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-Created by Leo Trostel on 17.08.2022
-
-This is a READme file for "smiles_to_mass_and_inclusion_list.py"
-
-Purpose:
-The purpose of the script is to generate a mass lists, which can be imported into Compound Discoverer.
-It also creates inclusion lists for positive and negative mode for the use on a QExactivePlus.
-
-Input:
-The scripts needs 1 txt file as input that contains the SMILES of compounds (one string per line).
-
-Output:
-
-Mass list as csv file that can be imported into Compound Discoverer and 2 inclusion lists.
-
-Important:
-The script uses the PubChem database and for every compound a request is sent, thus the code can run for some time.
-
-The csv files can be opened in Microsoft Excel and brought to a more readable form
-by selection of the "A" column and apply: Data > Text to columns > Next > Next > Finish > Ok
-However, this will override the Structure column and can not be imported into Compound Discoverer anymore.
-Nevertheless, it can be saved as an xlsx file, thus converting it to the Excel Workbook format.
-
-Step by step guide for non-python users:
-1. download Anaconda (link: https://docs.anaconda.com/anaconda/install/index.html) and install it, then run Anaconda Navigator
-2. create new environment under the environment tab, select python version 3.6.13
-3. you need to install some python packages for this script to work:
-	3.1. go to environments, click "play button" on newly created environment, open Terminal
-	3.2. run following lines individually (need to confirm: type "y" and press enter)(might take a while): 
-		conda install -c rdkit rdkit
-		pip install pubchempy
-	3.3. check if pandas is installed and active according to: https://docs.anaconda.com/anaconda/navigator/tutorials/pandas/
-4. open anaconda navigator, go to home tab, check if "Applications on" is set to the new environment
-5. click gear icon on "Spyder" > install specific version > 5.0.5 and wait for installation to finish
-6. click launch button below "Spyder"
-7. open the script: "smiles_to_mass_and_inclusion_list.py"
-8. change the pathway of the input files according to the filepath on your harddrive
-9. click somewhere in the left window and press F5 or click "Run File", if Run settings windows appears, click run
-10. wait for the script to finish running (you can see the progress in the bottom right window, "Script finished successfully" marks end of script)
-
diff --git a/readme.md b/readme.md
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+# Generate Mass and Inclusion Lists
+
+## Purpose
+
+The purpose of the script is to generate a mass lists, which can be imported into `Compound Discoverer`.
+It also creates inclusion lists for positive and negative mode with predicted NCE for the use on a QExactivePlus.
+The script uses the `PubChem` database and for every compound a request is sent, thus the code can run for some time.
+
+## Input
+
+The scripts needs 1 txt file as input that contains the SMILES of compounds (one string per line).
+
+## Output
+
+Mass and two inclusion lists as well as an overview with SMILES, Name, CAS, Formula, monoisotopic mass and InchiKey as csv file.
+Additionally, a txt file is created containing the maximal element count of C, H, O, N, S, P, Cl, Br an I (useful for `Compound Discoverer` workflow).
+The output paths are per default the same folder as the script.
+
+## Installation
+
+Step by step guide for non-python users:
+
+1. [Download Anaconda](https://docs.anaconda.com/anaconda/install/index.html) and install it, then run `Anaconda Navigator`
+2. create new environment under the `Environment` tab, select python version 3.6.13
+3. you need to install some python packages for this script to work:
+	3.1. go to environments, click `play button` on newly created environment, open Terminal
+	3.2. run following lines individually (need to confirm: type `y` and press `enter`)(might take a while): 
+		`conda install -c rdkit rdkit`
+		`pip install pubchempy`
+	3.3. check if pandas is installed and active according to [this Tutorial](https://docs.anaconda.com/anaconda/navigator/tutorials/pandas/)	
+4. open `Anaconda Navigator`, go to `Home` tab, check if `Applications on` is set to the new environment
+5. click `gear icon` on `Spyder` > install specific version > 5.0.5 and wait for installation to finish
+6. click `launch button` below `Spyder`
+7. open the script: `smiles_to_mass_and_inclusion_list.py`
+8. change the pathway of the input files according to the filepath on your harddrive
+9. click somewhere in the left window and press `F5` or click `Run File`, if Run settings windows appears, click `Run`
+10. wait for the script to finish running (may take a while, `Script finished successfully` marks end of script)
+