This repository contains a comprehensive critical commentary on the 2025 Nature article by Burger et al., titled “Synthetic alpha-synuclein fibrils replicate in mice causing MSA-like pathology.” The commentary, authored by Mengxi Zhu and Shu-Feng Zhou, presents a detailed, figure-by-figure evaluation of the study, including its Extended Data Figures and Supplementary Figures. Its purpose is to provide rigorous scientific scrutiny and enhance transparency in the interpretation of research claiming prion-like replication and in vivo pathogenicity of synthetic α-synuclein fibrils. The commentary identifies substantial methodological, conceptual, and interpretive issues that collectively challenge the strength and generalizability of the authors’ conclusions. Major points include concerns regarding the structural characterization of synthetic α-synuclein fibrils, the adequacy of in vivo pathology models, the specificity of glial cytoplasmic inclusion (GCI) identification, and the robustness of behavioral and biochemical assays used to support MSA-like phenotypes in mice. A key focus is the structural polymorphism problem. While the original study asserts that synthetic fibrils adopt an MSA-like conformation, the presented cryo-EM reconstructions lack essential validation, such as polymorph heterogeneity analyses, local resolution mapping, batch variability testing, protease-resistance profiling, and quantitative comparison with human-derived MSA fibrils. As a result, the purported structural similarity remains uncertain. The commentary also critiques the in vivo propagation evidence, highlighting insufficient stereology, ambiguous immunostaining procedures, lack of essential negative controls (heat-inactivated fibrils, endotoxin testing, scrambled-sequence fibrils), and inconsistent quantification thresholds. Claims of widespread pathological transmission are considered overstated in the absence of standardized, unbiased quantification methods. With regard to MSA-like pathology, the critique points out the absence of ultrastructural GCI validation via electron microscopy, inadequate differentiation between neuronal and glial inclusions, and incomplete cell-type–resolved imaging. Assertions of selective oligodendrocyte pathology are weakened by inconsistent staining intensities, missing g-ratio analyses, and limited high-resolution imaging. The behavioral data are evaluated as nonspecific, lacking assays that capture the core triad of MSA manifestations: autonomic failure, cerebellar dysfunction, and parkinsonism. Small sample sizes, unclear blinding, and incomplete longitudinal tracking further reduce interpretive strength. Biochemical propagation and “strain identity” experiments are found to rely heavily on qualitative or underpowered assays, with insufficient PK-digestion profiling, incomplete kinetic measurements, and potential contamination risks. Extended Data and Supplementary Figures are further examined for their methodological clarity, image normalization, and reproducibility, with multiple inconsistencies noted across quantification schemes, antibody validation, fibril preparation QC, and raw behavioral data presentation. Overall, this repository serves as a detailed and constructive scientific assessment aimed at improving rigor, transparency, and reproducibility in neurodegeneration research involving α-synuclein fibrils, prion-like propagation models, and MSA pathogenesis. It provides valuable guidance to researchers, peer reviewers, and institutions seeking to evaluate high-impact studies involving synthetic fibrils and neurodegenerative disease modeling.