Phosphoproteomic reanalysis of PRotein IDEntification database (PRIDE) datasets: PXD034120, PXD047134 and PXD037684

This repository contains reanalysis of published proteomics datasets for phosphorylation sites. Protein and phosphorylation data were analysed with reproducibility-optimized test statistic (ROTS) statistical test. ROTS was performed with PhosPiR pipeline. PXD034120: Mackmull, M. T. et al. Global, in situ analysis of the structural proteome in individuals with Parkinson’s diseaseto identify a new class of biomarker. Nat Struct Mol Biol 29, 978–989. ISSN: 1545-9985 (2022). Seach was done with Spectronaut 19 (Biognosys AG, Zurich, Switzerland) using sample-median normalization and MaxLFQ protein summarization. Phosphorylation of Ser, Thr, and Met oxidation and protein N-terminal acetylation were set as variable modifications, and Cys carbamidomethylation was set as a fixed modification. PXD037684: Jang, Y. et al. Mass Spectrometry–Based Proteomics Analysis of Human Substantia Nigra From Parkinson’sDisease Patients Identifies Multiple Pathways Potentially Involved in the Disease. Molecular Cellular Proteomics22, 100452. ISSN: 1535-9476 (2023). MaxQuant 2.7.5.0 was used to search the data. Phosphorylation of Ser, Thr, and Met oxidation and protein N-terminal acetylation were set as variable modifications, and Cys carbamidomethylation was set as a fixed modification. Data is tandem mass tag batches were normalized with using weighed ratio to reference channel. PXD047134: Blumenreich, S. et al. Large-scale proteomics analysis of five brain regions from Parkinson’s disease patientswith a GBA1 mutation. npj Parkinson’s Disease 10. ISSN: 2373-8057 (2024). MaxQuant 2.7.5.0 was used to search the data. Phosphorylation of Ser, Thr, and Met oxidation and protein N-terminal acetylation were set as variable modifications, and Cys carbamidomethylation was set as a fixed modification. Match between runs was turned on. Protein data analysed was downloaded from PXD047134 and LFQ intensities were used.