A method and apparatus for acquiring data from a mass spectrometer and its transmission to a computer system including a data acquisition engine, a network interface and a throughput optimization module which includes a ring buffer and a protocol stack. A compression engine may be provided between the acquisition engine and the ring buffer. The ring buffer is configured as a number of segments containing portions of memory matching the size of data words from the acquisition engine. When a segment is full of data corresponding to the words, or is partially full and has received data containing an end of scan marker, the number of words in the segment is written into a header word in the segment and the data in that segment are moved to the protocol stack. Subsequent data is received by the next segment in the buffer.