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.
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