the total number of feaures changes when different libraries are used for the identification

[vasiloa2]

Dear MSDIAL Team,

I would have two questions regarding the identification process, as described below:

A. I perform the identification step twice; first with an inhouse .msp MS/MS library and second with the MSMS_Public_Exp_Pos_VS17 from your website. I am doing this within the same project and I keep all other parameters the same. However, the exported files I get have different total number of features - and always higher with the library from your website.
For example I process and identify my samples with an inhouse library and I get 15.000 features (identified and unknowns. I then remove the inhouse libraray from the identification window and I add the library from your website and I get 16.000 features. So 1000 new features - that are not relevant with adducts. It is like the software performs again the peak finding process again and now finds new peaks.- Why is this happening? As a user, I would assume that the peak finding step has been completed and another round of identification would only annotate the existing peaks.

B. When I add both libraries (inhouse and from your website) in my identification window, the annotated molecules with the inhouse library are getting overwritten form the annotations of the website library. Is it possible to set one library as the preferred one and have a second one that annotates only the features that have not been annotated form the first one?

Thank you in advance for your support

My best regards
Katerina

[Bujee415]

Hell, Katerina!
Sorry for the late reply!
Does "total number of features" mean alignment peak spot number?
Just for your information, if you change your library from the "identification" button, it will do peak picking again. On the other hand, if you change from the "alignment" button, it won't do peak picking.