A culture medium processing system comprising: an extraction device including a filtration container and a collection container wherein the filtration container has an open upper surface, a filtration filter, disposed inside the filtration container, for deproteinizing a culture medium for cell culture, and an extraction port, disposed at a lower end of the filtration container, for extracting a filtrate downward that has passed through the filtration filter, the collection container being for collecting the filtrate extracted from the extraction port of the filtration container by being disposed immediately below the filtration container; an extraction device setting place at which the extraction device is set in an empty state; a sample container setting place at which sample containers containing culture medium to be deproteinized as samples are set; a reagent container setting place in which reagent containers containing at least a methanol solution and an acetonitrile solution respectively as reagents are set; a sample dispensing part configured to suck a sample from a sample container set at the sample container setting place and dispense the sucked sample into the filtration container disposed at a predetermined sample dispensing position; a reagent dispensing part configured to suck desired reagents from the reagent containers set at the reagent container setting place and to dispense the sucked reagents into the filtration container disposed at a predetermined reagent dispensing position; a filtration part including a filtration port at which the extraction device is set with the collection container disposed immediately below the filtration container, the filtration part being configured to collect a filtrate into the collection container by performing a filtration process for a solution in the filtration container of the extraction device set at the filtration port; a transport arm configured to hold the filtration container and/or the collection container of the extraction device set at the extraction device setting place and to transport the held filtration container and/or the held collection container to the sample dispensing position, the reagent dispensing position, and the filtration part; and a controller configured to control operation of the sample dispensing part, the reagent dispensing part and the transport arm to deproteinize a sample, wherein the controller is configured to perform conditioning for the filtration filter by dispensing a methanol solution into the empty filtration container, then to dispense a sample into the filtration container and add the acetonitrile solution as a deproteinization agent to the sample in the filtration container, and then to perform the filtration process in the filtration part. an extraction device including a filtration container and a collection container wherein the filtration container has an open upper surface, a filtration filter, disposed inside the filtration container, for deproteinizing a culture medium for cell culture, and an extraction port, disposed at a lower end of the filtration container, for extracting a filtrate downward that has passed through the filtration filter, the collection container being for collecting the filtrate extracted from the extraction port of the filtration container by being disposed immediately below the filtration container; an extraction device setting place at which the extraction device is set in an empty state; a sample container setting place at which sample containers containing culture medium to be deproteinized as samples are set; a reagent container setting place in which reagent containers containing at least a methanol solution and an acetonitrile solution respectively as reagents are set; a sample dispensing part configured to suck a sample from a sample container set at the sample container setting place and dispense the sucked sample into the filtration container disposed at a predetermined sample dispensing position; a reagent dispensing part configured to suck desired reagents from the reagent containers set at the reagent container setting place and to dispense the sucked reagents into the filtration container disposed at a predetermined reagent dispensing position; a filtration part including a filtration port at which the extraction device is set with the collection container disposed immediately below the filtration container, the filtration part being configured to collect a filtrate into the collection container by performing a filtration process for a solution in the filtration container of the extraction device set at the filtration port; a transport arm configured to hold the filtration container and/or the collection container of the extraction device set at the extraction device setting place and to transport the held filtration container and/or the held collection container to the sample dispensing position, the reagent dispensing position, and the filtration part; and a controller configured to control operation of the sample dispensing part, the reagent dispensing part and the transport arm to deproteinize a sample, wherein the controller is configured to perform conditioning for the filtration filter by dispensing a methanol solution into the empty filtration container, then to dispense a sample into the filtration container and add the acetonitrile solution as a deproteinization agent to the sample in the filtration container, and then to perform the filtration process in the filtration part.