EVALUATION OF LTQ-ORBITRAP

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 我们评估了离子丰度阈值设置对数据依赖采集的影响， 混合LTQ-Orbitrap质谱仪，分析特征，例如 所收集的光谱、全MS扫描的信噪比、所收集的光谱的光谱质量、以及所收集的光谱的质量。 获得的串联质谱，以及从一个样品中鉴定的肽和蛋白质的数量， 复杂混合物我们发现，增加数据依赖采集的阈值 通常减少了所获得的光谱的数量但提高了光谱的质量。这是 当阈值设置被设置为高于全MS扫描的噪声水平时尤其如此。我们 比较两种不同的实验配置：一种是在 在LTQ分析仪中采集串联MS扫描时， 在LTQ分析仪中获取全MS和串联MS扫描。我们研究了 的光谱，肽，和蛋白质在各种阈值条件下确定，我们发现 最佳阈值设置等于或低于仪器的相应噪声水平 无论是在Orbitrap还是在LTQ分析仪中执行完整的MS扫描。 当比较两种分析仪的高通量鉴定性能时，我们 结论是，在最佳阈值水平下使用，LTQ和Orbitrap识别类似的 肽和蛋白质的数量。LTQ的扫描速度越高， 收集的光谱，大致上被轨道阱的更高质量精度所补偿， 这导致改进的数据库搜索和肽验证软件 性能（J Am Soc Mass Spectrom 2009，xx，xxx）？2009年由Elsevier Inc.出版对 美国质谱学会American Society for Mass Spectrometry

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