The isobaric carrier approach, which combines small isobarically-labeled samples with a larger isobarically-labeled carrier sample, is finding diverse applications in ultrasensitive mass-spectrometry analysis of very small samples, such as single cells. To enhance the growing use of isobaric carriers, we characterized the trade-offs of using isobaric carriers in controlled experiments with complex human proteomes. The data indicate that isobaric carriers directly enhances peptide sequence identification without simultaneously increasing the number of protein copies sampled from small samples. The results also indicate strategies for optimizing the amount of isobaric carrier and analytical parameters, such as ion accumulation time, for different priorities such as improved quantification or increased number of identified proteins. Balancing these trade-offs enables adapting isobaric carrier experiments to different applications, such as quantifying proteins from limited biopsies or organoids, building single-cell atlases, or modeling protein networks in single cells. In all cases, the reliability of protein quantification should be estimated and incorporated in all subsequent analysis. We expect that these guidelines will aid in explicit incorporation of the characterized trade-offs in experimental designs and transparent error propagation in data analysis.

中文翻译：

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使用等压载体优化实验中蛋白质定量的准确性和深度

等压载体方法将等压标记的小样品与等压标记的大样品结合在一起，在超灵敏质谱分析非常小的样品（如单细胞）中发现了多种应用。为了增强同量异位载体的使用，我们在复杂的人类蛋白质组的受控实验中表征了使用同量异位载体的取舍。数据表明，同量异位载体直接增强了肽序列的鉴定，而没有同时增加从小样品中取样的蛋白质拷贝数。结果还表明了针对不同优先级（例如改进的定量或增加的鉴定蛋白质数量）优化等压载体和分析参数（例如离子积累时间）的策略。权衡这些折衷可以使等压载体实验适应不同的应用，例如从有限的活检或类器官中定量蛋白质，建立单细胞图谱或在单细胞中建立蛋白质网络模型。在所有情况下，都应评估蛋白质定量的可靠性，并将其纳入所有后续分析中。我们希望这些指导方针将有助于在实验设计中明确体现特征权衡，并在数据分析中透明地传播误差。应该估计蛋白质定量的可靠性，并将其纳入所有后续分析中。我们希望这些指导方针将有助于在实验设计中明确体现特征权衡，并在数据分析中透明地传播误差。应该估计蛋白质定量的可靠性，并将其纳入所有后续分析中。我们希望这些指导方针将有助于在实验设计中明确体现特征权衡，并在数据分析中透明地传播误差。