|Combined spectral library||n prust||2023-04-12|
I have a question regarding a combined spectral library.
When generating a spectral library containing multiple result files, is there an order in which the final spectral library entry to be matched to is picked?
I attached an example of a peptide that is identified in two result files that were used to generate one spectral library. The first result file is from a MQ search containing multiple fractions and the second result file is from a PD file. As you can see the peptide is identified multiple times and the spectra quality differs. Skyline decided to use the first entry in the spectral library for the result matching. This decision does not seem to be based on intensity, spectral quality or on alphabetical order, nor on the oder of loading the result files to generate the spectral library.
Could you provide me with some information on this decision process or if it's a random decision?