Palaeoproteomics of ochre-rich sediment from southern Africa

Palaeoproteomics of ochre-rich sediment from southern Africa Palaeoproteomic investigation of archaeological sediments associated with ochre use in the Klipdrift Shelter, Middle Stone Age of southern Africa Description This package consists of the following data and scripts. deamidation_peptidelength_kdsochre.R sequence_reconstruction_kdsochre.R compare_depth_kdsochre.R data evidence_blank.txt evidence_sample.txt my_proteins_dict_kdsochre.txt peptides_checked_blank.txt peptides_checked_sample.txt R scripts and data This package contains the data and R scripts to analyze and visualize the results of the study. The details of each data file are as follows: evidence_blank.txt: MaxQuant output 'evidence.txt' file for the experimental blanks. This file is used for the calculation of deamidation ratios. evidence_sample.txt: MaxQuant output 'evidence.txt' file for the sediment samples. This file is used for the calculation of deamidation ratios. my_proteins_dict_kdsochre.txt: Basic information (e.g., accessions and length) on the identified proteins used for downstream analyses. This file is used for sequence reconstruction. peptides_checked_blank.txt: Modified MaxQuant output 'peptide.txt' file for the experimental blanks. Please note that the MS2 spectra of the experimental blanks were not manually validated. This file is used for sequence reconstruction. peptides_checked_sample.txt: Modified MaxQuant output 'peptide.txt' file for the sediment samples. Peptide sequences revised by manual validation are also shown in the column 'Sequence_checked'. Peptides covering eland-specific variant positions are shown in the column 'classif', along with the contaminant and reverse hits. This file is used for sequence reconstruction. Each .R file is used to analyze the data as follows: deamidation_peptidelength_kdsochre.R: Prepares evidence.txt files for the calculation of deamidation rates. Also calculates and visualizes the peptide length results. sequence_reconstruction_kdsochre.R: Performs protein sequence reconstruction for the MaxQuant results. compare_depth_kdsochre.R: Visualizes the reconstructed protein sequences and their depth information. This must be executed after sequence_reconstruction_kdsochre.R. Importantly, please set the current working directory to where these files are located in each file. The points are shown with "TODO:" notifications. Session information session_info.txt: R software output of the sessionInfo() function in the developer's environment. License Creative Commons Attribution 4.0 International (CC BY 4.0)