De Novo Sequencing of DNA

A computer program product, comprising a non-transitory tangible computer-readable storage medium whose contents cause a processor to perform a method for locating a nucleotide of a nucleic acid during de novo sequencing, comprising:

• providing a system, wherein the system comprises one or more distinct software modules, and wherein the distinct software modules comprise an input module and an analysis module;
• (a) receiving a first product ion mass spectrum of a nucleic acid analyzed using a thermal dissociation method and receiving a second product ion mass spectrum of the nucleic acid analyzed using a radical-induced dissociation method using the input module;
• (b) optionally converting peak mass-to-charge ratio (m/z) values of the first spectrum, peak m/z values of the second spectrum, and an m/z value of a precursor ion of the nucleic acid to a single charge using the analysis module;
• and
• (c) determining a peak m/z value of the first spectrum that differs from a peak m/z value of the second spectrum by a mass value of a structure within the nucleic acid the radical-induced dissociation method is known to not be able to dissociate and the CID method is known to be able to dissociate using the analysis module.

A system for locating a nucleotide of a nucleic acid during de novo sequencing, comprising:

• a processor that
• (a) receives a first product ion mass spectrum of a nucleic acid analyzed using a thermal dissociation method and receives a second product ion mass spectrum of the nucleic acid analyzed using a radical-induced dissociation method,
• (b) converts peak mass-to-charge ratio (m/z) values of the first spectrum, peak m/z values of the second spectrum, and an m/z value of a precursor ion of the nucleic acid to a single charge, and
• (c) determines a peak m/z value of the first spectrum that differs from a peak m/z value of the second spectrum by a mass value of a structure within the nucleic acid the radical-induced dissociation method is known not to be able to dissociate and the thermal-dissociation method is known to be able to dissociate.