A column-sealing tool is provided for use during decoupling of a capillary column from a gas chromatography-mass spectrometry (GC-MS) system. The column-sealing tool includes an engagement structure for removably securing the column-sealing tool within a high vacuum enclosure of the GC-MS system, at a location between a high vacuum end of a transfer line and a mass analyzer of the GC-MS system. Additionally, the column-sealing tool includes a sealing element that is actuatable between a non-sealing position and a sealing position. During use the sealing element forms a secondary vacuum seal with the first end of the transfer line when the column-sealing tool is inserted into the GC-MS system and when the sealing element is in the sealing position.