Method and apparatus for de-convoluting a convoluted spectrum

1. A method comprising:

receiving a convoluted spectrum for a group of overlapping isotopic clusters by receiving intensity information for said convoluted spectrum that comprises a summary peak intensity that includes peak intensity ratio information for at least three peaks of each isotopic cluster of the group;

determining a main summary isotope peak intensity for each of a plurality of main summary isotope peaks using the peak intensity ratio information; and

storing said main summary isotope peak intensity for each of said plurality of main summary isotope peaks wherein each main summary isotope peak intensity represents a different isotopic cluster of the group of overlapping isotopic clusters.

2. A method comprising:

receiving a convoluted spectrum for a group of overlapping isotopic clusters obtained by using isobaric reagents and a mass spectrometer by receiving intensity information for said convoluted spectrum that comprises a summary peak intensity that includes peak intensity ratio information for at least three peaks of each isotopic cluster of the group;

determining a main summary isotope peak intensity for each of a plurality of main summary isotope peaks using the peak intensity ratio information; and

storing said main summary isotope peak intensity for each of said plurality of main summary isotope peaks wherein each main summary isotope peak intensity represents a different isotopic cluster of the group of overlapping isotopic clusters.

3. A method comprising:

receiving a convoluted spectrum for a group of overlapping isotopic clusters;

receiving peak intensity ratio information for at least three peaks of each isotopic cluster of the group, comprising at least receiving peak intensity ratio information for at least one down-mass side peak, a main summary isotope peak and at least one up-mass side peak for each isotopic cluster of the group;

determining a normalized peak intensity for each isotopic cluster in said convoluted spectrum by determining a main summary isotope peak for each of a plurality of main summary isotope peaks using the peak intensity ratio information;

fitting said convoluted spectrum to a given peak shape using a selected function; and

storing said normalized peak intensity for each of said plurality of main summary isotope peaks wherein each normalized peak intensity represents a different isotopic cluster of the group of overlapping isotopic clusters.

4. A method comprising:

performing a survey scan to determine a mass of one or more labeled analytes, or one or more labeled fragments thereof;

selecting one of the labeled analytes or labeled fragments;

subjecting the selected labeled analyte or labeled fragment to dissociative energy levels to thereby fragment the labeled analyte or labeled fragment;

performing an energy scan of the fragmented labeled analyte or labeled fragment; and

receiving a spectrum from the energy scan of the fragmented analyte or fragment, the spectrum including intensity peaks for one or more reporter ions and one or more daughter fragment ions of the selected labeled analyte or labeled fragment, wherein the intensity peaks associated with the reporter ion or ions are located in a quiet region of the spectrum and the reporter ions produce a convoluted spectrum of overlapping isotopic clusters associated with two or more different isotopic labeling reagents.

5. A method comprising:

receiving a convoluted spectrum for a group of overlapping isotopic clusters by receiving intensity information for said convoluted spectrum that comprises a summary peak intensity that includes ratio information for each isotopic cluster of the group;

determining a normalized peak intensity for each isotopic cluster in said convoluted spectrum by determining a main summary isotope peak for each of a plurality of main summary isotope peaks and for each main summary isotope peak determined, subtracting known intensity contributions for at least one lower mass isotope cluster up-mass side peak and at least one higher mass isotope cluster down-mass side peak from and adding known intensity contributions for at least one down-mass side peak and at least one up-mass side peak of the isotopic cluster to the respective main summary isotope peak;

storing said normalized peak intensity for each of said plurality of main summary isotope peaks wherein each normalized peak intensity represents a different isotopic cluster of the group of overlapping isotopic clusters; and

receiving peak intensity ratio information for at least three peaks of each isotopic cluster of the group.