Intact mass reconstruction from peptide level data and facilitated comparison with experimental intact observation

Inventors

Nichols, Andrew • Bern, Marshall • Kil, Yong Joo • Carlson, Eric

Assignees

Protein Metrics LLC

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 provides a method for reconstructing an intact mass spectrum of a protein or protein complex from peptide level data to form a pseudo intact mass spectrum of the protein or protein complex. Mass spectrum data associated with peptides of an enzyme-digested sample are received, where the mass spectrum data includes mass-to-charge ratio data associated with a set of modified peptide forms. The pseudo intact mass spectrum is derived from the peptide level data by using a comparison of the modified peptide forms to a reference list of peptide sequences.

A user selection is received for one or more modified peptide forms to include or to remove from the pseudo intact mass spectrum, where the selection is made from the set of modified peptide forms. The pseudo intact mass spectrum is generated from all or a subset of the received mass spectrum data based on the selected modified peptide forms to include or remove. Differences between the intact mass spectrum of the protein and the pseudo intact mass spectrum of the protein or protein complex are highlighted during an overlay display.

In an associated system, one or more processors execute computer-program instructions to perform the same computer-implemented method. The system receives the peptide-associated mass spectrum data from an enzyme-digested sample of a protein or protein complex, receives the user selection of modified peptide forms to include or to remove, generates the pseudo intact mass spectrum derived in part by comparison to a reference list of peptide sequences, and displays an overlay of the intact mass spectrum and the pseudo intact mass spectrum with differences highlighted.

Claims Coverage

Two independent claims are identified. Across the independent claims, the inventive coverage centers on reconstructing a pseudo intact mass spectrum from peptide level modified peptide form data with a user-controlled inclusion/removal selection and deriving the pseudo intact spectrum in part via comparison to a reference list of peptide sequences, followed by an overlay display that highlights differences.

The independent claims collectively cover generating a pseudo intact mass spectrum from peptide level mass-to-charge data associated with modified peptide forms, using a user selection to include or remove modified peptide forms, deriving the pseudo intact mass spectrum in part by comparison to a reference list of peptide sequences, and displaying an overlay of the intact and pseudo intact mass spectra with highlighted differences.

Stated Advantages

Documented Applications

No documented applications found