We present RawVegetable, a software for mass spectrometry data assessment and quality control tailored toward shotgun proteomics and cross-linking experiments. RawVegetable provides four main modules with distinct features: (A) The charge state chromatogram that independently displays the ion current for each charge state; useful for optimizing the chromatography for highly charged ions and with lower XIC values such as those typically found in cross-linking experiments. (B) The XL-Artefact determination, which flags possible noncovalently associated peptides. (C) The TopN density estimation, for detecting retention time intervals of under or over-sampling, and (D) The chromatography reproducibility module, which provides pairwise comparisons between multiple experiments. RawVegetable, a tutorial, and the example data are freely available for academic use at: http://patternlabforproteomics.org/rawvegetable.

Significance

Chromatography optimization is a critical step for any shotgun proteomic or cross-linking mass spectrometry experiment. Here, we present a nifty solution with several key features, such as displaying individual charge state chromatograms, highlighting chromatographic regions of under- or over-sampling and checking for reproducibility.

中文翻译：

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RawVegetable-用于蛋白质组学和交联质谱实验的数据评估工具。

我们将展示RawVegetable，这是一种针对gun弹枪蛋白质组学和交联实验量身定制的质谱数据评估和质量控制软件。RawVegetable提供了四个具有不同功能的主要模块：（A）电荷状态色谱图，可独立显示每种电荷状态的离子电流；对于优化带高电荷离子和较低XIC值（例如在交联实验中通常发现的XIC值）的色谱非常有用。（B）XL-人工产物测定，其标记可能的非共价结合的肽。（C）TopN密度估计，用于检测欠采样或过采样的保留时间间隔；以及（D）色谱再现性模块，该模块可提供多个实验之间的成对比较。RawVegetable，一个教程，

意义

色谱优化是任何shot弹枪蛋白质组学或交联质谱实验的关键步骤。在这里，我们提出了一个具有几个关键功能的精巧解决方案，例如显示单个电荷状态色谱图，突出显示欠采样或过采样的色谱区域以及检查可重复性。