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Spritz: A Proteogenomic Database Engine
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2020-09-23 , DOI: 10.1021/acs.jproteome.0c00407 Anthony J Cesnik 1, 2, 3, 4 , Rachel M Miller 1 , Khairina Ibrahim 1 , Lei Lu 1 , Robert J Millikin 1 , Michael R Shortreed 1 , Brian L Frey 1 , Lloyd M Smith 1
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2020-09-23 , DOI: 10.1021/acs.jproteome.0c00407 Anthony J Cesnik 1, 2, 3, 4 , Rachel M Miller 1 , Khairina Ibrahim 1 , Lei Lu 1 , Robert J Millikin 1 , Michael R Shortreed 1 , Brian L Frey 1 , Lloyd M Smith 1
Affiliation
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Proteoforms are the workhorses of the cell, and subtle differences between their amino acid sequences or post-translational modifications (PTMs) can change their biological function. To most effectively identify and quantify proteoforms in genetically diverse samples by mass spectrometry (MS), it is advantageous to search the MS data against a sample-specific protein database that is tailored to the sample being analyzed, in that it contains the correct amino acid sequences and relevant PTMs for that sample. To this end, we have developed Spritz (https://smith-chem-wisc.github.io/Spritz/), an open-source software tool for generating protein databases annotated with sequence variations and PTMs. We provide a simple graphical user interface for Windows and scripts that can be run on any operating system. Spritz automatically sets up and executes approximately 20 tools, which enable the construction of a proteogenomic database from only raw RNA sequencing data. Sequence variations that are discovered in RNA sequencing data upon comparison to the Ensembl reference genome are annotated on proteins in these databases, and PTM annotations are transferred from UniProt. Modifications can also be discovered and added to the database using bottom-up mass spectrometry data and global PTM discovery in MetaMorpheus. We demonstrate that such sample-specific databases allow the identification of variant peptides, modified variant peptides, and variant proteoforms by searching bottom-up and top-down proteomic data from the Jurkat human T lymphocyte cell line and demonstrate the identification of phosphorylated variant sites with phosphoproteomic data from the U2OS human osteosarcoma cell line.
中文翻译：
Spritz：蛋白质基因组数据库引擎
蛋白质型是细胞的主力军，它们的氨基酸序列或翻译后修饰 (PTM) 之间的细微差异可以改变它们的生物学功能。为了通过质谱法 (MS) 最有效地识别和量化遗传多样性样品中的蛋白质形式，根据针对被分析样品量身定制的样品特异性蛋白质数据库搜索 MS 数据是有利的，因为它包含正确的氨基酸该样本的序列和相关 PTM。为此，我们开发了 Spritz (https://smith-chem-wisc.github.io/Spritz/)，这是一种用于生成带有序列变异和 PTM 注释的蛋白质数据库的开源软件工具。我们为 Windows 和可在任何操作系统上运行的脚本提供简单的图形用户界面。Spritz 自动设置和执行大约 20 个工具，这些工具可以仅从原始 RNA 测序数据构建蛋白质基因组数据库。与 Ensembl 参考基因组比较后在 RNA 测序数据中发现的序列变异在这些数据库中的蛋白质上进行注释，而 PTM 注释则从 UniProt 转移。还可以使用 MetaMorpheus 中的自下而上质谱数据和全局 PTM 发现来发现修改并将其添加到数据库中。我们证明这种特定于样品的数据库允许识别变异肽、修饰的变异肽、
更新日期：2020-09-23
中文翻译：
Spritz：蛋白质基因组数据库引擎
蛋白质型是细胞的主力军，它们的氨基酸序列或翻译后修饰 (PTM) 之间的细微差异可以改变它们的生物学功能。为了通过质谱法 (MS) 最有效地识别和量化遗传多样性样品中的蛋白质形式，根据针对被分析样品量身定制的样品特异性蛋白质数据库搜索 MS 数据是有利的，因为它包含正确的氨基酸该样本的序列和相关 PTM。为此，我们开发了 Spritz (https://smith-chem-wisc.github.io/Spritz/)，这是一种用于生成带有序列变异和 PTM 注释的蛋白质数据库的开源软件工具。我们为 Windows 和可在任何操作系统上运行的脚本提供简单的图形用户界面。Spritz 自动设置和执行大约 20 个工具，这些工具可以仅从原始 RNA 测序数据构建蛋白质基因组数据库。与 Ensembl 参考基因组比较后在 RNA 测序数据中发现的序列变异在这些数据库中的蛋白质上进行注释，而 PTM 注释则从 UniProt 转移。还可以使用 MetaMorpheus 中的自下而上质谱数据和全局 PTM 发现来发现修改并将其添加到数据库中。我们证明这种特定于样品的数据库允许识别变异肽、修饰的变异肽、
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