Forum Replies Created
-
Posts
-
My generic method has stepped NCE at 30, 65, and 100. We’re running on a Q Exactive HF which uses an m/z of 500 for normalization. The degree of fragmentation will totally depend on the individual compounds; with this setup, I still see occasional compounds with only a precursor ion peak.
It may also help in your decision-making to consider what, if any, outside libraries for spectra searching you may be using. Incorporating the stepped energies can add some additional complexity since it’s a composite. mzCloud is supposed to be able to generate a composite spectrum to match, as closely as possible, your experimental spectrum. I have had some challenges, though, comparing my spectrum to spectra found on MoNA or Massbank where a single energy was used and it’s not clear if the spectrum was generated with absolute or normalized energies.
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”).
