Error while running MSstats and AvantGardeDIA external Tools

Error while running MSstats and AvantGardeDIA external Tools Chinmaya k  2020-01-02


I have installed both MSstats and AvantGardeDIA with all the R versions and libraries successfully. However, I am facing some issues while running both of these external tools right now. Such as;

MSstats - As you can see in the attached file. The MSstats function exports the results to a Temp directory with all the basic column information in it. But, the Fragment Ion column contains both fragment ions and precursors identified in the DIA search with respective "Area". According to MSstats, precursor information is not required for DIA analysis and how to exclude precursors from being exported by the MSstats as MSstats input file?

AvantGardeDIA - Whereas here in AvantGardeDIA, this tool is not able to change the working directory. I do not know what exactly is the reason here. I have also attached the screenshot of the current set working directory for AvantGardeDIA\Run_AvG_Module\GlobalRefinement below. Why this tool is not able to change the working directory and how can we resolve this issue?

Thank you,

Brian Pratt responded:  2020-01-02

Hi Chinmaya,

Questions about external tools are generally best directed to the teams that developed the individual tools. Have you tried their respective support sites yet?

We really should do a better job in Skyline of making that information easily available. I'll add that to our development queue.

Best Regards,

Brian Pratt

Nick Shulman responded:  2020-01-02

The MSstats external tool does not allow you to have both MS1 and MS2 precursors in your Skyline document.

You can find more information about that here:
-- Nick
Chinmaya k responded:  2020-01-03
Hi Brian,

I have not contacted the respective support sites yet.

Later, I found the AvantGardeDIA manual in their github repo and followed the steps they have provided. As of now, I am able to run the Global refinement module successfully. It took more than 5 hours to perform global refinement for 24k peptides (both target and decoy). It was confusing in-between as there were no indicators or tabs showing about the status of the analysis. This happed once before the SQlite database gets generated and later while all the Global refinement results being generated.

Nonetheless, now I am trying to understand the contents of the result files and AvG score generated from Global refinement steps.

Chinmaya k responded:  2020-01-03
Hi Nick,

Thank you for sharing that link.

I was able to remove the precursor being exported in MSstats input file.