|Title||»||Proteomics features still showing in small molecule mode|
|Assigned To||»||Brian Pratt|
During the latest iteration of Skyline-Online for small molecules, the following proteomics features were found to show up when Skyline is in small molecule UI mode:
1. Reports that no longer show up in the Document Grid - Reports (Peptide Quantification, Peptide Ratio Results, Peptide RT Results, etc.) show up in the list under File > Export > Report. If you click the "Edit list..." button in this form, you see a list with certain items grayed out. I think the grayed out items should no appear in the "Report:" list under File > Export > Report. Possibly, we should categorize tools by whether they are small molecule or proteomics tools and hide/show their reports based on this.
2. In the Molecule Settings - Library tab, clicking the "Build..." button shows a form with "Data source" for "Files" and "Prosit", but Prosit is a Proteomics-only tool. So, the small molecule form probably should have the "Data source" box hidden, and controls below it shifted up to its y-position.
3. If you give your library a name in the Build Library wizard and then click the "Add Files..." button, the file types drop-down list contains "Matched Peptides" and a very extensive list of peptide spectrum matching tools that produce output formats we recognize for library building. This should be changed to "Matched Molecules (*.ssl)" (adding any other output formats that we know we support for small molecules.