A method for characterising by tandem mass spectrometry a biological sample selected from the group consisting of a biological fluid; a plant fluid; a sample from a culture medium or in a biological culture reactor; a liquid obtained from an animal or plant tissue; an animal or plant tissue; one or more cells; a sample from a food matrix; a sample from a chemical reactor; a sample from a sewage plant; a sample from a composting plant; city water, river water, pond water, lake water, sea water, swimming pool water, air-cooled tower water or underground water; a sample from a liquid industrial effluent; waste water originating in particular from intensive farming or industries in the chemical, pharmaceutical or cosmetics field; a sample from air filtration or coating; a sample from an object; a pharmaceutical product; a cosmetic product; a perfume; a soil sample or one of the mixtures thereof, consisting in: a) chemically precipitating all the biological material containing proteins, present in said sample by adding a precipitating and denaturing agent to said sample, said biological material containing proteins being selected from the group consisting of a cell; a cell part; a virus; a prion and a protein present in the sample, said precipitating and denaturing agent being selected from the group consisting of an organic solvent, an acid or base inorganic compound, an acid organic compound, a chaotropic salt, one of the combinations thereof or one of the mixtures thereof; b) subjecting said sample to centrifugation whereby a pellet comprising the biological material containing proteins is obtained; c) subjecting the pellet obtained after step (b) and resolubilised under denaturing conditions to gel electrophoresis under denaturing conditions; d) after optional preparatory steps, subjecting all the proteins of the gel obtained after step (c) to proteolysis, and e) subjecting the peptides obtained after step (d) to tandem mass spectrometry, said preparatory steps consisting in: (d 1) staining the gel obtained after step (c); (d 2) cutting a part of this gel containing all the proteins initially contained in the sample; (d 3) destaining the cut gel in step (d 2); (d 4) subjecting the proteins contained in the gel cut and destained during step (d 3) to reduction and alkylation. a) chemically precipitating all the biological material containing proteins, present in said sample by adding a precipitating and denaturing agent to said sample, said biological material containing proteins being selected from the group consisting of a cell; a cell part; a virus; a prion and a protein present in the sample, said precipitating and denaturing agent being selected from the group consisting of an organic solvent, an acid or base inorganic compound, an acid organic compound, a chaotropic salt, one of the combinations thereof or one of the mixtures thereof; said biological material containing proteins being selected from the group consisting of a cell; a cell part; a virus; a prion and a protein present in the sample, said precipitating and denaturing agent being selected from the group consisting of an organic solvent, an acid or base inorganic compound, an acid organic compound, a chaotropic salt, one of the combinations thereof or one of the mixtures thereof; b) subjecting said sample to centrifugation whereby a pellet comprising the biological material containing proteins is obtained; c) subjecting the pellet obtained after step (b) and resolubilised under denaturing conditions to gel electrophoresis under denaturing conditions; d) after optional preparatory steps, subjecting all the proteins of the gel obtained after step (c) to proteolysis, and e) subjecting the peptides obtained after step (d) to tandem mass spectrometry, (d 1) staining the gel obtained after step (c); (d 2) cutting a part of this gel containing all the proteins initially contained in the sample; (d 3) destaining the cut gel in step (d 2); (d 4) subjecting the proteins contained in the gel cut and destained during step (d 3) to reduction and alkylation.