Issue 994: File > Import > Peptide Search - FASTA page should have Peptide Settings - Filter options

Assigned To:Matt Chambers
Opened:2023-12-07 10:26 by Brendan MacLean
Changed:2023-12-07 17:03 by Brendan MacLean
2023-12-07 10:26 Brendan MacLean
Title»File > Import > Peptide Search - FASTA page should have Peptide Settings - Filter options
Assigned To»Matt Chambers
Our defaults for SRM for the Peptide Settings - Filter values:

Min length: 8
Max length: 25
Exclude N-terminal AAs: 25

Seem less ideal for the Import > Peptide Search case where users often want to just include everything found by the search.

First, it would be nice to add these 3 settings to the Import > Peptide Search wizard, and maybe also include "Exclude potential ragged ends".
Second, the default should probably be to include everything found in the search:

Min length: min(length(RefSpectra.peptideSeq))
Max length: max(length(RefSpectra.peptideSeq))
Exclude N-terminal AAs: 0

Then the user can narrow things down from there if they want to.

2023-12-07 10:32 Matt Chambers
Did you mean:
Min length: min(srmSettings.Filter.MinLength, length(RefSpectra.peptideSeq))
Max length: max(srmSettings.Filter.MaxLength, length(RefSpectra.peptideSeq))

That control is used to execute DDA/DIA searches as well, so I'm thinking that leaving the fields blank should mean "this filter not applied". Because it sounds like you want the RefSpectra to override the srmSettings. But if there are no RefSpectra yet, there's no way to display what values will override the srmSettings.

2023-12-07 10:52 Brendan MacLean
No. I meant the defaults should be what I wrote, i.e. based on the spectral library contents. But, I see your point when we ask before the spectral library is built.

I do want to split those cases out to:
File > Execute > Peptide Search

But, I could maybe be convinced that these settings should be Nullable<int> and just not be applied when they are blank. Which at least for 2 of them would be the same as setting them to zero.

2023-12-07 10:55 Brendan MacLean
I am suggesting that these added fields would change SrmSettings values, as the other fields, like missed cleavages and protease enzymes already do.

Also, note that we are doing this for Transition Settings where we list different defaults for Import Peptide Search than are currently present in SrmSettings at the start of the wizard, but based on the data we are seeing during the wizard.

2023-12-07 11:08 Matt Chambers
OK , I now realize the min/max are meant to be vectorized over the peptide lengths. (duh)

I had been thinking the split between Import->Peptide Search and Execute->Peptide Search would only affect the first page, but I haven't thought very deeply about that split yet.

If these dialog options change the SrmSettings, then what happens if the user imports another peptide search? It overrides the "settings" from the previous peptide search? I suspect that might be somewhat counter-intuitive: for a later import to potentially change document settings to a more restrictive filter than the existing peptides require. That could be addressed with a warning dialog though if there are already peptides in the document and the new settings would filter out some existing peptides. This also applies for the existing way we do missed cleavages and enzyme, but we don't import those values from the peptide search and they're far more likely to be the same between import invocations.

2023-12-07 17:03 Brendan MacLean
Yeah. Sorry. AKA aggregate functions in SQL.