Proteomics最新文献_第4页

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 : 2024-07-14 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":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-14","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}

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Standard abbreviations 标准缩写。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-07-12 DOI: 10.1002/pmic.202470104

引用次数: 0

Contents: Proteomics 14'24 内容：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.202470103

引用次数: 0

Deep learning methods for protein function prediction. 用于蛋白质功能预测的深度学习方法。

IF 3.4 4区生物学

Proteomics Pub Date : 2024-07-12 DOI: 10.1002/pmic.202300471

Frimpong Boadu, Ahhyun Lee, Jianlin Cheng

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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":null,"pages":null},"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

引用次数: 0

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":null,"pages":null},"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}

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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":null,"pages":null},"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

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":null,"pages":null},"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