A method for mass spectral analysis of a sample containing a plurality of biomolecule species, comprising repeatedly performing data-dependent acquisition cycles across a chromatographic elution peak, each data-dependent acquisition cycle including steps of: A. acquiring a survey MS1 scan extending across a mass range of interest of an ensemble of ions generated from a sample; B. selecting a plurality of precursor ions based on the acquired MS1 scan, the selected plurality of precursor ions excluding precursor ions selected in a previous data-dependent acquisition cycle; and C. for each of the selected precursor ions, performing the following steps: i. determining a set of instrumental parameters for obtaining MS/MS spectra of a current selected precursor ion, the instrumental parameters determined at least partially on the basis of the relative abundance of a peak in the MS 1 scan associated with the current selected precursor ion, the set of instrumental parameters including an isolation window width, wherein the isolation window width is relatively narrower for relatively higher relative abundance precursors; and ii. obtaining a MS/MS spectrum corresponding to the current selected precursor ion using the determined instrumental parameters for the current selected precursor ion, wherein the MS/MS spectrum is acquired using an isolation window having the determined isolation window width, wherein the isolation windows used in the data-dependent acquisition cycles that are performed across the chromatographic elution peak cover, in the aggregate, across at least 70% of the mass range of interest. A. acquiring a survey MS1 scan extending across a mass range of interest of an ensemble of ions generated from a sample; B. selecting a plurality of precursor ions based on the acquired MS1 scan, the selected plurality of precursor ions excluding precursor ions selected in a previous data-dependent acquisition cycle; and C. for each of the selected precursor ions, performing the following steps: i. determining a set of instrumental parameters for obtaining MS/MS spectra of a current selected precursor ion, the instrumental parameters determined at least partially on the basis of the relative abundance of a peak in the MS 1 scan associated with the current selected precursor ion, the set of instrumental parameters including an isolation window width, wherein the isolation window width is relatively narrower for relatively higher relative abundance precursors; and ii. obtaining a MS/MS spectrum corresponding to the current selected precursor ion using the determined instrumental parameters for the current selected precursor ion, wherein the MS/MS spectrum is acquired using an isolation window having the determined isolation window width, wherein the isolation windows used in the data-dependent acquisition cycles that are performed across the chromatographic elution peak cover, in the aggregate, across at least 70% of the mass range of interest. i. determining a set of instrumental parameters for obtaining MS/MS spectra of a current selected precursor ion, the instrumental parameters determined at least partially on the basis of the relative abundance of a peak in the MS 1 scan associated with the current selected precursor ion, the set of instrumental parameters including an isolation window width, wherein the isolation window width is relatively narrower for relatively higher relative abundance precursors; and ii. obtaining a MS/MS spectrum corresponding to the current selected precursor ion using the determined instrumental parameters for the current selected precursor ion, wherein the MS/MS spectrum is acquired using an isolation window having the determined isolation window width,