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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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User provided spectral library #922

Open wenbostar opened 9 months ago

wenbostar commented 9 months ago

For a user provided spectral library, how does DIA-NN select fragment ions in the library for peptide detection?

vdemichev commented 8 months ago

This is described in the first Nature Methods DIA-NN paper, please see https://www.nature.com/articles/s41592-019-0638-x

wenbostar commented 6 months ago

Hi @vdemichev , after went through the NM paper, I got the following questions:

  1. Does DIA-NN remove b1, y1, b2 and y2 ions when it determines fragment ions to extract XICs for peptide identification?
  2. Does DIA-NN only consider the top-12 fragment ions from a spectral library for peptide identification?