Update README.md

README.md

@@ -163,32 +163,31 @@ for more examples.
 ### Prediction models
 
 DeepLC comes with multiple CNN models trained on data from various experimental
-settings:
-
-| Model filename | Experimental settings | Publication |
-| - | - | - |
-| full_hc_dia_fixed_mods.hdf5 | Reverse phase | [Rosenberger et al. 2014](https://doi.org/10.1038/sdata.2014.31) |
-| full_hc_LUNA_HILIC_fixed_mods.hdf5 | HILIC | [Spicer et al. 2018](https://doi.org/10.1016/j.chroma.2017.12.046) |
-| full_hc_LUNA_SILICA_fixed_mods.hdf5 | HILIC | [Spicer et al. 2018](https://doi.org/10.1016/j.chroma.2017.12.046) |
-| full_hc_PXD000954_fixed_mods.hdf5 | Reverse phase | [Rosenberger et al. 2014](https://doi.org/10.1038/sdata.2014.31) |
-
-By default, DeepLC selects the best model based on the calibration dataset. If
+settings. By default, DeepLC selects the best model based on the calibration dataset. If
 no calibration is performed, the first default model is selected. Always keep
-note of the used models and the DeepLC version.
-
-The table above is for an old version of DeepLC, the current version comes with:
+note of the used models and the DeepLC version. The current version comes with:
 
 | Model filename | Experimental settings | Publication |
 | - | - | - |
-| full_hc_hela_hf_psms_aligned_1fd8363d9af9dcad3be7553c39396960.hdf5 | Reverse phase | [Kelstrup et al. 2018](https://doi.org/10.1021/acs.jproteome.7b006021) |
-| full_hc_hela_hf_psms_aligned_8c22d89667368f2f02ad996469ba157e.hdf5 | Reverse phase | [Kelstrup et al. 2018](https://doi.org/10.1021/acs.jproteome.7b00602) |
-| full_hc_hela_hf_psms_aligned_cb975cfdd4105f97efa0b3afffe075cc.hdf5 | Reverse phase | [Kelstrup et al. 2018](https://doi.org/10.1021/acs.jproteome.7b00602) |
+| full_hc_PXD005573_mcp_8c22d89667368f2f02ad996469ba157e.hdf5 | Reverse phase | [Bruderer et al. 2017](https://pubmed.ncbi.nlm.nih.gov/29070702/) |
+| full_hc_PXD005573_mcp_1fd8363d9af9dcad3be7553c39396960.hdf5 | Reverse phase | [Bruderer et al. 2017](https://pubmed.ncbi.nlm.nih.gov/29070702/) |
 | full_hc_PXD005573_mcp_cb975cfdd4105f97efa0b3afffe075cc.hdf5 | Reverse phase | [Bruderer et al. 2017](https://pubmed.ncbi.nlm.nih.gov/29070702/) |
 
 For all the full models that can be used in DeepLC (including some TMT models!) please see:
 
 [https://github.com/RobbinBouwmeester/DeepLCModels](https://github.com/RobbinBouwmeester/DeepLCModels)
 
+Naming convention for the models is as follows:
+
+[full_hc]\_[dataset]\_[fixed_mods]\_[hash].hdf5
+
+The different parts refer to:
+
+**full_hc** - flag to indicated a finished, trained, and fully optimized model
+**dataset** - name of the dataset used to fit the model (see the original publication, supplementary table 2)
+**fixed mods** - flag to indicate fixed modifications were added to peptides without explicit indication (e.g., carbamidomethyl of cysteine)
+**hash** - indicates different architectures, where "1fd8363d9af9dcad3be7553c39396960" indicates CNN filter lengths of 8, "cb975cfdd4105f97efa0b3afffe075cc" indicates CNN filter lengths of 4, and "8c22d89667368f2f02ad996469ba157e" indicates filter lengths of 2
+
 
 ## Q&A