Add a filter so that the 'Fragment Ion' does not contain the value 'precursor' (see attached image). In the 'Edit report' window, go to the 'Filter' and select the 'Fragment Ion' field.

You can edit it and add a filter so you don't include data from MS1 into the report. The report is called 'AvantGardeDIA_Export' and should be under the External tools folder. Or you can modify the report template used by AvG. If you want to be able to do this now you can try, as you suggested, importing the MS1 after using AvG. The way I do it is, as you suggested, to only extract the data for MS2 and I add the MS1 traces later if I ever need them. I normally don't curate the data based on MS1. The issue is that any dotp (idotp and spectral dotp) require min 3 values, but MS1 usually has only 3 values to begin with so any refinement would automatically remove the idotp.Ĭould you please shortly comment on this and what would be the best way to run AVG on fragments while tagging MS1 along (import MS1 after AVG usage?) (not sure if including/excluding MS1 for peak picking and scoring would make sense but optionally excluding it from refinement certainly does, especially for DIA).

This might be solved by setting this value to 6, yet it would be nice having at least the option to tell avg to ignore MS1 for refinement and only refine MS2 chromatograms.

Does it treat MS1 and MS2 chromatograms as transitions in a similar/same fashion? I was surprised to see that also MS1 chromatograms get stripped of their quantitative state when going for MinimalNumberOfTransitionsAfterOptimization=3. I would like to adress one important question/issue of AVG. The connection will be released when they are closedĮrror in file(file, 'rt') : cannot open the connectionĬalls: Read_AndFormatResults -> read.csv -> read.table -> fileĬannot open file 'S:/avant garde test/AvantGardeDIA/DataFormatting/TempFiles/Report_GR_ColNamesName_Tag.csv': No such file or directory LaunchParallelTasks_ReadFromDB(ParamsFile,RefinementWorkflow) I noticed that AVG installed R-3.5.2 while some packages where built under R version 3.5.3 With the newest AVG and Skyline on Win 7 the issue remains that the temp file mentioned below is manually not observable in the folder and the program cannot continue. It doesnt hurt having transitions for decoys right? Are some files in the AVG folder supposed to contain 'Name_Tag' or is this meant contain the same name as the skyline document? These problems seem solved but there still can be sth wrong on my side. I also had other issues when R was not available for a few days (now fixed on its own) and also when the program was denied access to the R folders because of windows admin issues. AVG Version 0.0.1.3 (freshly installed from tool store). Thank you very much for the very swift response.

File avg update