Maillet Nicolas
Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France.
NAR Genom Bioinform. 2019 Oct 5;2(1):lqz004. doi: 10.1093/nargab/lqz004. eCollection 2020 Mar.
Recent developments in mass spectrometry techniques used in proteomics and proteogenomics have led to a constantly increasing interest in proteases. These proteases are used in different mass spectrometry analyses requiring protein digestions. To perform such digestions, one or multiple proteases are used. Few software exist that predict cleavage sites of proteases and simulate digestions. In this work, Rapid Peptides Generator (RPG), a new software developed in order to predict proteases-induced cleavage sites on sequences, is presented. RPG offers extra features and overcomes most issues of existing software in different ways. First, for each generated peptide, RPG gives its sequence, length and estimation of mass, measurements already provided by other software, as well as the peptide's isoelectric point. Moreover, contrary to existing software that limit the option of proteases to be used to a predefined list, users of RPG are able to easily define new proteases using a simple yet powerful grammar. This feature allows users to stay up-to-date to new or more specific proteases available on the market and optimizes time and effort before the actual mass spectrometry experiment. RPG is freely available through the well established package management system 'pip' and follows the standards for software development.
蛋白质组学和蛋白质基因组学中使用的质谱技术的最新进展引发了人们对蛋白酶的兴趣不断增加。这些蛋白酶用于需要蛋白质消化的不同质谱分析中。为了进行这种消化，会使用一种或多种蛋白酶。很少有软件能够预测蛋白酶的切割位点并模拟消化过程。在这项工作中，介绍了一种新开发的软件——快速肽生成器（RPG），用于预测序列上蛋白酶诱导的切割位点。RPG具有额外的功能，并以不同方式克服了现有软件的大多数问题。首先，对于每个生成的肽，RPG会给出其序列、长度和质量估计值（其他软件也已提供这些测量值）以及肽的等电点。此外，与将可用蛋白酶选项限制在预定义列表中的现有软件不同，RPG的用户能够使用一种简单而强大的语法轻松定义新的蛋白酶。此功能使用户能够跟上市场上新型或更特定蛋白酶的发展，并在实际质谱实验之前优化时间和精力。RPG可通过成熟的包管理系统“pip”免费获取，并遵循软件开发标准。
