METHODS AND COMPOSITIONS OF ACCELERATING REACTIONS FOR POLYPEPTIDE ANALYSIS AND RELATED USES

1 . (canceled)

2 . A method for treating a polypeptide, the method comprises the steps of:

a) contacting a polypeptide with a functionalizing reagent to modify an N-terminal amino acid (NTAA) of the polypeptide, thereby forming a modified NTAA;

b) optionally contacting the polypeptide with a removing reagent to remove the modified NTAA from the polypeptide; and

c) applying microwave energy to the polypeptide;

wherein either step a) or step b) is performed in the presence of the microwave energy.

3 . The method of claim 2 , further comprising: d) contacting the modified NTAA with a binding agent that binds to the modified NTAA.

4 . The method of claim 3 , wherein the step d) is conducted after step a) and before step b).

5 . (canceled)

6 . The method of claim 2 , wherein the polypeptide is contacted with the functionalizing reagent and then with the removing reagent.

7 . The method of claim 6 , wherein both step a) and step b) are performed in the presence of the microwave energy.

8 . The method of claim 2 , wherein the polypeptide is directly or indirectly joined to a support before contacting the polypeptide with the functionalizing reagent.

9 - 13 . (canceled)

14 . The method of claim 2 , wherein the functionalizing reagent adds a chemical moiety to the NTAA of the polypeptide.

15 . The method of claim 2 , wherein the functionalizing reagent selectively or specifically modifies the N-terminal amino acid (NTAA) of the polypeptide.

16 - 18 . (canceled)

19 . The method of claim 2 , wherein the functionalizing reagent comprises a compound selected from the group consisting of:

(i) a compound of Formula (I):

or a salt or conjugate thereof,

wherein

R 1 and R 2 are each independently H, C 1-6 alkyl, cycloalkyl, —C(O)R a , —C(O)OR b , or —S(O) 2 R c ;

R a , R b , and R c are each independently H, C 1-6 alkyl, C 1-6 haloalkyl, arylalkyl, aryl, or heteroaryl, wherein the C 1-6 alkyl, C 1-6 haloalkyl, arylalkyl, aryl, and heteroaryl are each unsubstituted or substituted;

R 3 is heteroaryl, —NR d C(O)OR e , or —SR f , wherein the heteroaryl is unsubstituted or substituted;

R d , R e , and R f are each independently H or C 1-6 alkyl; and

optionally wherein when R 3 is

wherein G 1 is N, CH, or CX where X is halo, C 1-3 alkyl, C 1-3 haloalkyl, or nitro, R 1 and R 2 are not both H;

(ii) a compound of Formula (II):

or a salt or conjugate thereof,

wherein

R 4 is H, C 1-6 alkyl, cycloalkyl, —C(O)R g , or —C(O)OR g ; and

R g is H, C 1-6 alkyl, C 2-6 alkenyl, C 1-6 haloalkyl, or arylalkyl, wherein the C 1-6 alkyl, C 2-6 alkenyl, C 1-6 haloalkyl, and arylalkyl are each unsubstituted or substituted;

(iii) a compound of Formula (III):

R 5 —N═C═S  (III)

or a salt or conjugate thereof,

wherein

R 5 is C 1-6 alkyl, C 2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl or heteroaryl;

wherein the C 1-6 alkyl, C 2-6 alkenyl, cycloalkyl, heterocycloalkyl, aryl or heteroaryl are each unsubstituted or substituted with one or more groups selected from the group consisting of halo, —NR h R i , —S(O) 2 R j , or heterocyclyl;

R h , R i , and R j are each independently H, C 1-6 alkyl, C 1-6 haloalkyl, arylalkyl, aryl, or heteroaryl, wherein the C 1-6 alkyl, C 1-6 haloalkyl, arylalkyl, aryl, and heteroaryl are each unsubstituted or substituted;

(iv) a compound of Formula (IV):

or a salt or conjugate thereof,

wherein

R 6 and R 7 are each independently H, C 1-6 alkyl, —CO 2 C 1-4 alkyl, —OR k , aryl, or cycloalkyl, wherein the C 1-6 alkyl, —CO 2 C 1-4 alkyl, —OR k , aryl, and cycloalkyl are each unsubstituted or substituted; and

R k is H, C 1-6 alkyl, or heterocyclyl, wherein the C 1-6 alkyl and heterocyclyl are each unsubstituted or substituted;

(v) a compound of Formula (V):

or a salt or conjugate thereof,

wherein

R 8 is halo or —OR m ;

R m is H, C 1-6 alkyl, or heterocyclyl; and

R 9 is hydrogen, halo, or C 1-6 haloalkyl;

(vi) a metal complex of Formula (VI):

ML n   (VI)

or a salt or conjugate thereof,

wherein

M is a metal selected from the group consisting of Co, Cu, Pd, Pt, Zn, and Ni;

L is a ligand selected from the group consisting of —OH, —OH 2 , 2,2′-bipyridine (bpy), 1,5 dithiacyclooctane (dtco), 1,2-bis(diphenylphosphino)ethane (dppe), ethylenediamine (en), and triethylenetetramine (trien); and

n is an integer from 1-8, inclusive;

wherein each L can be the same or different; and

(vii) a compound of Formula (VII):

or a salt or conjugate thereof,

wherein

G 1 is N, NR 13 , or CR 13 R 14 ;

G 2 is N or CH;

p is 0 or 1;

R 10 , R 11 , R 12 , R 13 , and R 14 are each independently selected from the group consisting of H, C 1-6 alkyl, C 1-6 haloalkyl, C 1-6 alkylamine, and C 1-6 alkylhydroxylamine, wherein the C 1-6 alkyl, C 1-6 haloalkyl, C 1-6 alkylamine, and C 1-6 alkylhydroxylamine are each unsubstituted or substituted, and R 10 and R 11 can optionally come together to form a ring; and

R 15 is H or OH.

20 . The method of claim 2 , which wherein removing the modified NTAA comprises contacting the polypeptide with a removing reagent, wherein the removing reagent comprises an acylpeptide hydrolase (APH), a dipeptidyl peptidase (DPP) and/or a dipeptidyl aminopeptidase enzyme.

21 . The method of claim 2 , wherein modification of the NTAA of the polypeptide is accelerated due to the application of the microwave energy to the polypeptide by at least 5% as compared to modification of the amino acid of the polypeptide without application of the microwave energy to the polypeptide.

22 - 59 . (canceled)

60 . The method of claim 2 , further comprising contacting the polypeptide with a peptide coupling reagent at step a).

61 - 73 . (canceled)

74 . A method for analyzing a polypeptide, which comprises the steps:

(a) providing a polypeptide optionally associated directly or indirectly with a recording tag;

(b) modifying an N-terminal amino acid (NTAA) of the polypeptide with a functionalizing reagent to yield a modified NTAA,

(c) contacting the polypeptide with a first binding agent comprising a first binding portion capable of binding to the modified NTAA and

(c1) a first coding tag with identifying information regarding the first binding agent, or

(c2) a first detectable label;

(d) (d1) transferring the information of the first coding tag to the recording tag to generate a first extended recording tag and analyzing the extended recording tag, or

(d2) detecting the first detectable label; and

(e) optionally contacting the polypeptide with a removing reagent to remove the modified NTAA to expose a new NTAA;

wherein

any one or more of steps (b), (c), (d1), (d2) and/or (e) are performed in the presence of microwave energy.

75 . (canceled)

76 . The method of claim 74 , wherein the polypeptide is contacted with the removing reagent at step (e).

77 . The method of claim 76 , further comprising repeating steps (b) to (e) at least one more time to determine a sequence of at least a portion of the polypeptide.

78 . (canceled)

79 . The method of claim 76 , wherein the steps (b) and (e) are performed in the presence of microwave energy.

80 - 127 . (canceled)

128 . The method of claim 74 , wherein the polypeptide is directly or indirectly joined to a support at step (a).

129 - 152 . (canceled)

153 . A kit or system for treating a polypeptide, which comprises:

a) a functionalizing reagent to modify an amino acid of a polypeptide, a binding agent capable of binding to said polypeptide, and/or a removing reagent to remove an amino acid from said polypeptide; and

b) a microwave energy source, e.g., a microwave energy source configured for applying a microwave energy to said polypeptide;

wherein the functionalizing reagent modifies an N-terminal amino acid (NTAA), the binding agent binds to an N-terminal amino acid (NTAA), and/or the removing reagent removes an N-terminal amino acid (NTAA).

154 - 155 . (canceled)

156 . A method for treating a polypeptide, the method comprises the steps of:

a) contacting a polypeptide with a functionalizing reagent to modify an amino acid of the polypeptide, thereby forming a modified amino acid;

b) contacting the modified amino acid with a binding agent that binds to the modified amino acid; and

c) applying microwave energy to the polypeptide, wherein step a) is performed in the presence of the microwave energy.

157 . The method of claim 156 , further comprising: d) removing the modified amino acid.

158 . The method of claim 157 , wherein both step a) and step d) are performed in the presence of the microwave energy.