EVALUATION OF LTQ-ORBITRAP

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 我们评估了用于数据依赖采集的离子丰度阈值设置对 一种混合LTQ-Orbitrap质谱仪，分析了 收集的光谱，全MS扫描的信噪比，光谱质量 获得串联质谱图，以及从一种植物中鉴定的多肽和蛋白质的数量 复杂的混合物。我们发现，提高数据依赖获取的门槛 通常会减少获取光谱的数量，但会提高获取的光谱的质量。这是 当阈值设置高于完全MS扫描的噪声级别时，尤其如此。我们 比较两种不同的实验配置：一种是在 Orbitrap分析器，而串联MS扫描是在LTQ分析器中获取的，其中 全MS和串联MS扫描均在LTQ分析仪中采集。我们检查了这个数字 在不同的阈值条件下鉴定出的光谱、多肽和蛋白质，我们发现 最佳阈值设置等于或低于仪器各自的噪声水平 无论是在Orbitrap还是在LTQ分析仪中执行全MS扫描。 在比较两种分析仪的高通量识别性能时，我们 结论是，在最佳阈值水平下，LTQ和Orbitrap识别出类似的 多肽和蛋白质的数量。LTQ的扫描速度越高，会产生更多 被收集的光谱，大致被轨道诱捕器更高的质量精度所补偿， 这带来了改进的数据库搜索和多肽验证软件 性能。(J am Soc MS Spectrm 2009，xx，xxx)？2009由Elsevier Inc.于 代表美国质谱学学会

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We evaluate the effect of ion-abundance threshold settings for data-dependent acquisition on a hybrid LTQ-Orbitrap mass spectrometer, analyzing features such as the total number of spectra collected, the signal to noise ratio of the full MS scans, the spectral quality of the tandem mass spectra acquired, and the number of peptides and proteins identified from a complex mixture. We find that increasing the threshold for data-dependent acquisition generally decreases the quantity but increases the quality of the spectra acquired. This is especially true when the threshold setting is set above the noise level of the full MS scan. We compare two distinct experimental configurations: one where full MS scans are acquired in the Orbitrap analyzer while tandem MS scans are acquired in the LTQ analyzer, and one where both full MS and tandem MS scans are acquired in the LTQ analyzer. We examine the number of spectra, peptides, and proteins identified under various threshold conditions, and we find that the optimal threshold setting is at or below the respective noise level of the instrument regardless of whether the full MS scan is performed in the Orbitrap or in the LTQ analyzer. When comparing the high-throughput identification performance of the two analyzers, we conclude that, used at optimal threshold levels, the LTQ and the Orbitrap identify similar numbers of peptides and proteins. The higher scan speed of the LTQ, which results in more spectra being collected, is roughly compensated by the higher mass accuracy of the Orbitrap, which results in improved database searching and peptide validation software performance. (J Am Soc Mass Spectrom 2009, xx, xxx) ? 2009 Published by Elsevier Inc. on behalf of American Society for Mass Spectrometry