Pseudo-electropherogram construction from peptide level mass spectrometry data
Inventors
Nichols, Andrew • Bern, Marshall • Kil, Yong Joo • Carlson, Eric
Assignees
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Publication Number
US-12352757-B2
Publication Date
2025-07-08
Expiration Date
Abstract
Methods and apparatuses for the identification and/or characterization of properties of a macromolecule based on mass spectrometry data. Specifically, described herein are methods and apparatuses for converting peptide-level data into a pseudo-intact mass spectra. Also described herein are methods and apparatuses for converting peptide-level data into a pseudo-electropherogram. The methods may be well suited for analyzing proteins and protein complexes, including estimating properties of post-translational modifications of the proteins and protein complexes. Methods may include generating a theoretical graph or spectrum based on peptide-level mass spectrometry data. In some embodiments, the theoretical graph may be a theoretical intact mass spectrum or a theoretical charge distribution spectrum.
Core Innovation
The invention converts peptide-level mass spectrometry data, including modified peptide forms, into reconstructed and theoretical intact protein representations. It generates a reconstructed/theoretical intact mass spectrum and a theoretical/reconstructed electropherogram for a large molecule, including proteins such as antibodies, so that the derived outputs can be compared to experimentally derived intact mass spectrometry and capillary isoelectric focusing (ciEF) electropherogram data.
A central aspect is determining masses of modified forms of molecular species based on associated mass-to-charge ratio data. Modified forms are matched to reference molecular sequences of the large molecule to map modified forms to locations in the large molecule, and calculated charge distributions of the modified forms are combined to generate a distribution of charge variant forms, with the charge distributions calculated based on isoelectric point and charge normalization.
The system supports iterative, interactive selection of modified peptide forms and modification groups to update the pseudo spectra and overlays. It uses data structures that track peptide and modification information, including position and probability and/or abundance, and it highlights differences related to PTMs or artifacts through overlay and peak alignment features. The implementation includes system/apparatus options, including cloud-based/web-based functionality, for generating and comparing theoretical spectra and charge distributions.
Claims Coverage
The document includes two independent claims, a method and a system. The claims cover receiving peptide-level mass spectrometry data with modified forms, mapping the modified forms to locations in a large molecule using reference molecular sequences, combining charge distributions calculated based on isoelectric point, and displaying a pseudo-electropherogram representing different charge variant forms.
Pseudo-electropherogram generation from peptide-level mass spectrometry with modified forms
Receiving mass spectrometry data including mass-to-charge ratio data associated with molecular species components of a large molecule, wherein the mass-to-charge ratio data includes mass-to-charge ratio data associated with modified forms of the molecular species; generating the pseudo-electropherogram based on all or a subset of the modified forms; determining masses of the modified forms based on the mass-to-charge ratio data; displaying the pseudo-electropherogram representing different charge variant forms of the large molecule.
Mapping modified forms to locations using reference molecular sequences and generating charge variant distributions
Matching reference molecular sequences of the large molecule against the determined masses of the modified forms of the molecular species to map the modified forms to locations in the large molecule; combining calculated charge distributions of the modified forms to generate a distribution of charge variant forms of the large molecule, wherein the calculated charge distributions are calculated based on isoelectric point; displaying the pseudo-electropherogram representing different charge variant forms of the large molecule.
System for pseudo-electropherogram generation using processors and computer-program instructions
A system comprising one or more processors and a memory configured to store computer-program instructions that perform a computer-implemented method comprising receiving mass spectrometry data with mass-to-charge ratio data associated with modified forms of molecular species components of a large molecule; generating the pseudo-electropherogram by determining masses of the modified forms, matching reference molecular sequences to map the modified forms to locations, combining charge distributions calculated based on isoelectric point, and displaying the pseudo-electropherogram representing different charge variant forms of the large molecule.
Across the independent method and system claims, the inventive coverage centers on generating a pseudo-electropherogram from mass spectrometry data containing modified forms by determining modified-form masses, mapping modified forms to large-molecule locations using reference molecular sequences, and combining isoelectric-point-based charge distributions to display different charge variant forms.
Stated Advantages
Not explicitly described in patent.
Documented Applications
Not explicitly described in patent.
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