Leeming Michael G, Ang Ching-Seng, Nie Shuai, Varshney Swati, Williamson Nicholas A
Bio21 Molecular Science & Biotechnology Institute, Melbourne Mass Spectrometry and Proteomics Facility, The University of Melbourne, Melbourne, VIC 3052, Australia.
Bioinform Adv. 2022 Dec 19;3(1):vbac096. doi: 10.1093/bioadv/vbac096. eCollection 2023.
A large number of experimental and bioinformatic parameters must be set to identify and quantify peptides in mass spectrometry experiments and each of these will impact the results. An ability to simulate raw data with known contents would allow researchers to rapidly explore the effects of varying experimental parameters and systematically investigate downstream processing software. A range of data simulators are available for established data-dependent acquisition methodologies, but these do not extend to the rapidly developing field of data-independent acquisition (DIA) strategies.
Here, we present a software package to simulate DIA liquid chromatography-mass spectrometry for bottom-up proteomics experiments. Synthedia can generate datasets with known peptide precursor ions and fragments and allows for the customization of a wide variety of chromatographic and mass spectrometry parameters.
Synthedia is freely available via the internet and can be used through a graphical website (https://synthedia.org/) or locally via the command line (https://github.com/mgleeming/synthedia/).
Supplementary data are available at online.
在质谱实验中，必须设置大量实验参数和生物信息学参数来识别和定量肽段，而其中每一个参数都将影响实验结果。能够模拟具有已知内容的原始数据，将使研究人员能够快速探索不同实验参数的影响，并系统地研究下游处理软件。对于已确立的数据依赖型采集方法，有一系列数据模拟器可供使用，但这些模拟器并不适用于快速发展的数据非依赖型采集（DIA）策略领域。
在此，我们展示了一个用于模拟自下而上蛋白质组学实验的DIA液相色谱 - 质谱的软件包。Synthedia可以生成具有已知肽前体离子和片段的数据集，并允许定制各种色谱和质谱参数。
Synthedia可通过互联网免费获取，可通过图形化网站（https://synthedia.org/）使用，也可通过命令行在本地使用（https://github.com/mgleeming/synthedia/）。
补充数据可在网上获取。
