AUC Data Import:

UltraScan supports import of experimental data from the following data sources:

  1. From the UltraScan data acquisition program for the Optima AUC for R+D data
  2. From the UltraScan data acquisition program for the Optima AUC for GMP data
  3. From disk or networked directories, including UltraScan-simulated data, and GMP acquisition
  4. From tar.gz files produced by the Beckman data acquisition program on the Optima AUC
  5. From legacy data generated by the ProteomeLab XLA/XLI/Aviv XLF (disk-based)
  6. From the Cölfen multi-wavelength instrument (disk-based)

Each method is further documented below:

  1. R+D Data Acquisition:

    • Select "Utilities:Data Acquisition from the main menu. This will place you in the "Manage Optima Runs - 1: Experiment" panel
    • Select "Define Another Experiment"
    • Fill out all fields each panel in this sequence: 1: General, 2: Lab/Rotor, 3: Speeds, 4: Cells, 5: Solutions, 6: Optics, 7: Ranges
    • In the Section "8: Submit", make sure all checks are completed and checked, except "Protocol Saved" and "Submit Completed". If everything has been correctly configured, submission should be enabled now, and you can submit the run information to the Optima. Once submitted, the program will shift to the "2: Live Update" stage. The program will wait for you to load the rotor, pull the vacuum, and to select the run ID entered in "1: General" on the Optima's touch screen and start the data acqisition.
    • After the data acquisition is completed, the program will switch to "3: LIMS Import" and allow you to review the data before saving it to the LIMS database.
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  2. GMP Data Acquisition:

    • Select "GMP:Data Acquisition Routine" from the main menu. This will place you in the "Manage Optima Runs - 1: Experiment" panel
    • Select "Define Another Experiment"
    • Fill out all fields each panel in this sequence: 1: General, 2: Lab/Rotor, 3: Speeds, 4: Cells, 5: Solutions, 6: Optics, 7: Ranges, 8: AProfile
    • In the Section "9: Submit", make sure all checks are completed and checked, except "Protocol Saved" and "Submit Completed". If everything has been correctly configured, submission should be enabled now, and you can submit the run information to the Optima. Once submitted, the program will shift to the "2: Live Update" stage. The program will wait for you to load the rotor, pull the vacuum, and to select the run ID entered in "1: General" on the Optima's touch screen and start the data acqisition.
    • After the data acquisition is completed, the program will switch to "3: LIMS Import" and allow you to review the data before saving it to the LIMS database.
    • After data import is completed, the program will switch to "4: Editing" and allow you to review the edited data before saving it to the LIMS database.
    • Once editing profiles for each triple have been saved the program will switch to "5: Analysis" and perform the analysis workflow in parallel for all triples in the experiment. Analysis jobs will be distributed over all available cores in the UltraScan in a Box server until they are either all running or the available cores are exhausted.
    • Once all analysis steps for all triples are completed, the program will switch to "6: Report" and generate a GMP report.
    • Please note: All actions taken by the operator must be electronically signed by the operator. Following this, the reviewer and approver will receive and email asking them to electronically sign the report. If a SME was selected, the SME will be notified by email about the signature progress.
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  3. Data Import from Disk:

    • Select if the data will imported into the LIMS system, or edited/analyzed without LIMS support by checking either the "Database" or "Local" radio button
    • Open "Utilities:Import Experimental Data" in the UltraScan main menu.
    • If you use the LIMS, and have user level 3 or higher, you can now select the data owner by changing the investigator field.
    • Click on "Import Experimental Data" and select the directory containing your data. By default, the program will look for data in $HOME/ultrascan/imports.
    • After loading the experimental data, the triples (and their ranges if it is a multi-wavelength experiment) will be listed in the listbox at the lower left.
    • You can now remove selected triples from the experiment using the "Drop Selected Triples" button
    • Follow the instructions (to do list) in the order in which it is entered.
    • Select a centerpiece for each triple
    • Select the solution for each triple. You can also edit the "Description" field for each triple at this time.
    • Before selecting solutions, make sure to enter applicable buffers and analytes for each triple, combining them as appropriate in a solution. Modules for creating buffers, analytes and solutions can be found in the respective "Database" menu entries.
    • If the data is intensity data, you will need to convert the data to pseudo-absorbance data before saving them to the LIMS database or disk. This is accomplished by clicking on "Define Reference Scans". You will need to select a point to the left of the meniscus of all scans by holding the control button while moving the mouse (all last scans from each triple will be shown). The point you select should define the highest intensity point in the air region above the meniscus.
    • Click on "Save" to save the data to disk or LIMS database.
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  4. Importing data from a tar.gz archive generated by the Beckman Optima AUC web application:

    • To extract a tar.gz file with experimental data generated by the Beckman web application, select "Utilities:Convert Optima Data (Beckman tar.gz)" from the main UltraScan menu. This module allows you to load a tar.gz file with legacy format data and convert it to the OpenAUC formatted file format, which UltraScan can read. The converted data will be stored in the $HOME/ultrascan/imports/ subdirectory in separate subdirectories for each data type and each speed according to this naming convention:

    • RunID-Intensity-RPM1
    • RunID-Intensity-RPM2
    • RunID-Intensity-RPM3
    • ...
    • RunID-Interference-RPM1
    • RunID-Interference-RPM2
    • RunID-Interference-RPM3
    • ...
    • RunID-Absorbance-RPM1
    • RunID-Absorbance-RPM2
    • RunID-Absorbance-RPM3
    • ...
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  5. Importing data from a Beckman XLA/XLI/XLF Proteomelab:

      XLA/XLI/XLF data are data that can be be copied to the $HOME/ultrascan/imports subdirectory and imported directly from there using the same procedure as explained in point (3) above.

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  6. Importing data from the Cölfen multi-wavelength instrument (disk-based):

      Cölfen multi-wavelength data can be be copied to the $HOME/ultrascan/imports subdirectory and imported directly from there using the same procedure as explained in point (3) above.
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