The recent development and implementation of the advanced peak determination (APD) algorithm with MS instrument dramatically increased the sampling of low abundance features for MS/MS fragmentation. After in‐depth evaluation, it is found that with APD on, many chimeric spectra are acquired through co‐fragmentation of high abundance contaminants with low abundance targets, and such co‐fragmentations are largely avoided when APD is off. To evaluate whether such a co‐fragmentation could significantly distort the accuracy of the isobaric‐labeling based quantitation of the low abundance target, a single‐shot TMT experiment is performed using a two‐proteome model, whereby each TMT channel contains premixed peptides from human and a cyanobacterium with a known ratio. Unexpectedly, it is found that APD does not significantly distort TMT ratios, probably because the majority of the APD‐specific chimeric spectra are not identifiable. Nevertheless, a few examples of significant distortion of TMT ratios of low abundance peptides caused by APD is found through manual inspection, and suggests that APD should be off in a single‐shot TMT experiment to avoid the laborious and time‐costing manual inspection.

中文翻译：

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在基于等压标记的单发蛋白质组定量分析中失真的高级峰测定的潜在风险评估。

带有MS仪器的先进峰测定（APD）算法的最新开发和实现极大地增加了MS / MS碎片检测低丰度特征的采样。经过深入评估，发现在打开APD时，通过对高丰度污染物和低丰度目标进行共片段化可以获得许多嵌合光谱，并且在APD关闭时可以避免这种共片段化。为了评估这种共片段化是否会严重扭曲基于等压标记的低丰度靶标定量的准确性，使用双蛋白质组模型进行了一次单次TMT实验，其中每个TMT通道均包含来自人的预混肽以及已知比例的蓝细菌。出乎意料的是，发现APD不会显着扭曲TMT比率，可能是因为大多数APD特定的嵌合光谱无法识别。但是，通过手动检查发现了一些由APD引起的低丰度肽的TMT比率显着失真的例子，建议在单次TMT实验中关闭APD，以避免费力和费时的手动检查。