Proteomics最新文献_第8页

mzIdentML 1.3.0 – Essential progress on the support of crosslinking and other identifications based on multiple spectra mzIdentML 1.3.0 - 在支持交联和其他基于多光谱的鉴定方面取得重要进展。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-07-12 DOI: 10.1002/pmic.202300385

Colin W. Combe, Lars Kolbowski, Lutz Fischer, Ville Koskinen, Joshua Klein, Alexander Leitner, Andrew R. Jones, Juan Antonio Vizcaíno, Juri Rappsilber

{"title":"mzIdentML 1.3.0 – Essential progress on the support of crosslinking and other identifications based on multiple spectra","authors":"Colin W. Combe, Lars Kolbowski, Lutz Fischer, Ville Koskinen, Joshua Klein, Alexander Leitner, Andrew R. Jones, Juan Antonio Vizcaíno, Juri Rappsilber","doi":"10.1002/pmic.202300385","DOIUrl":"10.1002/pmic.202300385","url":null,"abstract":"The mzIdentML data format, originally developed by the Proteomics Standards Initiative in 2011, is the open XML data standard for peptide and protein identification results coming from mass spectrometry. We present mzIdentML version 1.3.0, which introduces new functionality and support for additional use cases. First of all, a new mechanism for encoding identifications based on multiple spectra has been introduced. Furthermore, the main mzIdentML specification document can now be supplemented by extension documents which provide further guidance for encoding specific use cases for different proteomics subfields. One extension document has been added, covering additional use cases for the encoding of crosslinked peptide identifications. The ability to add extension documents facilitates keeping the mzIdentML standard up to date with advances in the proteomics field, without having to change the main specification document. The crosslinking extension document provides further explanation of the crosslinking use cases already supported in mzIdentML version 1.2.0, and provides support for encoding additional scenarios that are critical to reflect developments in the crosslinking field and facilitate its integration in structural biology. These are: (i) support for cleavable crosslinkers, (ii) support for internally linked peptides, (iii) support for noncovalently associated peptides, and (iv) improved support for encoding scores and the corresponding thresholds.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 17","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202300385","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141597983","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

A cross-omics data analysis strategy for metabolite-microbe pair identification 代谢物-微生物配对识别的交叉组学数据分析策略。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-07-12 DOI: 10.1002/pmic.202400035

Tao Sun, Dongnan Sun, Junliang Kuang, Xiaowen Chao, Yihan Guo, Mengci Li, Tianlu Chen

引用次数: 0

Editorial Board: Proteomics 14'24 编辑委员会：蛋白质组学 14'24

IF 3.4 4区生物学

Proteomics Pub Date : 2024-07-12 DOI: 10.1002/pmic.202470102

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Playing pin-the-tail-on-the-protein in extracellular vesicle (EV) proteomics 在细胞外囊泡 (EV) 蛋白组学中玩 "钉尾巴 "游戏。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-06-20 DOI: 10.1002/pmic.202400074

Natalie P. Turner

{"title":"Playing pin-the-tail-on-the-protein in extracellular vesicle (EV) proteomics","authors":"Natalie P. Turner","doi":"10.1002/pmic.202400074","DOIUrl":"10.1002/pmic.202400074","url":null,"abstract":"Extracellular vesicles (EVs) are anucleate particles enclosed by a lipid bilayer that are released from cells via exocytosis or direct budding from the plasma membrane. They contain an array of important molecular cargo such as proteins, nucleic acids, and lipids, and can transfer these cargoes to recipient cells as a means of intercellular communication. One of the overarching paradigms in the field of EV research is that EV cargo should reflect the biological state of the cell of origin. The true relationship or extent of this correlation is confounded by many factors, including the numerous ways one can isolate or enrich EVs, overlap in the biophysical properties of different classes of EVs, and analytical limitations. This presents a challenge to research aimed at detecting low-abundant EV-encapsulated nucleic acids or proteins in biofluids for biomarker research and underpins technical obstacles in the confident assessment of the proteomic landscape of EVs that may be affected by sample-type specific or disease-associated proteoforms. Improving our understanding of EV biogenesis, cargo loading, and developments in top-down proteomics may guide us towards advanced approaches for selective EV and molecular cargo enrichment, which could aid EV diagnostics and therapeutics research.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 18","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202400074","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141425818","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

A fast and sensitive size-exclusion chromatography method for plasma extracellular vesicle proteomic analysis 用于血浆细胞外囊泡蛋白质组分析的快速灵敏尺寸排阻色谱法。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-06-19 DOI: 10.1002/pmic.202400025

Ivo Díaz Ludovico, Samantha M. Powell, Gina Many, Lisa Bramer, Soumyadeep Sarkar, Kelly Stratton, Tao Liu, Tujin Shi, Wei-Jun Qian, Kristin E. Burnum-Johnson, John T. Melchior, Ernesto S. Nakayasu

{"title":"A fast and sensitive size-exclusion chromatography method for plasma extracellular vesicle proteomic analysis","authors":"Ivo Díaz Ludovico, Samantha M. Powell, Gina Many, Lisa Bramer, Soumyadeep Sarkar, Kelly Stratton, Tao Liu, Tujin Shi, Wei-Jun Qian, Kristin E. Burnum-Johnson, John T. Melchior, Ernesto S. Nakayasu","doi":"10.1002/pmic.202400025","DOIUrl":"10.1002/pmic.202400025","url":null,"abstract":"Extracellular vesicles (EVs) carry diverse biomolecules derived from their parental cells, making their components excellent biomarker candidates. However, purifying EVs is a major hurdle in biomarker discovery since current methods require large amounts of samples, are time-consuming and typically have poor reproducibility. Here we describe a simple, fast, and sensitive EV fractionation method using size exclusion chromatography (SEC) on a fast protein liquid chromatography (FPLC) system. Our method uses a Superose 6 Increase 5/150, which has a bed volume of 2.9 mL. The FPLC system and small column size enable reproducible separation of only 50 µL of human plasma in 15 min. To demonstrate the utility of our method, we used longitudinal samples from a group of individuals who underwent intense exercise. A total of 838 proteins were identified, of which, 261 were previously characterized as EV proteins, including classical markers, such as cluster of differentiation (CD)9 and CD81. Quantitative analysis showed low technical variability with correlation coefficients greater than 0.9 between replicates. The analysis captured differences in relevant EV proteins involved in response to physical activity. Our method enables fast and sensitive fractionation of plasma EVs with low variability, which will facilitate biomarker studies in large clinical cohorts.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 16","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202400025","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417076","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

Benefits and limits of decellularization on mass-spectrometry-based extracellular matrix proteome analysis of mouse kidney 脱细胞对基于质谱的小鼠肾脏细胞外基质蛋白质组分析的益处和局限。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-06-19 DOI: 10.1002/pmic.202400052

Teresa Frattini, Hanne Devos, Manousos Makridakis, Maria G. Roubelakis, Agnieszka Latosinska, Harald Mischak, Joost P. Schanstra, Antonia Vlahou, Jean-Sébastien Saulnier-Blache

{"title":"Benefits and limits of decellularization on mass-spectrometry-based extracellular matrix proteome analysis of mouse kidney","authors":"Teresa Frattini, Hanne Devos, Manousos Makridakis, Maria G. Roubelakis, Agnieszka Latosinska, Harald Mischak, Joost P. Schanstra, Antonia Vlahou, Jean-Sébastien Saulnier-Blache","doi":"10.1002/pmic.202400052","DOIUrl":"10.1002/pmic.202400052","url":null,"abstract":"The extracellular matrix (ECM) is composed of collagens, ECM glycoproteins, and proteoglycans (also named core matrisome proteins) that are critical for tissue structure and function, and matrisome-associated proteins that balance the production and degradation of the ECM proteins. The identification and quantification of core matrisome proteins using mass spectrometry is often hindered by their low abundance and their propensity to form macromolecular insoluble structures. In this study, we aimed to investigate the added value of decellularization in identifying and quantifying core matrisome proteins in mouse kidney. The decellularization strategy combined freeze-thaw cycles and sodium dodecyl sulphate treatment. We found that decellularization preserved 95% of the core matrisome proteins detected in non-decellularized kidney and revealed few additional ones. Decellularization also led to an average of 59 times enrichment of 96% of the core matrisome proteins as the result of the successful removal of cellular and matrisome-associated proteins. However, the enrichment varied greatly among core matrisome proteins, resulting in a misrepresentation of the native ECM composition in decellularized kidney. This should be brought to the attention of the matrisome research community, as it highlights the need for caution when interpreting proteomic data obtained from a decellularized organ.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 17","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202400052","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141425817","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

What proteomics has taught us about honey bee (Apis mellifera) health and disease. 蛋白质组学让我们了解蜜蜂（Apis mellifera）的健康和疾病。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-06-19 DOI: 10.1002/pmic.202400075

Maor Arad, Kenneth Ku, Connor Frey, Rhien Hare, Alison McAfee, Golfam Ghafourifar, Leonard J Foster

{"title":"What proteomics has taught us about honey bee (Apis mellifera) health and disease.","authors":"Maor Arad, Kenneth Ku, Connor Frey, Rhien Hare, Alison McAfee, Golfam Ghafourifar, Leonard J Foster","doi":"10.1002/pmic.202400075","DOIUrl":"https://doi.org/10.1002/pmic.202400075","url":null,"abstract":"The Western honey bee, Apis mellifera, is currently navigating a gauntlet of environmental pressures, including the persistent threat of parasites, pathogens, and climate change - all of which compromise the vitality of honey bee colonies. The repercussions of their declining health extend beyond the immediate concerns of apiarists, potentially imposing economic burdens on society through diminished agricultural productivity. Hence, there is an imperative to devise innovative monitoring techniques for assessing the health of honey bee populations. Proteomics, recognized for its proficiency in biomarker identification and protein-protein interactions, is poised to play a pivotal role in this regard. It offers a promising avenue for monitoring and enhancing the resilience of honey bee colonies, thereby contributing to the stability of global food supplies. This review delves into the recent proteomic studies of A. mellifera, highlighting specific proteins of interest and envisioning the potential of proteomics to improve sustainable beekeeping practices amidst the challenges of a changing planet.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e2400075"},"PeriodicalIF":3.4,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141425819","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

Editorial Board: Proteomics 12–13'24 编辑委员会：蛋白质组学 12-13'24

IF 3.4 4区生物学

Proteomics Pub Date : 2024-06-14 DOI: 10.1002/pmic.202470092

引用次数: 0

Contents: Proteomics 12–13'24 内容：蛋白质组学 12-13'24

IF 3.4 4区生物学

Proteomics Pub Date : 2024-06-14 DOI: 10.1002/pmic.202470093

引用次数: 0

Improved breast milk proteome coverage by DIA based LC-MS/MS method 基于 DIA 的 LC-MS/MS 方法提高了母乳蛋白质组的覆盖率。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-06-14 DOI: 10.1002/pmic.202300340

Jenni Viitaharju, Lauri Polari, Otto Kauko, Johannes Merilahti, Anne Rokka, Diana M. Toivola, Kirsi Laitinen

{"title":"Improved breast milk proteome coverage by DIA based LC-MS/MS method","authors":"Jenni Viitaharju, Lauri Polari, Otto Kauko, Johannes Merilahti, Anne Rokka, Diana M. Toivola, Kirsi Laitinen","doi":"10.1002/pmic.202300340","DOIUrl":"10.1002/pmic.202300340","url":null,"abstract":"The breast milk composition includes a multitude of bioactive factors such as viable cells, lipids and proteins. Measuring the levels of specific proteins in breast milk plasma can be challenging because of the large dynamic range of protein concentrations and the presence of interfering substances. Therefore, most proteomic studies of breast milk have been able to identify under 1000 proteins. Optimised procedures and the latest separation technologies used in milk proteome research could lead to more precise knowledge of breast milk proteome. This study (n = 53) utilizes three different protein quantification methods, including direct DIA, library-based DIA method and a hybrid method combining direct DIA and library-based DIA. On average we identified 2400 proteins by hybrid method. By applying these methods, we quantified body mass index (BMI) associated variation in breast milk proteomes. There were 210 significantly different proteins when comparing the breast milk proteome of obese and overweight mothers. In addition, we analysed a small cohort (n = 5, randomly selected from 53 samples) by high field asymmetric waveform ion mobility spectrometry (FAIMS). FAIMS coupled with the Orbitrap Fusion Lumos mass spectrometer, which led to 41.7% higher number of protein identifications compared to Q Exactive HF mass spectrometer.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 14","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202300340","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141316295","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