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Remove unimod dep
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RobbinBouwmeester committed Feb 3, 2025
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5 changes: 2 additions & 3 deletions README.md
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Expand Up @@ -298,12 +298,11 @@ os.environ['CUDA_VISIBLE_DEVICES'] = '1'
**__Q: What modification name should I use?__**

The names from unimod are used. The PSI-MS name is used by default, but the Interim name
is used as a fall-back if the PSI-MS name is not available. Please also see __unimod_to_formula.csv__
in the folder __unimod/__ for the naming of specific modifications.
is used as a fall-back if the PSI-MS name is not available. It should be fine as long as it is support by [proforma](https://pubs.acs.org/doi/10.1021/acs.jproteome.1c00771) and [psm_utils](https://github.com/compomics/psm_utils).

**__Q: I have a modification that is not in unimod. How can I add the modification?__**

Unfortunately since the V3.0 this is not possible any more via the GUI or commandline. You will need to use [psm_utils](https://github.com/compomics/psm_utils), above a minimal example is shown where we convert an identification file into a psm_list which is accepted by DeepLC. Here the sequence can for example include just the composition (e.g., SEQUEN[Formula:C12H20O2]CE).
Unfortunately since the V3.0 this is not possible any more via the GUI or commandline. You will need to use [psm_utils](https://github.com/compomics/psm_utils), above a minimal example is shown where we convert an identification file into a psm_list which is accepted by DeepLC. Here the sequence can for example include just the composition in proforma format (e.g., SEQUEN[Formula:C12H20O2]CE).

**__Q: Help, all my predictions are between [0,10]. Why?__**

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