• 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>Molecular & cellular proteomics: MCP >Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human endot
【24h】

Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human endot

机译：Mascot文件解析和量化（MFPaQ），一种用于解析，验证和量化ICAT和SILAC质谱分析生成的蛋白质组学数据的新软件：在人类原发性膜内膜蛋白的蛋白质组学研究中的应用

获取原文
获取原文并翻译 | 示例
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Proteomics strategies based on nanoflow (nano-) LC-MS/MS allow the identification of hundreds to thousands of proteins in complex mixtures. When combined with protein isotopic labeling, quantitative comparison of the proteome from different samples can be achieved using these approaches. However, bioinformatics analysis of the data remains a bottleneck in large scale quantitative proteomics studies. Here we present a new software named Mascot File Parsing and Quantification (MFPaQ) that easily processes the results of the Mascot search engine and performs protein quantification in the case of isotopic labeling experiments using either the ICAT or SILAC (stable isotope labeling with amino acids in cell culture) method. This new tool provides a convenient interface to retrieve Mascot protein lists; sort them according to Mascot scoring or to user-defined criteria based on the number, the score, and the rank of identified peptides; and to validate the results. Moreover the software extracts quantitative data from raw files obtained by nano-LC-MS/MS, calculates peptide ratios, and generates a non-redundant list of proteins identified in a multisearch experiment with their calculated averaged and normalized ratio. Here we apply this software to the proteomics analysis of membrane proteins from primary human endothelial cells (ECs), a cell type involved in many physiological and pathological processes including chronic inflammatory diseases such as rheumatoid arthritis. We analyzed the EC membrane proteome and set up methods for quantitative analysis of this proteome by ICAT labeling. EC microsomal proteins were fractionated and analyzed by nano-LC-MS/MS, and database searches were performed with Mascot. Data validation and clustering of proteins were performed with MFPaQ, which allowed identification of more than 600 unique proteins. The software was also successfully used in a quantitative differential proteomics analysis of the EC membrane proteome after stimulation with a combination of proinflammatory mediators (tumor necrosis factor-alpha, interferon-gamma, and lymphotoxin alpha/beta) that resulted in the identification of a full spectrum of EC membrane proteins regulated by inflammation.
机译：基于纳流（纳米）LC-MS / MS的蛋白质组学策略可鉴定复杂混合物中数百至数千种蛋白质。当与蛋白质同位素标记结合使用时，可以使用这些方法对不同样品中的蛋白质组进行定量比较。但是，数据的生物信息学分析仍然是大规模定量蛋白质组学研究的瓶颈。在这里，我们介绍了一个名为Mascot File Parsing and Quantification（MFPaQ）的新软件，该软件可以轻松处理Mascot搜索引擎的结果，并在使用ICAT或SILAC进行同位素标记实验的情况下对蛋白质进行定量（在氨基酸中添加稳定的同位素标记）细胞培养）方法。这个新工具提供了一个方便的界面来检索吉祥物蛋白质列表。根据已鉴定的肽的数量，分数和等级，根据Mascot评分或用户定义的标准对它们进行分类;并验证结果。此外，该软件还从通过nano-LC-MS / MS获得的原始文件中提取定量数据，计算出肽的比例，并生成在多重搜索实验中鉴定出的蛋白质的非冗余列表，并计算出它们的平均和标准化比例。在这里，我们将这个软件应用于人类原代内皮细胞（ECs）膜蛋白的蛋白质组学分析，这种内皮细胞参与许多生理和病理过程，包括类风湿性关节炎等慢性炎症疾病。我们分析了EC膜蛋白质组，并建立了通​​过ICAT标记对该蛋白质组进行定量分析的方法。 EC微粒体蛋白经分馏并通过nano-LC-MS / MS分析，并用Mascot进行数据库搜索。数据验证和蛋白质聚类使用MFPaQ进行，可以识别600多种独特的蛋白质。在结合促炎性介质（肿瘤坏死因子-α，干扰素-γ和淋巴毒素α/β）刺激后，该软件还成功用于EC膜蛋白质组的定量差异蛋白质组学分析，从而鉴定出完整的炎症调节的EC膜蛋白的光谱

著录项

相似文献

  • 外文文献
  • 中文文献
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号