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ChromEval: A Software Application for the Rapid Evaluation of HPLC System Performance in Proteomic Applications

机译：ChromEval：在蛋白质组学应用中快速评估HPLC系统性能的软件应用程序

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Mass spectrometry-based proteomics is typically performed using high performance liquid chromatography (HPLC) to introduce peptides into the instrument via electrospray ionization. A variety of configurations exist with varying degrees of precision and cost, but the ultimate goal is the reproducible delivery of peptides in well-separated elution peaks. It is well-known that the quality of chromatography can have a dramatic effect on sample identification as well as run-to-run reproducibility, which is especially important for quantitative analyses. Despite the importance of the HPLC system for both shotgun and targeted proteomics, there are few tools available to monitor HPLC performance. In this paper, we describe a new open-source software application, named ChromEval, to allow rapid assessment of HPLC performance, as well as to provide other metrics of mass spectrometer performance, including mass accuracy calibration. ChromEval permits the user to visually monitor the elution of a set of standard peptides in quality control runs interspersed among a regular workflow. To perform these tasks, ChromEval searches mzXML files using Tandem and presents the peptide results in a graphical user interface (GUI) that allows fast assessment of chromatography by visualization of superimposed elution peaks. This tool facilitates the identification and trouble-shooting of chromatography problems such as retention time shifts and variance in sample loading due to autosampler error. It also provides crude but consistent metrics of instrument performance including mass accuracy calibration and number of peptides identified from the standard mixture. ChromEval generates easily interpretable data quickly and thereby enables goo-go decision making during intensive instrument operation.
机译：基于质谱的蛋白质组学通常使用高效液相色谱（HPLC）进行，以通过电喷雾电离将肽引入仪器。存在各种配置，精度和成本各不相同，但最终目标是在分离良好的洗脱峰中可再现地输送肽。众所周知，色谱质量可以对样品鉴定以及批次间的重现性产生巨大影响，这对于定量分析尤为重要。尽管HPLC系统对于shot弹枪和靶向蛋白质组学都很重要，但几乎没有可用的工具来监控HPLC性能。在本文中，我们描述了一种名为ChromEval的新开源软件应用程序，该应用程序可以快速评估HPLC性能，并提供质谱仪性能的其他指标，包括质量准确度校准。 ChromEval允许用户可视化地监控散布在常规工作流程中的质量控制运行中一组标准肽的洗脱。为了执行这些任务，ChromEval使用Tandem搜索mzXML文件，并在图形用户界面（GUI）中显示肽段结果，从而可以通过可视化叠加的洗脱峰来快速评估色谱。该工具有助于识别和解决色谱问题，例如由于自动进样器错误而导致的保留时间偏移和样品上样量变化。它还提供了仪器性能的粗略但一致的指标，包括质量准确度校准和从标准混合物中鉴定出的肽数。 ChromEval可以快速生成易于解释的数据，从而可以在密集的仪器操作过程中进行通过/不通过决策。

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