Graphical User Interface

The Ion Mobility Dashboard was originally developed as a GUI and this guide was developed to hopefully answer all your questions related to this dashboard.

Run Overview

  1. Workflow choice will be dictated by which type of experiment you are running. The option to run any individual tool is also available.

  2. Depending on which workflow you’d like to run,a set of files and folders must be prepared ahead of time.

  3. Enter parameter values and use a unique experiment name. Avoid spaces or any special characters in this name.

  4. Double check parameter inputs, files, then run the experiment.

  5. If AutoCCS was performed, you will be able to view a preview of the results. If this does not appear, the experiment likely failed.

  6. Save results to folder. Do not use a duplicate folder name. Once results are saved, they will be removed from the application workspace.

First Step - Run PNNL PreProcessor

At this point in time, PNNL PreProcessor has not been integrated into the application. This tool has two important aspects in the workflow: 1) it filters and smooths data for quality control purposes, 2) it splits multi-field (.d) data into separate (.d) folders.
This spliting function adds a suffix to (.d) folders depending on the ms level as follows: ms1 would be in “filename_1.d”, ms2 would be in “filename_2.d”, etc.
This allows for both stepped-field and single-field to be processed in this application.
For singlefield, metadata must be extracted after splitting raw files.
For steppedfield, metadata must be extracted before splitting raw files.

Select your Workflow

There are three types of workflows to run. Each mode has separate needs for input files, but runs a combination of the modules depicted below.

DTIMS Single field

Drift tube ion mobility mass spectrometry requires knowledge of experiments and a table of calibration ions.

A note on Proteowizard and Nomenclature: For the single tool option, this application will convert all (.d) files to mzML. For the Single-Field workflow, this application will filter out all files suspected to come from multi-field data - this will be determined by the PNNL PreProcessor naming suffix. If a file suffix contains any number greater than (filename)1.d, it will be removed. For example, (filename)2.d would be removed from this workflow.

DTIMS Stepped field

Drift tube ion mobility mass spectrometry that requires specific known targets and their masses.

A Note on AutoCCS: For the stepped-field experiment, autoCCS does not generate a (hidden) metadata file. Instead, it extracts the ionization from the file name (POS or NEG). As such, any Feature files and Ims_Metadata files run through stepped-field AutoCCS must include POS or NEG in their names.

SLIM
Data from instrument performing Structures for Lossless Ion Manipulation.

Single Tool Option

This option is selected to run tools individually.

Select which tool you would like to run. Grey boxes are unavailable, white boxes are available, and the orange box indicates which is selected.

If AutoCCS is selected, choose single field, stepped field, or SLIM depending on your experiment.

Upload your files

Prior to uploading files, please sort each file type into their own folder, then select the folder by clicking “Browse”. For example, all Raw data files should be placed in a single folder without any other files. This includes data types such as Agilent (.d) which are folders themselves - ie: select the encompassing folder/directory which holds one or more raw data types, not the data files themselves.

Individual File uploads do not require folders and may be selected directly. These include: Calibrant File, Target List File, and Metadata File.

Once files are uploaded, select the Run tab.

Run Experiment

Prior to selecting “Run Experiment”, Docker Desktop must be open.

Please confirm all variables and path locations before running experiment.

When running experiment, do not exit the application or Docker. Doing so may result in temporary files (such as .tar files in data folders) not being deleted. If exited early, please ensure no temporary files exist in experimental folders before running again.

Viewing and Saving Results

After an experiment is completed, a “Save Results” button should appear. Select this button to find a folder to save results at.

If CCS Values were generated, a summary graph or PDF will be available to preview depending on the experiment type.

Running Additional Experiments

To clear all parameters and results, select the “Clear Experiment” button and confirm. Save results before clearing or they will be lost.