High-throughput experiments (HTE) result in large amounts of raw data that have to be evaluated for sample classification. Especially mass spectrometry, a widely used detection method in catalytic HTE applications, produces enormous amounts of data. In the past few years, in catalysts research, several test rigs based on mass spectrometric detection have been independently reported by different groups. In a typical HTE, the catalysts are tested sequentially; the recording of the scans, however, occurs continuously. For this reason, the scans of interest have to be extracted from the raw data, and scans belonging to the same sample have to be averaged in a tedious procedure before further processing. In this publication, we present our custom-designed software MS-Express (mass spectrometry data-extracting and -processing software), an efficient tool for HTE MS data evaluation. MS-Express not only sorts the data, it also establishes statistical significance with the help of reference and blank data and provides concise information about abundance and intensity distributions of expected peaks. A special feature is that the program also reports unexpected MS signals, which potentially lead to unexpected discoveries.