DIA-BERT Source Data and Supplementary Data

Source Data.xlsx includes the raw data for all figures from the main manuscript and Supplementary Information. The data is organized by each figure in separate sheets within the Excel file. Supplementary Data.zip contains five seperate Excels: File Name: Supplementary Data 1 Description: Comparison summary of identification between DIA-NN and DIA-BERT File Name: Supplementary Data 2 Description: Identified peptide precursors and proteins using DIA-NN (in library-based mode) and DIA-BERT File Name: Supplementary Data 3 Description: Parameters for simulated data by modified Synthedia File Name: Supplementary Data 4 Description: Quantification of peptide precursors and proteins using DIA-NN (in library-based mode) and DIA-BERT in combined search File Name: Supplementary Data 5 Description: Comparison of quantification performance on the three-species dataset using DIA-BERT with different quantification models and DIA-NN.