DDA-BERT Source Data

Description This dataset provides the source data for the manuscript related to DDA-BERT. It contains the underlying data for all figures and tables presented in the main text and supplementary information. File Organization Source_data.xlsx This primary Excel file contains the majority of the raw and processed data used to generate the charts and figures. Data is organized into individual worksheets, each labeled according to its corresponding Figure or Supplementary Figure number. Raw Data Archives (ZIP files) For figures involving large-scale datasets or numerous individual files (e.g., multi-species benchmark metrics), source data are archived into separate ZIP packages: Figure2.zip: Contains scoring data for human samples across different software tools: Figure2A-B_FragPipe_human_score.csv Figure2A-B_Sage_human_score.csv Figure2A-C_DDA-BERT_human_score.csv Figure6.zip: Contains source files for diagnostic analysis of overfitting and sequence memorization in DDA-BERT, along with four benchmark files used for FDP (False Discovery Proportion) calculation: Figure6A_box_plot.csv Figure6B_intensity.csv Figure6C_220627_GG_02_rep3_dil10_peptide.csv Figure6C_220627_GG_04_rep1_dil10_peptide.csv Figure6C_220627_GG_06_rep1_dil10_peptide.csv Figure6C_220627_GG_07_rep2_dil10_peptide.csv Supplementary Figure1.zip: Provides multi-species scoring data (fruit fly, Arabidopsis, and yeast) used for comparative analysis of different software tools: SFigure1A_DDA-BERT/FragPipe/Sage_fruit_fly_score.csv SFigure1B_DDA-BERT/FragPipe/Sage_artha_score.csv SFigure1C_DDA-BERT/FragPipe/Sage_yeast_score.csv Supplementary Figure4.zip: Contains summary tables of protein groups and peptide identification counts across all benchmark datasets, systematically organized by software tool: Sub-folders: AlphaPept, AlphaPeptDeep, DDA-BERT, FP (FragPipe), MS2Rescore, and Sage. Code and Visualization Scripts The scripts used for data processing, analysis, and figure generation are available on the official GitHub repository: Repository: zhiyuajun/DDA-BERT Path: DDA-BERT/scripts Model and Software Information For detailed implementation of the DDA-BERT model, including architecture, environment setup, and Docker images, please refer to the GitHub repository mentioned above.