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
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Publication Number
US-11222775-B2
Publication Date
2022-01-11
Expiration Date
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 disclosed approach provides an LC-MS data-independent acquisition framework in which sample product ion spectra are received for each mass selection window of a plurality of precursor mass selection windows for each time step of a plurality of time steps. Detectable compounds are separated over time, and at each time step a plurality of product ion scans is performed for the plurality of precursor mass selection windows selected across a mass range of the sample using a tandem mass spectrometer. The precursor mass selection windows include at least two overlapping precursor mass selection windows.
After acquisition, the received sample product ion spectra are searched a posteriori for one or more known compounds with known product ion spectra. A known product ion spectrum is retrieved from a library, and the sample product ion spectra corresponding to the precursor mass selection window expected to contain a precursor ion corresponding to the known product ion spectrum are retrieved. Product ion traces are generated by extracting product ion traces for product ions determined from the known product ion spectrum from the retrieved sample product ion spectra.
A score is then calculated to represent how well the retrieved sample product ion spectra and the known product ion spectrum match. The score is based on comparing mass accuracy of product ions, comparing relative intensities, and comparing at least one chromatographic characteristic of the product ions of the product ion traces. The identity of the precursor ion is confirmed using the score, and product ion traces and matching are stored as an electronic record to enable later a posteriori identification/quantitation by matching to reference library spectra.
The described framework supports identification and characterization beyond known compounds, including modified forms. Using retrieved sample product ion spectra, the system determines modified forms of known compounds, and characterizes a modification by comparing retrieved sample product ion spectra to masses predicted from known product ions and a modification to determine a type and location of the modification. The comparison uses predicted masses together with extracted product ion traces and the score-based matching approach.
Claims Coverage
The document includes three independent claims: clm-00001 (system), clm-00008 (method), and clm-00015 (computer program product). Across these independent claims, the coverage centers on a posteriori identification by receiving time-stepped product ion spectra acquired using overlapping precursor mass selection windows and performing library-based searching with a score that uses mass accuracy, relative intensities, and chromatographic characteristics to confirm precursor ion identity.
A posteriori compound identification with overlapping precursor mass selection windows and time-stepped product ion scans
Receives 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, where the sample product ion spectra are produced by separating detectable compounds over time and at each time step analyzing by performing product ion scans across a mass range with a tandem mass spectrometer, and wherein the precursor mass selection windows include at least two overlapping precursor mass selection windows.
Library-based product ion matching using extracted product ion traces
Searches the received sample product ion spectra for the presence of one or more known compounds with known product ion spectra by retrieving a known product ion spectrum 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 spectrum, and generating product ion traces by extracting product ion traces for product ions determined from the known product ion spectrum from the retrieved sample product ion spectra.
Score-based confirmation of precursor ion identity
Calculates a score for the product ion traces and the retrieved sample product ion spectra by comparing mass accuracy of product ions, comparing relative intensities of the known product ion spectrum and the product ion traces, and comparing at least one chromatographic characteristic of the product ions of the product ion traces, and confirms the identity of the precursor ion using the score.
The independent claims collectively cover a posteriori identification of detectable compounds using time-stepped tandem mass spectrometry product ion spectra acquired with overlapping precursor mass selection windows, followed by library retrieval, extraction of product ion traces, and score-based confirmation using mass accuracy, relative intensities, and chromatographic characteristics.
Stated Advantages
Improved confidence/coverage compared with SRM by avoiding prior transition design and enabling complete mining later without re-acquisition.
No prior transition design.
Complete mining later without re-acquisition.
Documented Applications
Not explicitly described in patent.
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