Calibration of analytical instrument

A method of determining a calibration for an analytical instrument, the analytical instrument comprising:

• an ion separator configured to perform ion separation scans, wherein in each ion separation scan the ion separator receives ions and separates them according to a first physico-chemical property;
• a mass filter arranged downstream of the ion separator, wherein the mass filter is operable in a filtering mode of operation, wherein in the filtering mode of operation the mass filter receives ions and transmits only those ions having mass to charge ratios within a m/z transmission window;
• and
• a mass analyser arranged downstream of the mass filter, wherein the mass analyser is configured to perform mass analysis scans, wherein in each mass analysis scan the mass analyser receives ions and mass analyses them;
• the method comprising:
• (i) ionising a calibrant to produce calibrant ions;
• (ii) the ion separator performing a sequence of ion separation scans, wherein in each ion separation scan, the ion separator receives calibrant ions and separates them according to the first physico-chemical property;
• (iii) operating the mass filter in its filtering mode of operation so as to filter separated calibrant ions, and during each ion separation scan of the sequence:
• scanning a centre mass to charge ratio of the m/z transmission window across a respective mass to charge ratio range Δm/zi, wherein the centre mass to charge ratio of the m/z transmission window is scanned across a respective different mass to charge ratio range Δm/zi for each ion separation scan of the sequence;
• (iv) the mass analyser performing a plurality of mass analysis scans by performing one or more mass analysis scan(s) during each ion separation scan of the sequence, wherein in each mass analysis scan the mass analyser receives filtered calibrant ions and mass analyses them;
• and
• (v) using data obtained from the plurality of mass analysis scans to determine a calibration for the analytical instrument.

A method of operating an analytical instrument, the analytical instrument comprising:

• an ion separator configured to perform ion separation scans, wherein in each ion separation scan the ion separator receives ions and separates them according to a first physico-chemical property;
• and
• a mass analyser arranged downstream of the ion separator, wherein the mass analyser is configured to perform mass analysis scans, wherein in each mass analysis scan the mass analyser receives ions and mass analyses them;
• the method comprising:
• (i) ionising a sample to produce sample ions;
• (ii) mass analysing sample ions in an MS1 mode of operation, so as to produce an MS1 mass spectrum of the sample ions;
• (iii) identifying a plurality of precursors of interest in the MS1 mass spectrum;
• (iv) determining an acquisition order for acquiring MS2 spectra of the plurality of precursors of interest, wherein the acquisition order is determined using an expected ion arrival time for each precursor of interest, and wherein the expected ion arrival time for each precursor of interest is determined using a calibration for the analytical instrument;
• and
• (iv) acquiring MS2 spectra for the plurality of precursors of interest by:
• sequentially selecting, in the acquisition order, each precursor of the plurality of precursors of interest;
• and
• for each selected precursor:
• fragmenting precursor ions so as to produce fragment ions, and mass analysing the fragment ions so as to produce an MS2 spectrum for that precursor.