Data-independent acquisition (DIA) is a promising technique for the proteomic analysis of complex protein samples. A number of studies have claimed that DIA experiments are more reproducible than data-dependent acquisition (DDA), but these claims are unsubstantiated since different data analysis methods are used in the two methods. Data analysis in most DIA workflows depends on spectral library searches, whereas DDA typically employs sequence database searches. In this study, we examined the reproducibility of the DIA and DDA results using both sequence database and spectral library search. The comparison was first performed using a cell lysate and then extended to an interactome study. Protein overlap among the technical replicates in both DDA and DIA experiments was 30% higher with library-based identifications than with sequence database identifications. The reproducibility of quantification was also improved with library search compared to database search, with the mean of the coefficient of variation decreasing more than 30% and a reduction in the number of missing values of more than 35%. Our results show that regardless of the acquisition method, higher identification and quantification reproducibility is observed when library search was used.

中文翻译：

---

鉴定策略对 DDA 和 DIA 结果再现性的影响。

数据独立采集（DIA）是一种用于复杂蛋白质样品蛋白质组分析的有前途的技术。许多研究声称 DIA 实验比数据依赖采集 (DDA) 更具可重复性，但这些说法未经证实，因为这两种方法使用了不同的数据分析方法。大多数 DIA 工作流程中的数据分析取决于谱库搜索，而 DDA 通常采用序列数据库搜索。在本研究中，我们使用序列数据库和谱库搜索检查了 DIA 和 DDA 结果的再现性。首先使用细胞裂解物进行比较，然后扩展到相互作用组研究。在 DDA 和 DIA 实验中，基于文库的鉴定技术重复之间的蛋白质重叠比序列数据库鉴定高 30%。与数据库检索相比，图书馆检索的量化重现性也得到了提高，变异系数平均值降低了 30% 以上，缺失值数量减少了 35% 以上。我们的结果表明，无论采用何种采集方法，当使用库搜索时，都会观察到更高的鉴定和定量重现性。