README ------ This file includes raw data information and search parameters used for PEAKS DIA demo project. The project analyzes 3 HeLa samples (5ng, 50ng and 500ng) with 3 replicates each. The DIA data is first searched using the spectral library generated by the PEAKS demo DDA project (Orbi_DDA_LFQ_Individual), where a database and de novo search is performed on the unmatched library scans. Using the results of the spectral library and database searches, identified peptides are analyzed using label-free quantification. In addition, we compare the efficiency of the analysis of DIA data without a spectral library. The data us analyzed directly using the de novo assisted database search workflow. Label-free quantification is then performed on the identified peptides. OVERVIEW -------- Project name: Orbi_DIA_LFQ_Individual Create Date: June 2, 2020 PEAKS Version: Xplus, 20200415 RAW DATA -------- Retrieved from: Bekker-Jensen, D.B., et.al. (2020). https://doi.org/10.1074/mcp.TIR119.001906 PXD016662 Files used in project: 20191114_EXP1_Evo1_AMV_DIA_Dil_5ng_30K1s_5min_01 20191114_EXP1_Evo1_AMV_DIA_Dil_5ng_30K1s_5min_02 20191114_EXP1_Evo1_AMV_DIA_Dil_5ng_30K1s_5min_03 20191114_EXP1_Evo1_AMV_DIA_Dil_50ng_15K1s_5min_01 20191114_EXP1_Evo1_AMV_DIA_Dil_50ng_15K1s_5min_02 20191114_EXP1_Evo1_AMV_DIA_Dil_50ng_15K1s_5min_03 20191114_EXP1_Evo1_AMV_DIA_Dil_500ng_15K1s_5min_01 20191114_EXP1_Evo1_AMV_DIA_Dil_500ng_15K1s_5min_02 20191114_EXP1_Evo1_AMV_DIA_Dil_500ng_15K1s_5min_02 DATA REFINEMENT --------------- Selected: Correct Precusor on Mass Only Associate features with chimera scans Filter features, charge between 2-8 SPECTRAL LIBRARY/DATABASE SEARCH PARAMETERS ------------------------------------------- Library: Generated from PEAKS DB results of PEAKS DDA demo project (Orbi_DDA_LFQ_Individual) Database: Human UniProt Reviewed Parent Error Tolerance: 10ppm Fragment Error Tolerance: 0.02 ppm Enzyme: Trypsin, Digest Mode: Specific 2 missed cleavages Modications Selected: Fixed:+57 Carbamidomethylation (C) Variable: +42 Aceytlation (Protein N-Term), +15.99 Oxidation (M), +0.98 Deamidation (NQ) Set maximum of 2 variable PTM/peptide