Determination of compatibility of a set chemical modifications with an amino-acid chain

A method for peptide analysis, comprising:

• comparing a measured mass of an analyte peptide against the masses of theoretical peptides derived from a reference protein;
• and
• applying a graph theory formulation to determine the chemical compatibility between a selected set of post-translational modifications (PTMs) with the theoretical peptides;
• whereby a set of candidate peptides is developed, comprising one or more peptides, including one or more peptides bearing one or more PTMs, having a mass consistent with that of said analyte peptide.

A program storage device readable by a machine, embodying a program of instructions executable by the machine to perform method steps for peptide analysis, said method steps comprising:

• (i) comparing a measured mass of an analyte peptide against the masses of theoretical peptides derived from a reference protein;
• and
• (ii) applying a graph theory formulation to determine the chemical compatibility of a selected set of post-translational modifications (PTMs) with the theoretical peptides;
• whereby a set of candidate peptides is developed, comprising one or more peptides, including one or more peptides bearing one or more PTMs, having a mass consistent with that of said analyte peptide.

A method in a computer system for analysis of an analyte peptide, comprising:

• receiving an input comprising a mass of an analyte peptide;
• presenting to a user a listing comprising a plurality of post-translational modifications (PTMs);
• and
• receiving from said user a user-selected set derived from said plurality of PTMs;

A method to select a set of candidate post-translational modifications based on the difference of a measured parameter between an analyte peptide and a theoretical peptide comprising:

• measuring a parameter of an analyte peptide;
• computing the same parameter as in the previous step for a corresponding theoretical peptide;
• computing a difference between the measured parameter of the analyte peptide and the computed parameter of the theoretical peptide;
• selecting from a database of post-translational modifications one or more post-translational modifications that could account for said difference;
• and
• reporting the set.

A program storage device readable by a machine, embodying a program of instructions executable by the machine to perform method steps for use in selecting a set of candidate post-translational modifications comprising:

• measuring a parameter of an analyte peptide;
• computing the same parameter as in the previous step for a corresponding theoretical peptide;
• computing a difference between the measured parameter of the analyte peptide and the computed parameter of the theoretical peptide;
• determining one or more sets of post-translational modifications that could account for said difference in the measured molecular weight of said peptide fragment and said unmodified fragment;
• and
• reporting the one or more sets.

A system for analyzing proteins or peptides, comprising:

• an input portion for receiving peptide mass data;
• a database of protein sequences;
• a peptide analysis module adapted for communication with said input portion and with said database of protein sequences;
• a microprocessor adapted for communication with said peptide analysis module;
• a database of post-translational modifications;
• a graphing module adapted for communication with said microprocessor and with said database of post-translational modifications;
• and
• an output portion, adapted for communication with said graphing module.