Palo Alto Research Center Inc.

Protein Metrics Inc.

Xerox Corporation

The Scripps Research Institute

Marshall Bern

David Goldberg

Yong Joo Kil

Peter Kiesel

Joerg Martini

Noble Marshall Johnson

Doron Kletter

Alejandro Enrique Brito

Michael I Recht

Bowen Cheng

Eric D Carlson

Ersin Uzun

Julien F Freudiger

Christopher Becker

Emiliano De Cristofaro

Andrew Nichols

Michael Taejong Kim

Malte Huck

Daniel H Greene

Michael Bassler

Francois Ragnet

Markus Beck

Boyan Zhang

Jan Matthias Ruhl

Steven Jay Harrington

Eric Saund

Michael J Natan

Prateek Sarkar

Annamaria B Amenta

John R Yates, Iii

Ming Ye

Nicholas Bern

Richard Seipert

This invention relates to graphical user-interactive displays for use in MS-based analysis of protein impurities, as well as methods and software for generating and using such. One aspect provides a user-interactive display comprising interactive and dynamic selection of one or more masses and concurrent display of peaks (points) corresponding to that predicted mass value across other displays (MS1, deconvolved mass spectrum, mass extracted ion chromatogram, etc.).

Interactive analysis of mass spectrometry data including peak selection and dynamic labeling

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.

Pseudo-electropherogram construction from peptide level mass spectrometry data

Methods and apparatuses for the identification and/or characterization of properties of a sample using mass spectrometry. Methods may include analyzing spacings between mass-to-charge ratio peaks from measured mass spectrum data, identifying and associating the spacings with mass delta values corresponding to masses of possible constituents of a molecule within the sample, calculating estimated charges of molecular species within the sample based on the spacings and mass delta values, and deconvoluting the measured mass spectrum data based on the estimated charges to provide a neutral mass spectrum. The methods and apparatuses (including software) described herein may result in more accurate characterization of peaks within the neutral mass spectrum, less false peaks within the neutral mass spectrum, and less noise in the neutral mass spectrum.

Methods and apparatuses for deconvolution of mass spectrometry data

Digital pathology is a promising alternative to manual slide analysis, but improvements in imaging and analysis methods are needed to provide an analysis data set of images that can easily be handled, stored, and importantly, delivered from one data location to another. Methods and software are described herein to improve image collection and analysis.

Apparatuses and methods for digital pathology

Methods and apparatuses for the identification and/or characterization of properties of a sample using mass spectrometry. The method involves using a measured spectrum of data from a sample taken with a mass spectrometer, deconvoluting the measured spectrum of data by applying parsimony weighting to minimize the number of charge states based on one or more of: the number of intense peaks in the mass spectrum; the number of harmonic relationships (e.g., masses in small integer ratios); and the number of off-by-one relationships (e.g., m/z bins with high probability for two adjacent charges). Thus, the underlying m/z spectrum may be inferred from the family of plausible deconvoluted spectra determined by applying parsimony and the inferred m/z spectrum may be used to identify and/or characterize the sample.

Methods and apparatuses for determining the intact mass of large molecules from mass spectrographic data

This invention relates to graphical user-interactive displays for use in MS-based analysis of protein impurities, as well as methods and software for generating and using such. One aspect provides a user-interactive display comprising interactive and dynamic selection of one or more masses and concurrent display of peaks (points) corresponding to that predicted mass value across other displays (MS1, deconvolved mass spectrum, etc.).

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

A system is configured to determine a color distribution of an object moving along a flow direction relative to a spatial filter. The light emanating from the object is time modulated according to the mask features of the spatial filter. First and second detectors are arranged to sense the modulated light. The first detector senses light having a first wavelength spectrum and generates a first electrical output signal in response to the sensed light. The second detector light senses light having a second wavelength spectrum and generates a second electrical output signal in response to the sensed light. Signals from the first and second detectors include information about color distribution of the object.

Determination of color characteristics of objects using spatially modulated light

Methods and apparatuses for the analysis of mass spectroscopic (MS) data as well as ultraviolet (UV) absorption data. In particular, described herein are tools and methods to assist in generating annotated peptide maps from a raw MS data.

Apparatuses and methods for annotated peptide mapping

Growing community of inventors

San Carlos, CA, United States of America

Marshall Bern