# Guides

```{toctree}
    :maxdepth: 1
    :hidden:

Library-free DIA <guides/libfree-gui>
DIA Transfer Learning <guides/transfer-dimethyl>
Evaluate Transfer Learning <guides/evaluate_model>

```


Below you will find a collection of guides how to use and configure alphaDIA for specific searches.

```{card} Library free DIA search using the GUI
:link: guides/libfree-gui.html
Perform a DIA search of label free bulk data usinmg a fully predicted spectral library from a FASTA digest.

{bdg-success}`GUI`
```

```{card} DIA Transfer Learning for Dimethyl labeled samples
:link: guides/transfer-dimethyl.html
Use the AlphaDIA GUI to train a custom peptdeep model for dimethyl labeled DIA data.
The custom model is then used to search non-multiplexed dimethyl labeled data with match between runs.

{bdg-success}`GUI` {bdg-primary}`Transfer Learning`
```

```{card} Evaluate Transfer Learning Metrics
:link: guides/evaluate_model.html
Evaluate the transfer learning by visualizing the metrics for the RT, Charge, Mobility and MS2 prediction tasks.

{bdg-warning}`Jupyter Notebook` {bdg-primary}`Transfer Learning`
```