CCMS-UCSD · mwang87 · Jan 21, 2022
diff --git a/docs/fileconversion_agilent.md b/docs/fileconversion_agilent.md
@@ -0,0 +1,17 @@
+## 1. Introduction
+
+This page describes how you can convert and process your raw data from Agilent Mass Spectrometers to work with various GNPS tools. There are several paths depending upon your goals
+
+1. Molecular Networking and qualitative comparison across multiple files using Classical Molecular Networking
+1. Molecular networking and relative quantitate analysis across multiple files using Feature Based Molecular Networking
+
+## Classical Molecular Networking
+
+Here, one concern is the scan numbers and multiple collision energies present in many untargeted mass spec data from Agilent Instruments. It is recommended that users convert to MGF files using ...
+
+
+## Feature Based Molecular Networking
+
+We recommend converting with MSConvert filtering to a single collision energy and analyzing with MZmine. 
+
+Lorem Ipsum for further instructions. 
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -21,6 +21,7 @@ nav:
     - Data Preparation/Upload:
         - Mass Spectrometry File Conversion: fileconversion.md
         - File Conversion (Waters): fileconversion_waters.md
+        - File Conversion (Agilent): fileconversion_agilent.md
         - GNPS File Upload: fileupload.md
         - Metadata: metadata.md
     - Recommended Data Analysis: