InjectionTimeGetterApp

This console line application is used to get MS1 and MS2 injection times from Thermo .raw files. It uses mzLib to load and get injection times. The source code for mzLib can be found at https://github.com/smith-chem-wisc/mzLib. This repository was built for a specific purpose in support of a specific paper. Support will be limited. Use the Issues tab to report bugs.

Requisites for running

1. .NET 6.0 (https://dotnet.microsoft.com/en-us/download)
2. Visual Studio (https://visualstudio.microsoft.com/#vs-section)
3. At least 16 GB of RAM.
4. Windows 11. Issues causes by running on Linux-based machines will not be supported.

Building InjectionTimeGetterApp

1. Clone this repository to your local machine.
2. Navigate to the directory on your local machine and open the InjectionTimeGetterApp.sln in Visual Studio.
3. Build the application either for debug or release mode (Ctrl + Shift + B, or the first option in the Build dropdown menu).
4. Make note of the final location of the .exe file output by release, which will be found in InjectionTimeGetterApp\bin\Debug\net6.0.

Command Line Interface Options

Option 1: PROCESS SELECTOR:

1. 1 : Gets retention times of all MS1 scans.
2. 2 : Gets all injection times of either MS1 or MS2 scans.
3. 3 : Combines Peaks output into a single file. This will not be supported in any issues. Option 2: MS LEVEL For PROCESS SELECTOR 2, selects what Ms Level you want to extract injection times for. Option 3: PATH TO FOLDER OF DATA The input folder of data to process.

Running InjectionTimeGetterApp

1. open command prompt.
2. type the following command

start /b "" "{path to InjectionTimeGetterApp.exe}" "{PROCESS SELECTOR}" "{MS LEVEL}" "{PATH TO FOLDER OF DATA}"