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

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


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.

Original languageEnglish
Pages (from-to)3007-3015
Number of pages9
JournalJournal of Proteome Research
Issue number12
StatePublished - 2 Dec 2022


  • FragPipe
  • Proteome Discoverer
  • labeled quantitative proteomics
  • mass spectrometry
  • tandem mass tag


Dive into the research topics of 'Comparative Evaluation of Proteome Discoverer and FragPipe for the TMT-Based Proteome Quantification'. Together they form a unique fingerprint.

Cite this