. We leveraged the strengths of flow-programmed (fp) denaturing online buffer exchange (dOBE) chromatography, including robust automation, relatively high ESI sensitivity, and long MS/MS window time, to support a TDMS platform for industrial protein characterization. We tested data-dependent (DDA) and targeted strategies using 14 different MS/MS scan types featuring combinations of collisional- and electron-based fragmentation as well as proton transfer charge reduction. This large, focused dataset was processed using a new software platform, named TDAcquireX, that improves proteoform characterization through TDMS data aggregation. A DDA-based workflow provided objective identification of αLac truncation proteoforms with a two-termini clipping search. A targeted TDMS workflow facilitated the characterization of αLac oxidation positional isomers. This strategy relied on using sliding window-based fragment ion deconvolution to generate composite proteoform spectral match (cPrSM) results amenable to fragment noise filtering, which is a fundamental enhancement relevant to TDMS applications generally.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e2400036"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141615392","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}

引用次数: 0

Automated multiplexed affinity-based enrichment of peptides for LC-MS/MS plasma proteomics. 用于 LC-MS/MS 血浆蛋白质组学的基于亲和力的多肽自动复用富集。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-11-01 Epub Date: 2024-08-27 DOI: 10.1002/pmic.202400049

Sergio Mosquim Junior, Fredrik Levander

{"title":"Automated multiplexed affinity-based enrichment of peptides for LC-MS/MS plasma proteomics.","authors":"Sergio Mosquim Junior, Fredrik Levander","doi":"10.1002/pmic.202400049","DOIUrl":"10.1002/pmic.202400049","url":null,"abstract":"Plasma proteomics offers high potential for biomarker discovery, as plasma is collected through a minimally invasive procedure and constitutes the most complex human-derived proteome. However, the wide dynamic range poses a significant challenge. Here, we propose a semi-automated method based on the use of multiple single chain variable fragment antibodies, each enriching for peptides found in up to a few hundred proteins. This approach allows for the analysis of a complementary fraction compared to full proteome analysis. Proteins from pooled plasma were extracted and digested before testing the performance of 29 different antibodies with the aim of reproducibly maximizing peptide enrichment. Our results demonstrate the enrichment of 3662 peptides not detected in neat plasma or negative controls. Moreover, most antibodies were able to enrich for at least 155 peptides across different levels of abundance in plasma. To further reduce analysis time, a combination of antibodies was used in a multiplexed setting. Repeated sample analyses showed low coefficients of variation, and the method is flexible in terms of affinity binders. It does not impose drastic increases in instrument time, thus showing excellent potential for usage in large scale discovery projects.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e2400049"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142078670","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}

引用次数: 0

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