Martens Lennart, Kohlbacher Oliver, Weintraub Susan T
†Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
‡Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
J Proteome Res. 2015 May 1;14(5):2002-4. doi: 10.1021/pr501318d. Epub 2015 Apr 22.
Computational tools are pivotal in proteomics because they are crucial for identification, quantification, and statistical assessment of data. The gateway to finding the best choice of a tool or approach for a particular problem is frequently journal articles, yet there is often an overwhelming variety of options that makes it hard to decide on the best solution. This is particularly difficult for nonexperts in bioinformatics. The maturity, reliability, and performance of tools can vary widely because publications may appear at different stages of development. A novel idea might merit early publication despite only offering proof-of-principle, while it may take years before a tool can be considered mature, and by that time it might be difficult for a new publication to be accepted because of a perceived lack of novelty. After discussions with members of the computational mass spectrometry community, we describe here proposed recommendations for organization of informatics manuscripts as a way to set the expectations of readers (and reviewers) through three different manuscript types that are based on existing journal designations. Brief Communications are short reports describing novel computational approaches where the implementation is not necessarily production-ready. Research Articles present both a novel idea and mature implementation that has been suitably benchmarked. Application Notes focus on a mature and tested tool or concept and need not be novel but should offer advancement from improved quality, ease of use, and/or implementation. Organizing computational proteomics contributions into these three manuscript types will facilitate the review process and will also enable readers to identify the maturity and applicability of the tool for their own workflows.
计算工具在蛋白质组学中至关重要，因为它们对于数据的识别、定量和统计评估至关重要。找到针对特定问题的最佳工具或方法的途径通常是期刊文章，但往往有大量的选择，这使得很难决定最佳解决方案。这对生物信息学的非专家来说尤其困难。由于出版物可能出现在不同的开发阶段，工具的成熟度、可靠性和性能可能会有很大差异。一个新颖的想法可能值得早期发表，尽管它只提供原理证明，而一个工具可能需要数年时间才能被认为是成熟的，到那时，由于缺乏新颖性，新的出版物可能很难被接受。在与计算质谱学界的成员进行讨论后，我们在此描述了关于信息学手稿组织的建议，作为一种通过基于现有期刊指定的三种不同手稿类型来设定读者（和审稿人）期望的方式。简短通讯是描述新颖计算方法的简短报告，其实现不一定准备好用于实际生产。研究文章展示了一个新颖的想法和经过适当基准测试的成熟实现。应用笔记侧重于成熟且经过测试的工具或概念，不一定新颖，但应在质量提高、易用性和/或实现方面有所进步。将计算蛋白质组学的贡献组织成这三种手稿类型将有助于审稿过程，也将使读者能够确定该工具对其自身工作流程的成熟度和适用性。
