Comparative Evaluation of Proteome Discoverer and FragPipe for the TMT-Based Proteome Quantification

Tianen He, Youqi Liu, Yan Zhou, Lu Li, He Wang, Shanjun Chen, Jinlong Gao, Wenhao Jiang, Yi Yu, Weigang Ge, Hui Yin Chang, Ziquan Fan, Alexey I. Nesvizhskii, Tiannan Guo, Yaoting Sun

研究成果: 雜誌貢獻期刊論文同行評審

7 引文 斯高帕斯(Scopus)


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.

頁(從 - 到)3007-3015
期刊Journal of Proteome Research
出版狀態已出版 - 2 12月 2022


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