Mass spectrometry data-independent analysis methods with improved efficiency

A mass spectrometer system comprising:

• an ion source configured to receive portions of a sample comprising compounds that are members of a compound class of interest;
• a mass filter configured to receive primary ion species generated by the ion source, the generated ions comprising a mass-to-charge (m/z) ratio range of interest;
• an ion fragmentation cell configured to receive a plurality of isolated subsets of the primary ion species from the mass filter;
• a mass analyzer configured to receive, from the fragmentation cell, product ions generated by fragmentation of the isolated subsets of the primary ion species;
• a detector configured to detect ions outlet from the mass analyzer;
• and
• one or more programmable processors electrically coupled to the mass filter, the ion fragmentation cell, the mass analyzer and the detector and comprising computer-readable instructions adapted to:
• determine or retrieve, a distribution, over the m/z ratio range of interest, of a number of primary ion species of members of said compound class having m/z ratios within each respective one of a plurality of sub-ranges of the m/z range of interest, wherein the determined or retrieved distribution comprises a histogram of a number of primary ion species versus m/z;
• define m/z positions of a set consisting of a number, nsb, of finite-width bins within the m/z ratio range of interest, the set of bins excluding m/z sub-ranges within the m/z ratio range of interest that encompass fewer than a threshold number, tsb, of the primary ion species, wherein the defining is based on the retrieved distribution;
• and
• cause the mass filter, ion fragmentation cell and mass analyzer to perform one or more cycles of tandem mass spectral analyses of compounds of the class, wherein each cycle of tandem mass spectral analyses comprises one or more tandem mass analyses pertaining to primary ion species within a respective of the defined bins, each tandem mass analysis of each cycle pertaining to a respective primary ion species,
• wherein the defining of the m/z positions of the non finite-width bins comprises either defining a center of a bin within an m/z range encompassed by an isolated histogram bar or defining a center of a bin at an average m/z value of a cluster or an isolated cluster of histogram bars.