Data for "Beyond Delta Masses: MS Andrea Directly Resolves Combinatorial Peptide Modifications in Open Searches"

This dataset contains reanalyzed data from four different datasets. The following three datasets were used to evaluate and compare the performance of MS Andrea, MSFragger and Sage. The first dataset contains phosphorylation-enriched peptides from HeLa cells. The original dataset was published by Bekker-Jensen et al. 2020 and the full dataset is available on ProteomeXchange via the PRIDE partner repository using ID PXD014525 The second dataset is phosphorylation-enriched peptides from Arabidopsis thaliana. The dataset was published by Mergner et al. 2020 and the full dataset is available on ProteomeXchange via the PRIDE partner repository using ID PXD013868 The third dataset is histone proteins isolated from breast cancer patients. The dataset was published by Noberini et al. 2016 and the full dataset is available on ProteomeXchange via the PRIDE partner repository using ID PXD002669 A folder for each of the datasets contains the following: .mzml files used for the database searches MS Andrea result files MS Andrea pin and pout files MSFragger result files Output files from Fragpipe Sage result files The fourth dataset is a synthetic phosphopeptide library which was used to evaluate the ability of MS Andrea to control FDR. The dataset was published by Marx et al. 2013, and the full peptide library is available on ProteomeXchange via the PRIDE partner repository using ID PXD000138 For this dataset the folder contains .mzml files used for the database searches MS Andrea result files