LC-MS/MS, PSM and BLG properties data from "Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins"

This dataset contains the data analyzed in:

Rodriguez Palomo I, Nair B, Chang Y, Dartigues B, Dekker K, Mackie M, Evans M, Macleod R, Olsen JV, Collins MJ. (2023)  "Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins"

It contains the following data:

raw_files.zip Thermo RAW files for the 0, 4 and 128 days samples

benchmark_results.zip PSMs data from the analysis of the RAW files

Data from runs in Mascot, Fragpipe, pFind, Metamorpheus, MaxQuant and DeNovoGUI

Parameters and workflow files for MaxQuant and Fragpipe

bovin_blg_prop.zip BLG properties files: amyloid formation, 3D structure and solvent accessibility

benchmark_table.csv Table with runs settings for benchmarking

parameters_table.xlsx Spreadsheet with software parameters, derived from files used to run each software