Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, No.18 Shilongshan Road, Hangzhou 310024, China.
Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, No.18 Shilongshan Road, Hangzhou 310024, China.
J Proteome Res. 2022 Dec 2;21(12):3007-3015. doi: 10.1021/acs.jproteome.2c00390. Epub 2022 Oct 31.
Isobaric labeling-based proteomics is widely applied in deep proteome quantification. Among the platforms for isobaric labeled proteomic data analysis, the commercial software Proteome Discoverer (PD) is widely used, incorporating the search engine CHIMERYS, while FragPipe (FP) is relatively new, free for noncommercial purposes, and integrates the engine MSFragger. Here, we compared PD and FP over three public proteomic data sets labeled using 6plex, 10plex, and 16plex tandem mass tags. Our results showed the protein abundances generated by the two software are highly correlated. PD quantified more proteins (10.02%, 15.44%, 8.19%) than FP with comparable NA ratios (0.00% vs. 0.00%, 0.85% vs. 0.38%, and 11.74% vs. 10.52%) in the three data sets. Using the 16plex data set, PD and FP outputs showed high consistency in quantifying technical replicates, batch effects, and functional enrichment in differentially expressed proteins. However, FP saved 93.93%, 96.65%, and 96.41% of processing time compared to PD for analyzing the three data sets, respectively. In conclusion, while PD is a well-maintained commercial software integrating various additional functions and can quantify more proteins, FP is freely available and achieves similar output with a shorter computational time. Our results will guide users in choosing the most suitable quantification software for their needs.
基于等压标记的蛋白质组学广泛应用于深度蛋白质组定量分析。在等压标记蛋白质组数据分析的平台中，商业软件 Proteome Discoverer（PD）被广泛应用，其内置搜索引擎为 CHIMERYS，而 FragPipe（FP）则相对较新，非商业用途免费，并集成了引擎 MSFragger。在这里，我们使用标记有 6 重、10 重和 16 重串联质量标签的三个公共蛋白质组数据集对 PD 和 FP 进行了比较。我们的结果表明，两种软件生成的蛋白质丰度高度相关。PD 定量的蛋白质比 FP 多（在三个数据集中分别为 10.02%、15.44%和 8.19%），但具有可比的 NA 比值（0.00%比 0.00%、0.85%比 0.38%和 11.74%比 10.52%）。使用 16 重数据集中，PD 和 FP 的输出在定量技术重复、批次效应和差异表达蛋白质的功能富集方面表现出高度一致性。然而，与 PD 相比，FP 分别节省了 93.93%、96.65%和 96.41%的处理时间来分析这三个数据集。总之，虽然 PD 是一款维护良好的商业软件，集成了各种附加功能，能够定量更多的蛋白质，但 FP 是免费提供的，并且在计算时间更短的情况下可以达到相似的输出。我们的研究结果将指导用户根据自己的需求选择最合适的定量软件。
