Searching FASTAs with Scaffold DIA, Resource-Intensive Process

Resource-Intensive Search Warning Message

If the user has selected a workflow that will require a FASTA search that will be particularly resource-intensive, a warning message is displayed. In a DIA search, because it is impossible to use precursor mass as a screening tool, every possible peptide match must be scored. As a result, searching against a large FASTA, or with a number of variable modifications, or with many samples can cause the search space to expand dramatically.

It is recommended that the user use an appropriate FASTA (e.g. limited by taxonomy) and limit the number of variable modifications searched. When analyzing a large number of samples, it is also better to use a DDA-based library or to create a chromatogram library and to search the full data set against that.

You may also see a warning if you try to load more than 12 raw files with a FASTA. This is just a warning, but it is advisable to search a DDA or DIA Chromatogram Library instead.

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