Example datasets including DIA-NN "basic" and "semi-tryptic" searches, and a "msms.txt" MaxQuant file before and after rescoring using mokapot from MS2Rescore.

The data.zip file contains: DIA-NN outputs and libraries from searches of raw files associated with Proteobench (https://proteobench.readthedocs.io/en/stable/available-modules/archived-modules/4-quant-lfq-ion-dia-aif/) and using the FASTA file provided on Proteobench ("ProteoBenchFASTA_MixedSpecies_HYE.fasta" file). Predicted libraries were first generated. One search is a "basic" search (using only the "ProteoBenchFASTA_MixedSpecies_HYE.fasta" file to predict a library), another is the same search where we also included the Arabiptosis Thaliana proteome ("uniprotkb_taxonomy_id_3702_AND_reviewed_2026_02_06.fasta"), and another is a search where we activated the "semi-tryptic" option (using only the "ProteoBenchFASTA_MixedSpecies_HYE.fasta" file to predict a library). All the predicted libraries of DIA-NN are included in the files. MS2Rescore outputs from rescoring a "msms.txt" MaxQuant file that corresponds to the raw file "20161213_NGHF_DBJ_SA_Exp3A_HeLa_1ug_7min_15000_02.mgf" searched using "uniprot-proteome-human-contaminants.fasta" with MaxQuant.