Start a new oligonucleotide analysis experiment - BioPharma Finder Software - Start a new oligonucleotide analysis experiment - BioPharma Finder Software - BioPharma Finder Software

Procedure

1. To open the Oligonucleotide Analysis page, from the BioPharma Finder home page, double-click Oligonucleotide Analysis in the Experiment Types area.
2. The Oligonucleotide Analysis page opens and contains five areas: Oligonucleotide Analysis Definition, Load Raw Data, Result Format for Multiple Raw Files, Oligonucleotide Sequence, and Processing Method.

3. 

2. In the Oligonucleotide Analysis Definition area, type the name of the experiment in the Experiment Name box.
3. Experiment names can contain up to 50 characters, including alphanumeric, space, underscore (“_”), and period (“.”) characters.
4. You can overwrite an existing experiment by entering the same experiment name. You cannot overwrite an experiment that is currently submitted to the run queue or is actively processing or canceling in the run queue.
5. See Process an experiment on the Queue page.
3. In the Load Raw Data area, select the Select Raw Data (“...”) button to locate and load the raw data files for the experiment.
4. See Select raw data files.
4. If you load multiple raw data files for an experiment, you must enter a condition for each raw data file and select the reference condition for the experiment. In the Condition box, type the condition for each raw data file, separated by a space. In the Reference Condition box, select the reference condition from the drop-down menu.
5. Below the Load Raw Data parameters, the application lists the raw data file names and their associated conditions. To change the condition assigned to a raw data file, use the drop-down menu in the Condition column to select a different condition.
5. If you load multiple raw data files for an experiment, in the Result Format for Multiple Raw Files area, select either Batch Processing or Multiconsensus.
6. See Batch and multiconsensus result formats.
7. You can process up to 10 raw data files in Multiconsensus mode.
8. If your experiment contains a single raw data file, the Result Format for Multiple Raw Files area is inactive.
6. In the table in the Oligonucleotide Sequence area, select the checkbox for a oligonucleotide sequence to assign the sequence to the experiment.
7. See Select one or more sequences.
8. This selection is optional.

9. NOTE

   For oligonucleotide analysis experiments, only sequences assigned the category “Sequencing" appear in the table. If your oligonucleotide sequence does not appear in the table, you can change its assigned category to “Sequencing” using the Oligonucleotide Sequence Editor.

7. In the table in the Processing Method area, select the checkbox for a processing method to assign the processing method to the experiment.
8. The application provides the Basic Default Method for basic oligonucleotide analysis experiments.
8. If the experiment contains multiple raw data files and you want to use certain component detection and identification parameters automatically determined by the application, select the Enable Automatic Parameter Values checkbox at the top of the Processing Method area. Otherwise, clear the Enable Automatic Parameter Values checkbox.
9. •The automatic component detection parameter values include:
10. •Absolute MS signal threshold (10³ counts, default S/N = 20)
11. •Typical chromatographic peak width (min)
12. •Maximum MS peak width (Da)
13. •Restricted retention time range (start and stop times)
14. •Mass tolerance (ppm or Da, depending on resolution)
15. •Maximum retention time shift (min)
16. •The automatic identification parameter value is the mass accuracy (ppm).
9. To proceed, do one of the following:
1. Select Start Processing to process the oligonucleotide analysis experiment without editing the method parameters.
2. Select Edit Method to review the processing method parameters, adjust the signal threshold and other parameters, and save the method before processing the oligonucleotide analysis experiment using the processing method editing wizard.
3. See Create or edit a processing method.

4. NOTE

   Thermo Fisher Scientific™ recommends that you review the method parameters before processing the experiment. If the default signal threshold value is too low, the experiment can take an excessive amount of time to process.

5. To process an experiment, the application requires the following input on the Oligonucleotide Analysis page:
6. •Experiment name
7. •One or more raw data files
8. •Conditions for each raw file (if there are multiple)
9. •Processing method
10. When you are finished editing the processing method, select the method in the Processing Method area and select Start Processing.
11. If the experiment contains all required information and the input processing method parameters are valid, the application begins processing the experiment.
12. If the experiment does not contain all required information or if the input processing method parameters are invalid, the application returns to the Oligonucleotide Analysis page.