Methods for prognosing the risk of progression in a ER-positive breast cancer (e.g., luminal B 1 breast cancer) subject are provided, such methods including the detection of levels of a variety of biomarkers prognostic of progression. Compositions in the form of kits and panels of reagents for detecting the biomarkers of the invention are also provided.

The present invention refers to p53 sequence and post translational modifications (PTMs) and to their use as biomarkers in the diagnosis of neurodegenerative disease and cognitive decline and/or in the prognosis of Alzheimer's disease at different stages and/or of neurodegenerative disease in a biological sample. The invention also provides for a 1) diagnostic method based on a highly accurate mass spectrometry analysis for the diagnosis of neurodegenerative disease, including Mild Cognitive Impairment (MCI), Alzheimer's disease (AD), fronto-temporal dementia (FTD), Lewi's Body (LB), and vascular dementia (VD) in a subject, by evaluating the PTMs to the said p53 linear sequence protein and possible cut of its full sequence specifically in human plasma of patients; and 2) prognosis of AD in CU and MCI patients.

The present invention generally pertains to methods of characterizing of a protein of interest. In particular, the present invention pertains to the use of post-column denaturation, size exclusion chromatography and mass spectrometry for detecting, identifying and characterizing crosslinking amino acid residues in a therapeutic antibody.

A method of utilizing the chymotrypsin level of an individual as a measure of the success of secretin, other neuropeptides, and peptides or digestive enzyme administration to such individuals, and in particular, as a prognosticative of potential secretin, other neuropeptides, peptides, and digestive enzyme administration for persons having ADD, ADHD, Autism and other PDD related disorders. In one aspect, a method for determining the efficacy of secretin, other neuropeptides, peptides, or digestive enzymes for the treatment of an individual diagnosed with a pervasive developmental disorder (PDD) comprises obtaining a sample of feces from an individual, determining a quantitative level of chymotrypsin present in the sample, and correlating the quantitative level of chymotrypsin determined to be present in the sample with the PDD to determine the efficacy of treating the individual with secretin, other neuropeptides, peptides, or digestive enzyme administration. In another aspect, a therapeutic method for treating an individual diagnosed with a PDD pervasive developmental disorder comprises determining the efficacy of secretin, other neuropeptides, peptides, and digestive enzyme administration for the treatment of the individual based on a measure of the individual's chymotrypsin level, and administering secretin, other neuropeptides, peptides, or digestive enzymes to the individual based on the determination of the measure of the individual's chymotrypsin level.

The present disclosure relates to methods of quantifying a target protein e.g., a tumor biomarker, in a sample by using a mass spectroscopy coupled with a chromatography method. The methods presented herein include incubating the sample with a composition comprising an amidase and a protease for a predetermined amount of time. Incubating the sample with a composition comprising an amidase and a protease in a single step improves the digestion efficiency of the target protein, leading to enhanced detectability e.g., signal to noise ratio, in mass spectroscopy.

Methods are provided for detecting and quantifying the Mesothelin protein (MSLN) in biological samples that have been fixed in formalin using Selected Reaction Monitoring (SRM)/Multiple Reaction Monitoring (MRM) mass spectrometry. The biological sample may be, for example, tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded. A protein sample is prepared from the biological sample and the MSLN protein is quantitated by SRM/MRM mass spectrometry by quantitating one or more MSLN fragment peptides in the protein sample.

Methods and systems for detecting allergens using mass spectrometry are provided herein. In some aspects, a sample can be screened for the presence or quantity of ovalbumin, lysozyme, casein (isoform S1 and S2), lactoglobulin, high and low glutens, wheat, rye, oats, barley, mustard, sesame, and various types of nuts including macadamia, pistachio, brazil, walnuts, peanuts and hazelnuts by detecting one or more peptides specific to the allergen of interest using selected MRM transitions.

Methods for interpretation of mass spectrometric tests for clinical biomarkers in which the amounts of internal standards are set to equal clinical evaluation thresholds, and preparations for adding stable isotope labeled peptide species to sample digests while minimizing losses and alterations in peptide stoichiometry.

The present invention relates to a method for measuring the levels of Protein C (PROC), preferably Activated Protein C (APC), in a subject in need thereof, the method comprising a step of performing an enzymatic digestion of one or more biological samples isolated from the subject, and a step of measuring the levels of the peptide of SEQ ID NO 1 (LGEYDLR) and/or SEQ ID NO 2 (TFVL-NFIK), wherein the levels of SEQ ID NO 1 and/or SEQ ID NO 2 correspond to the levels of PROC, preferably APC, present in said one or more biological samples. Methods for classifying subjects and prognosticating the response to treatments are also included.

Disclosed herein are stable isotope labeling (SIL) peptide mapping methods for accurate and sensitive conjugation site quantitation. Also disclosed herein are compositions comprising antibody drug conjugates (ADCs) that target BCMA.