How to modify the sum formula/mass of a user-defined nucleoside in the ProMass masses table to match the sequence of a modified oligonucleotide - WKB91954

OBJECTIVE or GOAL

Modify the sum formula/mass of a user-defined nucleoside in ProMass to match the sequence of a modified oligonucleotide.

ENVIRONMENT

• MassLynx 4.2
• ProMass for MassLynx 2.0
• ProMass for MassLynx HR

PROCEDURE

For the znova_masses.ini file, you calculate masses for nucleotide residues using the neutral formula of the nucleotide monomer residue with one linkage phosphate, and then subtract H2O from that formula. ProMass assumes that there is no phosphate at the 5’ or 3’ end of a full chain, so it leaves the full sequence with OH at the 3’ and 5’ ends by default. This is analogous to the way you would use amino acid residues. You would subtract H2O from the amino acid to get the residue mass.

For example, for the A MOE gapmer, this would be the correct monoisotopic mass:

#A MOE gapmer, C13H18N5O7P

xA = 387.0943842

ADDITIONAL INFORMATION

The above information was provided by Novatia.