Mass tags for quantitative analyses

1. A method comprising:

a) reacting two or more samples, each sample comprising one or more analytes, with a different labeling reagent, the labeling reagents being isotopic and/or isobaric to one another, to thereby produce two or more differently labeled samples each comprising one or more labeled analytes, wherein the labeling reagents are represented by the formula:

or a salt form and/or hydrate form thereof, wherein independently for each labeling reagent:

RP is a reporter group represented by either formula:

wherein ring A is aromatic; each Z can be independently CH, CR 2 or N provided that no more than two Z groups are N; and n can be 1 or 2, or

wherein ring B is non-aromatic; n is 1 or 2, each W is independently O, S, or NR 4 ; each W′ is independently CH 2 , CHR 2 , C(R 2 ) 2 , C(O), S(O), S(O) 2 , or C═N—R 4 ; and Q is CH or CR 2 ;

and each R 2 is independently hydrogen, deuterium, —OH, halogen, —CN, —NO 2 , alkyl, alkenyl, alkynyl, aryl, heteroaryl, arylalkyl, heteroarylalkyl, heteroalkyl, heterocycloalkyl, —R 3 or -T-R 3 , each R 3 can be independently hydrogen, deuterium, alkyl, alkenyl, alkynyl, aryl, arylalkyl, heteroalkyl, heterocycloalkyl, heteroaryl, or heteroaralkyl; T can be —O—, —NR 4 , —S—, —C(O)—, —S(O)—, —SO 2 —, —NR 4 C(O)—, —C(O)NR 4 —, —NR 4 SO 2 —, —SO 2 NR 4 —, —C(O)O—, —OC(O)—, —NR 4 C(O)O—, or —OC(O)NR 4 —; and each R 4 is independently hydrogen, deuterium, alkyl, heteroalkyl, aryl, or aralkyl; and

RP has a unique gross mass for each labeled analyte, and the remainder of the labeling reagent structure has a unique gross mass for each labeled analyte that compensates for the difference in unique gross mass between the RP for each labeled analyte such that the aggregate gross mass of the labeling reagent for each labeled analyte is the same; and

b) producing a mixture by mixing together the two or more differently labeled samples, and optionally one or more calibration standards.

2. The method of claim 1 further comprising:

c) performing a first mass spectrometric analysis on the mixture, or a fraction thereof;

d) treating selected ions, of a selected mass to charge ratio, of the labeled analytes from the first mass spectrometric analysis to dissociative energy levels to thereby form signature ions and ionized daughter fragment ions of at least some of the selected ion; and

e) performing a second mass analysis of the selected ions, the signature ions and the daughter fragment ions, or a fraction thereof.

3. The method of claim 2 , further comprising:

f) determining the gross mass and relative amount of each signature ion moiety in the second mass analysis and the gross mass of the daughter fragment ions.

4. The method of claim 3 , further comprising repeating steps (d) through (f) one or more times on selected ions of the labeled analytes at a different selected mass to charge ratio.

5. The method of claim 3 , further comprising repeating steps (a) through (f) one or more times, each time with a different fraction of the mixture.

6. The method of claim 1 , wherein the two or more samples are the products of an enzymatic digestion reaction.

7. The method of claim 1 , wherein each sample is a fraction from a separations process.

8. The method of claim 1 , wherein the one or more analytes are proteins, nucleic acid molecules, carbohydrates, lipids, steroids, amino acids, or small molecules of less than 1500 daltons.

9. The method of claim 1 , wherein the one or more analytes are peptides.

10. The method of claim 2 , wherein the reporter group does not substantially sub-fragment under conditions used to determine the analyte.

11. The method of claim 2 , wherein the reporter group does sub-fragment under conditions used to determine the analyte.

12. The method of claim 1 , wherein the one or more differentially labeled analytes each comprise a unique reporter group that identifies the sample from which it originated.

13. The method of claim 2 , wherein the identity of the labeled analyte associated with the selected ions of a selected mass to charge ratio is determined by analysis of the daughter fragment ions.

14. The method of claim 2 , wherein the relative amount of each signature ion in the second mass analysis is determined with respect to the other signature ions.

15. The method of claim 14 , wherein the relative amount of each signature ion associated with the identified analyte is correlated with the amount of each sample added to form the mixture to thereby determine the relative amount of the analyte in each of the two or more of the samples combined to form the mixture.

16. The method of claim 15 , wherein:

(i) the mixture further comprises a known amount of at least one calibration standard for the identified analyte and the absolute amount of each signature ion is determined with reference to the amount of signature ion associated with the calibration standard; and

(ii) the absolute amount of the identified analyte in each different sample of the mixture is determined with reference to the amount of each signature ion.

17. The method of claim 15 , further comprising repeating steps (d) through (f), on selected ions of the labeled analytes at a different selected mass to charge ratio, one or more times to thereby identify and/or determine the relative amount of one or more other analytes in each of the two or more of the samples combined to form the mixture.

18. The method of claim 15 , further comprising repeating steps (d) through (f), on selected ions of the labeled analytes at a different selected mass to charge ratio, one or more times to thereby identify and/or determine the absolute amount of one of more other analytes in each of the two or more of the samples combined to form the mixture.