High resolution ms1 based quantification

A mass spectrometer for performing data independent acquisition mass spectrometry on a sample, the mass spectrometer comprising:

• an ionisation source for producing a plurality of precursor ions;
• a mass analyser;
• a fragmentation apparatus;
• a mass selector;
• a chromatography system configured to separate molecules of the sample upstream from the mass selector such that they are introduced to the mass spectrometer as a series of chromatographic peaks;
• and
• a controller configured:
• (i) to cause the mass selector to select a precursor mass range of interest for the sample to be analysed;
• (ii) to cause the mass analyser to operate at a first, relatively higher resolution of at least 50,000 at m/z=200 amu and to perform a plurality of MS1 scans across a chromatographic peak of the precursor ions of the sample across the precursor mass range of interest, for quantitation and/or identification of the sample in the MS1 domain across that precursor mass range of interest;
• (iii) to divide the precursor mass range of interest into a plurality of precursor mass range segments;
• (iv) to control the mass selector so as to segment the precursor mass range of interest into the said plurality of mass range segments;
• (v) for each precursor mass range segment generated by the mass selector, to control the fragmentation apparatus so as to cause fragmentation of the precursor ions within that mass range segment;
• and
• (vi) for each precursor mass range segment, to cause the mass analyser to operate at a second, relatively lower resolution and to perform an MS2 scan of that fragmented sample segment, such that each of the fragmented sample segments across the precursor mass range of interest is fragmented and scanned to form a set of MS2 scans,
• wherein steps (iv), (v) and (vi) are performed in sequence repeatedly across the chromatographic peak, and
• wherein the controller is configured to interleave the plurality of MS1 scans throughout the set of MS2 scans, such that a ratio of the number of MS1 scans performed to the number of sets of MS2 scans performed during a width of the chromatographic peak is at least 3:1, the width being equal to four standard deviations of the chromatographic peak.