International journal of proteomics最新文献_第4页

Proteomic Analysis of the Ontogenetic Variability in Plasma Composition of Juvenile and Adult Bothrops jararaca Snakes. 幼蛇和成蛇血浆组成变异的蛋白质组学分析。

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-04-22 DOI: 10.1155/2013/135709

Karen de Morais-Zani, Kathleen Fernandes Grego, Aparecida Sadae Tanaka, Anita Mitico Tanaka-Azevedo

{"title":"Proteomic Analysis of the Ontogenetic Variability in Plasma Composition of Juvenile and Adult Bothrops jararaca Snakes.","authors":"Karen de Morais-Zani, Kathleen Fernandes Grego, Aparecida Sadae Tanaka, Anita Mitico Tanaka-Azevedo","doi":"10.1155/2013/135709","DOIUrl":"https://doi.org/10.1155/2013/135709","url":null,"abstract":"The ontogenetic variability in venom composition of some snake genera, including Bothrops, as well as the biological implications of such variability and the search of new molecules that can neutralize the toxic components of these venoms have been the subject of many studies. Thus, considering the resistance of Bothrops jararaca to the toxic action of its own venom and the ontogenetic variability in venom composition described in this species, a comparative study of the plasma composition of juvenile and adult B. jararaca snakes was performed through a proteomic approach based on 2D electrophoresis and mass spectrometry, which allowed the identification of proteins that might be present at different levels during ontogenetic development. Among the proteins identified by mass spectrometry, antihemorrhagic factor Bj46a was found only in adult plasma. Moreover, two spots identified as phospholipase A2 inhibitors were significantly increased in juvenile plasma, which can be related to the higher catalytic PLA2 activity shown by juvenile venom in comparison to that of adult snakes. This work shows the ontogenetic variability of B. jararaca plasma, and that these changes can be related to the ontogenetic variability described in its venom. ","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/135709","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31757013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Top-Down Characterization of the Post-Translationally Modified Intact Periplasmic Proteome from the Bacterium Novosphingobium aromaticivorans. 新香藻细菌翻译后修饰的完整质周蛋白质组的自顶向下表征

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-03-10 DOI: 10.1155/2013/279590

Si Wu, Roslyn N Brown, Samuel H Payne, Da Meng, Rui Zhao, Nikola Tolić, Li Cao, Anil Shukla, Matthew E Monroe, Ronald J Moore, Mary S Lipton, Ljiljana Paša-Tolić

{"title":"Top-Down Characterization of the Post-Translationally Modified Intact Periplasmic Proteome from the Bacterium Novosphingobium aromaticivorans.","authors":"Si Wu, Roslyn N Brown, Samuel H Payne, Da Meng, Rui Zhao, Nikola Tolić, Li Cao, Anil Shukla, Matthew E Monroe, Ronald J Moore, Mary S Lipton, Ljiljana Paša-Tolić","doi":"10.1155/2013/279590","DOIUrl":"https://doi.org/10.1155/2013/279590","url":null,"abstract":"The periplasm of Gram-negative bacteria is a dynamic and physiologically important subcellular compartment where the constant exposure to potential environmental insults amplifies the need for proper protein folding and modifications. Top-down proteomics analysis of the periplasmic fraction at the intact protein level provides unrestricted characterization and annotation of the periplasmic proteome, including the post-translational modifications (PTMs) on these proteins. Here, we used single-dimension ultra-high pressure liquid chromatography coupled with the Fourier transform mass spectrometry (FTMS) to investigate the intact periplasmic proteome of Novosphingobium aromaticivorans. Our top-down analysis provided the confident identification of 55 proteins in the periplasm and characterized their PTMs including signal peptide removal, N-terminal methionine excision, acetylation, glutathionylation, pyroglutamate, and disulfide bond formation. This study provides the first experimental evidence for the expression and periplasmic localization of many hypothetical and uncharacterized proteins and the first unrestrictive, large-scale data on PTMs in the bacterial periplasm.","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/279590","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40245327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 20

iTRAQ-Based and Label-Free Proteomics Approaches for Studies of Human Adenovirus Infections. 基于itraq和无标记的蛋白质组学方法研究人类腺病毒感染。

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-03-11 DOI: 10.1155/2013/581862

Hung V Trinh, Jonas Grossmann, Peter Gehrig, Bernd Roschitzki, Ralph Schlapbach, Urs F Greber, Silvio Hemmi

{"title":"iTRAQ-Based and Label-Free Proteomics Approaches for Studies of Human Adenovirus Infections.","authors":"Hung V Trinh, Jonas Grossmann, Peter Gehrig, Bernd Roschitzki, Ralph Schlapbach, Urs F Greber, Silvio Hemmi","doi":"10.1155/2013/581862","DOIUrl":"https://doi.org/10.1155/2013/581862","url":null,"abstract":"Both isobaric tags for relative and absolute quantitation (iTRAQ) and label-free methods are widely used for quantitative proteomics. Here, we provide a detailed evaluation of these proteomics approaches based on large datasets from biological samples. iTRAQ-label-based and label-free quantitations were compared using protein lysate samples from noninfected human lung epithelial A549 cells and from cells infected for 24 h with human adenovirus type 3 or type 5. Either iTRAQ-label-based or label-free methods were used, and the resulting samples were analyzed by liquid chromatography (LC) and tandem mass spectrometry (MS/MS). To reduce a possible bias from quantitation software, we applied several software packages for each procedure. ProteinPilot and Scaffold Q+ software were used for iTRAQ-labeled samples, while Progenesis LC-MS and ProgenesisF-T2PQ/T3PQ were employed for label-free analyses. R (2) correlation coefficients correlated well between two software packages applied to the same datasets with values between 0.48 and 0.78 for iTRAQ-label-based quantitations and 0.5 and 0.86 for label-free quantitations. Analyses of label-free samples showed higher levels of protein up- or downregulation in comparison to iTRAQ-labeled samples. The concentration differences were further evaluated by Western blotting for four downregulated proteins. These data suggested that the label-free method was more accurate than the iTRAQ method.","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/581862","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40245328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 66

Protein target quantification decision tree. 蛋白质目标量化决策树。

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-01-15 DOI: 10.1155/2013/701247

Jong Won Kim, Jinsam You

引用次数: 11

Advantageous uses of mass spectrometry for the quantification of proteins. 质谱法用于蛋白质定量的有利用途。

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-01-08 DOI: 10.1155/2013/219452

John E Hale

引用次数: 34

A Novel Peptide-Based SILAC Method to Identify the Posttranslational Modifications Provides Evidence for Unconventional Ubiquitination in the ER-Associated Degradation Pathway. 一种新的基于肽的SILAC方法识别翻译后修饰，为er相关降解途径中的非常规泛素化提供了证据。

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-02-03 DOI: 10.1155/2013/857918

Veronica G Anania, Daisy J Bustos, Jennie R Lill, Donald S Kirkpatrick, Laurent Coscoy

{"title":"A Novel Peptide-Based SILAC Method to Identify the Posttranslational Modifications Provides Evidence for Unconventional Ubiquitination in the ER-Associated Degradation Pathway.","authors":"Veronica G Anania, Daisy J Bustos, Jennie R Lill, Donald S Kirkpatrick, Laurent Coscoy","doi":"10.1155/2013/857918","DOIUrl":"https://doi.org/10.1155/2013/857918","url":null,"abstract":"The endoplasmic reticulum-associated degradation (ERAD) pathway is responsible for disposing misfolded proteins from the endoplasmic reticulum by inducing their ubiquitination and degradation. Ubiquitination is conventionally observed on lysine residues and has been demonstrated on cysteine residues and protein N-termini. Ubiquitination is fundamental to the ERAD process; however, a mutant T-cell receptor α (TCRα) lacking lysine residues is targeted for the degradation by the ERAD pathway. We have shown that ubiquitination of lysine-less TCRα occurs on internal, non-lysine residues and that the same E3 ligase conjugates ubiquitin to TCRα in the presence or absence of lysine residues. Mass-spectrometry indicates that WT-TCRα is ubiquitinated on multiple lysine residues. Recent publications have provided indirect evidence that serine and threonine residues may be modified by ubiquitin. Using a novel peptide-based stable isotope labeling in cell culture (SILAC) approach, we show that specific lysine-less TCRα peptides become modified. In this study, we demonstrate that it is possible to detect both ester and thioester based ubiquitination events, although the exact linkage on lysine-less TCRα remains elusive. These findings demonstrate that SILAC can be used as a tool to identify modified peptides, even those with novel modifications that may not be detected using conventional proteomic work flows or informatics algorithms.","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/857918","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31256813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Periodontal proteomics: wonders never cease! 牙周蛋白质组学：奇迹从未停止！

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-12-31 DOI: 10.1155/2013/850235

Harpreet Singh Grover, Shalini Kapoor, Neha Saksena

{"title":"Periodontal proteomics: wonders never cease!","authors":"Harpreet Singh Grover, Shalini Kapoor, Neha Saksena","doi":"10.1155/2013/850235","DOIUrl":"10.1155/2013/850235","url":null,"abstract":"Proteins are vital parts of living organisms, as they are integral components of the physiological metabolic pathways of cells. Periodontal tissues comprise multicompartmental groups of interacting cells and matrices that provide continuous support, attachment, proprioception, and physical protection for the teeth. The proteome map, that is, complete catalogue of the matrix and cellular proteins expressed in alveolar bone, cementum, periodontal ligament, and gingiva, is to be explored for more in-depth understanding of periodontium. The ongoing research to understand the signalling pathways that allow cells to divide, differentiate, and die in controlled manner has brought us to the era of proteomics. Proteomics is defined as the study of all proteins including their relative abundance, distribution, posttranslational modifications, functions, and interactions with other macromolecules, in a given cell or organism within a given environment and at a specific stage in the cell cycle. Its application to periodontal science can be used to monitor health status, disease onset, treatment response, and outcome. Proteomics can offer answers to critical, unresolved questions such as the biological basis for the heterogeneity in gingival, alveolar bone, and cemental cell populations. ","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893808/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32085460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Label-Free Quantitation and Mapping of the ErbB2 Tumor Receptor by Multiple Protease Digestion with Data-Dependent (MS1) and Data-Independent (MS2) Acquisitions. 基于数据依赖性(MS1)和数据非依赖性(MS2)获取的多重蛋白酶消化的ErbB2肿瘤受体的无标记定量和定位

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-04-04 DOI: 10.1155/2013/791985

Jason M Held, Birgit Schilling, Alexandria K D'Souza, Tara Srinivasan, Jessica B Behring, Dylan J Sorensen, Christopher C Benz, Bradford W Gibson

{"title":"Label-Free Quantitation and Mapping of the ErbB2 Tumor Receptor by Multiple Protease Digestion with Data-Dependent (MS1) and Data-Independent (MS2) Acquisitions.","authors":"Jason M Held, Birgit Schilling, Alexandria K D'Souza, Tara Srinivasan, Jessica B Behring, Dylan J Sorensen, Christopher C Benz, Bradford W Gibson","doi":"10.1155/2013/791985","DOIUrl":"https://doi.org/10.1155/2013/791985","url":null,"abstract":"The receptor tyrosine kinase ErbB2 is a breast cancer biomarker whose posttranslational modifications (PTMs) are a key indicator of its activation. Quantifying the expression and PTMs of biomarkers such as ErbB2 by selected reaction monitoring (SRM) mass spectrometry has several limitations, including minimal coverage and extensive assay development time. Therefore, we assessed the utility of two high resolution, full scan mass spectrometry approaches, MS1 Filtering and SWATH MS2, for targeted ErbB2 proteomics. Endogenous ErbB2 immunoprecipitated from SK-BR-3 cells was in-gel digested with trypsin, chymotrypsin, Asp-N, or trypsin plus Asp-N in triplicate. Data-dependent acquisition with an AB SCIEX TripleTOF 5600 and MS1 Filtering data processing was used to assess peptide and PTM coverage as well as the reproducibility of enzyme digestion. Data-independent acquisition (SWATH) was also performed for MS2 quantitation. MS1 Filtering and SWATH MS2 allow quantitation of all detected analytes after acquisition, enabling the use of multiple proteases for quantitative assessment of target proteins. Combining high resolution proteomics with multiprotease digestion enabled quantitative mapping of ErbB2 with excellent reproducibility, improved amino acid sequence and PTM coverage, and decreased assay development time compared to typical SRM assays. These results demonstrate that high resolution quantitative proteomic approaches are an effective tool for targeted biomarker quantitation.","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/791985","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31460190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 25

Current status and advances in quantitative proteomic mass spectrometry. 定量蛋白质组质谱技术的现状与进展。

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-03-06 DOI: 10.1155/2013/180605

Valerie C Wasinger, Ming Zeng, Yunki Yau

引用次数: 160

Additions to the Human Plasma Proteome via a Tandem MARS Depletion iTRAQ-Based Workflow. 通过串联MARS耗尽itraq工作流程添加到人类血浆蛋白质组。

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-02-19 DOI: 10.1155/2013/654356

Zhiyun Cao, Sachin Yende, John A Kellum, Renã A S Robinson

{"title":"Additions to the Human Plasma Proteome via a Tandem MARS Depletion iTRAQ-Based Workflow.","authors":"Zhiyun Cao, Sachin Yende, John A Kellum, Renã A S Robinson","doi":"10.1155/2013/654356","DOIUrl":"https://doi.org/10.1155/2013/654356","url":null,"abstract":"Robust platforms for determining differentially expressed proteins in biomarker and discovery studies using human plasma are of great interest. While increased depth in proteome coverage is desirable, it is associated with costs of experimental time due to necessary sample fractionation. We evaluated a robust quantitative proteomics workflow for its ability (1) to provide increased depth in plasma proteome coverage and (2) to give statistical insight useful for establishing differentially expressed plasma proteins. The workflow involves dual-stage immunodepletion on a multiple affinity removal system (MARS) column, iTRAQ tagging, offline strong-cation exchange chromatography, and liquid chromatography tandem mass spectrometry (LC-MS/MS). Independent workflow experiments were performed in triplicate on four plasma samples tagged with iTRAQ 4-plex reagents. After stringent criteria were applied to database searched results, 689 proteins with at least two spectral counts (SC) were identified. Depth in proteome coverage was assessed by comparison to the 2010 Human Plasma Proteome Reference Database in which our studies reveal 399 additional proteins which have not been previously reported. Additionally, we report on the technical variation of this quantitative workflow which ranges from ±11 to 30%.","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/654356","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31319069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 24