Edit the Manual Sequence parameters

On the Manual Sequence subpage, you can edit several parameters including the charge state, m/z, and mass ranges, as well as the number of isotopes for all or selected oligonucleotide sequences in the Results table. You can also choose to include adducts (Na+, K+) and base losses in the Results table by selecting the corresponding checkboxes.

Oligonucleotide Calculator and Workbook Editor > Manual Sequence subpage commands and parameters

Command or parameter

Description

Chain Name

Specifies the name of an added chain in the oligonucleotide sequence.

(Editor box)

Provides an area for you to manually type or paste new chain information.

Apply (button) (left side of page)

Adds the new chain to the Results table.

Apply to All Sequences (checkbox)

Specifies that changes to the parameters will be applied to all sequences in the Results table.

Apply to Selected Sequences (checkbox)

Specifies that changes to the parameters will be applied only to the sequences currently selected in the Results table.

Charge State Range

Specifies the range of charge states of the sequences in the Results table.

Charge state refers to the imbalance between the number of protons and the number of electrons in a molecular species (or an ion adduct).

Default values: −20 to −2

Range of values: −100 to 100

Note: The minimum and maximum charge state values must be of the same polarity (both values negative or positive).

m/z Range

Specifies the range of the mass-to-charge ratios of the sequences in the Results table.

Default values: 300 to 2500

Range of values: 10 to 100,000

Mass Range (M)

Specifies the range of masses of the sequences in the Results table.

Default values: 200 to 65,000

Range of values: 10 to 100,000

Number of Isotopes

Specifies the number of isotopes to include for each sequence in the Results table, based on the most abundant isotope per oligonucleotide.

Range of values: 0 to 15

Optional Columns (checkboxes)

(Selected by default) Select the checkbox to include columns listing the monoisotopic masses of several possible adducts and base losses in the Results table.

Adduct columns include:

  • Monoisotopic Mass [M] M+Na
  • Monoisotopic Mass [M] M+2Na
  • Monoisotopic Mass [M] M+K

Base loss (M−B) columns include:

  • Monoisotopic Mass [M] M-A
  • Monoisotopic Mass [M] M-C
  • Monoisotopic Mass [M] M-G
  • Monoisotopic Mass [M] M-T
  • Monoisotopic Mass [M] M-U

Apply (button) (right side of page)

Updates the Results table with the parameters specified for all or selected sequences.

Edit the Modification parameters

On the Modification subpage, you can make global changes the nucleotide bases, backbone linkers, 2' ribose groups, and 3'- and 5'-terminals for all or selected nucleotide sequences in the Results table. You can also make individual changes to the specific subunits.

TIP

The Modification subpage functions similarly to the Oligonucleotide Sequence Editor.

See Specify oligo building blocks.

Oligonucleotide Calculator and Workbook Editor > Modification subpage commands and parameters

Command or parameter

Description

Apply to All Sequences (checkbox)

Specifies that the modifications will be applied to all sequences in the Results table.

Apply to Selected Sequences (checkbox)

Specifies that the modifications will be applied only to the sequences currently selected in the Results table.

Update (button) (left side of page)

Updates the sequences in the Results table with the specified global subunit modifications.

Subunit/From/To (drop-down lists)

Specifies global changes to a subunit from one group to another.

5' Terminal (drop-down list)

Specifies the 5'-terminal group for a selected triplet.

(Subunit table)

Specifies subunit changes for a selected triplet.

3' Terminal (drop-down list)

Specifies the 3'-terminal group for a selected triplet.

Update (button) (right side of page)

Updates the sequences in the Results table with the specified triplet-specific subunit modifications.

Edit the Add/Edit Building Blocks parameters

On the Add/Edit Building Blocks subpage, you can edit or delete subunits in the table of building blocks. Changes made to oligo building blocks on the Add/Edit Building Blocks page are reflected by the subunits available on the Modification subpage.

TIP

The Add/Edit Building Blocks subpage functions similarly to the Oligonucleotide Sequence Editor.

See Edit custom modifications or oligo building blocks.

Oligonucleotide Calculator and Workbook Editor > Add/Edit Building Blocks subpage commands and parameters

Command or parameter

Description

(Table of building blocks)

Lists all of the individual subunits and their properties (name, symbol/site, formula, monoisotopic mass, and average mass).

Edit (button)

Select to modify the properties of the subunit selected in the table of building blocks.

Delete (button)

Select to delete the subunit selected in the table of building blocks.

Oligo building block properties (section)

Lists the editable properties of the subunit selected in the table of building blocks.

You can edit the name, symbol, and formula for each subunit. The monoisotopic mass and average mass fields are read only.

Note: You cannot edit any variable modifications or delete default subunits.

Apply (button)

Adds/updates the edited oligo building block in the table of building blocks.