Quadrupole time‐of‐flight (QTof) collision‐induced dissociation (CID) and Orbitrap higher‐energy collisional dissociation (HCD) are the most commonly used fragmentation techniques in mass spectrometry‐based proteomics workflows. The information content of the MS/MS spectra is first and foremost determined by the applied collision energy. How can we set up the two instrument types to achieve maximum transferability? To answer this question, we compared MS/MS spectra obtained on a Bruker QTof CID and a Thermo Q‐Exactive Focus Orbitrap HCD instrument as a function of collision energy using the similarity index. Results show that with a few eV lower collision energy setting on HCD (Orbitrap‐specific CID) than on QTof CID, nearly identical MS/MS spectra can be obtained for leucine enkephalin pentapeptide standard, for selected +2 and +3 enolase tryptic peptides and for a large number of peptides in a HeLa protein digest. The Bruker QTof was able to produce colder ions, which may be significant to study inherently labile compounds. Further, we examined energy dependence of peptide identification confidence, as characterized by Mascot scores, on the HeLa peptides. In line with earlier QTof results, this dependence shows one or two maxima (unimodal or bimodal behavior) on Orbitrap. The fraction of bimodal peptides is lower on Orbitrap. Optimal energies as a function of m/z show a similar linear trend on both instruments, which suggests that with appropriate collision energy adjustment, matching conditions for proteomics can be achieved. Data have been deposited in the MassIVE repository (MSV000086434).

中文翻译：

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QTof 和 Orbitrap 仪器上的碰撞能量：如何使蛋白质组学测量具有可比性？

四极杆飞行时间 (QTof) 碰撞诱导解离 (CID) 和 Orbitrap 高能碰撞解离 (HCD) 是基于质谱的蛋白质组学工作流程中最常用的碎裂技术。MS/MS 谱图的信息内容首先由施加的碰撞能量决定。我们如何设置两种仪器类型以实现最大的可转移性？为了回答这个问题，我们使用相似指数比较了在布鲁克 QTof CID 和 Thermo Q-Exactive Focus Orbitrap HCD 仪器上获得的 MS/MS 光谱作为碰撞能量的函数。结果表明，HCD（Orbitrap 特定 CID）上的碰撞能量设置比 CID 的 QT 低几 eV，可以获得几乎相同的亮氨酸脑啡肽五肽标准的 MS/MS 谱图，适用于选定的 +2 和 +3 烯醇化酶胰蛋白酶肽以及 HeLa 蛋白质消化物中的大量肽。Bruker QTof 能够产生更冷的离子，这对于研究固有不稳定的化合物可能具有重要意义。此外，我们检查了肽识别置信度的能量依赖性，以 Mascot 分数为特征，对 HeLa 肽。与早期的 QTof 结果一致，这种依赖性在 Orbitrap 上显示了一个或两个最大值（单峰或双峰行为）。Orbitrap 上双峰肽的比例较低。作为函数的最佳能量 在 HeLa 肽上。与早期的 QTof 结果一致，这种依赖性在 Orbitrap 上显示了一个或两个最大值（单峰或双峰行为）。Orbitrap 上双峰肽的比例较低。作为函数的最佳能量 在 HeLa 肽上。与早期的 QTof 结果一致，这种依赖性在 Orbitrap 上显示了一个或两个最大值（单峰或双峰行为）。Orbitrap 上双峰肽的比例较低。作为函数的最佳能量m / z在两种仪器上显示出类似的线性趋势，这表明通过适当调整碰撞能量，可以实现蛋白质组学的匹配条件。数据已存放在 MassIVE 存储库 (MSV000086434) 中。