Quantitation of biological molecules

A method for quantifying one or more peptides in a peptide mixture, comprising:

• receiving a first peptide mixture containing a plurality of peptides;
• separating one or more of the plurality of peptides of the first peptide mixture over a period of time;
• mass-to-charge analyzing one or more of the separated peptides of the first peptide mixture at a particular time in the period of time;
• calculating an abundance of one or more of the mass analyzed peptides of the first peptide mixture;
• and
• calculating a relative quantity for the one or more mass analyzed peptides of the first peptide mixture by comparing the calculated abundance of the one or more mass analyzed peptides of the first peptide mixture with an abundance of one or more peptides in a reference sample, the reference sample being external to the first peptide mixture.

A method of quantifying one or more peptides in a mixture, comprising:

• digesting a protein sample to generate a mixture of peptides;
• separating one or more peptides of the mixture of peptides using liquid chromatography;
• mass analyzing one or more of the separated peptides;
• identifying one or more of the mass analyzed peptides based on mass spectra for the peptides;
• calculating chromatogram peak areas for the identified peptides;
• calculating chromatogram peak areas for one or more proteins corresponding to the identified peptides based on the calculated peak areas for the corresponding peptides;
• normalizing the chromatogram peak area for the protein based on a chromatogram peak area for an internal standard;
• and
• determining a relative quantity for a protein of the one or more of the proteins by comparing the normalized chromatogram peak area for the protein to a chromatogram peak area for a corresponding protein in a reference sample.

An apparatus for quantifying one or more peptides in a peptide mixture, comprising:

• means for receiving a first peptide mixture containing a plurality of peptides;
• means for separating one or more of the plurality of peptides of the first peptide mixture over a period of time;
• means for mass analyzing one or more of the separated peptides of the first peptide mixture at a particular time in the period of time;
• means for calculating an abundance of one or more of the mass analyzed peptides of the first peptide mixture;
• means for calculating a relative quantity for the one or more mass analyzed peptides of the first peptide mixture by comparing the calculated abundance of the one or more mass analyzed peptides of the first peptide mixture with an abundance of one or more peptides in a reference sample which is external to first peptide mixture.

A computer program product on a computer-readable medium for quantifying one or more peptides in a first peptide mixture, the product comprising instructions operable to cause a programmable processor to:

• receive separation information representing a separation of one or more of a plurality of peptides of a first peptide mixture over a period of time;
• receive mass-to-charge analysis information for one or more of the separated peptides of the first peptide mixture at a particular time in the period of time;
• calculate an abundance of one or more of the mass analyzed peptides of the first peptide mixture;
• and
• calculate a relative quantity for the one or more mass analyzed peptides of the first peptide mixture by comparing the calculated abundance of the one or more mass analyzed peptides of the first peptide mixture with an abundance of one or more peptides in a reference sample, the reference sample being external to the first peptide mixture.

A computer program product on a computer-readable medium for quantifying one or more peptides in a first peptide mixture, the product comprising instructions operable to cause a programmable processor to:

• receive separation information representing a separation of one or more of a plurality of peptides of a first peptide mixture over a period of time;
• receive mass-to-charge analysis information for one or more of the separated peptides of the first peptide mixture at a particular time in the period of time;
• identify one or more of the mass analyzed peptides based on the mass-to-charge analysis information for the peptides;
• calculate chromatogram peak areas for the identified peptides;
• calculate chromatogram peak areas for one or more proteins corresponding to the identified peptides based on the calculated peak areas for the corresponding peptides;
• normalize the chromatogram peak area for the protein based on a chromatogram peak area for an internal standard;
• and
• determine a relative quantity for a protein of the one or more of the proteins by comparing the normalized chromatogram peak area for the protein to a chromatogram peak area for a corresponding protein in a reference sample.

Apparatus for quantifying one or more peptides in a first peptide mixture, the apparatus comprising digital circuitry configured to perform the following actions:

• receive separation information representing a separation of one or more of a plurality of peptides of a first peptide mixture over a period of time;
• receive mass-to-charge analysis information for one or more of the separated peptides of the first peptide mixture at a particular time in the period of time;
• calculate an abundance of one or more of the mass analyzed peptides of the first peptide mixture;
• and
• calculate a relative quantity for the one or more mass analyzed peptides of the first peptide mixture by comparing the calculated abundance of the one or more mass analyzed peptides of the first peptide mixture with an abundance of one or more peptides in a reference sample, the reference sample being external to the first peptide mixture.

Apparatus for quantifying one or more peptides in a first peptide mixture, the apparatus comprising digital circuitry configured to perform the following actions:

• receive separation information representing a separation of one or more of a plurality of peptides of a first peptide mixture over a period of time;
• receive mass-to-charge analysis information for one or more of the separated peptides of the first peptide mixture at a particular time in the period of time;
• identify one or more of the mass analyzed peptides based on the mass-to-charge analysis information for the peptides;
• calculate chromatogram peak areas for the identified peptides;
• calculate chromatogram peak areas for one or more proteins corresponding to the identified peptides based on the calculated peak areas for the corresponding peptides;
• normalize the chromatogram peak area for the protein based on a chromatogram peak area for an internal standard;
• and
• determine a relative quantity for a protein of the one or more of the proteins by comparing the normalized chromatogram peak area for the protein to a chromatogram peak area for a corresponding protein in a reference sample.

A method for quantifying one or more compounds in a biological sample, comprising:

• receiving a biological sample containing a plurality of compounds;
• separating one or more of the plurality of compounds of the biological sample over a period of time;
• mass-to-charge analyzing one or more of the separated compounds of the biological sample at a particular time in the period of time;
• calculating an abundance of one or more of the mass analyzed compounds of the biological sample;
• and
• calculating a relative quantity for the one or more mass analyzed compounds of the biological sample by comparing the calculated abundance of the one or more mass analyzed compounds of the biological sample with an abundance of one or more compounds in a reference sample, the reference sample being external to the biological sample.

Apparatus for quantifying one or more compounds in a biological sample, the apparatus comprising digital circuitry configured to perform the following actions:

• receive a biological sample containing a plurality of compounds;
• separate one or more of the plurality of compounds of the biological sample over a period of time;
• mass-to-charge analyze one or more of the separated compounds of the biological sample at a particular time in the period of time;
• calculate an abundance of one or more of the mass analyzed compounds of the biological sample;
• and
• calculate a relative quantity for the one or more mass analyzed compounds of the biological sample by comparing the calculated abundance of the one or more mass analyzed compounds of the biological sample with an abundance of one or more compounds in a reference sample, the reference sample being external to the biological sample.