How can I process MS1-level oligonucleotides in Molecule Profiler software?

For research use only. Not for use in diagnostic procedures.

Answer

The Molecule Profiler software includes workflows for oligonucleotide impurity studies conducted on an MS1-level. To start using these workflows for oligonucleotide studies, launch the software and select Processing Parameters from the Workflow menu on the left panel. Complete the following steps:

1) Create a new workflow by selecting the New menu and then selecting Oligonucleotides from the drop down list (see the red number 1 label in image below).
2) In the upper right corner of the software, the selected workflow is displayed next to the banner, Method type (red 2 below).
3) Next, name your oligonucleotide in the Compound name field (red 3 below), and then type the oligonucleotide sequence in the Sequence field (red 4 below). This sequence automatically creates a chemical formula and a mass over a range possible charge states (e.g., from 3-11).
4) Choose and confirm one of the three different oligonucleotide biotransformations listed (red 5 below): i) Oligonucleotide Basic, ii) Oligonucleotide Comprehensive, iii) Oligonucleotide Metabolites.
5) Fill in the necessary information in the Compound-Specific Parameters tab (red 6 below), which includes three additional tabbed windows. For oligonucleotides analyzed on an MS1 level, only the Catabolites and the Isotope Pattern tabs need to be completed (see Compound-Specific Parameters window in next image).



6) In the Compound-Specific Parameters tab, specify the maximum number of bonds that can break along the oligonucleotide backbone only, including the loss of dihydrogenphosphite.
7) Define the minimum number of nucleotides as shown below in the Min Nucleotides field.



8) After saving the processing method, select Batch under the Workspaces drop-down menu.
9) In the Batch workspace, add a sample from an MS1-level data set by selecting Sample in the first row of the batch table (see below in Batch workspace window).
10) In the Select Data window, select Browse to navigate to the appropriate data source folder. Then locate the desired .wiff file.
11) Select the folder which contains the processing method and then navigate to the processing parameters file.
12) In the Results File column in the Batch window, type the name of the file where the results will be stored. Note: The maximum number of rows that can be processed in one batch is 200.
13) After the batch is prepared and the batch options have been specified, submit the batch for data processing by clicking the green Find Metabolites button near the top left of the Batch window. A progress bar will show the status of the data processing workflow.



Displayed here is an example of one results file:

In the MS pane, the blue arrow indicates where the mono isotopic peak appears, and red arrow highlights all other isotopes. Light blue lines indicate the overlay of the oligo envelope. Yellow lines indicate the charge state of the oligo in between metabolites.