Update README.md

README.md

@@ -1,17 +1,18 @@
 # TFD/E
-This is a repository for algorithms for targeted detection, extraction, and characterisation of peptide features in [timsTOF](https://www.bruker.com/en/products-and-solutions/mass-spectrometry/timstof/timstof.html) data.
+This is a repository for algorithms exploring targeted detection, extraction, and characterisation of tryptic peptide features in [timsTOF](https://www.bruker.com/en/products-and-solutions/mass-spectrometry/timstof/timstof.html) data.
 
-There are a couple of approaches to feature detection here.
+There are three approaches to feature detection here.
 
-#### PASEF-based
+#### Targeted Detection and Extraction Pipeline
 A DDA pipeline that detects peptide features using the instrument isolation windows as a starting point. Code is [here](https://github.com/WEHI-Proteomics/tfde/tree/master/pipeline).
 
-#### YOLO feature detection
-Training a YOLO object detection ANN to detect features in ms1 frames. Intended to be used on the instrument at run-time to select precursors to fragment. Code is [here](https://github.com/WEHI-Proteomics/tfde/tree/master/yolo).
-
 #### 3D intensity descent
 Using the characteristic structure of peptides to detect and segment features for identification. Code is [here](https://github.com/WEHI-Proteomics/tfde/tree/master/3did).
 
+#### Feature detection with a YOLO-based CNN detector
+Training a YOLO object detection ANN to detect features in ms1 frames. Intended to be used on the instrument at run-time to select precursors to fragment. Code is [here](https://github.com/WEHI-Proteomics/tfde/tree/master/yolo).
+
 #### Also in this repository...
-- [Jupyter notebooks](https://github.com/WEHI-Proteomics/tfde/tree/master/notebooks) for prototypying ideas.
+- [Jupyter notebooks](https://github.com/WEHI-Proteomics/tfde/tree/master/notebooks/papers) for generating the figures for the papers.
+- [Jupyter notebooks](https://github.com/WEHI-Proteomics/tfde/tree/master/notebooks/prototyping) for prototypying ideas.
 - [Experiments](https://github.com/WEHI-Proteomics/tfde/tree/master/experiments), some of which helped develop ideas, while others didn't go very far.