Isobarically labeled analytes and fragment ions derived therefrom

1. A method for proteomic analysis of polypeptides, comprising:

a) reacting each of two or more polypeptide samples, each sample comprising a reactive polypeptide analyte, with a different isobaric and/or isomeric labeling reagent of a set of isobaric and/or isomeric labeling reagents to thereby produce two or more differentially labeled polypeptide analytes having the same mass, wherein each labeling reagent is a 6 membered heterocyclic ring comprising a ring nitrogen atom that is N-alkylated with a substituted or unsubstituted acetic acid moiety to which the polypeptide analyte is linked through a carbonyl carbon of the N-alkyl acetic acid moiety

b) mixing two or more of the differentially labeled polypeptide samples, or a portion thereof, and optionally one or more calibration standards to thereby produce a sample mixture comprising the same reactive polypeptide analyte labeled with two or more different labels having the same mass;

c) digesting each differentially labeled polypeptide sample with at least one enzyme to degrade components of the sample, to form degraded samples, after performing step (a); and

d) performing a mass analysis of the components of the degraded samples.

2. The method of claim 1 , wherein the polypeptide analyte is a protein.

3. The method of claim 1 , wherein the sample mixture comprises the same polypeptide analyte labeled with two or more different labels having the same mass, wherein at least two of the labeled polypeptide analytes are compounds of the formula selected from the group consisting of:

or a salt form and/or hydrate form thereof.

4. The method of claim 3 , wherein the polypeptide analyte is a full-length protein.

5. The method of claim 3 , wherein the fragmentation and further analysis produces at least two signature ions of the molecular formula selected from the group consisting of:

13 CC 5 H 13 N 2 + , 13 CC 5 H 13 15 NN + ′ 13 C 2 C 4 H 13 15 NN + and 13 C 3 C 3 H 13 15 NN + .

6. The method of claim 1 , wherein the polypeptide label comprises one or more heavy atom isotopes.

7. The method of claim 1 , further comprising the step of quantifying the concentration of the reactive polypeptide analyte present in the two or more samples.