Great advances have been made in sensitivity and acquisition speed on the Orbitrap mass analyzer, enabling increasingly deep proteome coverage. However, these advances have been mainly limited to the MS2 level, whereas ion beam sampling for the MS1 scans remains extremely inefficient. Here we report a data-acquisition method, termed BoxCar, in which filling multiple narrow mass-to-charge segments increases the mean ion injection time more than tenfold as compared to that of a standard full scan. In 1-h analyses, the method provided MS1-level evidence for more than 90% of the proteome of a human cancer cell line that had previously been identified in 24 fractions, and it quantified more than 6,200 proteins in ten of ten replicates. In mouse brain tissue, we detected more than 10,000 proteins in only 100 min, and sensitivity extended into the low-attomolar range.

Orbitrap质量分析仪在灵敏度和采集速度方面取得了长足的进步，可实现越来越深的蛋白质组覆盖。但是，这些进展主要限于MS2级别，而用于MS1扫描的离子束采样仍然效率极低。在这里，我们报告了一种称为BoxCar的数据获取方法，其中填充多个狭窄的质荷部分会使平均离子注入时间比标准全扫描的平均离子注入时间增加十倍以上。在1-h分析中，该方法为人类癌细胞系中90％以上的蛋白质组提供了MS1级证据，该蛋白质组先前已在24个馏分中鉴定出来，并且在十次重复中的十次中定量了6,200多种蛋白质。在老鼠的脑组织中，我们仅在100分钟内检测到10,000多种蛋白质，