A computer-implemented method for determining a reference proteomic profile of a pathological condition in a subject, comprising steps of: label free quantification of the relative protein abundances of a tissue sample from at least one subject for which a diagnosis of a pathological condition of said tissue has been previously established, said sample containing non-pathological and pathological tissue, determining the proteomic profile of said sample by calculating the ratio of the relative abundances, for each protein, of said protein in the pathological tissue with respect to said protein in the non-pathological tissue, determining a reference proteomic profile for the previously diagnosed pathological condition, by means of a statistical test established between at least two groups of subjects.

Systems and methods of monitoring treatment of a patient use information gained from exosomes, wherein the treatment target that was identified from a tumor is followed in exosomes in a biological fluid outside the tumor.

Methods of predicting an in vivo serum concentration of an antibody with a post-translational modification of interest after administration of the antibody are provided, as are methods for predicting a subject's exposure to post-translational variants of the antibody. The methods include predicting a percentage of the antibody with the post-translational modification of interest using an in vivo rate constant determined for the post-translational modification, and multiplying the predicted percentage of the antibody with the post-translational modification of interest by the in vivo concentration of the antibody to determine the concentration of the antibody with the post-translational modification of interest.

A method of generating an inclusion list for targeted mass spectrometric analysis is disclosed. Experimentally-acquired data for a plurality of isobarically-labeled peptides derived by proteolytic digestion of a corresponding protein. The data includes, for each of the isobarically-labeled peptides, a mass-to-charge (m/z) ratio, a charge state, and a chromatographic retention time (RT). The method includes determining a hydrophobicity index (HI) of an unlabeled peptide corresponding to the isobarically-labeled peptide. If the determined HI is less than a threshold value, a substitute unlabeled peptide is selected in accordance with predetermined criteria and predicted properties for the substitute peptide are determined and stored on an inclusion list. If the determined HI for the unlabeled peptide is at least as great as the threshold value, predicted properties for the unlabeled peptide are determined and stored on an inclusion list. The substitute unlabeled peptide may be selected from an available peptide library.

The description relates to a method and kits for determining the total carbonylation level on a polypeptide.

The invention discloses a detergent-compatible protein assay method, composition and kit based on bio-conjugation reaction between protein and Meldrum's acid activated furfural. The method includes adding MAF in dimethyl sulfoxide (DMSO) to a protein sample solution. The amine functionalities present on the amino acid residues reacts with the MAF instantaneously at room temperature to yield deep purple colored solutions of the corresponding conjugated proteins. The reagent composition added to protein may be in the range of 90-450 mM. The intensities of purple colored solutions were proportional to the protein concentration captured by spectrophotometric measurements. The assay is sensitive in the range of 0.125-15 mg/mL, is compatible with commonly used detergents and reducing agents in protein solutions and may be employed for estimation of protein samples in the presence of detergents and reducing agents.

Disclosed are methods for identifying one or more amino acid molecules and nucleic acid molecules encoding such amino acid molecules of at least two proteomes that are conserved, unique or express at higher or lower levels in at least one of the proteomes. Expression libraries are used that produce the proteome, and in one embodiment, may produce the proteome from at least one cDNA expression library in one to five reactions. Anti-proteome antibodies are prepared that selectively bind to one of the proteomes and binding with at least one second proteome compared.

The invention is directed to a process for preparing a library of saposin lipoprotein particles, wherein the particles comprise membrane components from a cell or an organelle membrane and a lipid binding polypeptide that is a saposin-like protein belonging to the SAPLIP family of lipid interacting proteins or a derivative form thereof, wherein the process comprises the steps of a) providing a mixture of crude membrane vesicles obtained from a cell or an organelle membrane; b) contacting the mixture of step a) with the lipid binding polypeptide in a liquid environment; and c) allowing for self-assembly of the particles. The invention also provides a process for preparing a purified saposin lipoprotein particle comprising the steps of preparing a library according to the process described above and the additional step of f) purifying the saposin lipoprotein particle from the library. In addition, the invention provides a library of saposin lipoprotein particles and saposin lipoprotein particles obtainable according to the processes of the invention. These can be used in medicine, in particular in preventing, treating or lessening the severity of a disease or for use in a diagnostic method, a cosmetic treatment or for use as vaccination formulation or as a tool for drug development, drug screening, drug discovery, antibody development, development of therapeutic biologies, for membrane or membrane protein purification, for membrane protein expression, for membrane and/or membrane protein research, in particular lipidomics and proteomics, preferably for the isolation, identification and/or study of membranes and/or membrane proteins or creation of a lipidome or proteome database.

The present invention relates to improved and integrated methods for the characterisation of an interaction site on a target protein that modulates the phenotype of a mammalian cell, such as a phenotype other than death and/or reduced growth. Such methods of the present invention include those to identify a target protein modulates such a phenotype of a mammalian cell, and optionally to characterise an interaction site on said target protein. Such identification and characterisation methods are useful in the development of research tools and/or therapeutics, such protein/peptide or small molecule therapeutics. Accordingly, the present invention also relates to methods of: identification of a ligand, such as a small molecule ligand, that binds to such a target protein; and identification a compound being a candidate modulator of said phenotype of a mammalian cell. The invention further relates to peptides or proteins, or fragments, variants and/or derivatives thereof) comprising certain amino acid sequences, nucleic acids encoding such peptides or proteins and uses of such peptides or proteins or of such nucleic acids.

The present invention is directed to methods for systematic identification of cellular ligands, disease-associated ligands, age-related ligands and receptor-specific ligands. Disease-associated ligands are promising targets to develop novel ligand-based therapies. The methods are broadly applicable to any type of cells or diseases in in vitro and in vivo settings. This invention further used the methods to identify Scg3 as a disease-related angiogenic factor for the therapy of diabetic retinopathy, diabetic macular edema, proliferative diabetic retinopathy, vascular age-related macular degeneration, diabetic foot and cancers.