Proteomics最新文献_第2页

An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources. 公共数据资源中元基因组学、元转录组学和宏蛋白质组学数据的整合方法

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-28 DOI: 10.1002/pmic.202500002

Shengbo Wang, Satwant Kaur, Benoit J Kunath, Patrick May, Lorna Richardson, Alexander B Rogers, Paul Wilmes, Robert D Finn, Juan Antonio Vizcaíno

{"title":"An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources.","authors":"Shengbo Wang, Satwant Kaur, Benoit J Kunath, Patrick May, Lorna Richardson, Alexander B Rogers, Paul Wilmes, Robert D Finn, Juan Antonio Vizcaíno","doi":"10.1002/pmic.202500002","DOIUrl":"https://doi.org/10.1002/pmic.202500002","url":null,"abstract":"The availability of public metaproteomics, metagenomics and metatranscriptomics data in public resources such as MGnify (for metagenomics/metatranscriptomics) and the PRIDE database (for metaproteomics), continues to increase. When these omics techniques are applied to the same samples, their integration offers new opportunities to understand the structure (metagenome) and functional expression (metatranscriptome and metaproteome) of the microbiome. Here, we describe a pilot study aimed at integrating public multi-meta-omics datasets from studies based on human gut and marine hatchery samples. Reference search databases (search DBs) were built using assembled metagenomic (and metatranscriptomic, where available) sequence data followed by de novo gene calling, using both data from the same sampling event and from independent samples. The resulting protein sets were evaluated for their utility in metaproteomics analysis. In agreement with previous studies, the highest number of peptide identifications was generally obtained when using search DBs created from the same samples. Data integration of the multi-omics results was performed in MGnify. For that purpose, the MGnify website was extended to enable the visualisation of the resulting peptide/protein information from three reanalysed metaproteomics datasets. A workflow (https://github.com/PRIDE-reanalysis/MetaPUF) has been developed allowing researchers to perform equivalent data integration, using paired multi-omics datasets. This is the first time that a data integration approach for multi-omics datasets has been implemented from public data available in the world-leading MGnify and PRIDE resources.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202500002"},"PeriodicalIF":3.4,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959677","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

Top-Down Proteomics: Why and When? 自上而下的蛋白质组学：为什么和何时？

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-27 DOI: 10.1002/pmic.202400338

Philipp T Kaulich, Andreas Tholey

{"title":"Top-Down Proteomics: Why and When?","authors":"Philipp T Kaulich, Andreas Tholey","doi":"10.1002/pmic.202400338","DOIUrl":"https://doi.org/10.1002/pmic.202400338","url":null,"abstract":"Manifold biological processes at all levels of transcription and translation can lead to the formation of a high number of different protein species (i.e., proteoforms), which outnumber the sequences encoded in the genome by far. Due to the large number of protein molecules formed in this way, which span an enormous range of different physicochemical properties, proteoforms are the functional drivers of all biological processes, creating the need for powerful analytical approaches to decipher this language of life. While bottom-up proteomics has become the most widely used approach, providing features such as high sensitivity, depth of analysis, and throughput, it has its limitations when it comes to identifying, quantifying, and characterizing proteoforms. In particular, the major bottleneck is to assign peptide-level information to the original proteoforms. In contrast, top-down proteomics (TDP) targets the direct analysis of intact proteoforms. Despite being characterized by a number of technological challenges, the TDP community has established numerous protocols that allow easy implementation in any proteomics laboratory. In this viewpoint, we compare both approaches, argue that it is worth embedding TDP experiments, and show fields of research in which TDP can be successfully implemented to perform integrative multi-level proteoformics.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400338"},"PeriodicalIF":3.4,"publicationDate":"2025-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956256","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

A Non-Metaproteomics Researchers' View on Metaproteomics in Microbiome Research. 非元蛋白质组学研究人员对微生物组学研究中宏蛋白质组学的看法

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-27 DOI: 10.1002/pmic.202500019

Velma T E Aho, Laure-Alix Clerbaux, Anne Kupczok, Bree Tillett, Neha Garg, Jannie G E Henderickx

{"title":"A Non-Metaproteomics Researchers' View on Metaproteomics in Microbiome Research.","authors":"Velma T E Aho, Laure-Alix Clerbaux, Anne Kupczok, Bree Tillett, Neha Garg, Jannie G E Henderickx","doi":"10.1002/pmic.202500019","DOIUrl":"https://doi.org/10.1002/pmic.202500019","url":null,"abstract":"Metaproteomics, an emerging field among the omic techniques, holds great promise for unraveling the function of microbiomes in host health and our environment. Metaproteomics can also be a valuable addition to multiomics studies of the microbiome, complementing genome-resolved metagenomics, metatranscriptomics, and metabolomics. The potential advancements from metaproteomics and multiomics research touch a breadth of disciplines, including ecology, biochemistry, immunology, medical microbiology, cell physiology, and medicine, and could lead to both fundamental and applied discoveries. However, there are significant roadblocks to widespread adoption of metaproteomics among microbiome researchers. In this Viewpoint article, we highlight the pivotal role of metaproteomics in microbiome research by showcasing its advantages, exploring opportunities to overcome challenges, and paving the way for its broader adoption as a mainstream technique. We hope that the recommendations provided in this Viewpoint article will inspire new, beneficial collaborations between proteomics experts, algorithm and infrastructure developers, biochemists, cell biologists, and microbiologists, enabling the construction of a knowledge base of microbiome function that can have an immediate and direct impact on host health and the environment.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202500019"},"PeriodicalIF":3.4,"publicationDate":"2025-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956585","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

Alpaca. A Simplified and Reproducible Python-Based Pipeline for Absolute Proteome Quantification Data Mining 羊驼。一个简化和可复制的基于python的绝对蛋白质组定量数据挖掘管道

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-26 DOI: 10.1002/pmic.202400417

Borja Ferrero-Bordera, Dörte Becher, Sandra Maaß

{"title":"Alpaca. A Simplified and Reproducible Python-Based Pipeline for Absolute Proteome Quantification Data Mining","authors":"Borja Ferrero-Bordera, Dörte Becher, Sandra Maaß","doi":"10.1002/pmic.202400417","DOIUrl":"https://doi.org/10.1002/pmic.202400417","url":null,"abstract":"The accurate construction of computational models in systems biology heavily relies on the availability of quantitative proteomics data, specifically, absolute protein abundances. However, the complex nature of proteomics data analysis necessitates specialised expertise, making the integration of this data into models challenging. Therefore, the development of software tools that ease the analysis of proteomics data and bridge between disciplines is crucial for advancing the field of systems biology. We developed an open access Python-based software tool available either as downloadable library or as web-based graphical user interface (GUI). The pipeline simplifies the extraction and calculation of protein abundances from unprocessed proteomics data, accommodating a range of experimental approaches based on label-free quantification. Our tool was conceived as a versatile and robust pipeline designed to ease and simplify data analysis, thereby improving reproducibility between researchers and institutions. Moreover, the robust modular structure of Alpaca allows its integration with other software tools.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 9-10","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202400417","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143945051","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}

引用次数: 0

Obituary: In Memory of Michael (Mike) J. Dunn (1946–2024) 讣告：纪念迈克尔（迈克）J.邓恩（1946-2024）

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-24 DOI: 10.1002/pmic.202500077

引用次数: 0

Contents: Proteomics 8'25 内容：蛋白质组学8'25

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-24 DOI: 10.1002/pmic.202570029

引用次数: 0

Editorial Board: Proteomics 8'25 编辑委员会：蛋白质组学8'25

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-24 DOI: 10.1002/pmic.202570028

引用次数: 0

Glycoproteomics and Its Role in Understanding Bacterial O-Linked Glycosylation. 糖蛋白组学及其在理解细菌o -链糖基化中的作用。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-21 DOI: 10.1002/pmic.202400256

Kristian I Karlic, Hamza Tahir, Nichollas E Scott

{"title":"Glycoproteomics and Its Role in Understanding Bacterial O-Linked Glycosylation.","authors":"Kristian I Karlic, Hamza Tahir, Nichollas E Scott","doi":"10.1002/pmic.202400256","DOIUrl":"https://doi.org/10.1002/pmic.202400256","url":null,"abstract":"Protein glycosylation is now recognized as a ubiquitous process observed in all domains of life. Within bacterial species, carbohydrates can be attached to multiple residues with glycosylation of serine, threonine, or tyrosine residues via their hydroxyl side chains referred to as O-linked glycosylation. To date, multiple bacterial enzymes have been identified that mediate O-linked glycosylation targeting either surface or periplasmic bacterial proteins, and in the case of toxin/effectors, host proteins. Within this review, we discuss the current understanding of common bacterial O-linked glycosylation systems and the glycoproteomic approaches which have been used to characterize these events. Focusing on O-oligosaccharyltransferases (O-OTases), flagellin-specific glycosylation systems, and glycosyltransferase toxin/effectors, we discuss the characteristics of known glycosylation systems. For the general O-linked systems mediated by the PglL oligosaccharyltransferases, we outline the key considerations when assessing glycosylation events across the Burkholderia, Neisseria, and Acinetobacter genera. In addition, we highlight the technologies and advancements in glycoproteomic techniques, as well as the bioinformatic tools that now facilitate high throughput studies of O-linked glycosylation within bacterial species. Combined, this review outlines our current understanding of O-linked glycosylation within well characterized Gram-negative genera and the current technologies available for exploring bacterial O-glycoproteomes.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400256"},"PeriodicalIF":3.4,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957310","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

Temporal Proteomic Profiling of Pheromone-Induced Cell Cycle Re-Entry in Saccharomyces cerevisiae

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-21 DOI: 10.1002/pmic.202400455

Sneha Parmar, Nathan R. Zuniga, Valentina Rossio, Xinyue Liu, Joao A. Paulo

{"title":"Temporal Proteomic Profiling of Pheromone-Induced Cell Cycle Re-Entry in Saccharomyces cerevisiae","authors":"Sneha Parmar, Nathan R. Zuniga, Valentina Rossio, Xinyue Liu, Joao A. Paulo","doi":"10.1002/pmic.202400455","DOIUrl":"https://doi.org/10.1002/pmic.202400455","url":null,"abstract":"<div>\u0000 \u0000 The regulation of cell cycle progression in response to environmental cues is essential for cellular adaptation. In Saccharomyces cerevisiae, the BAR1 gene modulates sensitivity to the mating pheromone α-factor, which induces cell cycle arrest in G1. Here, we investigated the dynamic proteomic response in the bar1 deletion strain using a 27-plex experimental design with TMTproD isobaric labeling. Asynchronous bar1Δ cells were treated with α-factor and then released from the pheromone-induced cell cycle arrest in G1. Using higher-order TMTpro sample multiplexing, we generated global temporal profiles of protein abundance associated with recovery from this arrest, with triplicate samples collected at eight time points from 0 to 165 min after washing out the pheromone. We identify specific proteins involved in cell cycle re-entry and in the attenuation of the pheromone signal, providing insights into the regulatory mechanisms of mating response in yeast. This study also contributes significantly to dynamic proteomic analysis of cell cycle progression. We present a versatile approach for investigating complex cellular processes and showcase cell cycle progression following release from pheromone-induced arrest in yeast.\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 9-10","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143945041","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

Cross-Species Molecular Similarities Based on Omics Approaches in CKD: Toward Improved Translation From Pre-Clinical Models to Humans. 基于组学方法的CKD跨物种分子相似性：从临床前模型到人类的改进翻译。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-21 DOI: 10.1002/pmic.202400136

Raquel María García-Sáez, Mariano Rodríguez

{"title":"Cross-Species Molecular Similarities Based on Omics Approaches in CKD: Toward Improved Translation From Pre-Clinical Models to Humans.","authors":"Raquel María García-Sáez, Mariano Rodríguez","doi":"10.1002/pmic.202400136","DOIUrl":"https://doi.org/10.1002/pmic.202400136","url":null,"abstract":"The prevalence of chronic kidney disease (CKD) is very high, and it is increasing. Obviously, the care is costly. The identification of biomarkers able to predict disease progression is key for optimal patient care. Tissue, blood, and urine omics are being used to discover new biomarkers. It is challenging to compare omics in animal models with that of CKD patients. The main obstacle is the enormous genetic difference between humans and rodents. Although animal models do not fully resemble CKD, there are possibilities to combine pathologies in an attempt to be closer to the human clinical picture. This manuscript describes Zucker rat model that has been modified to better resemble diabetic CKD: obesity, diabetes, cardiovascular disease, and renal function deterioration. This model has been used to evaluate treatments such as the administration of iSGLT2, VitE antioxidant therapy, or Mg supplementation. Plasma proteomics was performed in Nx-Zucker rats, and it was found change in families of proteins similar to those in CKD patients. Unfortunately, urine omics were not performed. It would be a good strategy to gather different research groups with similar aims to develop common strategies to share not only results but also samples obtained in patients and animals to optimize efforts.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400136"},"PeriodicalIF":3.4,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954592","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