Export AvG results

Export AvG results voellmy  2020-01-27 07:08


I'm posting regarding an issue with Avant-Garde for DIA using Skyline and am following the tutorial handed out at the 2019 Targeted Proteomics course in Barcelona. I believe I successfully went through all the described steps, but when I in the end pull up the Results Grid, the columns related to AvG (i.e. AvG_Score, Avg_SpectralLibSim_, etc.) do not appear. These columns are checked in the Document Settings>Annotations tab so I would expect that I can select them in the Results Grid or Document Grid, but this is not the case, even when opening the 'Customize View' option.

I'd appreciate if you could point me in the right direction in case this issue has come up in the past.
Thank you,

Nick Shulman responded:  2020-01-27 10:46

The set of columns that are available in the Results Grid depends on what you have selected in the Targets tree.

I am not familiar with the AvantGardeDIA tutorial but if you are not seeing the columns you expect you are probably supposed to select something else in the Targets tree. There is a different set of columns for Transitions, Precursors and Peptides.

When you define an annotation, you can specify which type of object the annotation applies to (Proteins, Peptides, Precursors, Transitions, Precursor Results, Transition Results, and Replicates). Which type of object(s) are the annotations that you care about applied to?

-- Nick
voellmy responded:  2020-02-07 01:54

Thank you, that was my bad that I couldn't locate the columns but now I can indeed add them.

In the meantime I have another AvantGarde-specific question regarding result output: is it correct that after running the GlobalRefinement module on a DIA dataset, I can export the AvantGardeDIA_Export report (again) and select only the rows where Quantitative=='True'. The areas corresponding to these rows are then my new dataset?

I understand that there are several outputs generated in the ResultsOptimization folder with scores, however it is not clear to me which score cutoffs to use etc.