Can you explain the difference between using "Blank Document" and inputting DIA peptide search?
Entering DIA peptide search will guide you step by step through the form you submitted. You can achieve the same or more results by selecting 'Blank Document', then using Settings > Peptide Settings and Transition Settings, File > Import FASTA, Refine > Add Decoys, File > Import > Results, and Refine > Reintegrate. In other words, if you know exactly what you want to achieve, you can navigate the options directly in the Skyline user interface for maximum functionality and flexibility. If not, you may find the Enter DIA Peptide Search option more convenient. After selecting 'Blank Document', you can also bring up this form via File > Import > Peptide Search and possibly make some initial adjustments for parts missing in the peptide search form.
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