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Pedro Magalhães

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May 17, 2023
Processing ZenoTOF data using the Human Pan-Human library from Swath Atlas (phl004_canonical_s32_osw.csv) and DIANN

Hello,

I am writing you based on the note you released entitled: “Processing ZenoTOF 7600 system data with DIA-NN software”

I have a question regarding the usage of the Human Pan-Human library from SwathAtlas (e.g. phl004_canonical_s32_osw.csv) in DIANN. The loading of the spectral library and the number of protein identifications are great, but we get always a warning using this spectral library as follows:

  • “Loading spectral library F:\Human_pan_SWATH.txt
  • WARNING: no neutral loss information found in the library – assuming fragments without losses
  • [0:04] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
  • [0:04] Spectral library loaded: 13911 protein isoforms, 13911 protein groups and 204564 precursors in 156396 elution groups.
  • [0:04] Initialising library
  • [0:04] Saving the library to F:\Human_pan_SWATH.txt.speclib”

I hope you can provide me with your feedback on this matter. Many thanks.

1 Comment

  1. Christie Hunter

    Yes, I’ve seen the same message when I use that library and also see that the search progresses just fine.

    I interpreted the message to mean that it parsed the library and didn’t find these specific ion types, like perhaps the b-17 and y-17 ions? But I don’t know that for sure.

    I checked on GitHub and couldn’t find any information but noticed there is a message board. Perhaps you could get an answer from Vadim on that message board!
    https://github.com/vdemichev/DiaNN

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