DIA-NN software is an innovative tool for processing proteomic data sets acquired using data-independent acquisition (DIA). Specific algorithms identify and quantify peptides and proteins in DIA data from fixed-window, variable-window (VW), or ZT Scan DIA experiments. (ZT Scan is achieved on a ZenoTOF 7600 system.)
Here, we describe the recommended data processing settings in DIA-NN software (v 1.81 or 1.9) that can significantly enhance accuracy and efficiency when processing ZT Scan data from the ZenoTOF 7600 system.
Adjust the following parameters to optimize the DIA-NN software for processing ZT Scan DIA data (below in red – screenshot is not displaying a raw data file or libraries):
- Additional Options: Update the command lines to include: “--report-lib-info”, “--out-measured-rt” and "--scanning-swath".
- Algorithm: set the MS2 mass accuracy to 20 ppm, and the MS1 accuracy to 0 ppm. (Mass accuracy automatically defaults to 20 ppm but can be lower if needed.) Scan window must be set to 6.
- MBR (match between runs): Ensures that only replicates of a given load or condition are searched together. (Never search data from varying loads together.) DIA-NN developers recommend occasionally turning off MBR for an unbiased health check of the instrument.)
- DIA-NN software v 1.9: Expect overall numbers of protein groups and precursors to be slightly less than v 1.8.1.
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