This dataset contains raw mass spectrometry (MS) data, including MS1 and MS/MS spectra, supporting the non-invasive prenatal diagnosis of genetic diseases in early pregnancy. The data were acquired using a SCIEX TripleTOF® 4600 mass spectrometer coupled with the DuoSpray™ Turbo V ion source operated in negative ion mode. The raw files are in WIFF format and can be viewed and analyzed using PeakView software. A detailed description of the files used for each figure is provided in the accompanying Readme.xlsx file.