From 6ba8cb715cdb9b3574ca9703a0bd5cd426c7660c Mon Sep 17 00:00:00 2001 From: RobbinBouwmeester Date: Tue, 18 Jun 2024 15:34:52 +0200 Subject: [PATCH] Update README.md --- README.md | 31 +++++++++++++++---------------- 1 file changed, 15 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index c729c09..70c434c 100644 --- a/README.md +++ b/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