Modern ion trap mass spectrometers are capable of collecting up to 60 tandem MS (MS/MS) scans per second, in theory providing acquisition speeds that can sample every eluting peptide precursor presented to the MS system. In practice, however, the precursor sampling capacity enabled by these ultrafast acquisition rates is often underutilized due to a host of reasons (e.g., long injection times and wide analyzer mass ranges). One often overlooked reason for this underutilization is that the instrument exhausts all the peptide features it identifies as suitable for MS/MS fragmentation. Highly abundant features can prevent annotation of lower abundance precursor ions that occupy similar mass-to-charge (m/z) space, which ultimately inhibits the acquisition of an MS/MS event. Here, we present an advanced peak determination (APD) algorithm that uses an iterative approach to annotate densely populated m/z regions to increase the number of peptides sampled during data-dependent LC-MS/MS analyses. The APD algorithm enables nearly full utilization of the sampling capacity of a quadrupole-Orbitrap-linear ion trap MS system, which yields up to a 40% increase in unique peptide identifications from whole cell HeLa lysates (approximately 53 000 in a 90 min LC-MS/MS analysis). The APD algorithm maintains improved peptide and protein identifications across several modes of proteomic data acquisition, including varying gradient lengths, different degrees of prefractionation, peptides derived from multiple proteases, and phosphoproteomic analyses. Additionally, the use of APD increases the number of peptides characterized per protein, providing improved protein quantification. In all, the APD algorithm increases the number of detectable peptide features, which maximizes utilization of the high MS/MS capacities and significantly improves sampling depth and identifications in proteomic experiments.

中文翻译：

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用于数据相关质谱的改进的前体表征

现代离子阱质谱仪每秒最多可收集60个串联MS（MS / MS）扫描，理论上提供了可以对提供给MS系统的每种洗脱肽前体进行采样的采集速度。然而，实际上，由于多种原因（例如，较长的进样时间和较宽的分析仪质量范围），这些超快采集速率所启用的前体采样能力经常得不到充分利用。这种未充分利用的一个经常被忽视的原因是该仪器耗尽了其鉴定为适合MS / MS片段化的所有肽特征。高度丰富的特征可以防止对占据相似质荷比（m / z）空间，这最终会阻止MS / MS事件的获取。在这里，我们提出了一种先进的峰值确定（APD）算法，该算法使用迭代方法来注释人口稠密的m / z数据依赖的LC-MS / MS分析过程中增加采样区域数量的区域。APD算法几乎可以充分利用四极杆-Orbitrap线性离子阱质谱系统的采样能力，从全细胞HeLa裂解物中分离出的独特肽段最多可增加40％（在90分钟的LC-分析中约为5.3万） MS / MS分析）。APD算法可在多种蛋白质组数据采集模式下保持改进的肽和蛋白质鉴定，包括不同的梯度长度，不同的预分离程度，衍生自多种蛋白酶的肽以及磷酸化蛋白质组分析。另外，APD的使用增加了每种蛋白质的特征肽数量，从而改善了蛋白质定量。总而言之，APD算法增加了可检测的肽特征的数量，