Identification parameters - BioPharma Finder Software - Oligonucleotide Analysis User Guide - Identification parameters - Work with an Oligonucleotide Analysis processing method - BioPharma Finder Software - BioPharma Finder Software

Oligonucleotide Identification

Search by Full MS Only

Indicates the type of data that application will use to search.

• Yes: Specifies that the application will search using full-scan data only.
• No: (Default) Specifies that the application will include MS/MS data along with full-scan data in the search.

Use MS/MS

Specifies the type of data to process.

• Ignore MS/MS: Uses only full-scan spectra in the raw data file to identify oligonucleotides.
• Use CID/HCD Only: Uses only CID/HCD spectra in the raw data file to identify oligonucleotides.
• Use ETD/ECD Only: Uses only the ETD/ECD spectra in the raw data file to identify oligonucleotides.
• Use All MS/MS: (Default) Uses all MS/MS spectra in the raw data file to identify oligonucleotides.

Maximum Oligonucleotide Mass

Specifies the maximum oligonucleotide mass to be identified.

• Default: 30,000
• Range: 500 to 500,000

Mass Accuracy (ppm)

Specifies the maximum deviation (ppm) between the mass of a theoretical oligonucleotide and the calculated mass of a particular ion used to identify an oligonucleotide

• Default: 250 (no raw data file loaded)
• Range: 1 to 2000

Minimum Confidence

Specifies the minimum confidence level for a reported oligonucleotide assignment on a 0-to-1 scale, with 1 being the highest confidence.

• Default: 0.80
• Range: 0.00 to 1.00

If “Yes” is selected in the Search by Full MS Only field, the minimum confidence will be set to 0.00.

Maximum Number of Modifications for an Oligonucleotide

Read-only. Specifies the maximum number of modifications allowed for each oligonucleotide; previously specified in the Assign Variable Modifications area of the Sequence Editor page. See Manage variable modifications.

In the Oligonucleotide Analysis workflow, only one modification for each oligonucleotide identified is supported at this time.

• Default: 1

Advanced Search

Enable Mass Search for Unspecified Modifications (checkbox)

Select the Enable Mass Search for Unspecified Modifications checkbox to allow the application to perform a mass search for unspecified modifications to the oligonucleotide.

Mass Changes for Unspecified Modifications

Defines the range of changes to the mass of a nucleotide resulting from an unspecified modification. Only integer values are possible.

• Default: 0 to 0 (no raw data file loaded)
• Range: -9,999 to 10,000

Read-only if the Enable Mass Search for Unspecified Modifications checkbox is not selected.

Enable Residue Deletion (checkbox)

Select the Enable Residue Deletion checkbox to allow the application to search for possible oligonucleotide sequences that may be missing a single nucleotide at any position.

Select Ribonuclease

RNase (drop-down menu)

Specifies the ribonuclease assigned to the currently open processing method.

• Nonspecific: A-, G-, U-, C-, T-, I-, H-
• RNase A: C-, U-
• RNase T1: G-
• RNase U2: A-
• Colicin E5: G-U
• mazF: -ACA
• None (default)

Ribonuclease notation information: A dash (-) indicates the cutting position of the indicated ribonuclease. For example, “-ACA” indicates a cut before the ACA sequence, “G-” indicates a cut after G bases, and “G-U” indicates a cut between G and U bases.

NOTICE The ribonuclease options "Nonspecific" or “None” are not supported for theoretical digestion at this time. Thus, if you enable the Customize Results page to view theoretical digestion results, do not use these ribonuclease options.

Custom Specificity (checkbox)

Specifies any custom specificity applied to the ribonuclease assigned to the currently open processing method.

By default, the Custom Specificity field is inactive (gray) but you can enable it for the selected RNase by selecting the Custom Specificity checkbox.

• When using a custom base, replace the standard oligonucleotide base with the base used in your experiment.
• For example, if you used RNase A in your experiment, but your oligonucleotide consisted of the base 5-methoxy-U (M) instead of U, you can create a custom specificity of RNase A = C-, M- so that the theoretical results correctly reflect the experiment.
• When applying custom activity to a ribonuclease, follow the notation pattern below.
• A dash (-) indicates the cutting location of the indicated ribonuclease.
• For example, “-ACA” indicates a cut before the ACA sequence, “G-” indicates a cut after G bases, and “G-U” indicates a cut between G and U bases.

Phosphate Location

Specifies the phosphate location defined for the currently open processing method.

• None
• 3’-linear
• 3’-cyclic
• 5"

Specificity Level

Defines the level of ribonuclease specificity for the ribonuclease assigned to the currently open processing method.

• Low
• Medium
• High (default)
• Strict

Specificity levels High, Medium, and Low correspond to confidence factors that the application uses to determine the final confidence score of component identification. The difference between these levels can impact your results when two or more components match the spectrum, but only one of the components adheres to the specificity requirements of the selected ribonuclease.