Tools for computational processing of LC-MS datasets:: A user's perspective
Tools for computational processing of LC-MS datasets:: A user's perspective
复制标题
DOI：
10.1016/j.cmpb.2007.03.001
复制
发表时间：
2007-06-01
影响因子：
6.1
通讯作者：
Marchiori, Elena
中科院分区：
文献类型：
--
作者：
Codrea, Marius C.;Jimenez, Connie R.;Marchiori, Elena
临床样品的液质联用(LC-MS)用于定量多肽和蛋白质的绝对离子丰度已成为一种很有前途的方法。对大量样本的蛋白质丰度变化进行量化是具有挑战性的，并且需要自动处理手段。数据分析软件的开发费时费力。幸运的是，最近已经引入了免费可用的工具，这些工具结合了可视化和数据处理的算法，并允许用户嵌入用于数据分析的外部例程。与这类工具的设计和评价有关的一个相关问题令人关切。易用性属性，如易于访问、大型数据集管理、模块化、与其他工具的集成等，对于使用来自不同(可能是集成的)工具的方法和可视化技术执行大规模综合数据分析非常重要。在这篇文章中，我们考虑了最近在顶级国际期刊上介绍的四个免费可用的工具，以确定这样的可用性描述符的列表。我们提出了10个描述符，它们既可以作为开发新工具时的指导方针，也可以作为评估现有工具可用性的参数。所考虑的工具表现出令人满意的可用性，最新的工具表现出更好的灵活性，表明工具的设计趋势是让用户在方法和工具的选择、使用和整合中发挥更核心的作用。(C)2007爱思唯尔爱尔兰有限公司。保留所有权利。
Liquid chromatography-mass spectrometry (LC-MS) profiling of clinical samples for quantifying absolute ion abundances of peptides and proteins has emerged as a promising approach. Quantitation of changes in protein abundance of large number of samples is challenging and requires automatic processing means. The development of data analysis software is laborious and time-consuming. Fortunately, freely available tools have been recently introduced, which incorporate algorithms for visualization and data processing and allow the user to embed external routines for data analysis. A relevant issue related to the design and evaluation of such tools concerns. usability Properties such as easy access, large datasets management, modularity, integration with other tools, etc, are important for performing large-scale integrative data analysis with methods and visual techniques from different (possibly integrated) tools. In this paper, we consider four freely available tools recently introduced in top international journals in order to identify a list of such usability descriptors. We propose 10 descriptors that can be used both as guidelines when developing new tools and as parameters for assessing usability of existing tools. The considered tools show satisfactory usability properties, and the most recent tools exhibit improved flexibility, indicating a trend towards the design of tools that give the user a more central role in the selection, use and integration of methods and tools. (c) 2007 Elsevier Ireland Ltd. All rights reserved.