Comparative analysis and optimization of proteomic information mining approaches for proteinaceous binders in painted artifacts

Abstract This study systematically compares the performance of two widely used proteomics software packages, FragPipe (FP) and Proteome Discoverer (PD), in the identification of proteinaceous binders in painted artifacts. While both tools deliver comparable performance in terms of protein identification numbers and accuracy, FP demonstrates a marked advantage in computational efficiency, completing database searches within one minute and achieving a 95.7–96.9% reduction in processing time relative to PD. Conversely, PD exhibits strengths in the nuanced analysis of specific proteins, particularly in complex matrices such as egg white glue and mixed adhesive formulations. As an open-source software freely available for non-commercial use, FP affords both high efficiency and robust accuracy in the analytical characterization of polychrome binders, whereas PD offers complementary value through its enhanced capacity for the detection of low-abundance proteins. These findings advance proteomics in archaeology and heritage conservation, optimizing protein identification strategies for ancient painted artifacts.