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.本仓库针对已发表的磷酸化位点蛋白质组学数据集开展了重新分析。研究采用可重复性优化检验统计量（reproducibility-optimized test statistic, ROTS）对蛋白质及磷酸化数据进行统计检验，并通过PhosPiR分析流程执行ROTS分析。 PXD034120： 相关研究为Mackmull M. T. 等人于2022年发表于《自然-结构与分子生物学》的论文《Global, in situ analysis of the structural proteome in individuals with Parkinson’s disease to identify a new class of biomarker》，卷29，页码978–989，ISSN：1545-9985。 本研究采用Spectronaut 19（瑞士苏黎世Biognosys AG公司）进行数据库检索，采用样本中位数归一化方法，并通过MaxLFQ完成蛋白质定量汇总。可变修饰设定为丝氨酸（Ser）、苏氨酸（Thr）磷酸化、甲硫氨酸氧化以及蛋白质N端乙酰化，固定修饰设定为半胱氨酸氨基甲酰化。 PXD037684： 相关研究为Jang Y. 等人于2023年发表于《分子与细胞蛋白质组学》的论文《Mass Spectrometry–Based Proteomics Analysis of Human Substantia Nigra From Parkinson’s Disease Patients Identifies Multiple Pathways Potentially Involved in the Disease》，卷22，文章编号100452，ISSN：1535-9476。 本研究采用MaxQuant 2.7.5.0进行数据库检索。可变修饰设定为丝氨酸、苏氨酸磷酸化、甲硫氨酸氧化以及蛋白质N端乙酰化，固定修饰设定为半胱氨酸氨基甲酰化。串联质量标签（tandem mass tag, TMT）批次数据采用基于参考通道的加权比率法进行归一化处理。 PXD047134： 相关研究为Blumenreich S. 等人于2024年发表于《npj 帕金森病》的论文《Large-scale proteomics analysis of five brain regions from Parkinson’s disease patients with a GBA1 mutation》，卷10，ISSN：2373-8057。 本研究采用MaxQuant 2.7.5.0进行数据库检索，并开启了运行间匹配（Match between runs）功能。可变修饰设定为丝氨酸、苏氨酸磷酸化、甲硫氨酸氧化以及蛋白质N端乙酰化，固定修饰设定为半胱氨酸氨基甲酰化。本次分析所用蛋白质数据下载自PXD047134数据集，采用无标记定量（label-free quantification, LFQ）强度值进行后续分析。