Progress in proteomics is mainly driven by advances in mass spectrometric (MS) technologies. Here we benchmarked the performance of the latest MS instrument in the benchtop Orbitrap series, the Q Exactive HF-X, against its predecessor for proteomics applications. A new peak-picking algorithm, a brighter ion source, and optimized ion transfers enable productive MS/MS acquisition above 40 Hz at 7500 resolution. The hardware and software improvements collectively resulted in improved peptide and protein identifications across all comparable conditions, with an increase of up to 50 percent at short LC–MS gradients, yielding identification rates of more than 1000 unique peptides per minute. Alternatively, the Q Exactive HF-X is capable of achieving the same proteome coverage as its predecessor in approximately half the gradient time or at 10-fold lower sample loads. The Q Exactive HF-X also enables rapid phosphoproteomics with routine analysis of more than 5000 phosphopeptides with short single-shot 15 min LC–MS/MS measurements, or 16 700 phosphopeptides quantified across ten conditions in six gradient hours using TMT10-plex and offline peptide fractionation. Finally, exciting perspectives for data-independent acquisition are highlighted with reproducible identification of 55 000 unique peptides covering 5900 proteins in half an hour of MS analysis.

中文翻译：

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Q Exactive HF-X用于Shot弹枪蛋白质组学的性能评估

蛋白质组学的进步主要是由质谱（MS）技术的进步推动的。在这里，我们将台式Orbitrap系列最新型MS仪器Q Exactive HF-X的性能与其蛋白质组学应用的前身进行了基准比较。一种新的峰采集算法，更明亮的离子源和优化的离子转移功能，可以在7500分辨率下在40 Hz以上的频率下进行高效的MS / MS采集。硬件和软件的改进共同改善了所有可比条件下的肽和蛋白质鉴定，在较短的LC-MS梯度条件下，肽和蛋白质鉴定增加了50％，每分钟可鉴定1000多种独特的肽。或者，Q Exactive HF-X能够在大约一半的梯度时间内或以低10倍的样品负载获得与其前代相同的蛋白质组覆盖率。Q Exactive HF-X还可以通过短时间的单次15分钟LC-MS / MS测量进行常规分析，对5000多种磷酸肽进行常规分析，或通过使用TMT10-plex和离线在六个梯度小时内在十种条件下定量分析的16700种磷酸肽，实现了快速的蛋白质组学研究肽分级分离。最后，在半小时的质谱分析中可重复鉴定55 000个覆盖5900种蛋白质的独特肽，突显了与数据无关的采集的令人兴奋的观点。使用TMT10-plex和离线肽分级分离法，在六个梯度小时内，在十个条件下对16个磷酸肽或16700个磷酸肽进行了定量。最后，在半小时的质谱分析中可重复鉴定55 000个覆盖5900种蛋白质的独特肽，突显了与数据无关的采集的令人兴奋的观点。使用TMT10-plex和离线肽分级分离法，在六个梯度小时内，在十种条件下对16个磷酸化肽或16700个磷酸肽进行了定量分析。最后，在半小时的质谱分析中可重复鉴定55 000个覆盖5900种蛋白质的独特肽，突显了与数据无关的采集的令人兴奋的观点。