Modification notation - BioPharma Finder Software - Modification notation - BioPharma Finder Software - BioPharma Finder Software

Variable modification

For example, 3:A9–T15 = 2104.4033M(A9+Deamination) shows:

• A9 = the modification occurs at the adenine at position 9 in oligonucleotide 3
• Deamination = the modification type

Multiple modifications

For example, 7G1–C15 = 4671.7648m[3’p](C6+C Depyrimidination) shows two modifications:

• A phosphate group (p) at the 3’ terminal (C15 end) of the sequence 7G1–C15 in oligonucleotide 7
• A depyrimidination at base C6 in the sequence 7G1–C15 in oligonucleotide 7

Unspecified modification

An unspecified modification is the addition or subtraction of a given mass of unspecified origin.

For example, 6:A1–G17 = 5159.9221m(~C10+14.0137) shows:

• ~C10 = the modification is on the C base at position 10 (approximately) in oligonucleotide 6
• +14.0137= the addition of a mass of 14.0137 amu

The Enable Mass Search for Unspecified Modifications option must be selected in the processing method (Parameters > Identification > Advanced Search) for the application to perform these identifications.

Nonspecific

For example, 1:A3–T17 = 4595.034m[nonspecific] shows that the identified oligonucleotide was produced from an unexpected cleavage for the specified ribonuclease.

3’-terminal modifications

The 3’-terminal of an oligonucleotide can be modified with the following groups:

• Phosphate (p): H₃PO₄
• Phosphorothioate (s): H₃PO₃S
• 3’-Triantennery GalNAc (g): C₇₈H₁₄₀N₁₁O₃₄P

For example, 7:G10–C21 = 3726.378m[3’p] shows that the 3’-terminal (C21 end) of the sequence G10–C21 of oligonucleotide 7 has been modified with a phosphate (p) group.

5’-terminal modifications

The 5’-terminal of an oligonucleotide can be modified with the following groups:

• Phosphate (p): H₃PO₄
• Phosphorothioate (s): H₃PO₃S
• Biotin (b): C₁₀H₁₆N₂O₃S
• cAG (a): C₃₂H₄₄O₂₇N₁₅P₅
• cAU (u): C₃₁H₄₃O₂₈N₁₂P₅
• cARCA (r): C₂₂H₃₂O₂₁N₁₀P₄
• mCAP (c): C₂₁H₃₀O₂₁N₁₀P₄

For example, 1:A26-G28 = 997.15180m[5'p] shows that the 5’-terminal (A26 end) of the sequence A26–G28 of oligonucleotide 1 has been modified with a phosphate (p) group.

Adducts

For example, 8:T1–G24 = 7342.2761m(Na+) shows that the oligonucleotide is a Na⁺ adduct.

The application detects adducts when an identified mass is higher than the expected precursor mass by a specific amount, for example, ~22 amu higher for a Na⁺ adduct, based on the given charge state.

The application search for many possible adducts, including Na⁺, 2Na⁺, Ca⁺², and Fe⁺³.

Deletion

A deletion (residual loss) is the loss of a nucleotide base within a given sequence identification.

The Enable Residue Deletion option must be selected in the processing method (Parameters > Identification > Advanced Search) for the application to perform these identifications.

The “Site” column in the Results table displays the deleted nucleotide base.

For example, 1:U1–G6 = 1897.3107m(G4+Deletion) shows that the application detected that nucleotide base G4 was deleted from the sequence U1–G6 in oligonucleotide 1. The Site column displays “G4”.