This repository contains analysis (Rmd) files defining various analyses of the ScanningSWATH mass spectromentry (MS)-based plasma proteome data of the CHRIS population study. The data is available for about 3,500 participants of the CHRIS baseline collection.
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sex_age_bmi_associated_proteins.Rmd: general overview of the data, multiple linear regression-based analysis to identify sex, age and BMI associated proteins. Identification of sex hormone treatment associated proteins and sensitivity analysis to evaluate impact of this treatment on general results.
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HCU_associated_proteins_baseII.Rmd: analysis for association of proteins with hormonal contraceptive use (HCU) in the serum proteome data of the BASE-II cohort.
The mass spectrometry proteomics data for QC samples, the fasta file used for spectral library annotation and peptide and protein quantities obtained from DIA-NN have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository. The corresponding PRIDE identifiers for the study pools and quality controls are PXD052861 and PXD052892 respectively.
Individual level data acquired as part of the CHRIS study data analyzed in here can be requested for research purposes by submitting a dedicated request to the CHRIS Access Committee. Please visit https://chrisportal.eurac.edu/ for more information on the process. A similar principle is applied for the BASE-II data. Please contact the scientific coordinator as outlined on https://www.base2.mpg.de/contact.