IF 3.4 4区生物学

Proteomics Pub Date : 2025-05-27 DOI: 10.1002/pmic.202400135

Riste Stojanov, Milos Jovanovik, Sasho Gramatikov, Igor Mishkovski, Eftim Zdravevski, Darko Sasanski, Zorica Karapancheva, Goce Spasovski, Ivona Vasileska, Tome Eftimov, Wu Zhuojun, Joachim Jankowski, Dimitar Trajanov

{"title":"Applicability Assessment of Technologies for Predictive and Prescriptive Analytics of Nephrology Big Data.","authors":"Riste Stojanov, Milos Jovanovik, Sasho Gramatikov, Igor Mishkovski, Eftim Zdravevski, Darko Sasanski, Zorica Karapancheva, Goce Spasovski, Ivona Vasileska, Tome Eftimov, Wu Zhuojun, Joachim Jankowski, Dimitar Trajanov","doi":"10.1002/pmic.202400135","DOIUrl":"https://doi.org/10.1002/pmic.202400135","url":null,"abstract":"The integration of big data into nephrology research will open new avenues for analyzing and understanding complex biological datasets, driving advances in personalized management of kidney diseases. This paper describes the multifaceted challenges and opportunities by incorporating big data in nephrology, emphasizing the importance of data standardization, advanced storage solutions, and advanced analytical methods. We discuss the role of data science workflows, including data collection, preprocessing, integration, and analysis, in facilitating comprehensive insights into disease mechanisms and patient outcomes. Furthermore, we highlight predictive and prescriptive analytics, as well as the application of large language models (LLMs) in improving clinical decision-making and enhancing the accuracy of disease predictions. The use of high-performance computing (HPC) is also examined, showcasing its role in processing large-scale datasets and accelerating machine learning algorithms. Through this exploration, we aim to provide a comprehensive overview of the current state and future directions of big data analytics in nephrology, with a focus on enhancing patient care and advancing medical research.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400135"},"PeriodicalIF":3.4,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144148882","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

Establishment of a Protocol for CE-MS Based Peptidome Analysis of Human Saliva. 基于CE-MS的人唾液肽球分析方案的建立。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-05-27 DOI: 10.1002/pmic.202400231

Carl-Johan Törnhage, Björn Peters, Agnieszka Latosinska, Ioanna K Mina, Marika Mokou, Harald Mischak, Justyna Siwy

{"title":"Establishment of a Protocol for CE-MS Based Peptidome Analysis of Human Saliva.","authors":"Carl-Johan Törnhage, Björn Peters, Agnieszka Latosinska, Ioanna K Mina, Marika Mokou, Harald Mischak, Justyna Siwy","doi":"10.1002/pmic.202400231","DOIUrl":"https://doi.org/10.1002/pmic.202400231","url":null,"abstract":"Proteins and peptides indicate physiological or pathological states and are investigated to identify markers to scrutinize health and disease surveillance. Saliva contains many proteins and peptides that could serve as biomarkers, offering a potential noninvasive approach for disease detection. To enable the assessment of the saliva proteome and peptidome as sources of biomarkers, protocols for sampling, sample preparation, and measurements have to be developed. We present the results of peptidome analysis from saliva samples collected at different time points before and after breakfast from 14 healthy adults (50% male, mean age 42.7 ± 10.3 years). While similar methods have been previously applied to urine, our aim was to adapt and demonstrate the effectiveness of these protocols for saliva. Specifically, we aimed to establish a salivary peptide dataspace, including peptide amino acid sequences, and to evaluate the impact of food intake and time of sampling. Capillary electrophoresis-mass spectrometry (CE-MS) and CE-MS/MS were used for peptidome analysis. Per sample, 3147 ± 559 peptides were detectable, without significant differences in the number of detected peptides between sample collection times. However, some peptides differed significantly in their abundance between samples collected before breakfast and 1, 2 and 4 h after breakfast. Samples collected after breakfast were more consistent in their peptide content. Sequencing identified 630 peptides, fragments of 82 proteins, with the majority derived from proline-rich proteins. The data indicate that saliva for peptidomics is best collected 1 to 4 h after breakfast.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e00231"},"PeriodicalIF":3.4,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144148885","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

Meeting Report: The Japanese-German Symposium on the "Advancement and Application of Proteoform-Centric Proteomics" (Kyoto, Japan, 2024). 会议报告：日德“以蛋白质形态为中心的蛋白质组学进展与应用”研讨会（日本京都，2024）。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-05-20 DOI: 10.1002/pmic.202400394

Nobuaki Takemori, Philipp T Kaulich, Jan Hahn, Hartmut Schlüter, Naoyuki Sugiyama, Kazuya Tsumagari, Yasushi Ishihama, Sabine Fuchs, Mio Iwasaki, Franz-Josef Müller, Christian Neusüß, Kyowon Jeong, Oliver Kohlbacher, Yoshihiro Shimizu, Yoichi Otsuka, Hisako Sato, Kazuki Sasaki, Yuriko Minegishi, Yoshio Kodera, Irene Fernandez-Cuesta, Boris Krichel, Norie Araki, Andreas Tholey

引用次数: 0

From Discovery to Implementation: Bringing Proteomics to the Clinic. 从发现到实施：将蛋白质组学带入临床。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-05-20 DOI: 10.1002/pmic.202500017

Agnieszka Latosinska, Harald Mischak, Antonia Vlahou

引用次数: 0

Contents: Proteomics 9–10'25

IF 3.4 4区生物学

Proteomics Pub Date : 2025-05-14 DOI: 10.1002/pmic.202570033

引用次数: 0

Editorial Board: Proteomics 9–10'25

IF 3.4 4区生物学

Proteomics Pub Date : 2025-05-14 DOI: 10.1002/pmic.202570032

引用次数: 0

Data-Driven Proteomics for Post-Translational Modification Discovery

IF 3.4 4区生物学

Proteomics Pub Date : 2025-05-14 DOI: 10.1002/pmic.202500064

Van-Nui Nguyen, Nguyen Quoc Khanh Le

引用次数: 0

Comparative Analysis of the Progesterone Receptor Interactome in the Human Ovarian Granulosa Cell Line KGN and Other Female Reproductive Cells. 人卵巢颗粒细胞系KGN与其他女性生殖细胞中孕激素受体相互作用组的比较分析。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-05-13 DOI: 10.1002/pmic.202400374

Natalie J Foot, Doan T Dinh, Samantha J Emery-Corbin, Jumana M Yousef, Laura F Dagley, Darryl L Russell

{"title":"Comparative Analysis of the Progesterone Receptor Interactome in the Human Ovarian Granulosa Cell Line KGN and Other Female Reproductive Cells.","authors":"Natalie J Foot, Doan T Dinh, Samantha J Emery-Corbin, Jumana M Yousef, Laura F Dagley, Darryl L Russell","doi":"10.1002/pmic.202400374","DOIUrl":"https://doi.org/10.1002/pmic.202400374","url":null,"abstract":"The nuclear steroid hormone receptor progesterone receptor (PGR) is expressed in granulosa cells in the ovarian follicle in a tightly regulated pattern in response to the surge of luteinizing hormone (LH) that stimulates ovulation. PGR plays a critical role in mediating ovulation in response to LH, however, the mechanism for this is still unknown. We performed immunoprecipitation-mass spectrometry using the KGN human granulosa cell line expressing the primary PGR isoforms PGR-A or PGR-B, to identify novel interacting proteins that regulate PGR function in these ovary-specific target cells. Proteomic analysis revealed protein interactions with both PGR isoforms that were gained (e.g., transcriptional coactivators) or lost (e.g., chaperone proteins) in response to the PGR agonist R5020. Additionally, isoform-specific interactions, including different families of transcriptional regulators, were identified. Comparison with published datasets of PGR-interacting proteins in human breast cancer cell lines and decidualized endometrial stromal cells demonstrated a remarkable number of tissue-specific interactions, shedding light on how PGR can maintain diverse functions in different tissues. In conclusion, we provide a comprehensive novel dataset of the PGR interactome in previously unstudied ovarian cells and offer new insights into ovary-specific PGR transcriptional mechanisms.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400374"},"PeriodicalIF":3.4,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959949","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

Advances in Spatial Multi-Omics: A Review of Multi-Modal Mass Spectrometry Imaging and Laser Capture Microdissection-LCMS Integration. 空间多组学研究进展：多模态质谱成像和激光捕获显微解剖- lcms集成综述。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-05-12 DOI: 10.1002/pmic.202400378

Jessica K Lukowski, Byoung-Kyu Cho, Antonia Zamacona Calderon, Borna Dianati, Katherine Stumpo, Savannah Snyder, Young Ah Goo

{"title":"Advances in Spatial Multi-Omics: A Review of Multi-Modal Mass Spectrometry Imaging and Laser Capture Microdissection-LCMS Integration.","authors":"Jessica K Lukowski, Byoung-Kyu Cho, Antonia Zamacona Calderon, Borna Dianati, Katherine Stumpo, Savannah Snyder, Young Ah Goo","doi":"10.1002/pmic.202400378","DOIUrl":"https://doi.org/10.1002/pmic.202400378","url":null,"abstract":"Mass spectrometry has long been utilized to characterize a variety of biomolecules such as proteins, metabolites, and lipids. Most MS-based omics studies rely on bulk analysis; however, bulk approaches often overlook low-abundance molecules that may exert critical biological effects. Recently, multi-omics analyses have been driving an explosion of knowledge about how biomolecules interact within biological systems. In particular, spatial multi-omics has emerged as a groundbreaking approach for implementing multi-omic and multi-modal analyses. Broadly defined, spatial omics has the ability to analyze biomolecules within their native spatial contexts, offering transformative insights. This review focuses on mass spectrometry-based spatial omics, specifically matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). We will explore how MALDI-MSI, in combination with laser capture microdissection (LCM) and traditional liquid chromatography-mass spectrometry (LC-MS) workflow, is advancing spatially resolved multi-omics research.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400378"},"PeriodicalIF":3.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954461","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

DICED (Database of Identified Cleavage Sites Endemic to Diseases States): A Searchable Web Interface for Terminomics/Degradomics. DICED（疾病状态特有的鉴定切割位点数据库）：术语组学/降解组学的可搜索Web界面。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-05-12 DOI: 10.1002/pmic.202500007

Jayadev Joshi, Sumit Bhutada, Daniel R Martin, Joyce Guzowski, Daniel Blankenberg, Suneel S Apte

{"title":"DICED (Database of Identified Cleavage Sites Endemic to Diseases States): A Searchable Web Interface for Terminomics/Degradomics.","authors":"Jayadev Joshi, Sumit Bhutada, Daniel R Martin, Joyce Guzowski, Daniel Blankenberg, Suneel S Apte","doi":"10.1002/pmic.202500007","DOIUrl":"https://doi.org/10.1002/pmic.202500007","url":null,"abstract":"Proteolysis is an irreversible posttranslational modification with immense biological impact. Owing to its high disease significance, there is growing interest in investigating proteolysis on the proteome scale, termed degradomics. We developed 'Database of Identified Cleavage sites Endemic to Disease states' (DICED; https://diced.lerner.ccf.org/), as a searchable knowledgebase to promote collaboration and knowledge sharing in degradomics. DICED was designed and constructed using Python, JavaScript, HTML, and PostgreSQL. Django (https://www.djangoproject.com) was chosen as the primary framework for its security features and support for agile development. DICED can be utilized on major web browsers and operating systems for easy access to high-throughput mass spectrometry-identified cleaved protein termini. The data was obtained using N-terminomics, comprising N-terminal protein labeling, labeled peptide enrichment, mass spectrometry and positional peptide annotation. The DICED database contains experimentally derived N-terminomics peptide datasets from tissues, diseases, or digests of tissue protein libraries using individual proteases and is searchable using UniProt ID, protein name, gene symbol or up to 100 peptide sequences. The tabular output format can be exported as a CSV file. Although DICED presently accesses data from a single laboratory, it is freely available as a Galaxy tool and the underlying database is scalable, permitting addition of new datasets and features.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202500007"},"PeriodicalIF":3.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143964686","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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