University of London

Hvivo Services Limited

Hospital Clinic I Provincial De Barcelona

Kinomica Limited

Institut De Investigacions Biomediques August Pi I Sunyer

Pedro Rodriguez Cutillas

Bart Vanhaesebroeck

Luisa Marie Beltran

Luis F Quintana Porras

Amanda Sole Gonzalez

Elisenda Bañón-Maneus

Josep M Campistol

Edmund Wilkes

Pedro Casado-izquierdo

Pedro Maria Casado Izquierdo

Elisenda BAÑÓN - Maneus

The present invention provides a method of quantifying the activity of a protein modifying enzyme in a sample, comprising calculating the value K for said protein-modifying enzyme on the basis of the number of modified peptides in a sample that are substrates of said protein modifying enzyme, the intensity of the modified peptides, each modified peptide in the sample that is a substrate of said protein modifying enzyme, the total number of modified peptides in the sample, the intensity of the modified peptides and all of the modified peptides in the sample. A method of quantifying the activity of a protein modifying enzyme in a sample, comprising calculating the value SC for said protein-modifying enzyme on the basis of a reduction in proliferation using an inhibitor at an inhibitor concentration at which proliferation is measured and the 'in vitro' IC50i of the inhibitor against a primary target is also provided. The invention further provides methods of identifying inhibitors with which to treat a patient, methods of treatment, a computer readable medium, a computer program product and devices for carrying out the methods.

Method for protein kinase activity ranking

The present invention provides a method of quantifying the activity of a protein modifying enzyme in a sample, comprising: (i) grouping modified peptides from a first sample and modified peptides from a second sample into a single group according to one of the following parameters: (a) modified peptides having a modification site that is modified by the same protein modifying enzyme; or (b) modified peptides having a modification site that is part of the same modification motif; (ii) calculating enrichment of the modified peptides from the first sample compared to the modified peptides from the second sample in the group; and (iii) calculating the statistical significance of said enrichment; wherein a statistically significant enrichment is indicative of a protein modifying enzyme being activated in the first sample compared to the second sample. In some embodiments, the method further comprises identifying modified peptides in a first sample and a second sample using mass spectrometry (MS) prior to step (i).

Methods for quantifying activity of protein modifying enzymes

The present invention provides a method for identifying differential activation of a bisubstrate protein modifying enzyme between samples, comprising:

Method for identifying activation of transferases

The present invention provides a method for quantifying modified peptides in a sample, the method comprising: (a) obtaining peptides from the sample; (b) adding reference modified peptides to the peptides obtained in step (a) to produce a mixture of peptides and reference modified peptides; (c) carrying out mass spectrometry (MS) on said mixture of peptides and reference modified peptides to obtain data relating to the peptides in the sample; and (d) comparing the data relating to the peptides in the sample with data in a database of modified peptides using a computer program; wherein the database of modified peptides is compiled by a method comprising: (i) obtaining peptides from a sample; (ii) enriching modified peptides from the peptides obtained in step (i); (iii) carrying out liquid chromatography-tandem mass spectrometry (LC-MS/MS) on the enriched modified peptides obtained in step (ii); (iv) comparing the modified peptides detected in step (iii) to a known reference database in order to identify the modified peptides; and (v) compiling data relating to the modified peptides identified in step (iv) into a database.

Method for quantifying modified peptides

The invention provides novel healthy kidney biomarkers useful in the monitoring of renal function and in the prognosis and diagnosis of renal dysfunctions, especially those related to graft rejection. The invention further relates to methods for aiding in the evaluation, and design of personalized therapies in transplantation nephrology.

Healthy kidney biomarkers

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London, United Kingdom

Pedro Rodriguez Cutillas