Add theoretical sequences to an oligo workbook - BioPharma Finder Software - Intact Mass Analysis User Guide - Add theoretical sequences to an oligo workbook - Create an oligo workbook - Getting started - Introduction to BioPharma Finder workbooks - BioPharma Finder Software - BioPharma Finder Software

Prerequisites

1. You are viewing the Calculator and Workbook page.

Procedure

1. On the Calculator and Workbook page, do one of the following:
1. To create a new oligo workbook, select New on the command bar.
2. To edit an existing oligo workbook, select the row (not the checkbox) for a workbook in the Workbook Manager table and then select Edit on the command bar.
3. The Oligonucleotide Calculator and Workbook Editor opens.

4. 

2. Add theoretical sequences the oligo workbook as appropriate.

3. TIP

   You can add one sequence at a time by manually entering the sequence in the Manual Sequence area. Otherwise, you can use the Import Sequence function to add up to 500 sequences at a time using a specifically-formatted .csv file.

4. The Results table displays the added sequences and contains information at three levels: sequence (top), charge state, and isotope (bottom).

5. 

3. (Optional) Edit the parameters on the Manual Sequence, Modification, and Add/Edit Building Blocks subpages of the Oligonucleotide Calculator and Workbook Editor.

4. NOTE

   The Oligonucleotide Calculator and Workbook Editor contains three subpages: Manual Sequence, Modification, Add/Edit Building Blocks. The Modification and Add/Edit Building Blocks subpages contain parameters that apply only to theoretical results, not experimental results. For oligo workbooks containing both theoretical and experimental results, updating the parameters on these subpages will affect only the theoretical results added to the workbook.

4. (Optional) View the Simulated Spectrum plots for any component in the Results table.
5. The Simulated Spectrum plot displays the peaks for each individual charge state for the sequence in a different color and labels the peaks with their respective m/z ratios. At the sequence level, the Simulated Spectrum plot displays all isotopes for all of the charge states of the sequence. At the charge state level, the Simulated Spectrum plot displays only the isotopes for the selected charge state.
6. The Predicted MS2 Spectrum plot displays the fragment ion peaks for a selected charge state and labels the peaks with their respective m/z ratios. At the sequence level, the Predicted MS2 Spectrum plot is blank. You must select a specific charge state to view the predicted spectrum for a sequence.