DeepLC

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Take Unimod modification compositions from psims.controlled_vocabulary.unimod

2

Currently, DeepLC hardcodes Unimod modification compositions in unimod_to_formula.csv. As new modifications are added, this file will grow out of date. It would be better to take modification compositions from a...

vrkosk

Tons of warnings when using iTRAQ4plex or iTRAQ8plex

3

If you use a modification like iTRAQ4plex or iTRAQ8plex, whose composition includes 13C or 15N, you get tons of warnings like: ``` 2024-07-16 15:36:18,842 WARNING Could not add the following...

vrkosk

I couldn't find any references to SciPy except for the dependency list. Is it required?

RalfG

Documentation or reference for missing models

2

I can map most of the model names from DeepLCModels to the supplementary table 2 in the 2021 publication. A couple gaps are filled by issue #77 (thanks!). I cannot...

vrkosk

Datasets

1

May I ask which file on the corresponding image of SWATH Library, HeLa HF, and DIA HF is used to evaluate the performance of unmodified peptides? 

xiaosiruwei