METHODS AND SYSTEMS FOR QUANTIFYING ISOBARIC LABELS AND PEPTIDES

• US 20090002703A1
• Filed: 08/16/2006
• Published: 01/01/2009
• Est. Priority Date: 08/16/2006
• Status: Abandoned Application

• Current Assignee: PerkinElmer LAS, Inc. (Perkinelmer Incorporated)
• Original Assignee: PerkinElmer LAS, Inc. (Perkinelmer Incorporated)
• Inventors: Parman, Craig Edward
• Application Number:
  US11/464,930
• Publication Number:
  US 20090002703A1
• Time in Patent Office: Days
• US Class Current: 356/326
• CPC Class Codes: G01N 33/6848 Methods of protein analysis involving mass spectrometry

Abstract

Methods and systems for quantifying at least two isobaric labels and/or peptides labeled with different isobaric labels are disclosed. In certain examples, the method comprises fitting a mathematical function to at least two isobaric label fragment peaks in a mass spectrum to quantify simultaneously an amount of at least one peptide present in two different samples.

Claims

1. A method of quantifying two or more isobaric labels comprising:

applying a mathematical function to at least two isobaric label fragment peaks in a mass spectrum to provide a fitted curve; and

determining a relative amount of each isobaric label from the fitted curve.

2. The method of claim 1 further comprising applying the mathematical function to at least two low mass, isobaric label fragment peaks in the mass spectrum.

3. The method of claim 1 further comprising applying the mathematical function to at least two high mass, isobaric label fragment peaks in the mass spectrum.

4. The method of claim 1 further comprising applying the mathematical function to all isobaric label fragment peaks in the mass spectrum.

5. The method of claim 1 wherein each isobaric label fragment peak has an intensity and in which the determining step further comprises:

determining the intensity of the at least two isobaric label fragment peaks in the mass spectrum from the fitted curve;

summing the intensity of the at least two isobaric label fragment peaks in the mass spectrum; and

dividing the intensity of at least one isobaric label fragment peak by the summed intensity to determine a relative amount of the at least one isobaric label fragment peak present in a sample.

6. The method of claim 1 in which the determining step further comprises:

determining an area for each of the at least two isobaric label fragment peaks in the mass spectrum from the fitted curve;

summing the areas of the at least two isobaric label fragment peaks in the mass spectrum; and

dividing the area of at least one isobaric label fragment peak by the summed areas to determine the relative amount of the at least one isobaric label fragment peak.

7. The method of claim 1 in which the applying a mathematical function comprises fitting the mathematical function to each of the at least two isobaric label fragment peaks in the mass spectrum to provide the fitted curve.

8. The method of claim 7 in which the mathematical function comprises at least one Gaussian function.

9. A method of quantifying peptides comprising:

subjecting a sample to fragmentation in a mass spectrometer, the sample comprising a first peptide labeled with a first isobaric label and a second peptide labeled with a second isobaric label, in which fragmentation in the mass spectrometer provides a low mass fragment peak and a high mass fragment peak for each of the first and second isobaric labels;

applying a mathematical function to at least one of the low mass fragment peaks or the high mass fragment peaks to provide a fitted curve; and

determining a relative amount of each of the first peptide and the second peptide from the fitted curve.

10. The method of claim 9 further comprising configuring the first isobaric label and the second isobaric label to provide low mass fragments having different mass-to-charge ratios.

11. The method of claim 10 further comprising configuring the mass-to-charge ratios to differ by at least 3 atomic mass units.

12. The method of claim 9 wherein each low mass fragment peak and each high mass fragment peak has an intensity, and in which the determining step further comprises:

determining the intensity of the peaks of the fitted curve;

summing the intensity of the peaks of the fitted curve;

dividing the intensity of at least one of the fitted curve peaks by the summed intensity to determine a relative amount of at least one isobaric label fragment peak; and

correlating the determined relative amount of the at least one isobaric label fragment peak with a relative amount of a peptide.

13. The method of claim 9 in which the first peptide and the second peptide have the same composition but are derived from at least two different samples.

14. The method of claim 9 in which the first peptide and the second peptide have different compositions or sequences.

15. A mass spectrometer comprising:

a first stage configured to select at least two peptides labeled with two, different isobaric labels;

a second stage in fluid communication with the first stage, the second stage configured to fragment the two, different isobaric labels of the selected at least two peptides to provide two low mass fragments and two high mass fragments;

a processing device electrically coupled to the second stage, the processing device configured to quantify simultaneously the two or more peptides.

16. The mass spectrometer of claim 15 in which each of the first stage and the second stage is configured as a quadrupole mass spectrometer.

17. The mass spectrometer of claim 15 in which the first stage is configured to pass two or more peptides with a mass-to-charge ratio within a selected mass-to-charge window.

18. The mass spectrometer of claim 15 in which the processing device further comprises an algorithm that is configured to quantify the peptides by fitting a mathematical function to the two low mass fragments to quantify simultaneously a relative amount of the at least two peptides.

19. A kit comprising:

an isobaric label;

a computer readable medium comprising an algorithm configured to quantify simultaneously at least two peptides; and

instructions for using the isobaric label and the algorithm to quantify peptides in a sample.

20. The kit of claim 19 in which the kit further comprises two or more isobaric labels.

21. The kit of claim 19 in which the algorithm is configured to quantify the at least two peptides by fitting a mathematical function to two low mass fragments from isobaric labels to quantify simultaneously a relative amount of the at least two peptides.

22. A method of quantifying at least two peptides labeled with different isobaric labels, the method comprising fitting a mathematical function to two isobaric label fragment peaks in a mass spectrum to quantify simultaneously a relative amount of the at least two peptides present in a sample.

23. A computer readable medium comprising an algorithm for simultaneously quantifying at least two peptides, the algorithm configured to fit a mathematical function to at least two isobaric label fragment peaks in a mass spectrum to quantify simultaneously a relative amount of the at least two peptides.