MS2 Column in Compound Discoverer

[gpblack]

Does anyone know how I get a “DIA only” assignment in the MS2 column of Compound Discoverer if my data was acquired in FS-ddMS2? And what does “DDA for other ion” mean?

[mnewmeyer]

According to the help menu, a “DIA only” flag happens when “Only data‑independent [all ions fragmentation (AIF)] scans are available.” I don’t know if a “DIA only” flag is possible if the data were collected with a DDA method. The “DDA for other ion” is dependent on the settings for “Ions” in the Detect Compounds node and for “Preferred Ions” in the Group Compounds node. For example, if you set your Ions to be [M+H]+ and [M+NH4]+ in Detect Compounds but only set your Preferred Ion to [M+H]+ in Group Compounds, you will get a “DDA for other ion” flag if there is an MS2 spectrum for an ion that the software assigned as an [M+NH4]+ adduct (since this wasn’t one of the Preferred Ions, it’s an “other ion”).

[gpblack]

That’s helpful! I am getting the “DIA only” flag on ddMS2 data which is perplexing, but your explanation for “DDA for other ion” is super helpful. Thanks!

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