PubChem serves as a comprehensive repository, housing over 100 million unique chemical structures representing the breadth of our chemical knowledge across numerous fields including metabolism, pharmaceuticals, toxicology, cosmetics, agriculture, and many more. Rapid identification of these small molecules increasingly relies on electrospray ionization (ESI) paired with tandem mass spectrometry (MS/MS), particularly by comparison to genuine standard MS/MS data sets. Despite its widespread application, achieving consistency in MS/MS data across various analytical platforms remains an unaddressed concern. This study evaluated MS/MS data derived from one hundred molecular standards utilizing instruments from five manufacturers, inclusive of quadrupole time-of-flight (QTOF) and quadrupole orbitrap “exactive” (QE) mass spectrometers by Agilent (QTOF), Bruker (QTOF), SCIEX (QTOF), Waters (QTOF), and Thermo QE. We assessed fragment ion variations at multiple collisional energies (0, 10, 20, and 40 eV) using the cosine scoring algorithm for comparisons and the number of fragments observed. A parallel visual analysis of the MS/MS spectra across instruments was conducted, consistent with a standard procedure that is used to circumvent the still prevalent issue of mischaracterizations as shown for dimethyl sphingosine and C20 sphingosine. Our analysis revealed a notable consistency in MS/MS data and identifications, with fragment ions’ m/z values exhibiting the highest concordance between instrument platforms at 20 eV, the other collisional energies (0, 10, and 40 eV) were significantly lower. While moving toward a standardized ESI MS/MS protocol is required for dependable molecular characterization, our results also underscore the continued importance of corroborating MS/MS data against standards to ensure accurate identifications. Our findings suggest that ESI MS/MS manufacturers, akin to the established norms for gas chromatography mass spectrometry instruments, should standardize the collision energy at 20 eV across different instrument platforms.

中文翻译：

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跨平台串联质谱分析

PubChem 是一个综合存储库，包含超过 1 亿个独特的化学结构，代表了我们在新陈代谢、制药、毒理学、化妆品、农业等众多领域的化学知识的广度。这些小分子的快速识别越来越依赖于电喷雾电离 (ESI) 与串联质谱 (MS/MS) 的配合，特别是通过与真正的标准 MS/MS 数据集进行比较。尽管其应用广泛，但在不同分析平台上实现 MS/MS 数据的一致性仍然是一个尚未解决的问题。本研究使用来自五家制造商的仪器评估了来自一百个分子标准品的 MS/MS 数据，包括安捷伦 (QTOF)、布鲁克 (QTOF) 的四极杆飞行时间 (QTOF) 和四极轨道阱“精确”(QE) 质谱仪)、SCIEX (QTOF)、沃特世 (QTOF) 和 Thermo QE。我们使用余弦评分算法评估了多个碰撞能量（0、10、20 和 40 eV）下的碎片离子变化，以进行比较和观察到的碎片数量。对跨仪器的 MS/MS 谱图进行了并行视觉分析，符合标准程序，该程序用于规避仍然普遍存在的二甲基鞘氨醇和 C20 鞘氨醇错误表征问题。我们的分析显示 MS/MS 数据和鉴定具有显着的一致性，碎片离子的m / z值在 20 eV 处表现出仪器平台之间的最高一致性，其他碰撞能量（0、10 和 40 eV）明显较低。虽然可靠的分子表征需要采用标准化的 ESI MS/MS 协议，但我们的结果也强调了根据标准验证 MS/MS 数据以确保准确识别的持续重要性。我们的研究结果表明，ESI MS/MS 制造商与气相色谱质谱仪器的既定标准类似，应将不同仪器平台的碰撞能量标准化为 20 eV。