|Correct spectrum selection for non-redundant library||Juan C. Rojas E.||2020-09-30|
Attached you can find a few slides displaying my issue.
In multiple instances I have observed that the spectrum selected for the non-redundant library is suboptimal compared to some other spectra available (Slide 1 and 2). For DDA files the problem is easily circumvented by working with the redundant library, but for library generation for DIA, MRM, and/or PRM methods could lead to comparisons to suboptimal representative library spectrum.
The .mzXML files (exported from PEAKS) for data acquired in resolution mode are kept in resolution mode format when exported (Slide 3). Maybe this is the reason for the mismatch due to better random matching (i.e. in mass tolerance consideration) to some of the "split" peaks of some spectra compared to others even if the absolute abundance is lower.
Is it possible to manually exchange the best representative spectrum for the non-redundant library?
If not, could a peak picking step be included in the library building procedure? Or should I just perform it with MSConvert externally?
As always, thank you for your time and support.