The present invention pertains to a new method for the diagnosis, prognosis, stratification and/or monitoring of a therapy, of cancer in a patient. The method is based on the determination of the level of a panel of biomarkers selected from CEA, AREG, IL-6, GDF-15, HGF-receptor, CXCL9, ErbB4-Her4, CXCL10, Flt3L, VEGFR-2, CD69, CXCL5, PSA, EMMPRIN, Cathepsin-D, Caspase-3, TNF-alpha, and INF-gamma. The new biomarker panel of the invention allows diagnosing and even stratifying various cancer diseases. Furthermore provided are diagnostic kits for performing the non-invasive methods of the invention.

The invention relates generally to compositions and methods for detecting protease activity in a subject or a biological sample using activatable antibodies, and the use of these compositions and methods in a variety of diagnostic indications.

A previously unrecognized fundamental property of .sub.1PI is to regulate the phenotypic composition of circulating and tissue-associated cells derived from hematopoietic stem cells. The present invention comprises screening for various unmodified and modified .sub.1PI's which are useful in the treatment of abnormalities in the number of cells of myeloid or lymphoid lineage that are associated with Human Immunodeficiency Virus-1 (HIV-1) infection, microbial infection, leukemia, solid tumor cancers, atherosclerosis, autoimmunity, stem cell transplantation, organ transplantation, and other diseases affected by cells of the immune system. The interaction of .sub.1PI with its receptors, cell surface Human Leucocyte Elastase (HLEcs) and Lipoprotein Receptor-related Protein (LRP), influences the level of cells of different lineages. Genetic and proteolytic modification of .sub.1PI is used to target these receptors to increase or decrease specific cell populations, as needed, in the various disease states.

The present invention is methods and assays for identifying single proteins from a sample, without the use of affinity reagents. The methods and assays combine endopeptidase-based component of conventional peptide mapping with single molecule labeling and a microreactor array platform. The invention also includes kits for performing the methods and assays.

The invention discloses a method for determining the molar ratio between wild type (WT) BRAF protein and protein variants thereof in a biological sample, comprising the steps of: a) Digesting said sample by using a serine proteinase which specifically cleaves peptide bonds C-terminal to glutamic acid residues or peptide bonds C-terminal to glutamic or aspartic acid residues, to obtain a composition comprising a peptide fragment resulting from digestion of the peptides by the proteinase, wherein the mass of said fragment differs between said wild type (WT) B-raf protein and one said BRAF protein variant. b) Quantitatively assaying the molar amount of the peptide fragment resulting from digestion of wild type (WT) B-raf protein and the molar amount of the peptide fragment resulting from digestion of variants of the wild type (WT) B-raf protein using a mass spectrometry technique. And, c) based on the quantitative assessment calculating the at least one specific ratio between said WT BRAF protein and said variants thereof. Further, a method for estimating a subject's susceptibility to a given drug treatment for a BRAF related disease. Also, a method of treatment for a subject with a BRAF related disease.

The present disclosure provides a method of identifying a polypeptide. The method can include steps of (a) attaching a polypeptide to a particle or solid support, thereby producing an immobilized polypeptide having a plurality of amino acids linked to the particle or solid support; (b) fragmenting the immobilized polypeptide, whereby the particle is attached to a set of fragments of the polypeptide; (c) performing a binding assay including contacting the set of fragments with a plurality of affinity reagents and detecting binding of affinity reagents of the plurality of affinity reagents to the set of fragments; and (d) identifying the polypeptide from results of the binding assay.

The present invention is methods and assays for identifying single proteins from a sample, without the use of affinity reagents. The methods and assays combine endopeptidase-based component of conventional peptide mapping with single molecule labeling and a microreactor array platform. The invention also includes kits for performing the methods and assays.

The present disclosure relates to methods of determining the amount of an anti-CD40 antibody in a sample. The present disclosure also relates to anti-CD40 antibody signature analytic peptides.

An in vitro method for the diagnosis, prognosis, stratification and/or monitoring of colorectal cancer in a subject includes detecting the level of AREG, CEA, HGF-receptor, ErbB4-Her4, CD69, PSA, EMMPRIN, and INF-gamma biomarkers in a biological sample of the subject. In an embodiment, the subject is administered a treatment when a differential level of the biomarkers compared to a healthy control or a reference value is indicative for the presence of colorectal cancer in the subject.

Provided herein are proteases that can be capable of cleaving immunoglobulins, including immunoglobulin G in a subject, which can be a canine. Also provided herein are methods of administering a protease provided herein to a subject, which can be a canine.