EP1929003A2

EP1929003A2 - Reagents for the detection of protein phosphorylation in carcinoma signaling pathways

Info

Publication number: EP1929003A2
Application number: EP06814000A
Authority: EP
Inventors: Roberto Polakiewicz; Kimberly Lee; Charles Farnsworth; Ailan Guo; Klarisa Rikova; Yu Li; Albrecht Moritz; Erik Spek
Original assignee: Cell Signaling Technology Inc
Current assignee: Cell Signaling Technology Inc
Priority date: 2005-08-31
Filing date: 2006-08-31
Publication date: 2008-06-11
Also published as: EP1929003A4; WO2007027867A3; WO2007027867A2; EP2182057A1

Abstract

The invention discloses nearly 474 novel phosphorylation sites identified in signal transduction proteins and pathways underlying human carcinoma, and provides phosphorylation-site specific antibodies and heavy-isotope labeled peptides (AQUA peptides) for the selective detection and quantification of these phosphorylated sites/proteins, as well as methods of using the reagents for such purpose. Among the phosphorylation sites identified are sites occurring in the following protein types: Kinase, Adaptor/Scaffold proteins, Phosphatase, G protein Regulator/Guanine Nucleotide Exchange Factors/GTPase Activating Proteins, Cytoskeleton Proteins, DNA Binding Proteins, Phospholipase, Receptor Proteins, Enzymes, DNA Repair/Replication Proteins, Adhesion Proteins, and Proteases , as well as other protein types.

Description

REAGENTS FOR THE DETECTION OF PROTEIN PHOSPHORYLATION IN CARCINOMA SIGNALING PATHWAYS

RELATED APPLICATIONS

This application claims the benefit of, and priority to, U. S.S.N. 60/713,041 , filed August 31 , 2005, presently pending, the disclosure of which is incorporated herein, in its entirety, by reference.

FIELD OF THE INVENTION

The invention relates generally to antibodies and peptide reagents for the detection of protein phosphorylation, and to protein phosphorylation in cancer.

BACKGROUND OF THE INVENTION

The activation of proteins by post-translational modification is an important cellular mechanism for regulating most aspects of biological organization and control, including growth, development, homeostasis, and cellular communication. Protein phosphorylation, for example, plays a critical role in the etiology of many pathological conditions and diseases, including cancer, developmental disorders, autoimmune diseases, and diabetes. Yet, in spite of the importance of protein modification, it is not yet well understood at the molecular level, due to the extraordinary complexity of signaling pathways, and the slow development of technology necessary to unravel it.

Protein phosphorylation on a proteome-wide scale is extremely complex as a result of three factors: the large number of modifying proteins, e.g. kinases, encoded in the genome, the much larger number of sites on substrate proteins that are modified by these enzymes, and the dynamic nature of protein expression during growth, development, disease states, and aging. The human genome, for example, encodes over 520 different protein kinases, making them the most abundant class of enzymes known. See Hunter, Nature 411: 355-65 (2001). Most kinases phosphorylate many different substrate proteins, at distinct tyrosine, serine, and/or threonine residues. Indeed, it is estimated that one-third of all proteins encoded by the human genome are phosphorylated, and many are phosphorylated at multiple sites by different kinases. Many of these phosphorylation sites regulate critical biological processes and may prove to be important diagnostic or therapeutic targets for molecular medicine. For example, of the more than 100 dominant oncogenes identified to date, 46 are protein kinases. See Hunter, supra. Understanding which proteins are modified by these kinases will greatly expand our understanding of the molecular mechanisms underlying oncogenic transformation. Therefore, the identification of, and ability to detect, phosphorylation sites on a wide variety of cellular proteins is crucially important to understanding the key signaling proteins and pathways implicated in the progression of diseases like cancer.

Carcinoma is one of the two main categories of cancer, and is generally characterized by the formation of malignant tumors or cells of epithelial tissue original, such as skin, digestive tract, glands, etc. Carcinomas are malignant by definition, and tend to metastasize to other areas of the body. The most common forms of carcinoma are skin cancer, lung cancer, breast cancer, and colon cancer, as well as other numerous but less prevalent carcinomas. Current estimates show that, collectively, various carcinomas will account for approximately 1.65 million cancer diagnoses in the United States alone, and more than 300,000 people will die from some type of carcinoma during 2005. (Source: American Cancer Society (2005)). The worldwide incidence of carcinoma is much higher.

As with many cancers, deregulation of receptor tyrosine kinases (RTKs) appears to be a central theme in the etiology of carcinomas. Constitutively active RTKs can contribute not only to unrestricted cell proliferation, but also to other important features of malignant tumors, such as evading apoptosis, the ability to promote blood vessel growth, the ability to invade other tissues and build metastases at distant sites (see Blume- Jensen et a/., Nature 411: 355-365 (2001)). These effects are mediated not only through aberrant activity of RTKs themselves, but, in turn, by aberrant activity of their downstream signaling molecules and substrates. I i

The importance of RTKs in carcinoma progression has led to a very active search for pharmacological compounds that can inhibit RTK activity in tumor cells, and more recently to significant efforts aimed at identifying genetic mutations in RTKs that may occur in, and affect progression of, different types of carcinomas (see, e.g., Bardell et al., Science 300: 949 (2003); Lynch et al., N. Eng. J.Med. 350: 2129-2139 (2004)). For example, non-small cell lung carcinoma patients carrying activating mutations in the epidermal growth factor receptor (EGFR), an RTK, appear to respond better to specific EGFR inhibitors than do patients without such mutations (Lynch et al., supra.; Paez et ai, Science 304: 1497-1500 (2004)).

Clearly, identifying activated RTKs and downstream signaling molecules driving the oncogenic phenotype of carcinomas would be highly beneficial for understanding the underlying mechanisms of this prevalent form of cancer, identifying novel drug targets for the treatment of such disease, and for assessing appropriate patient treatment with selective kinase inhibitors of relevant targets when and if they become available. However, although a few key RTKs involved in carcinoma progression are knowns, there is relatively scarce information about kinase-driven signaling pathways and phosphorylation sites that underly the different types of carcinoma. Therefore there is presently an incomplete and inaccurate understanding of how protein activation within signaling pathways is driving these complex cancers. Accordingly, there is a continuing and pressing need to unravel the molecular mechanisms of kinase-driven oncogenesis in carcinoma by identifying the downstream signaling proteins mediating cellular transformation in these cancers. Identifying particular phosphorylation sites on such signaling proteins and providing new reagents, such as phospho-specific antibodies and AQUA peptides, to detect and quantify them remains especially important to advancing our understanding of the biology of this disease.

Presently, diagnosis of carcinoma is made by tissue biopsy and detection of different cell surface markers. However, misdiagnosis can occur since some carcinoma cases can be negative for certain markers and because these markers may not indicate which genes or protein kinases may be deregulated. Although the genetic translocations and/or mutations characteristic of a particular form of carcinoma can be sometimes detected, it is clear that other downstream effectors of constitutively active kinases having potential diagnostic, predictive, or therapeutic value, remain to be elucidated. Accordingly, identification of downstream signaling molecules and phosphorylation sites involved in different types of carcinoma and development of new reagents to detect and quantify these sites and proteins may lead to improved diagnostic/prognostic markers, as well as novel drug targets, for the detection and treatment of this disease. SUMMARY OF THE INVENTION

The invention discloses nearly 474 novel phosphorylation sites identified in signal transduction proteins and pathways underlying human carcinomas and provides new reagents, including phosphorylation-site specific antibodies and AQUA peptides, for the selective detection and quantification of these phosphorylated sites/proteins. Also provided are methods of using the reagents of the invention for the detection, quantification, and profiling of the disclosed phosphorylation sites.

BRIEF DESCRIPTION OF THE DRAWINGS FIGURE 1 - Is a diagram broadly depicting the immunoaffinity isolation and mass-spectrometric characterization methodology (IAP) employed to identify the novel phosphorylation sites disclosed herein.

FIGURE 2 - Is a table (corresponding to Table 1) enumerating the 474 carcinoma signaling protein phosphorylation sites disclosed herein: Column A = the name of the parent protein; Column B = the

SwissProt accession number for the protein (human sequence); Column C = the protein type/classification; Column D = the tyrosine residue (in the parent protein amino acid sequence) at which phosphorylation occurs within the phosphorylation site; Column E = the phosphorylation site sequence encompassing the phosphorylatable residue (residue at which phosphorylation occurs (and corresponding to the respective entry in Column D) appears in lowercase; Column F = the type of carcinoma in which the phosphorylation site was discovered; Column G = the cell type(s) in which the phosphorylation site was discovered; and Column H= the SEQ ID NO.

FIGURE 3 - is an exemplary mass spectrograph depicting the detection of the tyrosine 2110 and 2114 phosphorylation sites in ROS (see Rows 364 and 365 in Figure 2/Table 1), as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); Y* (and pY) indicates the phosphorylated tyrosine (shown as lowercase "y" in Figure 2). <

FIGURE 4 - is an exemplary mass spectrograph depicting the detection of the tyrosine 975 phosphorylation site in ERBB2 (see Row 353 in Figure 2/Table 1), as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); Y^* (and pY) indicates the phosphorylated tyrosine (shown as lowercase "y" in Figure 2).

FIGURE 5 - is an exemplary mass spectrograph depicting the detection of the tyrosine 238 phosphorylation site in FLOT-1 (see Row 49 in Figure 2/Table 1), as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); Y* (and pY) indicates the phosphorylated tyrosine (shown as lowercase "y" in Figure 2) and M# (and lowercase "m") indicates an oxidized methionine also detected. FIGURE 6 - is an exemplary mass spectrograph depicting the detection of the tyrosine 455 phosphorylation site in RAN (see Row 274 in Figure 2/Table 1), as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); Y* (and pY) indicates the phosphorylated tyrosine (shown as lowercase "y" in Figure 2). FIGURE 7 - is an exemplary mass spectrograph depicting the detection of the tyrosine 736 phosphorylation site in ADAM9 (see Row 90 in Figure 2/ Table 1), as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); Y* (and pY) indicates the phosphorylated tyrosine (shown as lowercase "y" in Figure 2). FIGURE 8 - is an exemplary mass spectrograph depicting the detection of the tyrosine 136 phosphorylation site in CRK (see Row 44 in Figure 2/ Table 1), as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); Y* (and pY) indicates the phosphorylated tyrosine (shown as lowercase "y" in Figure 2). FIGURE 9 - is an exemplary mass spectrograph depicting the detection of the tyrosine 402 phosphorylation site in FER (see Row 339 in Figure 2/ Table 1), as further described in Example 1 (red and blue indicate ions detected in MS/MS spectrum); Y^* (and pY) indicates the phosphorylated tyrosine (shown as lowercase "y" in Figure 2).

DETAILED DESCRIPTION OF THE INVENTION

In accordance with the present invention, nearly 474 novel protein phosphorylation sites in signaling proteins and pathways underlying carcinoma have now been discovered. These newly described phosphorylation sites were identified by employing the techniques described in "Immunoaffinity Isolation of Modified Peptides From Complex Mixtures," U.S. Patent Publication No. 20030044848, Rush et al., using cellular extracts from a variety of human carcinoma-derived cell lines, such as H69 LS, HT29, MCF10, A431 , etc., as further described below. The novel phosphorylation sites (tyrosine), and their corresponding parent proteins, disclosed herein are listed in Table 1.

These phosphorylation sites correspond to numerous different parent proteins (the full sequences of which (human) are all publicly available in SwissProt database and their Accession numbers listed in Column B of Table 1/Figure 2), each of which fall into discrete protein type groups, for example Protein Kinases (Serine/Threonine nonreceptor, Tyrosine receptor, Tyrosine nonreceptor, dual specificity and other), Adaptor/Scaffold proteins, Cytoskeletal proteins, and Cellular Metabolism enzymes, etc. (see Column C of Table 1), the phosphorylation of which is relevant to signal transduction activity underlying carcinomas (e.g., skin, lung, breast and colon cancer), as disclosed herein.

The discovery of the nearly 474 novel protein phosphorylation sites described herein enables the production, by standard methods, of new reagents, such as phosphorylation site-specific antibodies and AQUA peptides (heavy-isotope labeled peptides), capable of specifically detecting and/or quantifying these phosphorylated sites/proteins. Such reagents are highly useful, inter alia, for studying signal transduction events underlying the progression of carcinoma. Accordingly, the invention provides novel reagents - phospho-specific antibodies and AQUA peptides ~ for the specific detection and/or quantification of a Carcinoma-related signaling protein/polypeptide only when phosphorylated (or only when not phosphorylated) at a particular phosphorylation site disclosed herein. The invention also provides methods of detecting and/or quantifying one or more phosphorylated Carcinoma-related signaling proteins using the phosphorylation-site specific antibodies and AQUA peptides of the invention, and methods of obtaining a phosphorylation profile of such proteins (e.g. Kinases).

In part, the invention provides an isolated phosphorylation site- specific antibody that specifically binds a given Carcinoma-related signaling protein only when phosphorylated (or not phosphorylated, respectively) at a particular tyrosine enumerated in Column D of Table 1 /Figure 2 comprised within the phosphorylatable peptide site sequence enumerated in corresponding Column E. In further part, the invention provides a heavy-isotope labeled peptide (AQUA peptide) for the detection and quantification of a given Carcinoma-related signaling protein, the labeled peptide comprising a particular phosphorylatable peptide site/sequence enumerated in Column E of Table 1/Figure 2 herein. For example, among the reagents provided by the invention is an isolated phosphorylation site-specific antibody that specifically binds the RIPK5 kinase (serine/threonine) only when phosphorylated (or only when not phosphorylated) at tyrosine 312 (see Row 310 (and Columns D and E) of Table 1/Figure 2). By way of further example, among the group of reagents provided by the invention is an AQUA peptide for the quantification of phosphorylated RIPK5 kinase, the AQUA peptide comprising the phosphorylatable peptide sequence listed in Column E, Row 310 of Table 1/Figure 2 (which encompasses the phosphorylatable tyrosine at position 312).

In one embodiment, the invention provides an isolated phosphorylation site-specific antibody that specifically binds a human Carcinoma-related signaling protein selected from Column A of Table 1 (Rows 2-475) only when phosphorylated at the tyrosine residue listed in corresponding Column D of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 1-2, 5-6, 9-11 , 13-35, 38-44, 46-49, 51-61 , 63-67, 69-80, 83-129, 131 , 133-147, 151-188, 191-210, 212-219, 221-240, 242- 317, 319-333, 335-344, 346-347, 349, 351-355, 357-400, 402-425, 427- 446, 449-.45I ₁ 453-459, and 461-474), wherein said antibody does not bind said signaling protein when not phosphorylated at said tyrosine. In another embodiment, the invention provides an isolated phosphorylation site-specific antibody that specifically binds a Carcinoma-related signaling protein selected from Column A of Table 1 only when not phosphorylated at the tyrosine residue listed in corresponding Column D of Table 1 , comprised within the peptide sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 1-2, 5-6, 9-11 , 13-35, 38-44, 46-49, 51-61 , 63- 67, 69-80, 83-129, 131 , 133-147, 151-188, 191-210, 212-219, 221-240, 242-317, 319-333, 335-344, 346-347, 349, 351-355, 357-400, 402-425, 427-446, 449-451 , 453-459, and 461-474), wherein said antibody does not bind said signaling protein when phosphorylated at said tyrosine. Such reagents enable the specific detection of phosphorylation (or non- phosphorylation) of a novel phosphorylatable site disclosed herein. The invention further provides immortalized cell lines producing such antibodies. In one preferred embodiment, the immortalized cell line is a rabbit or mouse hybridoma. In another embodiment, the invention provides a heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Carcinoma- related signaling protein selected from Column A of Table 1 , said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 1-2, 5-6, 9-11 , 13-35, 38-44, 46-49, 51-61 , 63-67, 69-80, 83-129, 131 , 133-147, 151-188, 191- 210, 212-219, 221-240, 242-317, 319-333, 335-344, 346-347, 349, 351- 355, 357-400, 402-425, 427-446, 449-451 , 453-459, and 461-474), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D of Table 1. In certain preferred embodiments, the phosphorylatable tyrosine within the labeled peptide is phosphorylated, while in other preferred embodiments, the phosphorylatable residue within the labeled peptide is not phosphorylated.

Reagents (antibodies and AQUA peptides) provided by the invention may conveniently be grouped by the type of Carcinoma-related signaling protein in which a given phosphorylation site (for which reagents are provided) occurs. The protein types for each respective protein (in which a phosphorylation site has been discovered) are provided in Column C of Table 1 /Figure 2, and include: Acetyltransferease, Actin binding proteins, Adaptor/Scaffold proteins, Adenylyl cyclase proteins, Adhesion proteins, Apoptosis proteins, Calcium-binding proteins, Cell Cycle Regulation proteins, Channel proteins, Cell surface proteins, Cellular metabolism proteins, Chaperone proteins, Cytokine proteins, Cytoskeleton proteins, DNA binding proteins, DNA repair proteins, Endoplasmic reticulum proteins, Extracellular Matrix proteins, G proteins regulatory proteins, GTP activating proteins, Guanine nucleotide exchange factor proteins, Hydrolase proteins, Inhibitor proteins, Kinases (Serine/ Threonine, dual specificity, Tyrosine etc.), Ligase proteins, Lipid binding proteins, Lyase proteins, Methyltransferase proteins, Mitochondrial proteins, Motor proteins, Oxidoreductase proteins, Phosphatases, Phospholipases, Proteases, Receptor proteins, and RNA binding proteins. Each of these distinct protein groups is considered a preferred subset of Carcinoma-related signal transduction protein phosphorylation sites disclosed herein, and reagents for their detection/quantification may be considered a preferred subset of reagents provided by the invention.

Particularly preferred subsets of the phosphorylation sites (and their corresponding proteins) disclosed herein are those occurring on the following protein types/groups listed in Column C of Table 1/Figure 2: 1) Kinases (including Serine/Threonine dual specificity, and Tyrosine kinases), 2) Adaptor/Scaffold proteins, 3) Phosphatases, 4) G protein regulators, Guanine Nucleotide Exchange factors, GTPase activating proteins, 5) Cytoskeleton proteins, 6) DNA binding proteins, 7) Phospholipase proteins, 8) Receptor proteins, 9) Enzymes, 10) DNA repair/replication proteins, 11) Adhesion proteins, and 12) Proteases. Accordingly, among preferred subsets of reagents provided by the invention are isolated antibodies and AQUA peptides useful for the detection and/or quantification of the foregoing preferred protein/phosphorylation site subsets.

In one subset of preferred embodiments there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a Kinase selected from Column A, Rows 296-365, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 296-365, of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 296-365, of Table 1 (SEQ ID NOs: 295-317, 319-333, 335-344, 346-347, 349, 351-355, and 357-364), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine. (ii) An equivalent antibody to (i) above that only binds the Kinase when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site).

(iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Carcinoma-related signaling protein that is a Kinase selected from Column A, Rows 296-365, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 296-365, of Table 1 (SEQ ID NOs: 295-317, 319-333, 335-344, 346- 347, 349, 351-355, and 357-364), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 296- 365, of Table t

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following Kinase phosphorylation sites are particularly preferred: PIK3C2B (Y127), RIPK5 (Y312), CDC2L5 (Y716), PRKCI (Y388), RPS6KA5 (Y423), FER (Y402), JAK3 (Y929), ZAP70 (Y451), DDR1 (Y755), ERBB2 (Y975), FGFR1 (Y397), FLT1 (Y1053), ROR1 (Y836), ROS1 (Y2110), (see SEQ ID NOs: 302, 309, 313, 324, 326, 338, 340, 343, 347, 352, 359, 360, 362, and 363). In one subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds an Adaptor/Scaffold protein selected from Column A, Rows 26-85, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 26-85, of Table 1 , comprised within the phosphorylatable > peptide sequence listed in corresponding Column E, Rows 26-85, of

Table 1 (SEQ ID NOs: 25-35, 38-44, 46-49, 51-61 , 63-67, 69-80, and 83- 84), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine. (ii) An equivalent antibody to (i) above that only binds the Adaptor/Scaffold protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site).

A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Carcinoma-related signaling protein that is an Adaptor/Scaffold protein selected from Column A, Rows 26-85, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 26-85, of Table 1 (SEQ ID NOs: 25-35, 38-44, 46-49, 51-61 , 63-67, 69-80, and 83-84), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 26- 85, of Table !

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following Adaptor/Scaffold protein phosphorylation sites are particularly preferred: CRK (Y136), FLOT1 (Y203), GAB2 (Y371), SPRY1 (Y53), (see SEQ ID NOs: 43, 49, 51 , and 74).

In a another subset of preferred embodiments there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a Phosphatase protein selected from Column A, Rows 408-419, 442, and 443, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 408-419, 442, and 443, of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 408-419, 442, and 443, of Table 1 (SEQ ID NOs: 407-418, 441 , and 442), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

(ii) An equivalent antibody to (i) above that only binds the Phosphatase protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site). (iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Carcinoma-related signaling protein that is a Phosphatase protein selected from Column A, Rows 408-419, 442, and 443, said labeled peptide comprising the phosphorγlatable peptide sequence listed in corresponding Column E, Rows 408-419, 442, and 443, of Table 1 (SEQ ID NOs: 407-418, 441 , and 442), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 408-419, 442, and 443, of Table 1.

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following Phosphatase protein phosphorylation sites are particularly preferred: INPP5D (Y40), PPP1 R14B (Y29), (see SEQ ID NOs: 413 and 442).

In still another subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a G protein regulator, guanine nucleotide exchange factors, GTPase activating proteins selected from Column A, Rows 270-283, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 270-283, of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 270-283, of Table 1 (SEQ ID NOs: 269-282), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

(ii) An equivalent antibody to (i) above that only binds the G protein regulator, guanine nucleotide exchange factors, or GTPase activating proteins when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site).

(iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Carcinoma-related signaling protein that is a G protein regulator, guanine nucleotide exchange factors, or GTPase activating proteins selected from Column A, Rows 270-283, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 270-283, of Table 1 (SEQ ID NOs: 269-282), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 270-283, of Table 1. Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following G protein regulator, guanine nucleotide exchange factors, or GTPase activating proteins phosphorylation sites are particularly preferred: RAN (Y155) and RASA3 (Y757) (see SEQ ID NOs: 273 and 277). In still another subset of preferred embodiments there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a Cytoskeletal protein selected from Column A, Rows 173-222, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 173-222, of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 173-222, of Table 1 (SEQ ID NOs: 172-188, 191-210, 212-219, and 221), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

(ii) An equivalent antibody to (i) above that only binds the Cytoskeletal protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site).

(iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Carcinoma-related signaling protein that is a Cytoskeletal protein selected from Column A, Rows 173-222, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 173-222, of Table 1 (SEQ ID NOs: 172- 188, 191-210, 212-219, and 221), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 173- 222, of Table t Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following Cellular metabolism enzyme phosphorylation sites are particularly preferred: PLEC1 (Y4505), VIM (Y38) (see SEQ ID NOs: 215 and 219).

In still another subset of preferred embodiments there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a DNA binding protein selected from Column A, Rows 223-231 , of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 223-231 , of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 223-231 , of Table 1 (SEQ ID NOs: 222-230), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

(ii) An equivalent antibody to (i) above that only binds the DNA binding protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site).

(iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Carcinoma-related signaling protein that is a DNA binding protein selected from Column A, Rows 223-231 , said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 223-231 , of Table 1 (SEQ ID NOs: 222- 230), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 223-231 , of Table 1.

In still another subset of preferred embodiments there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a Phospholipase protein selected from Column A, Rows 420-422, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 420-422, of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 420-422 of Table 1 (SEQ ID NOs: 419-421), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

(ii) An equivalent antibody to (i) above that only binds the Phospholipase protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site).

(iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Carcinoma-related signaling protein that is a Phospholipase protein selected from Column A, Rows 420-422, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 420-422, of Table 1 (SEQ ID NOs: 419- 421), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 420-422, of Table 1.

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following Phospholipase protein phosphorylation sites are particularly preferred: PLCB1 (Y239), PLD1 (Y420), (see SEQ ID NOs: 420 and 421).

In still another subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds an Receptor protein selected from Column A, Rows 444-459, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 444-459, of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 444-459, of Table 1 (SEQ ID NOs: 443-458), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine. (ii) An equivalent antibody to (i) above that only binds the Receptor protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site).

(iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Carcinoma-related signaling protein that is an Receptor protein selected from Column A, Rows 443-458, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 444-459, of Table 1 (SEQ ID NOs: 443-458), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 444-459, of Table 1.

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following Receptor protein phosphorylation sites are particularly preferred: GPRC5A (Y350 and Y347) (see SEQ ID NOs: 447 and 448).

In yet another subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds an Enzyme selected from Column A, Rows 243-262, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 243-262, of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 243-262, of Table 1 (SEQ ID NOs: 242-261), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

(ii) An equivalent antibody to (i) above that only binds the Enzyme when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site).

(iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Carcinoma-related signaling protein that is an Enzyme selected from Column A, Rows 243-262, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 243-262, of Table 1 (SEQ ID NOs: 242-261), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 243-262, of Table 1.

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following Enzyme phosphorylation sites are particularly preferred: C0X11 (Y111), (see SEQ ID NO: 246).

In yet another subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody specifically binds a DNA repair/DNA replication protein selected from Column A, Rows 232- 239, of Table 1 only when phosphorylated at the tyrosine listed in corresponding to Column D, Rows 232-239, of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 232-239, of Table 1 (SEQ ID NOs: 231-238), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

(ii) An equivalent antibody to (i) above that only binds the DNA repair/DNA replication protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site).

(iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Carcinoma-related signaling protein that is a DNA repair/DNA replication protein selected from Column A, Rows 232-239, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 232-239, of Table 1 (SEQ ID NOs: 231-238), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 232-239, of Table 1.

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following DNA repair/DNA replication protein phosphorylation sites are particularly preferred: PARP1 (Y176), ATRX (Y1667) (see SEQ ID NOs: 231 and 236). In yet another subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a Adhesion protein selected from Column A, Rows 89-137, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 89-137, of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 89-137, of Table 1 (SEQ ID NOs: 88-129, 131 , and 133-136), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

(ii) An equivalent antibody to (i) above that only binds the Adhesion protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site).

(iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Carcinoma-related signaling protein that is a Adhesion protein selected from Column A, Rows 89-137, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 89-137, of Table 1 (SEQ ID NOs: 88-129, 131 , and 133- 136), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 89-137, of Table 1.

Among this preferred subset of reagents, antibodies and AQUA peptides for the detection/quantification of the following Adhesion protein phosphorylation sites are particularly preferred: ADAM23 (Y375), ADAM9 (Y769), VCL (Y692) (see SEQ ID NOs: 88, 89, and 131).

In still another subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a Protease protein selected from Column A, Rows 423-441 , of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 423-441 , of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 423-441 , of Table 1 (SEQ ID NOs: 422-425, and 427-440), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine. (ii) An equivalent antibody to (i) above that only binds the Protease protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site).

(iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Carcinoma-related signaling protein that is a Protease protein selected from Column A, Rows 423-441 , said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 423-441 , of Table 1 (SEQ ID NOs: 422-425, and 427- 440), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 423-441 , of Table 1.

In still another subset of preferred embodiments, there is provided:

(i) An isolated phosphorylation site-specific antibody that specifically binds a protein selected from Column A, Rows 16, 19, and 291 , of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 16, 19, and 291 , of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 16, 19, and 291 , of Table 1 (SEQ ID NOs: 15, 18, and 290), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine. (ii) An equivalent antibody to (i) above that only binds the protein when not phosphorylated at the disclosed site (and does not bind the protein when it is phosphorylated at the site).

(iii) A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a Carcinoma-related signaling protein that is a protein selected from Column A, Rows 16, 19, and 291 , said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 16, 19, and 291 , of Table 1 (SEQ ID NOs: 15, 18, and 290), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 16, 19, and 291 , of Table 1. The invention also provides, in part, an immortalized cell line producing an antibody of the invention, for example, a cell line producing an antibody within any of the foregoing preferred subsets of antibodies. In one preferred embodiment, the immortalized cell line is a rabbit hybridoma or a mouse hybridoma.

In certain other preferred embodiments, a heavy-isotope labeled peptide (AQUA peptide) of the invention (for example, an AQUA peptide within any of the foregoing preferred subsets of AQUA peptides) comprises a disclosed site sequence wherein the phosphorylatable tyrosine is phosphorylated. In certain other preferred embodiments, a heavy-isotope labeled peptide of the invention comprises a disclosed site sequence wherein the phosphorylatable tyrosine is not phosphorylated.

The foregoing subsets of preferred reagents of the invention should not be construed as limiting the scope of the invention, which, as noted above, includes reagents for the detection and/or quantification of disclosed phosphorylation sites on any of the other protein type/group subsets (each a preferred subset) listed in Column C of Table 1/Figure 2.

Also provided by the invention are methods for detecting or quantifying a Carcinoma-related signaling protein that is tyrosine phosphorylated, said method comprising the step of utilizing one or more of the above-described reagents of the invention to detect or quantify one or more Carcinoma-related signaling protein(s) selected from Column A of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D of Table 1. In certain preferred embodiments of the methods of the invention, the reagents comprise a subset of preferred reagents as described above.

Also provided by the invention is a method for obtaining a phosphorylation profile of protein kinases that are phosphorylated in Carcinoma signaling pathways, said method comprising the step of utilizing one or more isolated antibody that specifically binds a protein kinase selected from Column A, Rows 296-365, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows296-365, of Table 1, comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 296-365, of Table 1 (SEQ ID NOs: 295-317, 319-333, 335-344, 346-347, 349, 351-355, and 357-364), to detect the phosphorylation of one or more of said protein kinases, thereby obtaining a phosphorylation profile for said kinases.

The identification of the disclosed nearly 474 novel Carcinoma- related signaling protein phosphorylation sites, and the standard production and use of the reagents provided by the invention are described in further detail below and in the Examples that follow.

All cited references are hereby incorporated herein, in their entirety, by reference. The Examples are provided to further illustrate the invention, and do not in any way limit its scope, except as provided in the claims appended hereto.

Table 1. Newly Discovered Carcinoma-Related Signaling Protein Phosphorylation Sites.

The short name for each protein in which a phosphorylation site has presently been identified is provided in Column A, and its SwissProt accession number (human) is provided Column B. The protein type/group into which each protein falls is provided in Column C. The identified tyrosine residue at which phosphorylation occurs in a given protein is identified in Column D, and the amino acid sequence of the phosphorylation site encompassing the tyrosine residue is provided in Column E (lower case y = the tyrosine (identified in Column D)) at which phosphorylation occurs. Table 1 above is identical to Figure 2, except that the latter includes the disease and cell type(s) in which the particular phosphorylation site was identified (Columns F and G). The identification of these 474 phosphorylation sites is described in more detail in Part A below and in Example 1.

Definitions.

As used herein, the following terms have the meanings indicated: "Antibody" or "antibodies" refers to all types of immunoglobulins, including IgG, IgM, IgA, IgD, and IgE, including F_ab or antigen-recognition fragments thereof, including chimeric, polyclonal, and monoclonal antibodies. The term "does not bind" with respect to an antibody's binding to one phospho-form of a sequence means does not substantially react with as compared to the antibody's binding to the other phospho-form of the sequence for which the antibody is specific.

"Carcinoma-related signaling protein" means any protein (or polypeptide derived therefrom) enumerated in Column A of Table 1/Figure 2, which is disclosed herein as being phosphorylated in one or more human carcinoma cell line(s). Carcinoma-related signaling proteins may be protein kinases, or direct substrates of such kinases, or may be indirect substrates downstream of such kinases in signaling pathways. A Carcinoma-related signaling protein may also be phosphorylated in other cell lines (non-carcinomic) harboring activated kinase activity. "Heavy-isotope labeled peptide" (used interchangeably with AQUA peptide) means a peptide comprising at least one heavy-isotope label, which is suitable for absolute quantification or detection of a protein as described in WO/03016861 , "Absolute Quantification of Proteins and Modified Forms Thereof by Multistage Mass Spectrometry" (Gygi et al.), further discussed below.

"Protein" is used interchangeably with polypeptide, and includes protein fragments and domains as well as whole protein. "Phosphorylatable amino acid" means any amino acid that is capable of being modified by addition of a phosphate group, and includes both forms of such amino acid.

"Phosphorylatable peptide sequence" means a peptide sequence comprising a phosphorylatable amino acid.

"Phosphorylation site-specific antibody" means an antibody that specifically binds a phosphorylatable peptide sequence/epitope only when phosphorylated, or only when not phosphorylated, respectively. The term is used interchangeably with "phospho-specific" antibody.

A. Identification of Novel Carcinoma-related Signaling Protein Phosphorylation Sites.

The nearly 474 novel Carcinoma-related signaling protein phosphorylation sites disclosed herein and listed in Table 1 /Figure 2 were discovered by employing the modified peptide isolation and characterization techniques described in "Immunoaffinity Isolation of Modified Peptides From Complex Mixtures," U.S. Patent Publication No. 20030044848, Rush et al. (the teaching of which is hereby incorporated herein by reference, in its entirety) using cellular extracts from the human carcinoma derived cell lines and patient samples indicated in Column G of Table 1/Figure 2. Exemplary cell lines used include Su-DHLI , MOLT15, H1703, 3T3-src, 3T3, AbI, A431 , pancreatic xenograft, H1993, HCC827, 3T3-EGFRwt, 3T3-EGFR(L858R), HCT 116, HT29, NCI-N87, HT29, CTV- 1, Karpas 299, MCF-10A (Y561F), MCF-10A (Y969F), Calu-3, H2347, H3255, H2170, U118MG, H1703, HCC366, H2228, HL61b, jurkat, SUPT- 13, Verona patient 4, PT9, DU145, DMS79, MDA-MB-468, A549, H1666, H1650, 831/13, K562, HL53B, HL66B, HL84B, HL87A, HPAC, H441 , SEM, Sor4, SorA, SEM, TgOVA, UT-7, MKPL-1 , H69 LS, A431 , DMS153 NS, SW620, HT116, MDA-MB-468, MCF10, HPAC, and HT29. The isolation and identification of phosphopeptides from these cell lines, using an immobilized general phosphotyrosine-specific antibody, is described in detail in Example 1 below. In addition to the nearly 474 previously unknown protein phosphorylation sites (tyrosine) discovered, many known phosphorylation sites were also identified (not described herein). The immunoaffinity/mass spectrometric technique described in the

'848 Patent Publication (the "IAP" method) - and employed as described in detail in the Examples - is briefly summarized below.

The IAP method employed generally comprises the following steps: (a) a proteinaceous preparation (e.g. a digested cell extract) comprising phosphopeptides from two or more different proteins is obtained from an organism; (b) the preparation is contacted with at least one immobilized general phosphotyrosine-specific antibody; (c) at least one phosphopeptide specifically bound by the immobilized antibody in step (b) is isolated; and (d) the modified peptide isolated in step (c) is characterized by mass spectrometry (MS) and/or tandem mass spectrometry (MS-MS). Subsequently, (e) a search program (e.g. Sequest) may be utilized to substantially match the spectra obtained for the isolated, modified peptide during the characterization of step (d) with the spectra for a known peptide sequence. A quantification step employing, e.g. SILAC or AQUA, may also be employed to quantify isolated peptides in order to compare peptide levels in a sample to a baseline.

In the IAP method as employed herein, a general phosphotyrosine- specific monoclonal antibody (commercially available from Cell Signaling Technology, Inc., Beverly, MA, Cat #9411 (p-Tyr-100)) was used in the immunoaffinity step to isolate the widest possible number of phospho- tyrosine containing peptides from the cell extracts. Extracts from the human carcinoma cell lines described above were employed.

As described in more detail in the Examples, lysates were prepared from these cells line and digested with trypsin after treatment with DTT and iodoacetamide to alkylate cysteine residues. Before the immunoaffinity step, peptides were pre-fractionated by reversed-phase solid phase extraction using Sep-Pak Cis columns to separate peptides from other cellular components. The solid phase extraction cartridges were eluted with varying steps of acetonitrile. Each lyophilized peptide fraction was redissolved in IAP buffer and treated with phosphotyrosine- specific antibody (P-Tyr-100, CST #9411) immobilized on protein Agarose. Immunoaffinity-purified peptides were eluted with 0.1% TFA and a portion of this fraction was concentrated with Stage or Zip tips and analyzed by LC-MS/MS, using a ThermoFinnigan LCQ Deca XP Plus ion trap mass spectrometer. Peptides were eluted from a 10 cm x 75 μm reversed-phase column with a 45-min linear gradient of acetonitrile. MS/MS spectra were evaluated using the program Sequest with the NCBI human protein database. This revealed a total of 474 novel tyrosine phosphorylation sites in signaling pathways affected by kinase activation or active in carcinoma cells. The identified phosphorylation sites and their parent proteins are enumerated in Table 1/Figure 2. The tyrosine (human sequence) at which phosphorylation occurs is provided in Column D, and the peptide sequence encompassing the phosphorylatable tyrosine residue at the site is provided in Column E. Figure 2 also shows the particular type of carcinoma (see Column G) and cell line(s) (see Column F) in which a particular phosphorylation site was discovered.

As a result of the discovery of these phosphorylation sites, phospho-specific antibodies and AQUA peptides for the detection of and quantification of these sites and their parent proteins may now be produced by standard methods, described below. These new reagents will prove highly useful in, e.g., studying the signaling pathways and events underlying the progression of carcinomas and the identification of new biomarkers and targets for diagnosis and treatment of such diseases. B. Antibodies and Cell Lines

Isolated phosphorylation site-specific antibodies that specifically bind a Carcinoma-related signaling protein disclosed in Column A of Table 1 only when phosphorylated (or only when not phosphorylated) at the corresponding amino acid and phosphorylation site listed in Columns D and E of Table 1/Figure 2 may now be produced by standard antibody production methods, such as anti-peptide antibody methods, using the phosphorylation site sequence information provided in Column E of Table 1. For example, previously unknown Ser/Thr kinase phosphorylation site (tyrosine 388) (see Row 325 of Table 1/Figure 2) is presently disclosed. Thus, antibodies that specifically bind this novel Ser/Thr kinase site can now be produced, e.g. by immunizing an animal with a peptide antigen comprising all or part of the amino acid sequence encompassing the respective phosphorylated residue (e.g. a peptide antigen comprising the sequence set forth in Rows 325 of Column E, of Table 1 (SEQ ID NO: 324) (which encompasses the phosphorylated tyrosine at positions 388 of the Ser/Thr kinase), to produce an antibody that only binds Ser/Thr kinase when phosphorylated at that site.

Polyclonal antibodies of the invention may be produced according to standard techniques by immunizing a suitable animal (e.g., rabbit, goat, etc.) with a peptide antigen corresponding to the Carcinoma-related phosphorylation site of interest (i.e. a phosphorylation site enumerated in Column E of Table 1 , which comprises the corresponding phosphorylatable amino acid listed in Column D of Table 1), collecting immune serum from the animal, and separating the polyclonal antibodies from the immune serum, in accordance with known procedures. For example, a peptide antigen corresponding to all or part of the novel Receptor tyrosine kinase phosphorylation site disclosed herein (SEQ ID NO: 352 = FWIQNEDLGPASPLDSTFyR, encompassing phosphorylated tyrosine 975 (lowercase y; see Row 353 of Table 1)) may be used to produce antibodies that only bind Receptor tyrosine kinase phosphorylation when phosphorylated at tyr975. Similarly, a peptide comprising all or part of any one of the phosphorylation site sequences provided in Column E of Table 1 may employed as an antigen to produce an antibody that only binds the corresponding protein listed in Column A of Table 1 when phosphorylated (or when not phosphorylated) at the corresponding residue listed in Column D. If an antibody that only binds the protein when phosphorylated at the disclosed site is desired, the peptide antigen includes the phosphorylated form of the amino acid. Conversely, if an antibody that only binds the protein when not phosphorylated at the disclosed site is desired, the peptide antigen includes the non-phosphorylated form of the amino acid.

Peptide antigens suitable for producing antibodies of the invention may be designed, constructed and employed in accordance with well- known techniques. See, e.g., ANTIBODIES: A LABORATORY MANUAL,

Chapter 5, p. 75-76, Harlow & Lane Eds., Cold Spring Harbor Laboratory (1988); Czernik, Methods In Enzymology, 201: 264-283 (1991); Merrifield, J. Am. Chem. Soc. 85: 21-49 (1962)).

It will be appreciated by those of skill in the art that longer or shorter phosphopeptide antigens may be employed. See Id. For example, a peptide antigen may comprise the full sequence disclosed in Column E of Table 1/Figure 2, or it may comprise additional amino acids flanking such disclosed sequence, or may comprise of only a portion of the disclosed sequence immediately flanking the phosphorylatable amino acid (indicated in Column E by lowercase "y"). Typically, a desirable peptide antigen will comprise four or more amino acids flanking each side of the phosphorylatable amino acid and encompassing it. Polyclonal antibodies produced as described herein may be screened as further described below. Monoclonal antibodies of the invention may be produced in a hybridoma cell line according to the well-known technique of Kohler and Milstein. See Nature 265: 495-97 (1975); Kohler and Milstein, Eur. J. Immunol. 6: 511 (1976); see also, CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Ausubel et al. Eds. (1989). Monoclonal antibodies so produced are highly specific, and improve the selectivity and specificity of diagnostic assay methods provided by the invention. For example, a solution containing the appropriate antigen may be injected into a mouse or other species and, after a sufficient time (in keeping with conventional techniques), the animal is sacrificed and spleen cells obtained. The spleen cells are then immortalized by fusing them with myeloma cells, typically in the presence of polyethylene glycol, to produce hybridoma cells. Rabbit fusion hybridomas, for example, may be produced as described in U. S Patent No. 5,675,063, C. Knight, Issued October 7, 1997. The hybridoma cells are then grown in a suitable selection media, such as hypoxanthine-aminopterin-thymidine (HAT), and the supernatant screened for monoclonal antibodies having the desired specificity, as described below. The secreted antibody may be recovered from tissue culture supernatant by conventional methods such as precipitation, ion exchange or affinity chromatography, or the like.

Monoclonal Fab fragments may also be produced in Escherichia coli by recombinant techniques known to those skilled in the art. See, e.g., W. Huse, Science 246: 1275-81 (1989); Mullinax et al., Proc. Nat'l Acad. Sci. 87: 8095 (1990). If monoclonal antibodies of one isotype are preferred for a particular application, particular isotypes can be prepared directly, by selecting from the initial fusion, or prepared secondarily, from a parental hybridoma secreting a monoclonal antibody of different isotype by using the sib selection technique to isolate class-switch variants (Steplewski, et al., Proc. Nat'l. Acad. Sci., 82: 8653 (1985); Spira et al., J. Immunol. Methods, 74: 307 (1984)). The preferred epitope of a phosphorylation-site specific antibody of the invention is a peptide fragment consisting essentially of about 8 to 17 amino acids including the phosphorylatable tyrosine, wherein about 3 to 8 amino acids are positioned on each side of the phosphorylatable tyrosine (for example, the FLOT1 tyrosine 238 phosphorylation site sequence disclosed in Row 49, Column E of Table 1), and antibodies of the invention thus specifically bind a target Carcinoma-related signaling polypeptide comprising such epitopic sequence. Particularly preferred epitopes bound by the antibodies of the invention comprise all or part of a phosphorylatable site sequence listed in Column E of Table 1 , including the phosphorylatable amino acid.

Included in the scope of the invention are equivalent non-antibody molecules, such as protein binding domains or nucleic acid aptamers, which bind, in a phospho-specific manner, to essentially the same phosphorylatable epitope to which the phospho-specific antibodies of the invention bind. See, e.g., Neuberger et al., Nature 312: 604 (1984). Such equivalent non-antibody reagents may be suitably employed in the methods of the invention further described below.

Antibodies provided by the invention may be any type of immunoglobulins, including IgG, IgM, IgA, IgD, and IgE, including F_ab or antigen-recognition fragments thereof. The antibodies may be monoclonal or polyclonal and may be of any species of origin, including (for example) mouse, rat, rabbit, horse, or human, or may be chimeric antibodies. See, e.g., M. Walker et al., Molec. Immunol. 26: 403-11 (1989); Morrision et al., Proc. Nat'l. Acad. Sci. 81: 6851 (1984); Neuberger et al., Nature 312: 604 (1984)). The antibodies may be recombinant monoclonal antibodies produced according to the methods disclosed in U.S. Pat. No. 4,474,893 (Reading) or U.S. Pat. No. 4,816,567 (Cabilly et al.) The antibodies may also be chemically constructed by specific antibodies made according to the method disclosed in U.S. Pat. No. 4,676,980 (Segel et al.)

The invention also provides immortalized cell lines that produce an antibody of the invention. For example, hybridoma clones, constructed as described above, that produce monoclonal antibodies to the Carcinoma- related signaling protein phosphorylation sties disclosed herein are also provided. Similarly, the invention includes recombinant cells producing an antibody of the invention, which cells may be constructed by well known techniques; for example the antigen combining site of the monoclonal antibody can be cloned by PCR and single-chain antibodies produced as phage-displayed recombinant antibodies or soluble antibodies in E. coli (see, e.g., ANTIBODY ENGINEERING PROTOCOLS, 1995, Humana Press, Sudhir Paul editor.)

Phosphorylation site-specific antibodies of the invention, whether polyclonal or monoclonal, may be screened for epitope and phospho- specificity according to standard techniques. See, e.g. Czernik et al., Methods in Enzymology, 201: 264-283 (1991). For example, the antibodies may be screened against the phospho and non-phospho peptide library by ELISA to ensure specificity for both the desired antigen (Ae. that epitope including a phosphorylation site sequence enumerated in Column E of Table 1) and for reactivity only with the phosphorylated (or non-phosphorylated) form of the antigen. Peptide competition assays may be carried out to confirm lack of reactivity with other phospho- epitopes on the given Carcinoma-related signaling protein. The antibodies may also be tested by Western blotting against cell preparations containing the signaling protein, e.g. cell lines over- expressing the target protein, to confirm reactivity with the desired phosphorylated epitope/target.

Specificity against the desired phosphorylated epitope may also be examined by constructing mutants lacking phosphorylatable residues at positions outside the desired epitope that are known to be phosphorylated, or by mutating the desired phospho-epitope and confirming lack of reactivity. Phosphorylation-site specific antibodies of the invention may exhibit some limited cross-reactivity to related epitopes in non-target proteins. This is not unexpected as most antibodies exhibit some degree of cross-reactivity, and anti-peptide antibodies will often cross-react with epitopes having high homology to the immunizing peptide. See, e.g., Czernik, supra. Cross-reactivity with non-target proteins is readily characterized by Western blotting alongside markers of known molecular weight. Amino acid sequences of cross-reacting proteins may be examined to identify sites highly homologous to the Carcinoma-related signaling protein epitope for which the antibody of the invention is specific.

In certain cases, polyclonal antisera may exhibit some undesirable general cross-reactivity to phosphotyrosine itself, which may be removed by further purification of antisera, e.g. over a phosphotyramine column. Antibodies of the invention specifically bind their target protein (Ae. a protein listed in Column A of Table 1) only when phosphorylated (or only when not phosphorylated, as the case may be) at the site disclosed in corresponding Columns D/E, and do not (substantially) bind to the other form (as compared to the form for which the antibody is specific).

Antibodies may be further characterized via immunohistochemical (IHC) staining using normal and diseased tissues to examine Carcinoma- related phosphorylation and activation status in diseased tissue. IHC may be carried out according to well-known techniques. See, e.g., ANTIBODIES: A LABORATORY MANUAL, Chapter 10, Harlow & Lane Eds., Cold Spring Harbor Laboratory (1988). Briefly, paraffin-embedded tissue (e.g. tumor tissue) is prepared for immunohistochemical staining by deparaffinizing tissue sections with xylene followed by ethanol; hydrating in water then PBS; unmasking antigen by heating slide in sodium citrate buffer; incubating sections in hydrogen peroxide; blocking in blocking solution; incubating slide in primary antibody and secondary antibody; and finally detecting using ABC avidin/biotin method according to manufacturer's instructions.

Antibodies may be further characterized by flow cytometry carried out according to standard methods. See Chow et al., Cytometry (Communications in Clinical Cytometry) 46: 72-78 (2001). Briefly and by way of example, the following protocol for cytometric analysis may be employed: samples may be centrifuged on Ficoll gradients to remove erythrocytes, and cells may then be fixed with 2% paraformaldehyde for 10 minutes at 37 °C followed by permeabilization in 90% methanol for 30 minutes on ice. Cells may then be stained with the primary phosphorylation-site specific antibody of the invention (which detects a Carcinoma-related signal transduction protein enumerated in Table 1), washed and labeled with a fluorescent-labeled secondary antibody.

Additional fluorochrome-conjugated marker antibodies (e.g. CD45, CD34) may also be added at this time to aid in the subsequent identification of specific hematopoietic cell types. The cells would then be analyzed on a flow cytometer (e.g. a Beckman Coulter FC500) according to the specific protocols of the instrument used.

Antibodies of the invention may also be advantageously conjugated to fluorescent dyes (e.g. Alexa488, PE) for use in multi- parametric analyses along with other signal transduction (phospho-CrkL, phospho-Erk 1/2) and/or cell marker (CD34) antibodies.

Phosphorylation-site specific antibodies of the invention specifically bind to a human Carcinoma-related signal transduction protein or polypeptide only when phosphorylated at a disclosed site, but are not limited only to binding the human species, perse. The invention includes antibodies that also bind conserved and highly homologous or identical phosphorylation sites in respective Carcinoma-related proteins from other species (e.g. mouse, rat, monkey, yeast), in addition to binding the human phosphorylation site. Highly homologous or identical sites conserved in other species can readily be identified by standard sequence comparisons, such as using BLAST, with the human Carcinoma-related signal transduction protein phosphorylation sites disclosed herein.

C. Heavy-Isotope Labeled Peptides (AQUA Peptides).

The novel Carcinoma-related signaling protein phosphorylation sites disclosed herein now enable the production of corresponding heavy- isotope labeled peptides for the absolute quantification of such signaling proteins (both phosphorylated and not phosphorylated at a disclosed site) in biological samples. The production and use of AQUA peptides for the absolute quantification of proteins (AQUA) in complex mixtures has been described. See WO/03016861 , "Absolute Quantification of Proteins and Modified Forms Thereof by Multistage Mass Spectrometry," Gygi et al. and also Gerber et al. Proc. Natl. Acad. Sci. U.S.A. 100: 6940-5 (2003) (the teachings of which are hereby incorporated herein by reference, in their entirety).

The AQUA methodology employs the introduction of a known quantity of at least one heavy-isotope labeled peptide standard (which has a unique signature detectable by LC-SRM chromatography) into a digested biological sample in order to determine, by comparison to the peptide standard, the absolute quantity of a peptide with the same sequence and protein modification in the biological sample. Briefly, the AQUA methodology has two stages: peptide internal standard selection and validation and method development; and implementation using validated peptide internal standards to detect and quantify a target protein in sample. The method is a powerful technique for detecting and quantifying a given peptide/protein within a complex biological mixture, such as a cell lysate, and may be employed, e.g., to quantify change in protein phosphorylation as a result of drug treatment, or to quantify differences in the level of a protein in different biological states.

Generally, to develop a suitable internal standard, a particular peptide (or modified peptide) within a target protein sequence is chosen based on its amino acid sequence and the particular protease to be used to digest. The peptide is then generated by solid-phase peptide synthesis such that one residue is replaced with that same residue containing stable isotopes (¹³C, ¹⁵N). The result is a peptide that is chemically identical to its native counterpart formed by proteolysis, but is easily distinguishable by MS via a mass shift. A newly synthesized AQUA internal standard peptide is then evaluated by LC-MS/MS. This process provides qualitative information about peptide retention by reverse-phase chromatography, ionization efficiency, and fragmentation via collision- induced dissociation. Informative and abundant fragment ions for sets of native and internal standard peptides are chosen and then specifically monitored in rapid succession as a function of chromatographic retention to form a selected reaction monitoring (LC-SRM) method based on the unique profile of the peptide standard.

The second stage of the AQUA strategy is its implementation to measure the amount of a protein or modified protein from complex mixtures. Whole cell lysates are typically fractionated by SDS-PAGE gel electrophoresis, and regions of the gel consistent with protein migration are excised. This process is followed by in-gel proteolysis in the presence of the AQUA peptides and LC-SRM analysis. (See Gerber et al. supra.) AQUA peptides are spiked in to the complex peptide mixture obtained by digestion of the whole cell lysate with a proteolytic enzyme and subjected to immunoaffinity purification as described above. The retention time and fragmentation pattern of the native peptide formed by digestion (e.g. trypsinization) is identical to that of the AQUA internal standard peptide determined previously; thus, LC-MS/MS analysis using an SRM experiment results in the highly specific and sensitive measurement of both internal standard and analyte directly from extremely complex peptide mixtures. Because an absolute amount of the AQUA peptide is added (e.g. 250 fmol), the ratio of the areas under the curve can be used to determine the precise expression levels of a protein or phosphorylated form of a protein in the original cell lysate. In addition, the internal standard is present during in-gel digestion as native peptides are formed, such that peptide extraction efficiency from gel pieces, absolute losses during sample handling (including vacuum centrifugation), and variability during introduction into the LC-MS system do not affect the determined ratio of native and AQUA peptide abundances.

An AQUA peptide standard is developed for a known phosphorylation site sequence previously identified by the IAP-LC-MS/MS method within a target protein. One AQUA peptide incorporating the phosphorylated form of the particular residue within the site may be developed, and a second AQUA peptide incorporating the non- phosphorylated form of the residue developed. In this way, the two standards may be used to detect and quantify both the phosphorylated and non-phosphorylated forms of the site in a biological sample. Peptide internal standards may also be generated by examining the primary amino acid sequence of a protein and determining the boundaries of peptides produced by protease cleavage. Alternatively, a protein may actually be digested with a protease and a particular peptide fragment produced can then sequenced. Suitable proteases include, but are not limited to, serine proteases (e.g. trypsin, hepsin), metallo proteases (e.g. PUMP1), chymotrypsin, cathepsin, pepsin, thermolysin, carboxypeptidases, etc.

A peptide sequence within a target protein is selected according to one or more criteria to optimize the use of the peptide as an internal standard. Preferably, the size of the peptide is selected to minimize the chances that the peptide sequence will be repeated elsewhere in other non-target proteins. Thus, a peptide is preferably at least about 6 amino acids. The size of the peptide is also optimized to maximize ionization frequency. Thus, peptides longer than about 20 amino acids are not preferred. The preferred ranged is about 7 to 15 amino acids. A peptide sequence is also selected that is not likely to be chemically reactive during mass spectrometry, thus sequences comprising cysteine, tryptophan, or methionine are avoided.

A peptide sequence that does not include a modified region of the target region may be selected so that the peptide internal standard can be used to determine the quantity of all forms of the protein. Alternatively, a peptide internal standard encompassing a modified amino acid may be desirable to detect and quantify only the modified form of the target protein. Peptide standards for both modified and unmodified regions can be used together, to determine the extent of a modification in a particular sample (i.e. to determine what fraction of the total amount of protein is represented by the modified form). For example, peptide standards for both the phosphorylated and unphosphorylated form of a protein known to be phosphorylated at a particular site can be used to quantify the amount of phosphorylated form in a sample.

The peptide is labeled using one or more labeled amino acids (i.e. the label is an actual part of the peptide) or less preferably, labels may be attached after synthesis according to standard methods. Preferably, the label is a mass-altering label selected based on the following considerations: The mass should be unique to shift fragment masses produced by MS analysis to regions of the spectrum with low background; the ion mass signature component is the portion of the labeling moiety that preferably exhibits a unique ion mass signature in MS analysis; the sum of the masses of the constituent atoms of the label is preferably uniquely different than the fragments of all the possible amino acids. As a result, the labeled amino acids and peptides are readily distinguished from unlabeled ones by the ion/mass pattern in the resulting mass spectrum. Preferably, the ion mass signature component imparts a mass to a protein fragment that does not match the residue mass for any of the 20 natural amino acids.

The label should be robust under the fragmentation conditions of MS and not undergo unfavorable fragmentation. Labeling chemistry should be efficient under a range of conditions, particularly denaturing conditions, and the labeled tag preferably remains soluble in the MS buffer system of choice. The label preferably does not suppress the ionization efficiency of the protein and is not chemically reactive. The label may contain a mixture of two or more isotopically distinct species to generate a unique mass spectrometric pattern at each labeled fragment position. Stable isotopes, such as ¹³C, ¹⁵N, ¹⁷O, ¹⁸O, or ³⁴S, are among preferred labels. Pairs of peptide internal standards that incorporate a different isotope label may also be prepared. Preferred amino acid residues into which a heavy isotope label may be incorporated include leucine, praline, valine, and phenylalanine.

Peptide internal standards are characterized according to their mass-to-charge (m/z) ratio, and preferably, also according to their retention time on a chromatographic column (e.g. an HPLC column). Internal standards that co-elute with unlabeled peptides of identical sequence are selected as optimal internal standards. The internal standard is then analyzed by fragmenting the peptide by any suitable means, for example by collision-induced dissociation (CID) using, e.g., argon or helium as a collision gas. The fragments are then analyzed, for example by multi-stage mass spectrometry (MS") to obtain a fragment ion spectrum, to obtain a peptide fragmentation signature. Preferably, peptide fragments have significant differences in m/z ratios to enable peaks corresponding to each fragment to be well separated, and a signature that is unique for the target peptide is obtained. If a suitable fragment signature is not obtained at the first stage, additional stages of MS are performed until a unique signature is obtained.

Fragment ions in the MS/MS and MS³ spectra are typically highly specific for the peptide of interest, and, in conjunction with LC methods, allow a highly selective means of detecting and quantifying a target peptide/protein in a complex protein mixture, such as a cell lysate, containing many thousands or tens of thousands of proteins. Any biological sample potentially containing a target protein/peptide of interest may be assayed. Crude or partially purified cell extracts are preferably employed. Generally, the sample has at least 0.01 mg of protein, typically a concentration of 0.1-10 mg/mL, and may be adjusted to a desired buffer concentration and pH.

A known amount of a labeled peptide internal standard, preferably about 10 femtomoles, corresponding to a target protein to be detected/quantified is then added to a biological sample, such as a cell lysate. The spiked sample is then digested with one or more protease(s) for a suitable time period to allow digestion. A separation is then performed (e.g. by HPLC, reverse-phase HPLC, capillary electrophoresis, ion exchange chromatography, etc.) to isolate the labeled internal standard and its corresponding target peptide from other peptides in the sample. Microcapillary LC is a preferred method.

Each isolated peptide is then examined by monitoring of a selected reaction in the MS. This involves using the prior knowledge gained by the characterization of the peptide internal standard and then requiring the MS to continuously monitor a specific ion in the MS/MS or MS^π spectrum for both the peptide of interest and the internal standard. After elution, the area under the curve (AUC) for both peptide standard and target peptide peaks are calculated. The ratio of the two areas provides the absolute quantification that can be normalized for the number of cells used in the analysis and the protein's molecular weight, to provide the precise number of copies of the protein per cell. Further details of the AQUA methodology are described in Gygi et a/., and Gerber et a/, supra.

In accordance with the present invention, AQUA internal peptide standards (heavy-isotope labeled peptides) may now be produced, as described above, for any of the nearly 474 novel Carcinoma-related signaling protein phosphorylation sites disclosed herein (see Table 1 /Figure 2). Peptide standards for a given phosphorylation site (e.g. the tyrosine 40 site in INPP5D kinase- see Row 414 of Table 1) may be produced for both the phosphorylated and non-phosphorylated forms of the site (e.g. see INPP5D site sequence in Column E, Row 414 of Table 1 . (SEQ ID NO: 413)) and such standards employed in the AQUA methodology to detect and quantify both forms of such phosphorylation site in a biological sample. AQUA peptides of the invention may comprise all, or part of, a phosphorylation site peptide sequence disclosed herein (see Column E of Table 1/Figure 2). In a preferred embodiment, an AQUA peptide of the invention consists of, or comprises, a phosphorylation site sequence disclosed herein in Table 1/Figure 2. For example, an AQUA peptide of the invention for detection/quantification of FGFR1 kinase when phosphorylated at tyrosine 397 may consist of, or comprise, the sequence PAVMTSPLYLEIIIYCTGAFLISCMVGSVIVyK (y=phosphotyrosine), which comprises phosphorylatable tyrosine 397 (see Row 360, Column E; (SEQ ID NO: 359)). Heavy-isotope labeled equivalents of the peptides enumerated in Table 1/Figure 2 (both in phosphorylated and unphosphorylated form) can be readily synthesized and their unique MS and LC-SRM signature determined, so that the peptides are validated as AQUA peptides and ready for use in quantification experiments.

The phosphorylation site peptide sequences disclosed herein (see Column E of Table 1/Figure 2) are particularly well suited for development of corresponding AQUA peptides, since the IAP method by which they were identified (see Part A above and Example 1) inherently confirmed that such peptides are in fact produced by enzymatic digestion (trypsinization) and are in fact suitably fractionated/ionized in MS/MS. Thus, heavy-isotope labeled equivalents of these peptides (both in phosphorylated and unphosphorylated form) can be readily synthesized and their unique MS and LC-SRM signature determined, so that the peptides are validated as AQUA peptides and ready for use in quantification experiments. Accordingly, the invention provides heavy-isotope labeled peptides

(AQUA peptides) for the detection and/or quantification of any of the Carcinoma-related phosphorylation sites disclosed in Table 1/Figure 2 (see Column E) and/or their corresponding parent proteins/polypeptides (see Column A). A phosphopeptide sequence consisting of, or comprising, any of the phosphorylation sequences listed in Table 1 may be considered a preferred AQUA peptide of the invention. For example, an AQUA peptide comprising the sequence

LGGGTyGEVFKARDKVSGDLVALK (SEQ ID NO: 317) (where y may be either phosphotyrosine or tyrosine, and where V = labeled valine (e.g. ¹⁴C)) is provided for the quantification of phosphorylated (or non- phosphorylated) kinase (Tyr 28) in a biological sample (see Row 318 of Table 1 , tyrosine 28 being the phosphorylatable residue within the site). However, it will be appreciated that a larger AQUA peptide comprising a disclosed phosphorylation site sequence (and additional residues downstream or upstream of it) may also be constructed. Similarly, a smaller AQUA peptide comprising less than all of the residues of a disclosed phosphorylation site sequence (but still comprising the phosphorylatable residue enumerated in Column D of Table 1/Figure 2) may alternatively be constructed. Such larger or shorter AQUA peptides are within the scope of the present invention, and the selection and production of preferred AQUA peptides may be carried out as described above (see Gygi et al., Gerber et al. supra.).

Certain particularly preferred subsets of AQUA peptides provided by the invention are described above (corresponding to particular protein types/groups in Table 1 , for example, Kinases or Adaptor/Scaffold proteins). Example 4 is provided to further illustrate the construction and use, by standard methods described above, of exemplary AQUA peptides provided by the invention. For example, the above-described AQUA peptides corresponding to the both the phosphorylated and non- phosphorylated forms of the disclosed MAP4K1 kinase tyrosine 28 phosphorylation site (see Row 318 of Table 1/Figure 2) may be used to quantify the amount of phosphorylated MAP4K1 (Tyr 28) in a biological sample, e.g. a tumor cell sample (or a sample before or after treatment with a test drug). AQUA peptides of the invention may also be employed within a kit that comprises one or multiple AQUA peptide(s) provided herein (for the quantification of a Carcinoma-related signal transduction protein disclosed in Table 1/Figure 2), and, optionally, a second detecting reagent conjugated to a detectable group. For example, a kit may include AQUA peptides for both the phosphorylated and non-phosphorylated form of a phosphorylation site disclosed herein. The reagents may also include ancillary agents such as buffering agents and protein stabilizing agents, e.g., polysaccharides and the like. The kit may further include, where necessary, other members of the signal-producing system of which system the detectable group is a member (e.g., enzyme substrates), agents for reducing background interference in a test, control reagents, apparatus for conducting a test, and the like. The test kit may be packaged in any suitable manner, typically with all elements in a single container along with a sheet of printed instructions for carrying out the test. AQUA peptides provided by the invention will be highly useful in the further study of signal transduction anomalies underlying cancer, including carcinomas, and in identifying diagnostic/bio-markers of these diseases, new potential drug targets, and/or in monitoring the effects of test compounds on Carcinoma-related signal transduction proteins and pathways.

D. Immunoassay Formats

Antibodies provided by the invention may be advantageously employed in a variety of standard immunological assays (the use of AQUA peptides provided by the invention is described separately above). Assays may be homogeneous assays or heterogeneous assays. In a homogeneous assay the immunological reaction usually involves a phosphorylation-site specific antibody of the invention), a labeled analyte, and the sample of interest. The signal arising from the label is modified, directly or indirectly, upon the binding of the antibody to the labeled analyte. Both the immunological reaction and detection of the extent thereof are carried out in a homogeneous solution. Immunochemical labels that may be employed include free radicals, radioisotopes, fluorescent dyes, enzymes, bacteriophages, coenzymes, and so forth. In a heterogeneous assay approach, the reagents are usually the specimen, a phosphorylation-site specific antibody of the invention, and suitable means for producing a detectable signal. Similar specimens as described above may be used. The antibody is generally immobilized on a support, such as a bead, plate or slide, and contacted with the specimen suspected of containing the antigen in a liquid phase. The support is then separated from the liquid phase and either the support phase or the liquid phase is examined for a detectable signal employing means for producing such signal. The signal is related to the presence of the analyte in the specimen. Means for producing a detectable signal include the use of radioactive labels, fluorescent labels, enzyme labels, and so forth. For example, if the antigen to be detected contains a second binding site, an antibody which binds to that site can be conjugated to a detectable group and added to the liquid phase reaction solution before the separation step. The presence of the detectable group on the solid support indicates the presence of the antigen in the test sample. Examples of suitable immunoassays are the radioimmunoassay, immunofluorescence methods, enzyme-linked immunoassays, and the like. Immunoassay formats and variations thereof that may be useful for carrying out the methods disclosed herein are well known in the art. See generally E. Maggio, Enzyme-lmmunoassay, (1980) (CRC Press, Inc., Boca Raton, FIa.); see also, e.g., U.S. Pat. No. 4,727,022 (Skold et al., "Methods for Modulating Ligand-Receptor Interactions and their Application"); U.S. Pat. No. 4,659,678 (Forrest et al., "Immunoassay of Antigens"); U.S. Pat. No. 4,376,110 (David et al., "Immunometric Assays Using Monoclonal Antibodies"). Conditions suitable for the formation of antigen-antibody complexes are well described. See id. Monoclonal antibodies of the invention may be used in a "two-site" or "sandwich" assay, with a single cell line serving as a source for both the labeled monoclonal antibody and the bound monoclonal antibody. Such assays are described in U.S. Pat. No. 4,376,110. The concentration of detectable reagent should be sufficient such that the binding of a target Carcinoma- related signal transduction protein is detectable compared to background. Phosphorylation site-specific antibodies disclosed herein may be conjugated to a solid support suitable for a diagnostic assay (e.g., beads, plates, slides or wells formed from materials such as latex or polystyrene) in accordance with known techniques, such as precipitation. Antibodies, or other target protein or target site-binding reagents, may likewise be conjugated to detectable groups such as radiolabels (e.g., ³⁵S, ¹²⁵I, ¹³¹I), enzyme labels (e.g., horseradish peroxidase, alkaline phosphatase), and fluorescent labels (e.g., fluorescein) in accordance with known techniques.

Antibodies of the invention may also be optimized for use in a flow cytometry (FC) assay to determine the activation/phosphorylation status of a target Carcinoma-related signal transduction protein in patients before, during, and after treatment with a drug targeted at inhibiting phosphorylation at such a protein at the phosphorylation site disclosed herein. For example, bone marrow cells or peripheral blood cells from patients may be analyzed by flow cytometry for target Carcinoma-related signal transduction protein phosphorylation, as well as for markers identifying various hematopoietic cell types. In this manner, activation status of the malignant cells may be specifically characterized. Flow cytometry may be carried out according to standard methods. See, e.g. Chow et al., Cytometry (Communications in Clinical Cytometry) 46: 72-78 (2001). Briefly and by way of example, the following protocol for cytometric analysis may be employed: fixation of the cells with 1 % paraformaldehyde for 10 minutes at 37 ⁰C followed by permeabilization in 90% methanol for 30 minutes on ice. Cells may then be stained with the primary antibody (a phospho-specific antibody of the invention), washed and labeled with a fluorescent-labeled secondary antibody. Alternatively, the cells may be stained with a fluorescent-labeled primary antibody. The cells would then be analyzed on a flow cytometer (e.g. a Beckman Coulter EPICS-XL) according to the specific protocols of the instrument used. Such an analysis would identify the presence of activated

Carcinoma-related signal transduction protein(s) in the malignant cells and reveal the drug response on the targeted protein.

Alternatively, antibodies of the invention may be employed in immunohistochemical (IHC) staining to detect differences in signal transduction or protein activity using normal and diseased tissues. IHC may be carried out according to well-known techniques. See, e.g., ANTIBODIES: A LABORATORY MANUAL, supra. Briefly, paraffin-embedded tissue (e.g. tumor tissue) is prepared for immunohistochemical staining by deparaffinizing tissue sections with xylene followed by ethanol; hydrating in water then PBS; unmasking antigen by heating slide in sodium citrate buffer; incubating sections in hydrogen peroxide; blocking in blocking solution; incubating slide in primary antibody and secondary antibody; and finally detecting using ABC avidin/biotin method according to manufacturer's instructions. Antibodies of the invention may be also be optimized for use in other clinically-suitable applications, for example bead-based multiplex- type assays, such as IGEN, Luminex™ and/or Bioplex™ assay formats, or otherwise optimized for antibody arrays formats, such as reversed- phase array applications (see, e.g. Paweletz et al., Oncogene 20(16): 1981-89 (2001)). Accordingly, in another embodiment, the invention provides a method for the multiplex detection of Carcinoma-related protein phosphorylation in a biological sample, the method comprising utilizing two or more antibodies or AQUA peptides of the invention to detect the presence of two or more phosphorylated Carcinoma-related signaling proteins enumerated in Column A of Table 1/Figure 2. In one preferred embodiment, two to five antibodies or AQUA peptides of the invention are employed in the method. In another preferred embodiment, six to ten antibodies or AQUA peptides of the invention are employed, while in another preferred embodiment eleven to twenty such reagents are employed.

Antibodies and/or AQUA peptides of the invention may also be employed within a kit that comprises at least one phosphorylation site- specific antibody or AQUA peptide of the invention (which binds to or detects a Carcinoma-related signal transduction protein disclosed in Table 1/Figure 2), and, optionally, a second antibody conjugated to a detectable group. In some embodies, the kit is suitable for multiplex assays and comprises two or more antibodies or AQUA peptides of the invention, and in some embodiments, comprises two to five, six to ten, or eleven to twenty reagents of the invention. The kit may also include ancillary agents such as buffering agents and protein stabilizing agents, e.g., polysaccharides and the like. The kit may further include, where necessary, other members of the signal-producing system of which system the detectable group is a member (e.g., enzyme substrates), agents for reducing background interference in a test, control reagents, apparatus for conducting a test, and the like. The test kit may be packaged in any suitable manner, typically with all elements in a single container along with a sheet of printed instructions for carrying out the test.

The following Examples are provided only to further illustrate the invention, and are not intended to limit its scope, except as provided in the claims appended hereto. The present invention encompasses modifications and variations of the methods taught herein which would be obvious to one of ordinary skill in the art.

EXAMPLE 1 Isolation of Phosphotyrosine-Containing Peptides from Extracts of Carcinoma Cell Lines and Identification of Novel Phosphorylation Sites.

In order to discover previously unknown Carcinoma-related signal transduction protein phosphorylation sites, IAP isolation techniques were employed to identify phosphotyrosine-containing peptides in cell extracts from human carcinoma cell lines and patient cell lines identified in Column G of Table 1 including Su-DHLI , MOLT15, H1703, 3T3-src, 3T3, AbI, A431 , pancreatic xenograft, H1993, HCC827, 3T3-EGFRwt, 3T3- EGFR(L858R), HCT 116, HT29, NCI-N87, HT29, CTV-1 , Karpas 299, MCF-10A (Y561 F), MCF-10A (Y969F), Calu-3, H2347, H3255, H2170, U118MG, H1703, HCC366, H2228, HL61b, jurkat, SUPT-13, Verona patient 4, PT9, DU145, DMS79, MDA-MB-468, A549, H1666, H1650, 831/13, K562, HL53B, HL66B, HL84B, HL87A, HPAC₁ H441 , SEM, Sor4, SorA, SEM, TgOVA, UT-7, MKPL-1, H69 LS, A431 , DMS153 NS, SW620, HT116, MDA-MB-468, MCF10, HPAC, and HT29. Tryptic phosphotyrosine-containing peptides were purified and analyzed from extracts of each of the cell lines mentioned above, as follows. Cells were cultured in DMEM medium or RPMI 1640 medium supplemented with 10% fetal bovine serum and penicillin/streptomycin.

Suspension cells were harvested by low speed centrifugation. After complete aspiration of medium, cells were resuspended in 1 ml_ lysis buffer per 1.25 x 10⁸ cells (20 mM HEPES pH 8.0, 9 M urea, 1 mM sodium vanadate, supplemented or not with 2.5 mM sodium pyro- phosphate, 1 mM β-glycerol-phosphate) and sonicated.

Adherent cells at about 80% confluency were starved in medium without serum overnight and stimulated, with ligand depending on the cell type or not stimulated. After complete aspiration of medium from the plates, cells were scraped off the plate in 10 ml lysis buffer per 2 x 10⁸ cells (20 mM HEPES pH 8.0, 9 M urea, 1 mM sodium vanadate, supplemented with 2.5 mM sodium pyrophosphate, 1 mM β-glycerol- phosphate) and sonicated.

Sonicated cell lysates were cleared by centrifugation at 20,000 x g, and proteins were reduced with DTT at a final concentration of 4.1 mM and alkylated with iodoacetamide at 8.3 mM. For digestion with trypsin, protein extracts were diluted in 20 mM HEPES pH 8.0 to a final concentration of 2 M urea and soluble TLCK-trypsin (Worthington) was added at 10-20 μg/mL Digestion was performed for 1-2 days at room temperature. Trifluoroacetic acid (TFA) was added to protein digests to a final concentration of 1%, precipitate was removed by centrifugation, and digests were loaded onto Sep-Pak Ci₈ columns (Waters) equilibrated with 0.1 % TFA. A column volume of 0.7-1.0 ml was used per 2 x 10⁸ cells. Columns were washed with 15 volumes of 0.1 % TFA, followed by 4 volumes of 5% acetonitrile (MeCN) in 0.1 % TFA. Peptide fraction I was obtained by eluting columns with 2 volumes each of 8, 12, and 15% MeCN in 0.1% TFA and combining the eluates. Fractions Il and III were a combination of eluates after eluting columns with 18, 22, 25% MeCN in 0.1% TFA and with 30, 35, 40% MeCN in 0.1% TFA, respectively. All peptide fractions were lyophilized.

Peptides from each fraction corresponding to 2 x 10⁸ cells were dissolved in 1 ml of IAP buffer (20 mM Tris/HCI or 50 mM MOPS pH 7.2, 10 mM sodium phosphate, 50 mM NaCI) and insoluble matter (mainly in peptide fractions III) was removed by centrifugation. IAP was performed on each peptide fraction separately. The phosphotyrosine monoclonal antibody P-Tyr-100 (Cell Signaling Technology, Inc., catalog number 9411) was coupled at 4 mg/ml beads to protein G (Roche), respectively. Immobilized antibody (15 μl, 60 μg) was added as 1:1 slurry in IAP buffer to 1 ml of each peptide fraction, and the mixture was incubated overnight at 4° C with gentle rotation. The immobilized antibody beads were washed three times with 1 ml IAP buffer and twice with 1 ml water, all at 4° C. Peptides were eluted from beads by incubation with 75 μl of 0.1 % TFA at room temperature for 10 minutes. Alternatively, one single peptide fraction was obtained from Sep-Pak

C18 columns by elution with 2 volumes each of 10%, 15%, 20 %, 25 %, 30 %, 35 % and 40 % acetonitirile in 0.1% TFA and combination of all eluates. IAP on this peptide fraction was performed as follows: After lyophilization, peptide was dissolved in 50 ml IAP buffer (MOPS pH 7.2, 10 mM sodium phosphate, 50 mM NaCI) and insoluble matter was removed by centrifugation. Immobilized antibody (40 μl, 160 μg) was added as 1:1 slurry in IAP buffer, and the mixture was incubated overnight at 4° C with gentle shaking. The immobilized antibody beads were washed three times with 1 ml IAP buffer and twice with 1 ml water, all at 4° C. Peptides were eluted from beads by incubation with 55 μl of 0.15% TFA at room temperature for 10 min (eluate 1), followed by a wash of the beads (eluate 2) with 45 μl of 0.15% TFA. Both eluates were combined.

Analysis by LC-MS/MS Mass Spectrometry. 40 μl or more of IAP eluate were purified by 0.2 μl StageTips or

ZipTips. Peptides were eluted from the microcolumns with 1 μl of 40% MeCN, 0.1 % TFA (fractions I and II) or 1 μl of 60% MeCN, 0.1% TFA (fraction III) into 7.6-9.0 μl of 0.4% acetic acid/0.005% heptafluorobutyric acid. For single fraction analysis, 1 μl of 60% MeCN, 0.1% TFA, was used for elution from the microcolumns. This sample was loaded onto a 10 cm x 75 μm PicoFrit capillary column (New Objective) packed with Magic C18 AQ reversed-phase resin (Michrom Bioresources) using a Famos autosamplerwith an inert sample injection valve (Dionex). The column was then developed with a 45-min linear gradient of acetonitrile delivered at 200 nl/min (Ultimate, Dionex), and tandem mass spectra were collected in a data-dependent manner with an LTQ ion trap mass spectrometer essentially as described by Gygi et a/., supra.

Database Analysis & Assignments.

MS/MS spectra were evaluated using TurboSequest in the Sequest Browser package (v. 27, rev. 12) supplied as part of BioWorks 3.0 (ThermoFinnigan). Individual MS/MS spectra were extracted from the raw data file using the Sequest Browser program CreateDta, with the following settings: bottom MW, 700; top MW, 4,500; minimum number of ions, 20; minimum TIC, 4 x 10⁵; and precursor charge state, unspecified. Spectra were extracted from the beginning of the raw data file before sample injection to the end of the eluting gradient. The IonQuest and VuDta programs were not used to further select MS/MS spectra for Sequest analysis. MS/MS spectra were evaluated with the following TurboSequest parameters: peptide mass tolerance, 2.5; fragment ion tolerance, 0.0; maximum number of differential amino acids per modification, 4; mass type parent, average; mass type fragment, average; maximum number of internal cleavage sites, 10; neutral losses of water and ammonia from b and y ions were considered in the correlation analysis. Proteolytic enzyme was specified except for spectra collected from elastase digests.

Searches were performed against the NCBI human protein database (NCBI RefSeq protein release #11 ; 8 May 2005; 1 ,826,611 proteins, including 47,859 human proteins. Peptides that did not match RefSeq were compared to NCBI GenPept release #148; 15 June 2005 release date; 2,479,172 proteins, including 196,054 human proteins.). Cysteine carboxamidomethylation was specified as a static modification, and phosphorylation was allowed as a variable modification on serine, threonine, and tyrosine residues or on tyrosine residues alone. It was determined that restricting phosphorylation to tyrosine residues had little effect on the number of phosphorylation sites assigned. Furthermore, it should be noted that certain peptides were originally isolated in mouse and later normalized to human sequences as shown by Table1/Figure2.

In proteomics research, it is desirable to validate protein identifications based solely on the observation of a single peptide in one experimental result, in order to indicate that the protein is, in fact, present in a sample. This has led to the development of statistical methods for validating peptide assignments, which are not yet universally accepted, and guidelines for the publication of protein and peptide identification results (see Carr et a/., MoI. Cell Proteomics 3: 531-533 (2004)), which were followed in this Example. However, because the immunoaffinity strategy separates phosphorylated peptides from unphosphorylated peptides, observing just one phosphopeptide from a protein is a common result, since many phosphorylated proteins have only one tyrosine- phosphorylated site. For this reason, it is appropriate to use additional criteria to validate phosphopeptide assignments. Assignments are likely to be correct if any of these additional criteria are met: (i) the same sequence is assigned to co-eluting ions with different charge states, since the MS/MS spectrum changes markedly with charge state; (ii) the site is found in more than one peptide sequence context due to sequence overlaps from incomplete proteolysis or use of proteases other than trypsin; (iii) the site is found in more than one peptide sequence context due to homologous but not identical protein isoforms; (iv) the site is found in more than one peptide sequence context due to homologous but not identical proteins among species; and (v) sites validated by MS/MS analysis of synthetic phosphopeptides corresponding to assigned sequences, since the ion trap mass spectrometer produces highly reproducible MS/MS spectra. The last criterion is routinely employed to confirm novel site assignments of particular interest. All spectra and all sequence assignments made by Sequest were imported into a relational database. The following Sequest scoring thresholds were used to select phosphopeptide assignments that are likely to be correct: RSp < 6, XCorr > 2.2, and DeltaCN > 0.099. Further, the sequence assignments could be accepted or rejected with respect to accuracy by using the following conservative, two-step process.

In the first step, a subset of high-scoring sequence assignments should be selected by filtering for XCorr values of at least 1.5 for a charge state of +1 , 2.2 for +2, and 3.3 for +3, allowing a maximum RSp value of 10. Assignments in this subset should be rejected if any of the following criteria are satisfied: (i) the spectrum contains at least one major peak (at least 10% as intense as the most intense ion in the spectrum) that can not be mapped to the assigned sequence as an a, b, or y ion, as an ion arising from neutral-loss of water or ammonia from a b or y ion, or as a multiply protonated ion; (ii) the spectrum does not contain a series of b or y ions equivalent to at least six uninterrupted residues; or (iii) the sequence is not observed at least five times in all the studies conducted (except for overlapping sequences due to incomplete proteolysis or use of proteases other than trypsin).

In the second step, assignments with below-threshold scores should be accepted if the low-scoring spectrum shows a high degree of similarity to a high-scoring spectrum collected in another study, which simulates a true reference library-searching strategy.

EXAMPLE 2

Production of Phospho-specific Polyclonal Antibodies for the Detection of Carcinoma-related Signaling Protein Phosphorylation

Polyclonal antibodies that specifically bind a Carcinoma-related signal transduction protein only when phosphorylated at the respective phosphorylation site disclosed herein (see Table 1 /Figure 2) are produced according to standard methods by first constructing a synthetic peptide antigen comprising the phosphorylation site sequence and then immunizing an animal to raise antibodies against the antigen, as further described below. Production of exemplary polyclonal antibodies is provided below.

A. JAK3 (tyrosine 929). A 24 amino acid phospho-peptide antigen,

LDASRLLLy^*SSQICKGMEYLGSRR (where y^*= phosphotyrosine) that corresponds to the sequence encompassing the tyrosine 929 phosphorylation site in human JAK3 kinase (see Row 341 of Table 1 ; SEQ ID NO: 340), plus cysteine on the C-terminal for coupling, is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer. See ANTIBODIES: A LABORATORY MANUAL, supra.; Merrifield, supra. This peptide is then coupled to KLH and used to immunize animals to produce (and subsequently screen) phospho-specific JAK3 (tyr 929) polyclonal antibodies as described in Immunization/Screening below.

B. SPRY1 (tyrosine 53).

A 13 amino acid phospho-peptide antigen, GSNEy*TEGPSWK (where y*= phosphotyrosine) that corresponds to the sequence encompassing the tyrosine 53 phosphorylation site in human SPRY1 (see Row 75 of Table 1 (SEQ ID NO: 74)), plus cysteine on the C-terminal for coupling, is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer. See ANTIBODIES: A LABORATORY MANUAL, supra.; Merrifield, supra. This peptide is then coupled to KLH and used to immunize animals to produce (and subsequently screen) phospho-specific SPRY1 (tyr 53) polyclonal antibodies as described in Immunization/Screening below.

C. INPP5D (tyrosine 40).

A 16 amino acid phospho-peptide antigen, ASESISRAy*ALCVLYR (where y*= phosphotyrosine) that corresponds to the sequence encompassing the tyrosine 40 phosphorylation site in human INPP5D protein (see Row 414 of Table 1 (SEQ ID NO: 413), plus cysteine on the C-terminal for coupling, is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer. See ANTIBODIES: A LABORATORY MANUAL, supra.; Merrifield, supra. This peptide is then coupled to KLH and used to immunize animals to produce (and subsequently screen) phospho-specific INPP5D (tyr 40) antibodies as described in Immunization/Screening below.

Immunization/Screening.

A synthetic phospho-peptide antigen as described in A-C above is coupled to KLH, and rabbits are injected intradermally (ID) on the back with antigen in complete Freunds adjuvant (500 μg antigen per rabbit). The rabbits are boosted with same antigen in incomplete Freund adjuvant (250 μg antigen per rabbit) every three weeks. After the fifth boost, bleeds are collected. The sera are purified by Protein A-affinity chromatography by standard methods (see ANTIBODIES: A LABORATORY MANUAL, Cold Spring Harbor, supra.). The eluted immunoglobulins are further loaded onto a non-phosphorylated synthetic peptide antigen-resin Knotes column to pull out antibodies that bind the non-phosphorylated form of the phosphorylation site. The flow through fraction is collected and applied onto a phospho-synthetic peptide antigen-resin column to isolate antibodies that bind the phosphorylated form of the site. After washing the column extensively, the bound antibodies (i.e. antibodies that bind a phosphorylated peptide described in A-C above, but do not bind the non-phosphorylated form of the peptide) are eluted and kept in antibody storage buffer.

The isolated antibody is then tested for phospho-specificity using Western blot assay using an appropriate cell line that expresses (or overexpresses) target phospho-protein (i.e. phosphorylated JAK3, SPRY1 or INPP5D), for example, A431 , and A549, respectively. Cells are cultured in DMEM or RPMI supplemented with 10% FCS. Cell are collected, washed with PBS and directly lysed in cell lysis buffer. The protein concentration of cell lysates is then measured. The loading buffer is added into cell lysate and the mixture is boiled at 100 ⁰C for 5 minutes. 20 μl (10 μg protein) of sample is then added onto 7.5% SDS-PAGE gel. A standard Western blot may be performed according to the lmmunoblotting Protocol set out in the CELL SIGNALING TECHNOLOGY, INC. 2003-04 Catalogue, p. 390. The isolated phospho-specific antibody is used at dilution 1 :1000. Phosphorylation-site specificity of the antibody will be shown by binding of only the phosphorylated form of the target protein. Isolated phospho-specific polyclonal antibody does not (substantially) recognize the target protein when not phosphorylated at the appropriate phosphorylation site in the non-stimulated cells (e.g. JAK3 is not bound when not phosphorylated at tyrosine 929). In order to confirm the specificity of the isolated antibody, different cell lysates containing various phosphorylated signal transduction proteins other than the target protein are prepared. The Western blot assay is performed again using these cell lysates. The phospho-specific polyclonal antibody isolated as described above is used (1 :1000 dilution) to test reactivity with the different phosphorylated non-target proteins on Western blot membrane. The phospho-specific antibody does not significantly cross-react with other phosphorylated signal transduction proteins, although occasionally slight binding with a highly homologous phosphorylation-site on another protein may be observed. In such case the antibody may be further purified using affinity chromatography, or the specific immunoreactivity cloned by rabbit hybridoma technology.

EXAMPLE 3

Production of Phospho-specific Monoclonal Antibodies for the Detection of Carcinoma-related Signaling Protein Phosphorylation Monoclonal antibodies that specifically bind a Carcinoma-related signal transduction protein only when phosphorylated at the respective phosphorylation site disclosed herein (see Table 1/Figure 2) are produced according to standard methods by first constructing a synthetic peptide antigen comprising the phosphorylation site sequence and then immunizing an animal to raise antibodies against the antigen, and harvesting spleen cells from such animals to produce fusion hybridomas, as further described below. Production of exemplary monoclonal antibodies is provided below.

A. RAN (tyrosine 155).

An 14 amino acid phospho-peptide antigen, SNy*NFEKPFLWLAR (where y*= phosphotyrosine) that corresponds to the sequence encompassing the tyrosine 155 phosphorylation site in human RAN phosphatase (see Row 274 of Table 1 (SEQ ID NO: 273)), plus cysteine on the C-terminal for coupling, is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer. See ANTIBODIES: A LABORATORY MANUAL, supra.; Merrifield, supra. This peptide is then coupled to KLH and used to immunize animals and harvest spleen cells for generation (and subsequent screening) of phospho-specific monoclonal RAN (tyr 155) antibodies as described in Immunization/Fusion/Screening below.

B. PLEC1 (tyrosine 4505).

A 18 amino acid phospho-peptide antigen, GYYSPy*SVSGSGSTAGSR (where y*= phosphotyrosine) that corresponds to the sequence encompassing the tyrosine 4505 phosphorylation site in human PLEC1 (see Row 216 of Table 1 (SEQ ID NO: 215)), plus cysteine on the C-terminal for coupling, is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer. See ANTIBODIES: A LABORATORY MANUAL, supra.; Merrifield, supra. This peptide is then coupled to KLH and used to immunize animals and harvest spleen cells for generation (and subsequent screening) of phospho-specific monoclonal PLEC1 (tyr 4505) antibodies as described in Immunization/Fusion/Screening below. C. PLCB1 (tyrosine 239).

A 15 amino acid phospho-peptide antigen, Py*LTVDQMMDFINLK (where y*= phosphotyrosines) that corresponds to the sequence encompassing the tyrosine 239 phosphorylation site in human PLCB1 protein (see Row 421 of Table 1 (SEQ ID NO: 420)), plus cysteine on the C-terminal for coupling, is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer. See ANTIBODIES: A LABORATORY MANUAL, supra.; Merrifield, supra. This peptide is then coupled to KLH and used to immunize animals and harvest spleen cells for generation (and subsequent screening) of phospho-specific monoclonal PLCB1 (tyr 239) antibodies as described in Immunization/Fusion/Screening below.

Immunization/Fusion/Screening.

A synthetic phospho-peptide antigen as described in A-C above is coupled to KLH, and BALB/C mice are injected intradermal^ (ID) on the back with antigen in complete Freunds adjuvant (e.g. 50 μg antigen per mouse). The mice are boosted with same antigen in incomplete Freund adjuvant (e.g. 25 μg antigen per mouse) every three weeks. After the fifth boost, the animals are sacrificed and spleens are harvested. Harvested spleen cells are fused to SP2/0 mouse myeloma fusion partner cells according to the standard protocol of Kohler and Milstein (1975). Colonies originating from the fusion are screened by ELISA for reactivity to the phospho-peptide and non-phospho-peptide forms of the antigen and by Western blot analysis (as described in Example 1 above). Colonies found to be positive by ELISA to the phospho-peptide while negative to the non-phospho-peptide are further characterized by Western blot analysis. Colonies found to be positive by Western blot analysis are subcloned by limited dilution. Mouse ascites are produced from a single clone obtained from subcloning, and tested for phospho- specificity (against the RAN, PLEC1 , or PLCB1) phospho-peptide antigen, as the case may be) on ELISA. Clones identified as positive on Western blot analysis using cell culture supernatant as having phospho-specificity, as indicated by a strong band in the induced lane and a weak band in the uninduced lane of the blot, are isolated and subcloned as clones producing monoclonal antibodies with the desired specificity.

Ascites fluid from isolated clones may be further tested by Western blot analysis. The ascites fluid should produce similar results on Western blot analysis as observed previously with the cell culture supernatant, indicating phospho-specificity against the phosphorylated target (e.g. PLCB1 phosphorylated at tyrosine 239).

EXAMPLE 4

Production and Use of AQUA Peptides for the Quantification of Carcinoma-related Signaling Protein Phosphorylation Heavy-isotope labeled peptides (AQUA peptides (internal standards)) for the detection and quantification of a Carcinoma-related signal transduction protein only when phosphorylated at the respective phosphorylation site disclosed herein (see Table 1/Figure 2) are produced according to the standard AQUA methodology (see Gygi et al., Gerber et al., supra.) methods by first constructing a synthetic peptide standard corresponding to the phosphorylation site sequence and incorporating a heavy-isotope label. Subsequently, the MS^π and LC-SRM signature of the peptide standard is validated, and the AQUA peptide is used to quantify native peptide in a biological sample, such as a digested cell extract. Production and use of exemplary AQUA peptides is provided below. A. PIK3C2B (tyrosine 127).

An AQUA peptide comprising the sequence,

GSLSGDy*LYIFDGSDGGVSSSPGPGDIEGSCK (y*= phosphotyrosine; sequence incorporating ¹⁴C/¹⁵N-labeled valine (indicated by bold V), which corresponds to the tyrosine 127 phosphorylation site in human PIK3C2B kinase (see Row 303 in Table 1 (SEQ ID NO: 302)), is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer (see Merrifield, supra.) as further described below in Synthesis & MS/MS Signature. The Met (tyr 835) AQUA peptide is then spiked into a biological sample to quantify the amount of phosphorylated PIK3C2B (tyr 127) in the sample, as further described below in Analysis & Quantification.

B. GAB2 (tyrosine 371). An AQUA peptide comprising the sequence ASSCETyEYPQR (y*= phosphotyrosine; sequence incorporating ¹⁴C/¹⁵N-labeled proline (indicated by bold P), which corresponds to the tyrosine 371 phosphorylation site in human GAB2 protein (see Row 52 in Table 1 (SEQ ID NO: 51)), is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer (see Merrifield, supra.) as further described below in Synthesis & MS/MS Signature. The GAB2 (tyr 287) AQUA peptide is then spiked into a biological sample to quantify the amount of phosphorylated GAB2 (tyr 371) in the sample, as further described below in Analysis & Quantification.

C. VIM (tyrosine 38).

An AQUA peptide comprising the sequence, Ty*SLGSALRPSTSR (y^*= phosphotyrosine; sequence incorporating ¹⁴C/¹⁵N-labeled Leucine (indicated by bold L), which corresponds to the tyrosine 38 phosphorylation site in human VIMprotein (see Row 220 in Table 1 (SEQ ID NO: 219)), is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer (see Merrifield, supra.) as further described below in

Synthesis & MS/MS Signature. The VIM (tyr 38) AQUA peptide is then spiked into a biological sample to quantify the amount of phosphorylated VIM (tyr 38) in the sample, as further described below in Analysis & Quantification.

D. GPRC5A (tyrosine 350).

An AQUA peptide comprising the sequence AHAWPSPYKDyEVK (y^*= phosphotyrosine; sequence incorporating ¹⁴C/¹⁵N-labeled proline (indicated by bold P), which corresponds to the tyrosine 350 phosphorylation site in human GPRC5A protein (see Row 448 in Table 1 (SEQ ID NO: 447)), is constructed according to standard synthesis techniques using, e.g., a Rainin/Protein Technologies, Inc., Symphony peptide synthesizer (see Merrifield, supra.) as further described below in Synthesis & MS/MS Signature. The GPRC5A (tyr 350) AQUA peptide is then spiked into a biological sample to quantify the amount of phosphorylated GPRC5A (tyr 350) in the sample, as further described below in Analysis & Quantification.

Synthesis & MS/MS Spectra.

Fluorenylmethoxycarbonyl (Fmoc)-derivatized amino acid monomers may be obtained from AnaSpec (San Jose, CA). Fmoc-derivatized stable- isotope monomers containing one ¹⁵N and five to nine ¹³C atoms may be obtained from Cambridge Isotope Laboratories (Andover, MA). Preloaded Wang resins may be obtained from Applied Biosystems. Synthesis scales may vary from 5 to 25 μmol. Amino acids are activated in situ with 1-H- benzotriazolium, i-bis(dimethylamino) methylene]-hexafluorophosphate (1-),3-oxide:1-hydroxybenzotriazole hydrate and coupled at a 5-fold molar excess over peptide. Each coupling cycle is followed by capping with acetic anhydride to avoid accumulation of one-residue deletion peptide byproducts. After synthesis peptide-resins are treated with a standard scavenger-containing trifluoroacetic acid (TFA)-water cleavage solution, and the peptides are precipitated by addition to cold ether. Peptides (i.e. a desired AQUA peptide described in A-D above) are purified by reversed- phase C18 HPLC using standard TFA/acetonitrile gradients and characterized by matrix-assisted laser desorption ionization-time of flight (Biflex III, Bruker Daltonics, Billerica, MA) and ion-trap (ThermoFinnigan, LCQ DecaXP) MS.

MS/MS spectra for each AQUA peptide should exhibit a strong y-type ion peak as the most intense fragment ion that is suitable for use in an SRM monitoring/analysis. Reverse-phase microcapillary columns (0.1 A~ 150-220 mm) are prepared according to standard methods. An

Agilent 1100 liquid chromatograph may be used to develop and deliver a solvent gradient [0.4% acetic acid/0.005% heptafluorobutyric acid (HFBA)/7% methanol and 0.4% acetic acid/0.005% HFBA/65% methanol/35% acetonitrile] to the microcapillary column by means of a flow splitter. Samples are then directly loaded onto the microcapillary column by using a FAMOS inert capillary autosampler (LC Packings, San Francisco) after the flow split. Peptides are reconstituted in 6% acetic acid/0.01% TFA before injection.

Analysis & Quantification. Target protein (e.g. a phosphorylated protein of A-D above) in a biological sample is quantified using a validated AQUA peptide (as described above). The IAP method is then applied to the complex mixture of peptides derived from proteolytic cleavage of crude cell extracts to which the AQUA peptides have been spiked in. LC-SRM of the entire sample is then carried out. MS/MS may be performed by using a ThermoFinnigan (San Jose, CA) mass spectrometer (LCQ DecaXP ion trap or TSQ Quantum triple quadrupole). On the DecaXP, parent ions are isolated at 1.6 m/z width, the ion injection time being limited to 150 ms per microscan, with two microscans per peptide averaged, and with an AGC setting of 1 x 10⁸; on the Quantum, Q1 is kept at 0.4 and Q3 at 0.8 m/z with a scan time of 200 ms per peptide. On both instruments, analyte and internal standard are analyzed in alternation within a previously known reverse-phase retention window; well-resolved pairs of internal standard and analyte are analyzed in separate retention segments to improve duty cycle. Data are processed by integrating the appropriate peaks in an extracted ion chromatogram (60.15 m/z from the fragment monitored) for the native and internal standard, followed by calculation of the ratio of peak areas multiplied by the absolute amount of internal standard (e.g., 500 fmol).

Claims

WHAT IS CLAIMED IS:

1. A method for obtaining a phosphorylation profile of protein Kinases that are phosphorylated in Carcinoma signaling pathways, said method comprising the step of utilizing one or more isolated antibody that specifically binds a protein Kinase selected from Column A, Rows 296- 365, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 296-365, of Table 1 , comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 296-365, of Table 1 (SEQ ID NOs: 295-317, 319-333, 335-344, 346-347, 349, 351-355, and 357-364), to detect the phosphorylation of one or more of said protein Kinases, thereby obtaining a phosphorylation profile for said Kinases.

2. A method for detecting or quantifying a signaling protein that is tyrosine-phosphorylated in carcinoma signaling pathways, said method comprising the step of utilizing one or more of the following reagents to detect or quantify one or more Carcinoma-related signaling protein(s) selected from Column A of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D of Table 1 :

(i) an isolated phosphorylation site-specific antibody that specifically binds said protein only when phosphorylated at the tyrosine listed in corresponding Column D of Table 1, comprised within the phosphorylation site sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 1-2, 5-6, 9-11, 13-35, 38-44, 46-49, 51-61 , 63-67, 69-80, 83-129, 131 , 133-147, 151-188, 191-210, 212-219, 221-240, 242- 317, 319-333, 335-344, 346-347, 349, 351-355, 357-400, 402-425, 427- 446, 449-451 , 453-459, and 461-474), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine; and/or

(ii) a heavy-isotope labeled peptide (AQUA peptide) for the quantification of said protein, said labeled peptide comprising the phosphorylation site peptide sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 1-2, 5-6, 9-11 , 13-35, 38-44, 46-49, 51-61 , 63- 67, 69-80, 83-129, 131 , 133-147, 151-188, 191-210, 212-219, 221-240, 242-317, 319-333, 335-344, 346-347, 349, 351-355, 357-400, 402-425, 427-446, 449-451 , 453-459, and 461-474).

3. The method of claim 2, wherein said protein is a kinase protein selected from Column A, Rows 296-365, of Table 1 , and wherein

(i) said antibody specifically binds said kinase protein only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 296-365, of Table 1, comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 296-365, of Table 1 (SEQ ID NOs: 295-317, 319-333, 335-344, 346-347, 349, 351-355, and 357-364), and

(ii) said labeled peptide comprises the phosphorylation site peptide sequence listed in corresponding Column E, Rows 296-365, of Table 1 (SEQ ID NOs: 295-317, 319-333, 335-344, 346-347, 349, 351-355, and 357-364), comprising the phosphorylated tyrosine listed in corresponding Column D, Rows 296-365, of Table 1.

4. The method of claim 2, wherein said protein is an adaptor/scaffold protein selected from Column A, Rows 26-85 of Table 1 , and wherein

(i) said antibody specifically binds said adaptor/scaffold protein only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 26-85, of Table 1 , comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 26-85, of Table 1 (SEQ ID NOs: 25-35, 38-44, 46-49, 51-61 , 63-67, 69-80, and 83-84), and

(ii) said labeled peptide comprises the phosphorylation site peptide sequence listed in corresponding Column E, Rows 26-85, of Table 1 (SEQ ID NOs: 25-35, 38-44, 46-49, 51-61, 63-67, 69-80, and 83-84), comprising the phosphorylated tyrosine listed in corresponding Column D, Rows 26-85, of Table 1.

5. The method of claim 2, wherein said protein is a phosphatase protein selected from Column A, Rows 408-419, 442 and 443, of Table 1 , and wherein

(i) said antibody specifically binds said phosphatase protein only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 408-419, 442 and 443, of Table 1 , comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 408-419, 442 and 443 of Table 1 (SEQ ID NOs: 407-418, 441 and 442), and

(ii) said labeled peptide comprises the phosphorylation site peptide sequence listed in corresponding Column E, Rows 408-419, 442 and 443, of Table 1 (SEQ ID NOs: 407-418, 441 and 442), comprising the phosphorylated tyrosine listed in corresponding Column D, Rows 408- 419, 442 and 443, of Table 1.

6. The method of claim 2, wherein said protein is a G protein regulator, Guanine Nucleotide Exchange factor, or GTPase activating protein selected from Column A, Rows 270-283 of Table 1 , and wherein (i) said antibody specifically binds said G protein regulator,

Guanine Nucleotide Exchange factor, or GTPase activating protein only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 270-283, of Table 1 , comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 270-283, of Table 1 (SEQ ID NOs: 269-282), and

(ii) said labeled peptide comprises the phosphorylation site peptide sequence listed in corresponding Column E, Rows 270-283, of Table 1 (SEQ ID NOs: 269-282), comprising the phosphorylated tyrosine listed in corresponding Column D, Rows 270-283, of Table 1.

7. The method of claim 2, wherein said protein is a cytoskeletal protein selected from Column A, Rows 173-222, of Table 1 , and wherein (i) said antibody specifically binds said Cytoskeletal protein only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 173-222, of Table 1, comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 173-222, of Table 1 (SEQ ID NOs: 172-188, 191-210, 212-219, and 221), and (ii) said labeled peptide comprises the phosphorylation site peptide sequence listed in corresponding Column E, Rows 173-222, of Table 1 (SEQ ID NOs: 172-188, 191-210, 212-219, and 221), comprising the phosphorylated tyrosine listed in corresponding Column D, Rows 173- 222, of Table t

8. The method of claim 2, wherein said protein is a DNA binding protein selected from Column A, Rows 223-231 , of Table 1 , and wherein

(i) said antibody specifically binds said DNA binding protein only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 223-231 , of Table 1 , comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 223-231 , of Table 1 (SEQ ID NOs: 222-230), and

(ii) said labeled peptide comprises the phosphorylation site peptide sequence listed in corresponding Column E, Rows 223-231 , of Table 1 (SEQ ID NOs: 222-230), comprising the phosphorylated tyrosine listed in corresponding Column D, Rows 223-231 , of Table 1.

9. The method of claim 2, wherein said protein is a phospholipase protein selected from Column A, Rows 420-422, of Table 1 , and wherein (i) said antibody specifically binds said phospholipase protein only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 420-422, of Table 1 , comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 420-422, of Table 1 (SEQ ID NOs: 419-421), and

(ii) said labeled peptide comprises the phosphorylation site peptide sequence listed in corresponding Column E, Rows 420-422, of Table 1 (SEQ ID NOs; 419-421), comprising the phosphorylated tyrosine listed in corresponding Column D, Rows 420-422, of Table 1.

10. The method of claim 2, wherein said protein is a receptor protein selected from Column A, Rows 444-459, of Table 1, and wherein

(i) said antibody specifically binds said receptor protein only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 444-459, of Table 1 , comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 444-459, of Table 1 (SEQ ID NOs: 443-458), and

(ii) said labeled peptide comprises the phosphorylation site peptide sequence listed in corresponding Column E, Rows 444-459, of Table 1 (SEQ ID NOs: 443-458), comprising the phosphorylated tyrosine listed in corresponding Column D, Rows 444-459, of Table 1.

11. The method of claim 2, wherein said protein is an enzyme selected from Column A, Rows 243-262, of Table 1 , and wherein

(i) said antibody specifically binds said enzyme only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 243-262, of Table 1, comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 243-262, of Table 1 (SEQ ID NOs: 242-261), and (H) said labeled peptide comprises the phosphorylation site peptide sequence listed in corresponding Column E, Rows 243-262, of Table 1 (SEQ ID NOs: 242-261), comprising the phosphorylated tyrosine listed in corresponding Column D, Rows 243-262, of Table 1.

12. The method of claim 2, wherein said protein is a DNA repair/replication protein selected from Column A, Rows 232-239, of Table 1 , and wherein

(i) said antibody specifically binds said DNA repair/replication protein only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 232-239, of Table 1 , comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 232-239, of Table 1 (SEQ ID NOs: 231-238), and

(ii) said labeled peptide comprises the phosphorylation site sequence listed in corresponding Column E, Rows 232-239, of Table 1 (SEQ ID NOs: 231-238), comprising the phosphorylated tyrosine listed in corresponding Column D, Rows 232-239, of Table 1.

13. The method of claim 2, wherein said protein is a adhesion protein selected from Column A, Rows 89-137, of Table 1 , and wherein

(i) said antibody specifically binds said adhesion protein only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 89-137, of Table 1 , comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 89-137, of Table 1 (SEQ ID NOs: 88-129, 131 , and 133-136), and

(ii) said labeled peptide comprises the phosphorylation site peptide sequence listed in corresponding Column E, Rows 89-137, of Table 1

(SEQ ID NOs: 88-129, 131, and 133-136), comprising the phosphorylated tyrosine listed in corresponding Column D, Rows 89-137, of Table 1.

14. The method of claim 2, wherein said protein is a protease protein selected from Column A, Rows 423-441 , of Table 1 , and wherein

(i) said antibody specifically binds said protease protein only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 423-441 , of Table 1 , comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 423-441 , of Table 1 (SEQ ID NOs: 422-425, and 427-440), and

(ii) said labeled peptide comprises the phosphorylation site peptide sequence listed in corresponding Column E, Rows 423-441 , of Table 1 (SEQ ID NOs: 422-425, and 427-440), comprising the phosphorylated tyrosine listed in corresponding Column D, Rows 423-441 of Table 1.

15. The method of claim 2, wherein said protein is a protein selected from Column A, Rows 16, 19, and 291, of Table 1 , and wherein

(i) said antibody specifically binds said protein only when phosphorylated at the tyrosine listed in corresponding Column D, Rows

16. 19, and 291 , of Table 1, comprised within the phosphorylation site sequence listed in corresponding Column E, Rows 16, 19, and 291 , of Table 1 (SEQ ID NOs: 15, 18, and 290), and

(ii) said labeled peptide comprises the phosphorylation site peptide sequence listed in corresponding Column E, Rows 16, 19, and 291 , of Table 1 (SEQ ID NOs: 15, 18, and 290), comprising the phosphorylated tyrosine listed in corresponding Column D, Rows 16, 19, and 291 of Table 1.

16. An isolated phosphorylation site-specific antibody that specifically binds a human Carcinoma-related signaling protein selected from Column A of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 1-2, 5-6, 9-11, 13-35, 38-44, 46-49, 51-61 , 63-67, 69-80, 83-129, 131 , 133-147, 151-188, 191-210, 212-219, 221-240, 242- 317, 319-333, 335-344, 346-347, 349, 351-355, 357-400, 402-425, 427- 446, 449-451 , 453-459, and 461-474), wherein said antibody does not bind said signaling protein when not phosphorylated at said tyrosine.

17. An isolated phosphorylation site-specific antibody that specifically binds a human Carcinoma-related signaling protein selected from Column A of Table 1 only when not phosphorylated at the tyrosine listed in corresponding Column D of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 1-2, 5-6, 9-11 , 13-35, 38-44, 46-49, 51-61 , 63-67, 69-80, 83-129, 131 , 133-147, 151-188, 191-210, 212-219, 221-240, 242- 317, 319-333, 335-344, 346-347, 349, 351-355, 357-400, 402-425, 427- 446, 449-451 , 453-459, and 461-474), wherein said antibody does not bind said signaling protein when phosphorylated at said tyrosine.

18. A heavy-isotope labeled peptide (AQUA peptide) for the quantification of a human Carcinoma-related signaling protein selected from Column A of Table 1 , said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E of Table 1 (SEQ ID NOs: 1-2, 5-6, 9-11, 13-35, 38-44, 46-49, 51-61 , 63-67, 69-80, 83-129, 131 , 133-147, 151-188, 191-210, 212-219, 221-240, 242- 317, 319-333, 335-344, 346-347, 349, 351-355, 357-400, 402-425, 427- 446, 449-451 , 453-459, and 461-474), comprising the phosphorylatable tyrosine listed in corresponding Column D, Rows 2-475, of Table 1.

19. The labeled peptide of claim 18, wherein said phosphorylatable tyrosine is phosphorylated.

20. The labeled peptide of claim 18, wherein said phosphorylatable tyrosine is not phosphorylated.

21. An immortalized cell line producing the antibody of claim 16 or 17.

22. The cell line of claim 21 , wherein said immortalized cell line is a rabbit hybridoma or a mouse hybridoma.

23. The antibody of claim 16, wherein said antibody specifically binds a kinase protein selected from Column A, Rows 296-365, of

Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 296-365, of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E,

Rows 296-365, of Table 1 (SEQ ID NOs: 295-317, 319-333, 335-344, 346- 347, 349, 351-355, and 357-364), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

24. The heavy-isotope labeled peptide (AQUA peptide) of claim 18, wherein said labeled peptide is for the quantification of a kinase protein selected from Column A, Rows 296-365, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 296-365, of Table 1 (SEQ ID NOs: 295-317, 319-333, 335-344, 346- 347, 349, 351-355, and 357-364), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 296- 365, of Table t

25. The antibody of claim 16, wherein said antibody specifically binds an adaptor/scaffold protein selected from Column A, Rows 26-85, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 26-85, of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 26-85, of Table 1 (SEQ ID NOs: 25-35, 38-44, 46-49, 51-61 , 63-67, 69-80, and 83- 84), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

26. The heavy-isotope labeled peptide (AQUA peptide) of claim 18, wherein said labeled peptide is for the quantification of an adaptor/scaffold protein selected from Column A, Rows 26-85, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 26-85, of Table 1 (SEQ ID NOs: 25-35, 38-44, 46-49, 51- 61 , 63-67, 69-80, and 83-84), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 26-85, of Table !

27. The antibody of claim 16, wherein said antibody specifically binds a phosphatase protein selected from Column A, Rows 408-419, 442 and 443, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 408-419, 442 and 443, of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 408-419, 442 and 443, of Table 1 (SEQ ID NOs: 407-418, 441 and 442), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

28. The heavy-isotope labeled peptide (AQUA peptide) of claim 18, wherein said labeled peptide is for the quantification of a phosphatase protein selected from Column A, Rows 408-419, 442 and 443, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 408-419, 442 and 443, of Table 1 (SEQ ID NOs: 407-418, 441 and 442), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 408- 419, 442 and 443, of Table 1.

29. The antibody of claim 14, wherein said antibody specifically binds a G protein regulator, Guanine Nucleotide Exchange factor, or GTPase activating protein selected from Column A, Rows 270-283, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 270-283, of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 270-283, of Table 1 (SEQ ID NOs: 269-282), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

30. The heavy-isotope labeled peptide (AQUA peptide) of claim 18, wherein said labeled peptide is for the quantification of a G protein regulator, Guanine Nucleotide Exchange factor, or GTPase activating protein selected from Column A, Rows 270-283, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 270-283, of Table 1 (SEQ ID NOs: 269-282), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 270-283, of Table 1.

31. The antibody of claim 16, wherein said antibody specifically binds a cytoskeletal protein selected from Column A, Rows 173-222, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 173-222, of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 173-222 of Table 1 (SEQ ID NOs: 172-188, 191-210, 212-219, and 221), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

32. The heavy-isotope labeled peptide (AQUA peptide) of claim 18, wherein said labeled peptide is for the quantification of a cytoskeletal protein selected from Column A, Rows 173-222, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 173-222, of Table 1 (SEQ ID NOs: 172-188, 191-210, 212-219, and 221), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 173-222, of Table 1.

33. The antibody of claim 16, wherein said antibody specifically binds a DNA binding protein selected from Column A, Rows 223-231 of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 223-231 of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 223-231 , of Table 1 (SEQ ID NOs: 222-230), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

34. The heavy-isotope labeled peptide (AQUA peptide) of claim 18, wherein said labeled peptide is for the quantification of a DNA binding protein selected from Column A, Rows 223-231 , said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 223-231 , of Table 1 (SEQ ID NOs: 222-230), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 223-231 , of Table 1.

35. The antibody of claim 16, wherein said antibody specifically binds a phospholipase protein selected from Column A, Rows 420-422, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 420-422, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 420-422, of Table 1 (SEQ ID NOs: 419-421), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

36. The heavy-isotope labeled peptide (AQUA peptide) of claim 18, wherein said labeled peptide is for the quantification of a phospholipase protein selected from Column A, Rows 420-422, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 420-422, of Table 1 (SEQ ID NOs: 419-421), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 420-422, of Table 1.

37. The antibody of claim 16, wherein said antibody specifically binds a receptor protein selected from Column A, Rows 444-459, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 444-459, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 444-459, of Table 1 (SEQ ID NOs: 443-458), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

38. The heavy-isotope labeled peptide (AQUA peptide) of claim 18, wherein said labeled peptide is for the quantification of a receptor protein selected from Column A, Rows 444-459, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 444-459, of Table 1 (SEQ ID NOs: 443-458), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 444-459, of Table 1.

39. The antibody of claim 16, wherein said antibody specifically binds an enzyme selected from Column A, Rows 242-262, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 242-262, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 242-262, of Table 1 (SEQ ID NOs: 241-261), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

40. The heavy-isotope labeled peptide (AQUA peptide) of claim 18, wherein said labeled peptide is for the quantification of an enzyme selected from Column A, Rows 242-262, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 242-262, of Table 1 (SEQ ID NOs: 241-261), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 242-262, of Table 1.

41. The antibody of claim 16, wherein said antibody specifically binds a DNA repair/replication protein selected from Column A, Rows 232-239, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 232-239, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 232-239, of Table 1 (SEQ ID NOs: 231-238), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

42. The heavy-isotope labeled peptide (AQUA peptide) of claim 18, wherein said labeled peptide is for the quantification of a DNA repair/replication protein selected from Column A, Rows 232-239, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 232-239, of Table 1 (SEQ ID NOs: 231- 238), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 232-239, of Table 1.

43. The antibody of claim 16, wherein said antibody specifically binds an adhesion protein selected from Column A, Rows 89-137, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 89-137, of Table 1, comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 89-137, of Table 1 (SEQ ID NOs: 88-129, 131 , and 133-136), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

44. The heavy-isotope labeled peptide (AQUA peptide) of claim 18, wherein said labeled peptide is for the quantification of an adhesion protein selected from Column A, Rows 89-137, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 89-137, of Table 1 (SEQ ID NOs: 88-129, 131 , and 133- 136), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 89-137, of Table 1.

45. The antibody of claim 16, wherein said antibody specifically binds a protease selected from Column A, Rows 423-441, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 423-441 , of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 423-441 , of Table 1 (SEQ ID NOs: 422-425, and 427-440), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

46. The heavy-isotope labeled peptide (AQUA peptide) of claim 18, wherein said labeled peptide is for the quantification of a protease selected from Column A, Rows 423-441, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 423-441 , of Table 1 (SEQ ID NOs: 422-425, and 427-440), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 423-441 , of Table 1.

47. The antibody of claim 16, wherein said antibody specifically binds a protein selected from Column A, Rows 16, 19, and 291, of Table 1 only when phosphorylated at the tyrosine listed in corresponding Column D, Rows 16, 19, and 291 , of Table 1 , comprised within the phosphorylatable peptide sequence listed in corresponding Column E, Rows 16, 19, and 291 , of Table 1 (SEQ ID NOs: 15, 18, and 290), wherein said antibody does not bind said protein when not phosphorylated at said tyrosine.

48. The heavy-isotope labeled peptide (AQUA peptide) of claim 18, wherein said labeled peptide is for the quantification of a protein selected from Column A₁ Rows 16, 19, and 291, said labeled peptide comprising the phosphorylatable peptide sequence listed in corresponding Column E, Rows 16, 19, and 291 , of Table 1 (SEQ lD NOs: 15, 18, and 290), which sequence comprises the phosphorylatable tyrosine listed in corresponding Column D, Rows 16, 19, and 291, of Table 1.

49. An immortalized cell line producing the antibody of any one of claims 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45 and 47.

50. The cell line of claim 49, wherein said immortalized cell line is a rabbit hybridoma or a mouse hybridoma.

51. The heavy-isotope labeled peptide of any one of claims 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46 and 48, wherein said phosphorylatable tyrosine is phosphorylated.

52. The heavy-isotope labeled peptide of any one of claims 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46 and 48, wherein said phosphorylatable tyrosine is not phosphorylated.