Lower section of Modification Results table parameters - BioPharma Finder Software - Lower section of Modification Results table parameters - BioPharma Finder Software

Lower section of Modification Results table parameters - BioPharma Finder Software - Lower section of Modification Results table parameters - BioPharma Finder Software - BioPharma Finder Software

BioPharma Finder 5.2 Oligonucleotide Analysis User Guide

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Ardia Platform > Software > BioPharma Finder Software

Desktop Software > BioPharma Finder Software

Document Type

User Guide

Software version

5.2

The following table describes the types of information in the lower section of the Modification Results table on the Modification Summary page.

Modification Results table, lower section parameters
Parameter	Description
Field Chooser	Displays the Field Chooser dialog box so that you can select the columns to display in the lower section of the Modification Results pane.
(Check box)	Select or clear the checkbox in the table header row to select/deselect all rows in the lower section. You can also select the checkbox in individual rows for export.
Oligonucleotide	Displays the oligonucleotide sequence.
Residue #	Displays the nucleotide residue (site) number of the modification within the oligonucleotide sequence.
Modification	Displays the type and site of modification.
Category	Displays the type of modification by category. Unknown Modification: Modifications identified using the Mass Search for Unspecified Modifications functionality when the application cannot identify the exact location of the modification. Unknown modifications are indicated by a tilde (~). Modification: Common modifications. Artifact: Modifications resulting from sampling errors.
Comment	Displays any comments about the modification to support the identification, the % Abundance, or both. Examples of comments include None, Possible artifact, or Poor recovery.
Normalized Time Shift (NTS)	Displays the experimental shift of the retention time after modification as a percentage of the abundance-weighted average retention time of all identified components. A negative NTS values indicates that the modified oligonucleotide elutes earlier than the unmodified oligonucleotide. A positive NTS value indicates that the modified oligonucleotide elutes later than the unmodified oligonucleotide.
Predicted Time Shift	Displays the predicted retention time shift for a modified component compared to the unmodified component. This parameters is based on empirically-determined Normalized Time Shift values of common modifications.
Modified Oligonucleotides	Displays the nucleotide sequence range and sequence mass for the component within the oligonucleotide.
Oligonucleotide Sequence	Displays the oligonucleotide sequence for the component.
Confidence	Displays the confidence score for the modification assignment.
Recovery	Displays the general abundance of the component. This value is the total peak area (including modified and unmodified forms of the component) as a percentage of the self-weighted average of all components. The recovery value can be over 100% because of the way the application calculates the reference peak intensity. Good: Recovery > 10% Fair: 1% < Recovery < 10% Poor: Recovery < 1%
% Abundance raw_data_file_name	Displays the % Abundance value for a modification in a particular raw data file.
Custom % Abundance raw_data_file_name	Displays the custom % Abundance value for a modification in a particular raw data file. Visible only when you change the list of components used for the % Abundance calculation.