IP2Daemon is a software to automatically convert raw files into ms1/ms2/ms3 files and upload them to the ip2 server.
Currently, IP2Daemon supports the following features.

  1. RAW file to spectral files
  2. WATERS files to spectral files
  3. WATERS-DDA file to spectral files


1.Java 1.7+(click to download check whether java is installed or not, open the command prompt and type “java -version”
2. Microsoft .NET Framework 4.5 (click to download) You can check the existing installation of the dot net framework by checking installed software from the control panel.
3. Thermo MSFileReader (click to download)

Figure 5.2.1: Download IP2Daemon software

Download IP2Daemon software from ip2 download page (Figure 5-2-1).

Figure 5.2.2: Launching IP2Daemon software

4. After extracting zip file, follow these steps:

  • Open in your favorite editor.
  • Change the IP2_SERVER_HOST with your ip2 server hostname (port is not required) – Make sure you have enabled the scp access on your IP2 server
  • Change REMOTE_DATA_PATH with your ip2_data folder configured on the server (Normally its /ip2_data)
  • Change IP2_SERVER_SSH_PORT with your scp port (Default is 22).
  • Change IP2_SERVER_SSH_PORT with your scp port (Default is 22).
    Note : Make sure you separate the path with “\\”

Figure 5.2.3: Updating configuration

double click IP2Daemon.jar file to launch the software (Figure 5-2-2).

Figure 5.2.4: Launch IP2Daemon

5. User can see the processing of the files (Figure 5-2-4)
After launching the program, you can find C:\Users\\ip2data folder in your system

Figure 5.2.5: ip2_data structure

  • Create a new folder with your ip2 username in raw_files, waters_files, and waters_dda_files directory. (e.g if you have ip2 application with user ‘ip2test’ then create ip2test folder in raw_files folder)
  • Drop your all raw files in your newly created folder in raw_files folder (e.g C:\Users\\ip2data\raw_files\ip2test – if your username is ip2test)
  • Same way you can drop the waters files in waters_files folder and waters dda in waters_dda_files folder.

6.Update ms params configuration for waters files located (Figure 5-2-6) and add new required params (Figure 5-2-7)

Figure 5.2.6: Params file location in waters folder

Figure 5.2.7: Params file

On cheezer follow these steps

1.After log in to your account select project tab as shown in the figure to get your projects.

Figure 5.2.8: Go to Project

2. Select your project using view tab.
3.Select IP2Daemon files tab as shown in below image

Figure 5.2.9

4. You can select a new experiment tab as shown in the image.

Figure 5.2.10: Select New Experiment

5. You can select either single or multiple Experiments

Figure 5.2.11: Single/Multiple Experiments

6. If you want from selected experiments instead of new experiments then select option selected experiments and select experiments from the drop-down as shown in image

Figure 5.2.12: Use selected Experiments

7. Select for raw files you want to select and submit your job by clicking the “Submit” button as shown in the image.

Figure 5.2.13: SUBMIT RAW files


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