Merge pull request #1 from ypriverol/main

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ypriverol · Feb 23, 2023 · dc3edb4 · dc3edb4
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diff --git a/absolute-expression/PXD000865/PXD000865-IBAQ-normalization.csv b/absolute-expression/PXD000865/PXD000865-IBAQ-normalization.csv
diff --git a/absolute-expression/PXD004452/PXD004452-IBAQ-normalization.csv b/absolute-expression/PXD004452/PXD004452-IBAQ-normalization.csv
diff --git a/absolute-expression/PXD020192/PXD020192-IBAQ-normalization.csv b/absolute-expression/PXD020192/PXD020192-IBAQ-normalization.csv
diff --git a/proteogenomics-research/README.md b/proteogenomics-research/README.md
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+
diff --git a/proteogenomics-research/deepLC/9-1/legacy_calibration/can1_deeplc_predictions.csv b/proteogenomics-research/deepLC/9-1/legacy_calibration/can1_deeplc_predictions.csv
diff --git a/proteogenomics-research/deepLC/9-1/legacy_calibration/can1_deeplc_predictions.png b/proteogenomics-research/deepLC/9-1/legacy_calibration/can1_deeplc_predictions.png
diff --git a/proteogenomics-research/deepLC/9-1/no_calibration/can1_deeplc_predictions.csv b/proteogenomics-research/deepLC/9-1/no_calibration/can1_deeplc_predictions.csv
diff --git a/proteogenomics-research/deepLC/9-1/pygam_calibration/can1_deeplc_predictions.csv b/proteogenomics-research/deepLC/9-1/pygam_calibration/can1_deeplc_predictions.csv
diff --git a/proteogenomics-research/deepLC/9-1/pygam_calibration/can1_deeplc_predictions.png b/proteogenomics-research/deepLC/9-1/pygam_calibration/can1_deeplc_predictions.png
diff --git a/proteogenomics-research/deepLC/DeepLC_with_retrainer.ipynb b/proteogenomics-research/deepLC/DeepLC_with_retrainer.ipynb
diff --git a/proteogenomics-research/deepLC/README.md b/proteogenomics-research/deepLC/README.md
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+# Dataset Analyzed
+
+The dataset used in this project is the result of the PXD014145 project filtered by spectrumAI (removing low confident mutations). The dataset description can be found in the following link: https://www.ebi.ac.uk/pride/archive/projects/PXD014145. 
+
+Dataset details: 
+- TMT dataset
+- Cells were lysed in 0.1% RapiGest SF (0.1M HEPES pH8) and protease inhibitors. Proteins were reduced using 5mM DTT and afterwards alkylated using 15 mM 2-Iodoacetamide (each at 37°C for 15 min). Two-step digestion was performed using trypsin in 1:25 enzmy:protein ration. 
+- TMT labelled samples were fractionated using an Waters reversed phase XBridge C18 column (150mm x 1mm column containing 3.5µm particles) on a Agilent1100 HPLC system. 
+- Q Exactive plus mass spectrometer coupled to EASY-nLC™ 1000 UHPLC system. 
+
+# DeepLC_Report
+
+In order to use DeepLC to predict the retention time of non-canonical peptides, we did a prediction of canonical peptide to see how the model works. All canonical peptides are divided into ten parts, nine for model calibration and one for prediction. I used two calibration model methods. At the same time, the direct prediction method of uncalibrated model is also used. Here are the results of the predicted canonical peptide.
+
+### pygam_calibration
+
+```python
+deeplc --file_pred can1.csv --file_cal can9.csv --plot_predictions
+```
+
+![can1_deeplc_predictions](https://user-images.githubusercontent.com/83333440/218061182-2f28b887-e4cc-499e-b261-c118ad8b2902.png)
+
+### legacy_calibration
+```python
+deeplc --file_pred can1.csv --file_cal can9.csv --plot_predictions --legacy_calibration
+```
+
+![can1_deeplc_predictions](https://user-images.githubusercontent.com/83333440/218061300-4d052787-25e4-41d0-add2-fe4faf716cfa.png)
+### no calibration
+```python
+deeplc --file_pred can1.csv --plot_predictions
+```
+
+![image](https://user-images.githubusercontent.com/83333440/218063568-0b5c5838-3876-4e46-96f0-0f220c8c40f2.png)
+
+At the same time, I used canonical peptides to calibrate the model to predict non-canonical peptides, and the results are as follows:
+
+### pygam_calibration
+```python
+ deeplc --file_pred non.csv --file_cal can.csv --plot_predictions
+```
+
+![non_to_rt_deeplc_predictions](https://user-images.githubusercontent.com/83333440/218064924-9fceb3d2-eab5-4dab-a3e4-44b34b622c15.png)
+
+### legacy_calibration
+
+```python 
+deeplc --file_pred non.csv --file_cal can.csv --plot_predictions --legacy_calibration
+```
+
+![non_deeplc_predictions](https://user-images.githubusercontent.com/83333440/218066151-bb1f5f2e-0c35-4dcf-9e41-2671cadb6512.png)
+
+### no calibration
+
+```python 
+deeplc --file_pred non.csv --plot_predictions
+```
+
+![image](https://user-images.githubusercontent.com/83333440/218065199-7efd37ae-81bc-4677-9c7e-7d09d92bd804.png)