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

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.