Data independent acquisition of product ion spectra and reference spectra library matching

Inventors

Bonner, Ronald F. • Tate, Stephen A. • AEBERSOLD, RUDOLF • Navarro ALvarez, Pedro Jose • Rinner, Oliver • Reiter, Lukas • Gillet, Ludovic

Assignees

Eidgenoessische Technische Hochschule Zurich ETHZ • Biognosys AG • DH Technologies Development Pte Ltd

Abstract

Systems and methods are disclosed for analyzing a sample using overlapping precursor isolation windows. A mass analyzer of a tandem mass spectrometer is instructed to select and fragment at least two overlapping precursor isolation windows across a precursor ion mass range of a sample using a processor. The tandem mass spectrometer includes a mass analyzer that allows overlapping precursor isolation windows across the mass range of the sample.

Core Innovation

The invention relates to data-independent LC-MS/MS acquisition and downstream processing that generate complete product ion spectra maps across a full precursor m/z range. It uses step-wise, optionally overlapping, precursor isolation windows across a plurality of time steps to produce sample product ion spectra for each mass selection window at each time step. The generated results are stored as an electronic record for later mining and searching.

A processor receives the sample product ion spectra for each precursor mass selection window across time steps and searches for the presence of one or more known compounds with known product ion spectra. The processor retrieves the sample product ion spectra corresponding to a precursor mass selection window expected to contain a precursor ion corresponding to the known product ion spectra. It generates product ion traces in time for the sample product ion spectra for one or more of the known product ion spectra and calculates a score that represents how well the known product ions and sample product ions match.

When the score exceeds a threshold value, the processor calculates a quantitative value for a known compound from the product ion traces. The known product ion spectra are received from in-silico predictions, and matching sample product ions can be used to identify a modified form of one or more compounds of the known compounds. Further characterization is performed by comparing matching sample ions to masses predicted from known product ions and extracting spectra to determine modification type and location.

Claims Coverage

The independent claims are directed to a system, a method, and a computer program product for quantitating detectable compounds using data-independent acquisition results organized by precursor mass selection windows and time steps. Across the independent claims, there are five main inventive features: receiving time-resolved sample product ion spectra by mass selection windows, matching to known product ion spectra provided via in-silico predictions, generating product ion traces in time, scoring match quality and applying a threshold, and calculating a quantitative value from the traces.

Across the independent claims, quantitation is performed by time-resolved matching of sample product ion spectra by precursor mass selection windows to known product ion spectra provided by in-silico predictions, using retrieval, generation of product ion traces, scoring, thresholding, and calculation of a quantitative value from the traces. Dependent claims additionally support modified form identification and characterization based on matching sample product ions, comparison to predicted masses, and extracting spectra for modification type and location.

Stated Advantages

Documented Applications