Capture compounds, collections thereof and methods for analyzing the proteome and complex compositions

• US 20030119021A1
• Filed: 07/16/2002
• Published: 06/26/2003
• Est. Priority Date: 07/16/2001
• Status: Active Grant

• Current Assignee: Caprotec Bioanalytics GmbH
• Original Assignee: Caprotec Bioanalytics GmbH
• Inventors: Little, Daniel P., Siddiqi, Suhaib, Koster, Hubert
• Granted Patent: US 7,858,560 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00581 Mass
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/0072 Organic compounds
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: C12Q 2565/627 being a mass spectrometer
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: G01N 33/6803 General methods of protein analysis not limited to specific proteins or families of proteins
• CPC Class Codes: G01N 33/6842 Proteomic analysis of subsets of protein mixtures with reduced complexity, e.g. membrane proteins, phosphoproteins, organelle proteins
• CPC Class Codes: G01N 33/6848 Methods of protein analysis involving mass spectrometry
• CPC Class Codes: G01N 33/6851 Methods of protein analysis involving laser desorption ionisation mass spectrometry

Abstract

Capture compounds and collections thereof and methods using the compounds for the analysis of biomolecules are provided. In particular, collections, compounds and methods are provided for analyzing complex protein mixtures, such as the proteome. The compounds are multifunctional reagents that provide for the separation and isolation of complex protein mixtures. Automated systems for performing the methods also provided.

Claims

1. A collection of capture compounds, comprising:

a plurality of capture compounds, comprising sets of capture compounds, wherein set of each capture compounds includes a moiety X that is selected to covalently bind to biomolecules or to bind with sufficiently high affinity so that the resulting complexes of biomolecule/capture compounds are stable under conditions of mass spectrometric analysis;

a moiety Y that increases the selectivity of the binding by X such that the capture compound binds to fewer biomlecules when the selectivity moiety is present than in its absence;

a moiety Q, such that each set contains a different Q, wherein Q permits separation of each set; and

a moiety Z for presenting X, Y and Q.

2. The collection of claim 1, wherein the biomolecules are proteins.

3. The collection of claim 1, wherein Q permits separation by arraying of the capture compounds on a solid support by binding to the surface or a molecule thereon.

4. The collection of claim 1 that includes at least ten different capture compounds.

5. The collection of claim 3 that includes at least ten different capture compounds.

6. The collection of claim 1 that includes at least fifty different capture compounds.

7. The collection of claim 3 that includes at least fifty different capture compounds.

8. The collection of claim 1 that includes at least 100 different capture compounds.

9. The collection of claim 3 that includes at least 100 different capture compounds.

10. The collection of claim 1, wherein Q is chemical group for arraying at addressable loci on a solid supports.

11. A solid support, comprising the collection of compounds of claim 1, wherein each set of compounds is arrayed at a single locus.

12. A solid support, comprising the collection of compounds of claim 3, wherein each set of compounds is arrayed at a single locus.

13. The collection of claim 1, wherein:

component capture compounds are selected from the group consisting of compounds that have the formula(e);

Q-Z-(X)_m and Q-Z-(Y)_n;

Z is a moiety that is cleavable prior to or during mass spectrometric analysis biomolecules bound to the capture compound;

m is an integer that is 1 to 100; and

n in an integer from 1 to 100.

14. The collection of claim 13, wherein component capture compounds are selected from the group consisting of

Q-Z-X and Q-Z-Y.

15. The collection of claim 1, wherein:

component capture compounds are selected from the group consisting of compounds that have the formula(e);

Q-Z-(X)_m and Q-Z-(Y)_n;

Z is a moiety that is not cleavable prior to or during mass spectrometric analysis of biomolecules bound to the capture compound;

m is an integer that is 1 to 100; and

n in an integer from 1 to 100.

16. The collection of claim 15, wherein:

component capture compounds are selected from the group consisting of compounds that have the formula(e);

Q-Z-(X)_m and Q-Z-(Y)_n;

m is an integer that is 1 to 100;

n in an integer from 1 to 100; and

Q is a oligonucleotide or oligonucleotide analog that includes a single-stranded portion of sufficient length “

j”

to form a stable hybrid with a base-complementary single stranded nucleic acid molecule or analog.

17. The collection of claim 1, wherein:

component capture compounds are selected from the group consisting of

m is an integer that is 1 to 100; and

n in an integer from 1 to 100.

18. The collection of claim 1, wherein:

component capture compounds are selected from the group consisting of compounds that the formula(e);

Q-Z-X and Q-Z-Y; and

Q is a oligonucleotide or oligonucleotide analog that includes a single-stranded portion of sufficient length “

j”

to form a stable hybrid with a base-complementary single stranded nucleic acid molecule or analog.

19. The collection of claim 15, wherein:

Q is a oligonucleotide or oligonucleotide analog that includes a single-stranded portion of sufficient length to form a stable hybrid with a base-complementary single stranded nucleic acid molecule or analog.

20. The collection of claim 1, wherein Q has formula N¹_s—

B_i—

N²_u—

, wherein;

N¹, B and N² are oligonucleotides or oligonucleotide analogs comprising s, t and u members, respectively;

B is a region of sequence permutations that contains at least two bases; and

sum of s, i and u is at least 5.

21. The collection of claim 20, wherein the sum of s, i and u is about 5 up to about 50.

22. The collection of claim 20, wherein each member of N¹, B and N² is independently selected from among monomer building blocks of deoxyribonucleic acid, ribonucleic acid, protein nucleic acid and analogs thereof.

23. The collection of claim 13, wherein Z is a photocleavable, acid cleavable, alkaline cleavable, oxidatively cleavable, or reductively cleavable group.

24. The collection of claim 1, wherein Z comprises an insoluble support to which each X, Y and Q is linked either directly or via a linker.

25. The collection claim 24, wherein the insoluble support is selected from the group consisting of a bead, capillary, plate, membrane, wafer, comb, pin, a wafer with pits, an array of pits or nanoliter wells and a flat surface for receiving or linking samples at discrete loci.

26. The collection claim 24, wherein the support comprises silicon, silica gel, glass, nylon, Wang resin, Merrifield resin, dextran cross-linked with epichlorohydrin, agarose, cellulose, magnetic beads, Dynabeads, a metal surface or a plastic material.

27. The collection claim 24, wherein Z comprises hydrophobic beads comprising polystyrene, polyethylene, polypropylene or teflon, or hydrophilic beads comprising cellulose, dextran cross-linked with epichlorohydrin, agarose, polyacrylamide, silica gel and controlled pore glass.

28. The collection claim 24, wherein the Z moiety comprises spacer groups S¹ and/or S², and a cleavable linkage, where the S¹ and/or S² moieties are attached to insoluble support and the cleavable linkage is attached to S², if present, otherwise to the insoluble support.

29. The collection of claim 1, wherein Z is at least a trivalent moiety and has less than 50 members and is selected from straight or branched chain alkylene, straight or branched chain alkenylene, straight or branched chain alkynylene, straight or branched chain alkylenoxy, straight or branched chain alkylenthio, straight or branched chain alkylencarbonyl, straight or branched chain alkylenamino, cycloalkylene, cycloalkenylene, cycloalkynylene, cycloalkylenoxy, cycloalkylenthio, cycloalkylencarbonyl, cycloalkylenamino, heterocyclylene, arylene, arylenoxy, arylenthio, arylencarbonyl, arylenamino, heteroarylene, heteroarylenoxy, heteroarylenthio, heteroarylencarbonyl, heteroarylenamino, oxy, thio, carbonyl, carbonyloxy, ester, amino, amido, phosphino, phosphineoxido, phosphoramidato, phosphinamidato, sulfonamido, sulfonyl, sulfoxido, carbamato, ureido, and combinations thereof, and is unsubstituted or substituted with one or more substituents each independently selected from R¹⁵;

each R¹⁵ is independently a monovalent group selected from straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, heterocyclyl, straight or branched chain heterocyclylalkyl, straight or branched chain heterocyclylalkenyl, straight or branched chain heterocyclylalkynyl, aryl, straight or branched chain arylalkyl, straight or branched chain arylalkenyl, straight or branched chain arylalkynyl, heteroaryl, straight or branched chain heteroarylalkyl, straight or branched chain heteroarylalkenyl, straight or branched chain heteroarylalkynyl, halo, straight or branched chain haloalkyl, pseudohalo, azido, cyano, nitro, OR⁶⁰, NR⁶⁰R⁶¹, COOR⁶⁰, C(O)R⁶⁰, C(O)NR⁶⁰R⁶¹, S(O)_qR⁶⁰, S(O)_qOR⁶⁰, S(O)_qNR⁶⁰R⁶¹, NR⁶⁰C(O)R⁶¹, NR⁶⁰C(O)NR⁶⁰R⁶¹, NR⁶⁰S(O)_qR⁶⁰, SiR⁶⁰R⁶¹R⁶², P(R⁶⁰)₂, P(O)(R⁶⁰)₂, P(OR⁶⁰)₂, P(O)(OR⁶⁰)₂, P(O)(OR⁶⁰)(R⁶¹) and P(O)NR⁶⁰R⁶¹;

q is an integer from 0 to 2;

each R⁶⁰, R⁶¹ and R⁶² is independently hydrogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, aryl, straight or branched chain aralkyl, straight or branched chain aralkenyl, straight or branched chain aralkynyl, heteroaryl, straight or branched chain heteroaralkyl, straight or branched chain heteroaralkenyl, straight or branched chain heteroaralkynyl, heterocyclyl, straight or branched chain heterocyclylalkyl, straight or branched chain heterocyclylalkenyl or straight or branched chain heteorcyclylalkynyl;

with the proviso that Z is cleavable prior to or during analysis of the biomolecule.

30. The collection of claim 1, wherein Z is at least a trivalent moiety and is selected from straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, —

(C(R¹⁵)₂)_d—

, —

O—

, —

S—

, —

(CH₂)_d—

, —

(CH₂)_dO—

, —

(CH₂)_dS—

, >

N(R¹⁵), —

(S(O)_u)—

, —

(S(O)₂)_w—

, >

C(O), —

(C(O))_w—

, —

(C(S(O)_u))_w—

, —

(C(O)O)_w—

, —

(C(R¹⁵)₂)_dO—

, —

(C(R¹⁵)₂)_dS(O)_u—

, —

O(C(R¹⁵)₂)_d—

, —

S(O)_u(C(R¹⁵)₂)_d—

, —

(C(R¹⁵)₂)_dO(C (R¹⁵)₂)_d—

, —

(C(R¹⁵)₂)_dS(O)_u(C(R¹⁵)₂)_d—

, —

N(R¹⁵)(C(R¹⁵)₂)_d—

, —

(C(R¹⁵)₂)_dNR¹⁵—

, —

(C(R¹⁵)₂)_dN(R¹⁵)(C(R¹⁵)₂)_d—

, —

(S(R¹⁵)(O_u)_w—

, —

(C(R¹⁵)₂)_d—

, —

(C(R¹⁵)₂)_dO(C(R¹⁵)₂)_d—

, —

(C(R¹⁵)₂)_d(C(O)O)_w(C(R¹⁵) ₂)_d—

, —

(C(O)O)_w(C(R¹⁵)₂)_d—

, —

(C(R¹⁵)₂)_d(C(O)O)_w—

, —

(C(S)(R¹⁵)_w—

, —

(C(O))_w(CR¹⁵₂)_d—

, —

(CR¹⁵)_d(C(O))_w(CR¹⁵)_d—

, —

(C(R¹⁵)₂)_d(C(O))_w—

, —

N(R¹⁵) (C(R¹⁵)₂)_w—

, —

OC(R¹⁵)₂C(O)—

, —

O((R¹⁵)₂C(O)N(R¹⁵)—

, —

(C(R¹⁵)₂)_wN(R¹⁵) (C(R¹⁵)₂)_w—

, —

(C(R¹⁵)₂)_wN(R¹⁵)—

, >

P(O)_v(R¹⁵)_x, >

P(O)_u(R¹⁵)₃, >

P(O)U(C (R¹⁵)₂)_d, >

Si(R¹⁵)₂ and combinations of any of these groups;

u, v and x are each independently 0 to 5;

each d is independently an integer from 1 to 20, or 1 to 12, or 1-6, or 1 to 3;

each w is independently an integer selected from 1 to 6, or 1 to 3, or 1 to 2;

with the proviso that Z is cleavable prior to or during analysis of the biomolecule.

31. The collection of claim 1, wherein Z is a trivalent group having any combination a group selected from the group consisting of arylene, heteroarylene, cycloalkylene, >

C(R¹⁵)₂, —

C(R¹⁵)═

C(R¹⁵)—

, >

C═

C(R²³)(R²⁴), >

C(R²³)(R²⁴), —

C≡

C—

, —

O—

, >

S(A)_u, >

P(D)_v(R¹⁵), >

P(D)_v(ER¹⁵), >

Si(R¹⁵)₂, >

N(R¹⁵), >

N⁺(R²³)(R²⁴) and >

C(E);

where u is 0, 1 or 2;

v is 0, 1, 2 or 3;

A is —

O—

or —

NR¹⁵;

D is —

S—

or —

O—

; and

E is —

S—

, —

O—

or —

NR¹⁵;

that groups can be combined in any order;

each R¹⁵ is a monovalent group independently selected from the group consisting of hydrogen and Y¹—

R¹⁸;

each Y¹ is a divalent group independently having any combination of the following groups;

a direct link, arylene, heteroarylene, cycloalkylene, >

C(R¹⁷)₂, —

C(R¹⁷)═

C(R¹⁷)—

, >

C═

C(R²³)(R²⁴), >

C(R²³) (R²⁴), —

C≡

C—

, —

O—

, >

S(A)_u, >

P(D)_v(R¹⁷), >

P(D)_v(ER¹⁷), >

N(R¹⁷), >

N(COR¹⁷), >

N⁺(R²³)(R²⁴), >

Si(R¹⁷)₂ and >

C(E);

where u is 0, 1 or 2;

v is 0, 1, 2 or 3;

A is —

O—

or —

NR¹⁷;

D is —

S—

or —

O—

; and

E is —

S—

, —

O—

or —

NR¹⁷;

that groups can be combined in any order;

R¹⁷ and R¹⁸ are each independently selected from the group consisting of hydrogen, halo, pseudohalo, cyano, azido, nitro, —

SiR²⁷R²⁸R²⁵, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy and —

NR¹⁹R²⁰;

R¹⁹ and R²⁰ are each independently selected from hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, aralkyl, heteroaryl, heteroaralkyl and heterocyclyl;

R²³ and R²⁴ are selected from (i) or (ii) as follows;

(i) R²³ and R²⁴ are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl and heteroaryl;

or

(ii) R²³ and R²⁴ together form alkylene, alkenylene or cycloalkylene;

R²⁵, R²⁷ and R²⁸ are each independently a monovalent group selected from hydrogen, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy and —

NR¹⁹R²⁰;

R¹⁵, R¹⁷, R¹⁸, R¹⁹, R²⁰, R²³, R²⁴, R²⁵, R²⁷ and R²⁸ can be substitut with one or more substituents each independently selected from Z²;

Z² is selected from alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, hydroxy, —

S(O)_hR³⁵;

h is 0, 1 or 2, —

NR³⁵R³⁶, —

COOR³⁵, —

COR³⁵, —

CONR³⁵R³⁶, —

OC(O)NR³⁵R³⁶, —

N(R³⁵)C(O)R³⁶, alkoxy, aryloxy, heteroaryl, heterocyclyl, heteroaryloxy, heterocyclyloxy, aralkyl, aralkenyl, aralkynyl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, aralkoxy, heteroaralkoxy, alkoxycarbonyl, carbamoyl, thiocarbamoyl, alkoxycarbonyl, carboxyaryl, halo, pseudohalo, haloalkyl and carboxamido;

R³⁵ and R³⁶ are each independently selected from among hydrogen, halo, pseudohalo, cyano, azido, nitro, trialkylsilyl, dialkylarylsilyl, alkyldiarylsilyl, triarylsilyl, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy, amino, amido, alkylamino, dialkylamino, alkylarylamino, diarylamino and arylamino;

with the proviso that Z is cleavable prior to or during analysis, including mass spectrometric analysis of the compound.

32. The collection of claim 1, wherein Z has the formula:

—

(S¹)_t—

M(R¹⁵)_a—

(S²)_b-L-, wherein;

S¹ and S² are spacer moieties;

t and b are each independently 0 or 1;

a is an integer from 0 to 4;

M is a central moiety possessing three or more points of attachment;

each R¹⁵ is a monovalent group independently selected from Y²—

R¹⁸;

each Y² is a divalent group independently having any combination of the following groups;

a direct link, arylene, heteroarylene, cycloalkylene, >

C(R¹⁷)₂, —

C(R¹⁷)═

C(R¹⁷)—

, >

C═

C(R²³)(R²⁴), >

C(R²³)(R²⁴), —

C≡

C—

, —

O—

, >

S(A)_u, >

P(D)_v(R¹⁷), >

P(D)_v(ER¹⁷), >

N(R¹⁷), >

N(COR¹⁷), >

N⁺(R²³)(R²⁴), >

Si(R¹⁷)₂ and >

C(E);

where u is 0, 1 or 2;

v is 0, 1, 2 or 3;

A is —

O—

or —

NR¹⁷;

D is —

S—

or —

O—

; and

E is —

S—

, —

O—

or —

NR¹⁷;

that groups can be combined in any order;

R¹⁷ and R¹⁸ are each independently selected from the group consisting of hydrogen, halo, pseudohalo, cyano, azido, nitro, —

SiR²⁷R²⁸R²⁵, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy and —

NR¹⁹R²⁰;

R¹⁹ and R²⁰ are each independently selected from hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, aralkyl, heteroaryl, heteroaralkyl and heterocyclyl;

R²³ and R²⁴ are selected from (i) or (ii) as follows;

(i) R²³ and R²⁴ are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl and heteroaryl;

or

(ii) R²³ and R²⁴ together form alkylene, alkenylene or cycloalkylene;

R²⁵, R²⁷ and R²⁸ are each independently a monovalent group selected from hydrogen, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy and —

NR¹⁹R²⁰;

R¹⁵, R¹⁷, R¹⁸, R¹⁹, R²⁰, R²³, R²⁴, R²⁵, R²⁷ and R²⁸ can be substituted with one or more substituents each independently selected from Z²;

Z² is selected from alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, hydroxy;

—

S(O)_hR³⁵;

h is 0, 1 or 2, —

NR³⁵R³⁶, —

COOR³⁵, —

COR³⁵, —

CONR³⁵R³⁶, —

OC(O)NR³⁵R³⁶, —

N(R³⁵)C(O)R³⁶, alkoxy, aryloxy, heteroaryl, heterocyclyl, heteroaryloxy, heterocyclyloxy, aralkyl, aralkenyl, aralkynyl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, aralkoxy, heteroaralkoxy, alkoxycarbonyl, carbamoyl, thiocarbamoyl, alkoxycarbonyl, carboxyaryl, halo, pseudohalo, haloalkyl and carboxamido;

R³⁵ and R³⁶ are each independently selected from among hydrogen, halo, pseudohalo, cyano, azido, nitro, trialkylsilyl, dialkylarylsilyl, alkyldiarylsilyl, triarylsilyl, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy, amino, amido, alkylamino, dialkylamino, alkylarylamino, diarylamino and arylamino; and

L is a group that is cleavable prior to or during mass spectrometric analysis of the compound.

33. The collection of claim 32, wherein M is a tetravalent alkylene, tetravalent phenylene, tetravalent biphenylene or a tetravalent heterobifunctional trityl derivative, and is unsubstituted or is substituted with 1 to 4 groups, each independently selected from R¹⁵.

34. The collection of claim 32, wherein M is at least a trivalent group selected from the following groups absent a hydrogen atom:

—

(CH₂)_r—

, —

(CH₂O)_r—

, —

(CH₂CH₂—

O)_r—

, —

(NH—

(CH₂)_r—

C(═

O))_s—

, —

(NH—

CH(R⁵²)—

C(═

O))_r—

, —

(O—

(CH)_r—

C(═

O))_s—

,

35. The collection of claim 32, wherein S¹ and S² are each independently selected from —

(CH₂)_r—

, —

(CH₂O)—

, —

(CH₂CH₂—

O)_r—

, —

(NH—

(CH₂)_r—

C(═

O))_s—

, —

(NH—

CH(R⁵²)—

C(═

O))_s—

, —

(O—

(CH)_r—

C(═

O))_s—

,

36. The collection of claim 32, wherein L is a disulfide moiety, a photocleavable group, an acid cleavable group, an alkaline cleavable group, a oxidatively cleavable group, or a reductively cleavable group.

37. The collection of claim 32, wherein L is a trityl ether, an ortho nitro substituted aryl group, an o-nitrobenzyl, a phenacyl, nitrophenylsulfenyl group.

38. The collection of claim 32, wherein:

L has formula I, II or III as follow;

R²⁰ is ω

-(4,4′

-dimethoxytrityloxy)alkyl or ω

-hydroxyalkyl;

R²¹ is selected from hydrogen, alkyl, aryl, alkoxycarbonyl, aryloxycarbonyl and carboxy;

R²¹ is selected from hydrogen, alkyl, aryl, alkoxycarbonyl, aryloxycarbonyl and carboxy;

R²² is hydrogen;

t is 0-3;

R⁵⁰ is alkyl, alkoxy, aryl or aryloxy;

X²⁰ is hydrogen, alkyl or OR²⁰.

R¹ is hydrogen;

R² is selected from among ω

-hydroxyalkoxy, ω

-(4,4′

-dimethoxytrityloxy)alkoxy, ω

-hydroxyalkyl and ω

-(4,4′

-dimethoxytrityloxy)alkyl, and is unsubstituted or substituted on the alkyl or alkoxy chain with one or more alkyl groups; and

c and e are each independently 0-4.

39. The collection of claim 32, wherein:

L is selected from among —

S—

S—

, —

O—

P(═

O)(OR⁵¹)—

NH—

, p-Me-o-NO₂—

PhCH₂—

, —

O—

C(═

O)—

, and

R⁵¹ is straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, aryl, heteroaryl, cycloalkyl, heterocyclyl, straight or branched chain aralkyl, straight or branched chain aralkenyl, straight or branched chain aralkynyl, straight or branched chain heteroaralkyl, straight or branched chain heteroaralkenyl, straight or branched chain heteroaralkynyl, straight or branched chain cycloalkylalkyl, straight or branched chain cycloalkylalkenyl, straight or branched chain cycloalkylalkynyl, straight or branched chain heterocyclylalkyl, straight or branched chain heterocyclylalkenyl or straight or branched chain heterocyclylalkynyl; and

y is an integer from 0 to 4.

40. The collection of claim 32, wherein R¹⁵ is —

H, —

OH, —

OR⁵¹, —

SH, —

SR⁵¹, —

NH₂, —

NHR⁵¹, —

N(R⁵¹)₂, —

F, —

Cl, —

Br, —

I, —

SO₃H, —

PO<sup>−

2</sup>₄, —

CH₃, —

CH₂CH₃, —

CH(CH₃)₂ or —

C(CH₃)₃;

where R⁵¹ is straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, aryl, heteroaryl, cycloalkyl, heterocyclyl, straight or branched chain aralkyl, straight or branched chain aralkenyl, straight or branched chain aralkynyl, straight or branched chain heteroaralkyl, straight or branched chain heteroaralkenyl, straight or branched chain heteroaralkynyl, straight or branched chain cycloalkylalkyl, straight or branched chain cycloalkylalkenyl, straight or branched chain cycloalkylalkynyl, straight or branched chain heterocyclylalkyl, straight or branched chain heterocyclylalkenyl or straight or branched chain heterocyclylalkynyl.

41. The collection of claim 1, wherein each X is selected from the group consisting of an active ester, an active halo moiety, an amino acid side chain-specific functional group, a reagent that binds to active site of an enzyme, a ligand that binds to a receptor, a specific peptide that binds to a biomolecule surfaces, a lectin, an antibody, an antigen, biotin;

streptavidin.

42. The collection of claim 41, wherein an X is an α

-halo ether, an α

-halo carbonyl group, maleimido, a metal complex, an expoxide, an isothiocyanate, or an antibody against phosphorylated or glycosylated peptides/proteins.

43. The collection of claim 41, wherein X is —

C(═

O)O-Ph-pNO₂, —

C(═

O)O—

C₆F₅, —

C(═

O)—

O—

(N-succinimidyl), —

OCH₂—

I, —

OCH₂—

Br, —

OCH₂—

Cl, —

C(O)CH₂I, —

C(O)CH₂Br or —

C(O)CH₂Cl.

44. The collection of claim 1, wherein member compounds comprise a mass modifying tag linked to Z.

45. The collection of claim 28, wherein member compounds comprise a mass modifying tag;

and the mass modifying tag is linked to Z or is S².

46. The collection of claim 32, wherein:

the mass modified Z moiety has the formula;

—

(S¹)_t—

M(R¹⁵)_a—

(S²)_b-L-T-; and

T is a mass modifying tag.

47. The collection of claim 44, wherein the mass modifying tag is a divalent group having the formula —

X¹R¹⁰— and

is selected from (i)-(vii) as follows;

(i) X¹ is a divalent group selected from —

O—

, —

O—

C(O)—

(CH₂)_y—

C(O)O—

, —

NH—

C(O)—

, —

C(O)—

NH—

, —

NH—

C(O)—

(CH₂)_y—

C(O)O—

, —

NH—

C(S)—

NH—

, —

O—

P(O-alkyl)-O—

, —

O—

SO₂—

O—

, —

O—

C(O)—

CH₂—

S—

, —

S—

, —

NH— and

 

R¹⁰ is a divalent group selected from —

(CH₂CH₂O)_z—

CH₂CH₂O—

, —

(CH₂CH₂O)_z—

CH₂CH₂O-alkylene, alkylene, alkenylene, alkynylene, arylene, heteroarylene, —

(CH₂)_z—

CH₂—

O—

, —

(CH₂)_z—

CH₂—

O-alkylene, —

(CH₂CH₂NH)_z—

CH₂CH₂NH—

, —

CH₂—

CH(OH)—

CH₂O—

, —

Si(R¹²)(R¹³)—

, —

CHF— and

—

CF₂—

;

where y is an integer from 1 to 20;

z is an integer from 0 to 200;

R¹¹ is the side chain of a naturally occurring α

-amino acid; and

R¹² and R¹² are each independently selected from alkyl, aryl and aralkyl;

(ii) —

S—

S—

;

(iii) —

S—

;

(iv) —

(NH—

(CH₂)_y—

NH—

C(O)—

(CH₂)_y—

C(O))_z—

NH—

(CH₂)_y—

NH—

C(O)—

(CH₂)_y—

C(O)O—

, where y and z are selected as in (i);

(v) —

(NH—

(CH₂)_y—

C(O))_z—

NH—

(CH₂)_y—

C(O)O—

, where y and z are selected as in (i);

(vi) —

(NH—

CH(R¹¹)—

C(O))_z—

NH—

CH(R¹¹)—

C(O)O—

, where R¹¹ and z are selected as in (i);

or

(vii) —

(O—

(CH₂)_y—

C(O))_z—

NH—

(CH₂)_y—

C(O)O—

, where y and z are selected as in (i).

48. The collection of claim 45, wherein S² has the formula —

X¹R¹⁰—

, where —

X¹R¹⁰—

is selected from (i)-(vii) as follows;

(i) X¹ is a divalent group selected from —

O—

, —

O—

C(O)—

(CH₂)_y—

C(O)O—

, —

NH—

C(O)—

, —

C(O)—

NH—

, —

NH—

C(O)—

(CH₂)_y—

C(O)O—

, —

NH—

C(S)—

NH—

, —

O—

P(O-alkyl)-O—

, —

O—

SO₂—

O—

, —

O—

C(O)—

CH₂—

S—

, —

S—

, —

NH— and

 

R¹⁰ is a divalent group selected from —

(CH₂CH₂O)_z—

CH₂CH₂O—

, —

(CH₂CH₂O)_z—

CH₂CH₂O-alkylene, alkylene, alkenylene, alkynylene, arylene, heteroarylene, —

(CH₂)_z—

CH₂—

O—

, —

(CH₂)_z—

CH₂—

O-alkylene, —

(CH₂CH₂NH)_z—

CH₂CH₂NH—

, —

CH₂—

CH(OH)—

CH₂O—

, —

Si(R¹²)(R¹³)—

, —

CHF— and

—

CF₂—

;

where y is an integer from 1 to 20;

z is an integer from 0 to 200;

R¹¹ is the side chain of a naturally occurring α

-amino acid; and

R¹² and R¹² are each independently selected from alkyl, aryl and aralkyl;

(ii) —

S—

S—

;

(iii) —

S—

;

(iv) —

(NH—

(CH₂)_y—

NH—

C(O)—

(CH₂)_y—

C(O))_z—

NH—

(CH₂)_y—

NH—

C(O)—

(CH₂)_y—

C(O)O—

, where y and z are selected as in (i);

(v) —

(NH—

(CH₂)_y—

C(O))_z—

NH—

(CH₂)_y—

C(O)O—

, where y and z are selected as in (i);

(vi) —

(NH—

CH(R¹¹)—

C(O))_z—

NH—

CH(R¹¹)—

C(O)O—

, where R¹¹ and z are selected as in (i);

or

(vii) —

(O—

(CH₂)_y—

C(O))_z—

NH—

(CH₂)_y—

C(O)O—

, where y and z are selected as in (i).

49. A collection of claim 17, wherein Q is an oligonucleotide comprising at least “

j”

nucleotides; and

the collection comprises about 10 to 4^j compounds of any, wherein, where j is the number of bases in the single-stranded portion of the oligonucleotide.

50. The collection of claim 49, wherein Z is a moiety that is cleavable during mass spectrometric analysis of the compounds.

51. The collection of claim 49, wherein Z is a moiety that is not cleavable during mass spectrometric analysis of the compounds.

52. A composition, comprising a collection of claim 16, hybridized to a plurality of oligonucleotides or analogs thereof that comprise oligonucleotides that are complementary to each each Q.

53. The composition of claim 52, wherein the oligonucleotides or analog thereof that are complementary to Q are immobilized on a solid support as an array.

54. The composition of claim 53 that is an addressable array.

55. The collection of claim 1, further comprising biomolecules covalently bound to one or more capture compounds in the collection.

56. The collection of claim 55, wherein the biomolecules comprise proteins.

57. The solid support of claim 11, wherein the array is an addressable array.

58. A method for analysis of biomolecules, comprising:

a) contacting a composition comprising a biomolecule with a collection of capture compounds of claim 1 to form capture compound-biomolecule complexes; and

b) identifying or detecting bound biomolecules.

59. The method of claim 58, wherein capture compounds in the collection further comprises a solubility group W that influences the solubility properties of the capture compound

60. The method of claim 58, wherein the biomolecules are proteins.

61. The method of claim 58, wherein:

the capture compounds are in an addressable array; and

each locus in the array contains a different set of capture compounds.

62. The method of claim 58, wherein identification comprises mass spectrometric analysis of the bound biomolecules.

63. The method are claim 58, wherein the biomolecules are proteins.

64. The method are claim 62, wherein the biomolecules are proteins.

65. The method of claim 62, wherein the biomolecules bound to the capture compounds are treated with a protease prior to mass spectrometric analysis.

66. The method of claim 58, wherein each set of compounds in the collection comprises the same X moiety but differs in Y moiety.

67. The method of claim 58, wherein each set of compounds in the collection comprises different X, Y and Q moieties.

68. The method of claim 58, wherein each set of compounds in the collection comprises different X and Y moieties.

69. A method for separating protein conformers, comprising:

contacting a composition comprising a biomolecule with a collection of capture compounds of claim 1;

separating the members of the collection; and

identifying the bound proteins from the mixture, whereby each conformer has different binding specificity for members of the collection.

70. The method of claim 69, wherein identification is effected by mass spectrometry

71. The method of claim 69, wherein at least one conformer is associated with a disease.

72. The collection of claim 1, wherein capture compounds comprise:

a central core Z linked to a reactive functionality X and a selectivity functionality Y, whereby a capture compound forms a covalent bond with a biomolecule in the mixture or interacts with high stabilty such that the affinity of binding of the capture compound to the biomolecule through the reactive functionality in the presence of the selectivity functionality is at least ten-fold greater than in the absence of the selectivity functionality.

73. A method for reducing diversity of complex mixture of biomolecules, comprising:

contacting the mixture with a collection of capture compounds of claim 1 to form complexes of capture compounds with bound biomolecules; and

either before, during or after contacting,

separating each set of complexes of capture compounds with biomolecules from the other sets.

74. A method for identification of phenotype-specific biomolecules, comprising:

sorting cells from a single subject according to a predetermined phenotype to produce at least two separated sets of cells;

contacting mixtures of biomolecules from each set of sorted cells with a collection of capture compounds of claim 1;

and

comparing the patterns of biomolecules binding from each set to identify biomolecules that differ for each set, thereby identifying phenotype-specific biomolecules.

75. The method of claim 74, wherein the cells are synchronized or frozen in a metabolic state before sorting and/or after sorting.

76. The method of claim 74, wherein the biomolecules comprise proteins.

77. The method of claim 74, wherein the bound biomolecules are identified by mass spectrometry.

78. The method of claim 74, wherein each capture compound includes a moiety X that covalently binds to proteins;

a moiety that increases the selectivity of the binding such that the capture compound binds to fewer proteins when the selectivity moiety is present than in its absence.

79. The method of claim 74, wherein each capture compound further comprises a moiety Q for arraying of the capture compounds at different loci on a solid support.

80. The method of claim 74, wherein capture compounds comprise a moiety X that covalently binds to proteins;

and a moiety Q that permits arraying of the capture compounds on a solid support by binding to the surface or a molecule thereon.

81. The method of claim 74, wherein the phenotypes are diseased and healthy phenotypes.

82. Thee method of claim 81, wherein the cells are disease phenotype is a tumor and the healthy phenotype is non-tumor.

83. The method of claim 58, wherein:

each sorting function Q is an oligonucleotide that includes a single-stranded portion of length “

j”

for hybridizing to a complementary oligonucleotide, wherein j is at least 5 bases; and

the method further comprises;

hybridizing the capture compounds to a set of complementary oligonucleotides, which attached to a solid support, wherein the hybridizing is effected before or after the contacting step, thereby immobilizing the capture compounds or capture compound biomolecule complexes on the solid support.

84. The method of claim 83, wherein the single-stranded oligonucleotides or oligonucleotide analogs that are complementary to the Q moiety on the capture compounds are immobilized on a solid support.

85. The method of claim 84, wherein the single stranded oligonucleotides or oligonucleotide analogs that are complementary to the Q moiety of the comprise an addressable array.

86. The method of claim 58, wherein the collection comprises at least 60, 200, 500, 1000 or 1500 sets of different capture ragents.

87. The method of claim 58, wherein the contacting step is performed in an aqueous medium and the biomolecules are hydrophilic.

88. The method of claim 58, wherein the contacting step is performed in a hydrophobic medium and the biomolecules are hydrophobic.

89. The method of claim 58, wherein identification or detection is effected by mass spectrometric analysis of the biomolecule-capture compound complexes.

90. The method of claim 89, wherein the mass spectrometric format is matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry.

91. The method of claim 58, wherein the biomolecules comprise proteins.

92. The method of claim 58, wherein:

the capture compounds comprise a sorting function Q for arraying the compounds on a solid support; and

the method further comprises arraying the capture compounds on a solid support before, during or after the contacting step, wherein;

the resulting biomolecule-capture compound complexes are at discrete spots on a solid support.

93. The method of claim 92, wherein mass spectrometric analysis of the bound biomolecules, comprises:

(i) addition of matrix to the biomolecule-capture agent complexes;

(vi) spot-by-spot matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry.

94. The method of claim 58, further comprising:

chemical or enzymatic treatment of the biomolecule-capture compound complexes to remove or cleave portions thereof.

95. The method of claim 62, wherein mass spectrometric analysis of the bound biomolecules, comprises:

(i) addition of matrix to the sets of biomolecule-capture agent complexes; and

(ii) matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry of each set of biomolecule-capture agent complexes.

96. The method of claim 58, wherein the composition comprising a biomolecule is a cell lysate.

97. The method of claim 96, wherein the cells from which the lysate is produced are synchronized or frozen in a metabolic state.

101. A method of processing the mass spectrometric data produced by the method claim 62, comprising:

(a) subtracting any background;

(b) reducing noise;

(c) calibrating molecular weight; and

(d) refining peaks.

102. The method of claim 101, wherein step (d) comprises peak integration.

103. The method of claim 101, further comprising:

(e) comparing the processed data with existing protein databases or DNA databases containing open reading frames to determine whether the protein is known, and

(f) if the protein is known, identifying modifications

104. The method of claim 101, further comprising:

comparing data from tissues of healthy and diseased individuals, or from different physiological or developmental stages, or from different parts of a tissue.

105. A method of analysis of biomolecules, comprising:

(a) reacting a first mixture of biomolecules with the collection of claim 1 to form a mixture of compound-biomolecule complexes, wherein the compounds comprising the mixture have a first mass modifying tag;

(b) reacting a second mixture of biomolecules with the collection of claim 1 to form a mixture of compound-biomolecule complexes, wherein the compounds comprising the complexes have either (a) no mass modifying tag;

or (b) a second mass modifying tag;

(c) pooling the products of steps (i) and (ii) to produce a mixture thereof;

(d) sorting the compound-biomolecule complexes in the mixture of step c) according to Q moiety to produce an array of sorted complexes;

(v) analyzing the complexes at each locus.

106. The collection of claim 1, wherein compounds in the collection comprises Z, which comprises a reagent of a luminescence assay or a group that is detected in a calorimetric assay;

and a sorting group Q that comprises a single-stranded oligonucleotide.

107. The collection of claim 17, wherein Z is a solid support.

108. The collectin of claim 17, wherein Z is a particulate support.

109. A method for analyzing biomolecules, comprising:

(i) reacting a mixture of biomolecules with the composition of claim 106 to form a mixture of compound-biomolecule complexes;

(ii) hybridizing the compound-biomolecule conjugate mixture to single stranded oligonucleotides or oligonucleotide analogs that are complementary to the Q moiety of the compound-biomolecule complexes to form double stranded hybrids and

(iii) analyzing the double stranded hybridized complexes.

110. The method of claim 109, wherein the quantity of a biomolecule from different experiments is determined by luminescence or by detecting the colorometric tag.

111. The method of claim 109, wherein spectrophotometrically differentiatable dyes are used in the quantification analysis.

112. The method of claim 62, wherein the analysis is orthogonal time of flight (O-TOF) mass spectrometry.

113. The method of claim 62, wherein the analysis is electrospray (ES) mass spectrometry.

114. A method for analyzing biomolecule interactions, comprising:

a) contacting a mixture of biomolecules with a collection of capture compounds of claim 1, to form a compound-biomolecule complexes, wherein;

Z is a moiety that is not cleavable prior to or during mass spectrometric analysis of biomolecules bound to the capture compound; and

the complexes are stable to matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry conditions;

b) contacting the capture compound-biomolecule complexes with a mixture containing compounds selected from the group consisting of mixtures of biomolecules amd small molecules test compounds, wherein compounds in the mixture bind to biomolecules in the complexes;

c) before or after step b) immobilizing the capture compounds on a solid support via the Q group of each set of capture compounds;

d) analyzing the bound compounds by mass spectrometry.

115. The method of claim 114, wherein the small molecule test compounds candidates drugs and are selected from the group consisting of small organic molecules, peptides, peptide mimetics, antisense molecules or dsRNA, antibodies, fragments of antibodies and recombinant or synthetic antibodies and fragments thereof;

and

the method is a method for identifying candidate drugs that bind to biomolecules.

116. The method of claim 114, wherein the capture compound-biomolecule complexes are contacted in step a) with a mixture of biomolecules to identify components of biomolecule complexes or biochemical pathways.

117. The method of claim 114, wherein the biomolecules are proteins.

119. The collection of claim 1, wherein the capture compounds further comprise a solubility group W that influences the solubility properties of the capture compound.

120. The collection of claim 1, wherein the selectivity function Y is selected from those set forth in FIG. 17 and/or the reactivity function X is selected from those set forth in FIG. 16.

98. A system for analysis of mixtures of biomolecules, comprising:

a collection of capture compounds, comprising sets of capture compounds, wherein set of each capture compounds includes a moiety X, which is different in each set, that is selected to covalently bind to biomolecules or to bind with sufficiently high affinity so that complexes of biomolecule/capture compounds are stable under conditions of mass spectrometric analysis;

a moiety Y that increases the selectivity of the binding such that the capture compound binds to fewer biomlecules when the selectivity moiety is present than in its absence;

a computer programmed with instructions for controlling and directing analysis of biomolecules using the collections;

a mass spectrometer; and

software for analysis of data produced by the mass spectrometer.

99. The system of claim 98 that is an automated system.

100. The system of claim 98, further comprising a liquid chromatographic device.

118. A collection of capture compounds, comprising:

a plurality of capture compounds, comprising sets of capture compounds, wherein set of each capture compounds includes a moiety X, which is different in each set, that is selected to covalently bind to biomolecules or to bind with sufficiently high affinity so that the resulting complexes of biomolecule/capture compounds are stable under conditions of mass spectrometric analysis;

a moiety Y that increases the selectivity of the binding by X such that the capture compound binds to fewer biomlecules when the selectivity moiety is present than in its absence; and

a moiety Z for presenting X and Y.

121. A capture compound, comprising a moiety Z that is a trivalent trityl for presenting functional moieties X, Y and Q, wherein moiety X is selected to covalently bind to biomolecules or to bind with sufficiently high affinity so that the resulting complexes of biomolecule/capture compounds are stable under conditions of mass spectrometric analysis;

moiety Y increases the selectivity of the binding by X such that the capture compound binds to fewer biomlecules when Y is present than in its absence; and

moiety Q permits separation of sets of capture compounds.

122. The capture compound of claim 121, wherein Z has the formula:

123. The capture compound of claim 122, wherein X is selected from the groups set forth in FIG. 16.

124. The capture compound of claim 122, wherein Y is selected from the groups set forth in FIG. 17.

125. The capture compound of claim 122, wherein Q is an oligonucleotide or oligonucleotide analog that includes a single-stranded portion of sufficient length “

j”

to form a stable hybrid with a base-complementary single stranded nucleic acid molecule or analog.