search

MannLabs / alphadia

modular & open DIA search
https://alphadia.readthedocs.io
Apache License 2.0
41 stars 3 forks source link

Which specLib formats are supported by alphabase #209

Closed tobiasko closed 3 months ago

tobiasko commented 3 months ago

Hi developers,

which specLib formats are currently supported by alphabase? The alphaDIA manuscript just talks about spectral libraries in .tsv format...which could be just anything. Which columns are required? I tried a lib generated by DIA-NN, this did not work. How about libs generated by other tools like Spectronaut? Are predicted libs from tools like Koina ok?

jalew188 commented 3 months ago

Diann generated TSV library is supported, check https://github.com/MannLabs/alphabase/blob/main/alphabase/constants/const_files/psm_reader.yaml#L191.

The only problem is if this is called by AlphaDIA. I transfer this issue to AlphaDIA repo

tobiasko commented 3 months ago

ok. THX!

tobiasko commented 3 months ago

Where can I find a description of your supported .tsv library format?

GeorgWa commented 3 months ago

Hi,

DIA-NN, MSFragger and Spectraonaut spectral libraries should be supported. Furthermore alphaBase HDF. If you have a DIA-NN .tsv library which does not work, please let us know and send the library. We are happy to fix it and include in our test suite.