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生物信息学作为评估亚细胞蛋白质组学策略质量和推断蛋白质功能的工具：以植物细胞壁蛋白质组学为例

Bioinformatics as a tool for assessing the quality of sub-cellular proteomic strategies and inferring functions of proteins: plant cell wall proteomics as a test case.

作者信息

Clemente Hélène San, Pont-Lezica Rafael, Jamet Elisabeth

机构信息

Surfaces cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS-UPS-Université de Toulouse, Pôle de Biotechnologie Végétale, 24 chemin de Borde-Rouge, BP 42617 Auzeville, 31326 Castanet-Tolosan, France.

出版信息

Bioinform Biol Insights. 2009 Feb 18;3:15-28. doi: 10.4137/bbi.s2065.

DOI:10.4137/bbi.s2065
PMID:20140071
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2808182/
Abstract

Bioinformatics is used at three different steps of proteomic studies of sub-cellular compartments. First one is protein identification from mass spectrometry data. Second one is prediction of sub-cellular localization, and third one is the search of functional domains to predict the function of identified proteins in order to answer biological questions. The aim of the work was to get a new tool for improving the quality of proteomics of sub-cellular compartments. Starting from the analysis of problems found in databases, we designed a new Arabidopsis database named ProtAnnDB (http://www.polebio.scsv.ups-tlse.fr/ProtAnnDB/). It collects in one page predictions of sub-cellular localization and of functional domains made by available software. Using this database allows not only improvement of interpretation of proteomic data (top-down analysis), but also of procedures to isolate sub-cellular compartments (bottom-up quality control).

摘要

生物信息学用于亚细胞区室蛋白质组学研究的三个不同步骤。第一个步骤是从质谱数据中鉴定蛋白质。第二个步骤是预测亚细胞定位，第三个步骤是搜索功能域以预测已鉴定蛋白质的功能，从而回答生物学问题。这项工作的目的是获得一种新工具，以提高亚细胞区室蛋白质组学的质量。从对数据库中发现的问题进行分析开始，我们设计了一个名为ProtAnnDB（http://www.polebio.scsv.ups-tlse.fr/ProtAnnDB/）的拟南芥新数据库。它在一个页面中收集了可用软件对亚细胞定位和功能域的预测。使用这个数据库不仅可以改进蛋白质组学数据的解释（自上而下分析），还可以改进分离亚细胞区室的程序（自下而上质量控制）。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/a3e2343016d6/bbi-2009-015f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/10eed5240c8e/bbi-2009-015f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/9c325b19bd9e/bbi-2009-015f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/0cf106a2770a/bbi-2009-015f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/9c0674306447/bbi-2009-015f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/32817d3cf77d/bbi-2009-015f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/5349c14c3193/bbi-2009-015f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/a3e2343016d6/bbi-2009-015f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/10eed5240c8e/bbi-2009-015f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/9c325b19bd9e/bbi-2009-015f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/0cf106a2770a/bbi-2009-015f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/9c0674306447/bbi-2009-015f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/32817d3cf77d/bbi-2009-015f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/5349c14c3193/bbi-2009-015f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/65ef/2808182/a3e2343016d6/bbi-2009-015f7.jpg

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