Usage

ORIGAMI-MS can be operated using the command line or graphical user interface

Graphical User Interface - easier of the two

  1. Go to ORIGAMI-MS folder
  2. Select polarity, activation region, activation method and then fill-in appropriate parameters. If you miss any parameter or the parameter does not match its requirements, you will be prompted to try again.
  3. Ensure your parameters are correct by clicking on the Calculate button. If everything worked fine, you will see not error messages and the code compiled correctly.
  4. Examine one of the three available plots to make sure you are happy.
  5. Go to MassLynx tune page and start acquisition. You can either set the acquisition time in MassLynx (make sure to add at least a minute to the run time) or you can come back to ORIGAMI-MS after the pre-calculated amount of time and stop the acquisition.
  6. Go back to ORIGAMI-MS and press on Go button. If successful, a new window will appear with print out messages.
  7. Let it do its thing and come back when the acquisition is finished.
  8. Analyse your data in ORIGAMI-ANALYSE

Important

Make sure you set the scan time to whatever you've set in ORIGAMI-MS. If you do not, data acquisition will be out of sync and it will be useless.

Important

If you need to cancel the run, just press on the Stop button - this will stop ORIGAMI-MS script. Subsequently, go to MassLynx, stop the acquisition and reinitilize MassLynx.

Command line interface - quicker of the two

  1. Open command prompt and navigate to wherever the WREnS ScriptRunnerLight.exe is located. Usually C:\Program Files (x86)\Wrens\Bin
  2. The general rules are ScriptRunnerLight.exe SCRIPT_NAME.dll PARAMETERS where you replace the SCRIPT_NAME.dll with whatever method you are using and put in appropriate parameters in the PARAMETERS section.

Important

You can stop the script from running by pressing CTRL+C or CTRL+PAUSE on your keyboard. To be safe, I would also run the CIU_RESET.dll script using the ScriptRunnerLight.exe CIU_RESET.dll command.

Example command line inputs

Linear method

ScriptRunnerLight.exe CIU_LINEAR.dll TRAP,POSITIVE,3,5,4.0,200.0,2.0,25.5
  • region: TRAP
  • polarity: POSITIVE
  • SPV: 3
  • scan time: 5
  • start V: 4
  • end V: 200
  • step V: 2V
  • approx. run time – 25.5 (can be any number!)

Exponential method

ScriptRunnerLight.exe CIU_EXPONENT.dll TRAP,POSITIVE,3,5,4.0,200.0,2.0,20.0,0.03,92.75
  • region: TRAP
  • polarity: POSITIVE
  • SPV: 3
  • scan time: 5
  • start V: 4
  • end V: 200
  • step V: 2V
  • exponential percent - 20
  • exponential increment – 0.03
  • approx. run time – 92.75 (can be any number!)

Boltzmann method

ScriptRunnerLight.exe CIU_FITTED.dll TRAP,POSITIVE,3,5,4.0,200.0,2.0,50.0,61.25
  • region: TRAP
  • polarity: POSITIVE
  • SPV: 3
  • scan time: 5
  • start V: 4
  • end V: 200
  • step V: 2V
  • Boltzmann offset – 50
  • approx. run time – 61.25 (can be any number!)

User-defined method

ScriptRunnerLight.exe CIU_LIST.dll "TRAP,POSITIVE,5, [3 3 3 3 3 3],[4 6 8 10 12 14]
  • region: TRAP
  • polarity: POSITIVE
  • scan time: 5
  • list of scans per voltage (SPVs): [3 3 3 3 3 3]
  • list of collision voltages (CVs): [4 6 8 10 12 14]

Note

This is probably the hardest method to get right. The parameters must start with quotation mark (“) and values cannot be separated by anything other than comma, apart from the values inside the square brackets ([ ]) which have to be separated by single space. Of course, the lists of SPVs and CVs must of the same length.

Note

In general, the values inside the PARAMETERS section of the code must not be separated by anything other than a comma (,)

Tip

Make sure you save the ORIGAMIMS parameters in your notebook, in the header of the MassLynx .raw file or as configuration file inside the MassLynx .raw file. This way, you will make your life a lot easier and your analysis will be swift and pain-free.