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don't know the difference between the meaning of the two definitions in red circles here. Can I understand that the upper one is the spectrum of the identified compound, and the lower one means every fragment scanned by EI?
Yes - the top spectrum is of the compound as determined by the 'Find by Chromatogram Deconvolution' algorithm. The bottom spectrum is the raw spectrum of the data file averaged over the same time range used in the top spectrum. This is a quick way to determine what ions were identified by the algorithm as belonging together vs. all the ions acquired at that range in time.
Next, I right click and search using NIST-MS program, sometimes it doesn't show valid compounds, unless I double click the area in red circle, why? Do I make a mistake when I use Masshunter or NIST-MS?
I believe this is because you need to have a spectrum selected in Qual to "pass" to the NIST software. If you don't have a spectrum selected - NIST will be opened but not have any spectra to process. Selection of a spectrum will result in a blue box drawn around the spectrum as you can see in your first screenshot. Next time you encounter this issue - return to Qual and see if that blue highlighting was present or not. If not - that confirms my suspicion. If so - then we'll need to investigate further.
The problem of NIST MSSearch not searching may be the Automation setting. Its location is revision dependent. In MSSearch
select Options>Library Search Options. Highlight the Automation tab. Look for "Automatic Search On" and make sure it is checked. Select Okay.
When you close MSSearch this setting is saved. Try NIST Search from Qual again. I have found that without this checkmark, NIST MSSearch will open but no action will be taken, as designed. Usually the software that is calling MSSearch will set the Automation flag, but apparently not in this case.
With regard to the Double-Click in the red circle. You have the Structures tab selected for the unknown spectrum. If you had the Names tab selected you could also double-click on the Cpd # - R.T. The double-click is just a shortcut to Search this spectrum. Typically this is used after you have made changes in MSSearch and wish to re-Search an existing spectrum.
I looked into Hexatriene's suggestions regarding the blue box around the spectrum in Qual. When I right-click on a spectrum, I find the blue box always appears. I then select Search Using NIST MS program. I have also found I can search each compound by right-clicking it in the Data Navigator list and selecting Search Using NIST MS program. This appears to be completely independent of whether or not the spectrum is displayed or the compound has a checkmark next to it.