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 used to store an electronic record of all product ion spectra of all detectable compounds of a sample. A plurality of product ion scans are performed on a tandem mass spectrometer one or more times in a single sample analysis across a mass range using a plurality of mass selection windows. All sample product ion spectra of all detectable compounds for each mass selection window are produced. All sample product ion spectra for each mass selection window are received from the tandem mass spectrometer using a processor. All sample product ion spectra for each mass selection window are stored as an electronic record of all detectable compounds of the sample using the processor. The electronic record is used to characterize compounds known at the time the electronic record is stored or to characterize compounds that became known after the electronic record was stored.

Core Innovation

A problem being addressed is the quantitation of detectable compounds of a sample using tandem mass spectrometry while avoiding the need to preselect specific target compounds or transitions. The disclosed approach performs data acquisition and analysis in a way that supports later searching against known compounds with known product ion spectra, including characterization of modified forms by locating matching ions across precursor mass selection windows.

The invention acquires sample product ion spectra by separating detectable compounds over time and analyzing the detectable compounds at each time step by performing product ion scans for precursor mass selection windows selected across a mass range using a tandem mass spectrometer. A processor receives the sample product ion spectra for each mass selection window of a plurality of precursor mass selection windows for each time step of a plurality of time steps, thereby generating an electronic record of product ion spectra across windows and time.

The processor searches the received product ion spectra for the presence of one or more known compounds with known product ion spectra by retrieving known product ion spectra from a library, retrieving the sample product ion spectra corresponding to the precursor mass selection window expected to contain a precursor ion corresponding to the known product ion spectra, and generating product ion traces in time. The processor calculates a score representing how well known product ions and sample product ions match, and calculates a quantitative value for a known compound when the score exceeds a threshold value.

In refinements, the system identifies a modified form of one or more compounds of the known compounds using one or more matching sample product ions, and characterizes a type and location of the modification by comparing matching sample ions to masses predicted from known product ions. Further refinement includes extracting a spectrum from the sample product ion spectra in order to characterize the type and location of the modification in the identified modified form.

Claims Coverage

The independent claims are directed to a system, a method, and a computer program product that quantitate detectable compounds by acquiring time-resolved tandem mass spectrometer product ion spectra across multiple precursor mass selection windows, then searching against known product ion spectra from a library using scoring and thresholding. Across the independent claims, the inventive features include (i) time-resolved product ion acquisition across precursor mass selection windows, (ii) library-based retrieval of known product ion spectra, (iii) generation of time-based product ion traces, and (iv) scoring and threshold-based quantitation, with further support in refinements for modified forms and modification type/location characterization.

Across the independent claim set, quantitation is achieved by receiving time-resolved tandem mass spectrometer product ion spectra across precursor mass selection windows, searching the spectra against library-provided known product ion spectra with window-correspondence retrieval, generating time-based product ion traces, and calculating a score with threshold-based quantitation. Refinements further identify modified forms using matching sample product ions and characterize modification type and location by comparing matching sample ions to masses predicted from known product ions.

Stated Advantages

Documented Applications