Method for Real Time Encoding of Scanning SWATH Data and Probabilistic Framework for Precursor Inference

A method for encoding and storing tandem mass spectrometry data measured from overlapping precursor ion transmission windows, comprising:

• moving a precursor ion transmission window with precursor ion mass-to-charge ratio (m/z) width Win overlapping steps across a precursor ion mass range with a step size S m/z using a mass filter of a tandem mass spectrometer, producing a series of overlapping transmission windows across the mass range, wherein the mass filter transmits precursor ions within the transmission window at each overlapping step;
• fragmenting or transmitting the precursor ions transmitted at each overlapping step by the mass filter using a fragmentation device of the spectrometer, producing one or more resulting product ions for each overlapping window of the series;
• detecting intensities or counts for each of the one or more resulting product ions for each overlapping window of the series that form mass spectrum data for each overlapping window of the series using a mass analyzer of the spectrometer;
• and
• encoding each unique product ion detected by the mass analyzer in real-time during data acquisition using a processer by
• identifying a first appearance overlapping window of the series with a first appearance of the each unique ion,
• selecting a group of G overlapping windows of the series immediately preceding the first appearance overlapping window so that the group spans at least the width W of the transmission window, calculating a sum of counts or intensities of the each unique ion detected from each window of the G overlapping windows of the group, and associating the sum with a position of an overlapping window of the group, and
• shifting the group of G overlapping windows of the series selected one overlapping window forward, calculating a sum of counts or intensities of the each unique ion detected from each window of the G overlapping windows of the group, associating the sum with a position of an overlapping window of the group, storing the sum and the position in the memory device, and repeating these steps until at least one overlapping window of the group no longer overlaps with the first appearance overlapping window.

A computer program product, comprising a non-transitory and tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor to perform a method for encoding and storing tandem mass spectrometry data measured from overlapping precursor ion transmission windows, the method comprising:

• providing a system, wherein the system comprises one or more distinct software modules, and wherein the distinct software modules comprise a control module and an encode and store module;
• instructing a mass filter of a tandem mass spectrometer to move a precursor ion transmission window with precursor ion mass-to-charge ratio (m/z) width Win overlapping steps across a precursor ion mass range with a step size S m/z using the control module, producing a series of overlapping transmission windows across the mass range, wherein the mass filter transmits precursor ions within the transmission window at each overlapping step;
• instructing a fragmentation device of the spectrometer to fragment or transmit the precursor ions transmitted at each overlapping step by the mass filter using the control module, producing one or more resulting product ions for each overlapping window of the series;
• instructing a mass analyzer of the spectrometer that detects intensities or counts for each of the one or more resulting product ions for each overlapping window of the series that form mass spectrum data for each overlapping window of the series using the control module;
• and
• encoding each unique product ion detected by the mass analyzer in real-time during data acquisition using the encode and store module by
• identifying a first appearance overlapping window of the series with a first appearance of the each unique ion,
• selecting a group of G overlapping windows of the series immediately preceding the first appearance overlapping window so that the group spans at least the width W of the transmission window, calculating a sum of counts or intensities of the each unique ion detected from each window of the G overlapping windows of the group, and associating the sum with a position of an overlapping window of the group, and
• shifting the group of G overlapping windows of the series selected one overlapping window forward, calculating a sum of counts or intensities of the each unique ion detected from each window of the G overlapping windows of the group, associating the sum with a position of an overlapping window of the group, storing the sum and the position in the memory device, and repeating these steps until at least one overlapping window of the group no longer overlaps with the first appearance overlapping window.