Fig. 2.

The dependence of well-performing manipulation chains on the selection of quantification tool comprehensively assessed by the precision of 3,128 potential chains. First, the clustering analyses among manipulation chains across multiple datasets were conducted for three quantification tools: (A) MaxQuant, (B) Progenesis, and (C) OpenMS. Then, three neighboring partitions of varied performance were identified, which included partition αcontaining the chains of consistently superior precision (PMADs <0.14) across multiple datasets, partition βincluding the chain of good precision (PMADs <0.3) across multiple datasets, partition γ consisting of the chains of fair precision (PMADs <0.7) for multiple datasets. Finally, the Venn diagrams showing the chains shared by multiple tools or demonstrating tool-specific characteristics were provided for the chains within (D) partition α, (E) partition α and β, and (F) partition α and β and γ.