Methods and systems of proteome analysis and imaging

Piehowski, Paul D.; Zhu, Ying; Kelly, Ryan T.; Burnum-Johnson, Kristin E.; Moore, Ronald J.

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Title: Methods and systems of proteome analysis and imaging

Abstract

Provided herein are methods and systems for proteome analysis that are at least partially automated and/or performed robotically. In some aspects, the methods and systems described herein can rapidly and efficiently provide protein identification of each of the proteins from a proteome, or a complement of proteins, obtained from extremely small amounts of biological samples. The identified proteins can be imaged quantitatively over a spatial region. Automation and robotics facilitates the throughput of the methods and systems, which enables protein imaging and/or rapid proteome analysis.

Inventors:: Piehowski, Paul D.; Zhu, Ying; Kelly, Ryan T.; Burnum-Johnson, Kristin E.; Moore, Ronald J.

Issue Date:: 2023-08-08

Research Org.:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 2222078

Patent Number(s):: 11719702

Application Number:: 15/993,949

Assignee:: Battelle Memorial Institute (Richland, WA)

DOE Contract Number:: AC05-76RL01830; P41GM103493; R21EB020976; R21HD084788; R33CA225248

Resource Type:: Patent

Resource Relation:: Patent File Date: 05/31/2018

Country of Publication:: United States

Language:: English

Citation Formats


                    Piehowski, Paul D., Zhu, Ying, Kelly, Ryan T., Burnum-Johnson, Kristin E., and Moore, Ronald J. Methods and systems of proteome analysis and imaging.  United States: N. p., 2023. 
        Web.

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                    Piehowski, Paul D., Zhu, Ying, Kelly, Ryan T., Burnum-Johnson, Kristin E., & Moore, Ronald J. Methods and systems of proteome analysis and imaging.  United States.

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                    Piehowski, Paul D., Zhu, Ying, Kelly, Ryan T., Burnum-Johnson, Kristin E., and Moore, Ronald J. Tue .  
        "Methods and systems of proteome analysis and imaging".  United States.  https://www.osti.gov/servlets/purl/2222078.

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@article{osti_2222078,

  title        = {Methods and systems of proteome analysis and imaging},

  author       = {Piehowski, Paul D. and Zhu, Ying and Kelly, Ryan T. and Burnum-Johnson, Kristin E. and Moore, Ronald J.},

  abstractNote = {Provided herein are methods and systems for proteome analysis that are at least partially automated and/or performed robotically. In some aspects, the methods and systems described herein can rapidly and efficiently provide protein identification of each of the proteins from a proteome, or a complement of proteins, obtained from extremely small amounts of biological samples. The identified proteins can be imaged quantitatively over a spatial region. Automation and robotics facilitates the throughput of the methods and systems, which enables protein imaging and/or rapid proteome analysis.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2023},

  month        = {8}

}

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Similar Records

Title: Methods and systems of proteome analysis and imaging

Abstract

Citation Formats

The pancreas in human type 1 diabetes journal, May 2010

High-Efficiency On-Line Solid-Phase Extraction Coupling to 15−150-μm-i.d. Column Liquid Chromatography for Proteomic Analysis journal, July 2003

Molecular imaging of proteins in tissues by mass spectrometry journal, September 2008

Obtaining Analytes for a Tissue Specimen patent-application, May 2013

Single-cell sequencing-based technologies will revolutionize whole-organism science journal, July 2013

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics journal, October 2016

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum journal, May 2011

Quantitative Studies on Cell Proteins in Suspension Cultures journal, January 1970

Ultrasensitive nanoelectrospray ionization-mass spectrometry using poly(dimethylsiloxane) microchips with monolithically integrated emitters journal, January 2010

NIH Image to ImageJ: 25 years of image analysis journal, June 2012

Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module journal, August 2016

Ultrasensitive and Fast Bottom-up Analysis of Femtogram Amounts of Complex Proteome Digests journal, October 2013

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells journal, February 2018

Getting intimate with trypsin, the leading protease in proteomics: TRYPSIN IN PROTEOMICS journal, June 2013

A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards journal, September 2014

Printing 2-Dimentional Droplet Array for Single-Cell Reverse Transcription Quantitative PCR Assay with a Microfluidic Robot journal, April 2015

Virtual wells for use in high throughput screening assays patent, May 2003

Sequential Operation Droplet Array: An Automated Microfluidic Platform for Picoliter-Scale Liquid Handling, Analysis, and Screening journal, June 2013

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin journal, April 2015

Quantification of islet size and architecture journal, March 2012

Quantitative proteomic analysis of single pancreatic islets journal, October 2009

The ion funnel: Theory, implementations, and applications journal, April 2009

High Throughput Miniaturized Assay System and Methods patent-application, August 2014

SNaPP: Simplified Nanoproteomics Platform for Reproducible Global Proteomic Analysis of Nanogram Protein Quantities journal, March 2016

Integrated Droplet Analysis System with Electrospray Ionization-Mass Spectrometry Using a Hydrophilic Tongue-Based Droplet Extraction Interface journal, October 2010

Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples journal, December 2016

Apparatus for Assay, Synthesis and Storage, and Methods of Manufacture, Use, and Manipulation Thereof patent-application, October 2010

Development and Evaluation of a Micro- and Nanoscale Proteomic Sample Preparation Method journal, December 2005

Enzyme-Friendly, Mass Spectrometry-Compatible Surfactant for In-Solution Enzymatic Digestion of Proteins journal, November 2003

Proteomic profiling of human islets collected from frozen pancreata using laser capture microdissection journal, January 2017

Nanoliter-Scale Protein Crystallization and Screening with a Microfluidic Droplet Robot journal, May 2014

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types journal, February 2014

An Integrated Platform for Isolation, Processing, and Mass Spectrometry-based Proteomic Profiling of Rare Cells in Whole Blood journal, March 2015

Methods for processing biological tissue patent-application, July 2006

Apparatus and method for analyzing a metabolite profile patent-application, January 2007

High-throughput microfluidic single-cell RT-qPCR journal, August 2011

The importance of using the optimal plasticware and glassware in studies involving peptides journal, July 2011

Development of Mass Spectrometry-Based Shotgun Method for Proteome Analysis of 500 to 5000 Cancer Cells journal, March 2010

Heterogeneity and Lobularity of Pancreatic Pathology in Type 1 Diabetes during the Prediabetic Phase journal, July 2015

Automatic Combination of Microfluidic Nanoliter-Scale Droplet Array with High-Speed Capillary Electrophoresis journal, May 2016

High Recovery FASP Applied to the Proteomic Analysis of Microdissected Formalin Fixed Paraffin Embedded Cancer Tissues Retrieves Known Colon Cancer Markers journal, July 2011

A Protein Epitope Signature Tag (PrEST) Library Allows SILAC-based Absolute Quantification and Multiplexed Determination of Protein Copy Numbers in Cell Lines journal, September 2011

High-Precision Dispensing of Nanoliter Biofluids on Glass Pedestal Arrays for Ultrasensitive Biomolecule Detection journal, April 2016

Tissue preparation for laser capture microdissection and RNA extraction from fresh frozen breast tissue journal, July 2007

Single-Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16-Cell Frog ( Xenopus ) Embryo journal, January 2016

Ultrasensitive Proteomics Using High-Efficiency On-Line Micro-SPE-NanoLC-NanoESI MS and MS/MS journal, January 2004

BoxPlotR: a web tool for generation of box plots journal, January 2014

The Perseus computational platform for comprehensive analysis of (prote)omics data journal, June 2016

New Mass-Spectrometry-Compatible Degradable Surfactant for Tissue Proteomics journal, January 2015

Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling journal, April 2016

Ultrasensitive and Quantitative Analyses from Combined Separations−Mass Spectrometry for the Characterization of Proteomes journal, April 2004

Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics journal, November 2014

Single Cell Proteomics Using Frog ( Xenopus laevis ) Blastomeres Isolated from Early Stage Embryos, Which Form a Geometric Progression in Protein Content journal, June 2016

Ultrasensitive Proteome Profiling for 100 Living Cells by Direct Cell Injection, Online Digestion and Nano-LC-MS/MS Analysis journal, June 2015

Quantitative analysis of cell composition and purity of human pancreatic islet preparations journal, August 2010

Islet cell hyperexpression of HLA class I antigens: a defining feature in type 1 diabetes journal, August 2016

The pancreas in human type 1 diabetes
journal, May 2010

High-Efficiency On-Line Solid-Phase Extraction Coupling to 15−150-μm-i.d. Column Liquid Chromatography for Proteomic Analysis
journal, July 2003

Molecular imaging of proteins in tissues by mass spectrometry
journal, September 2008

Obtaining Analytes for a Tissue Specimen
patent-application, May 2013

Single-cell sequencing-based technologies will revolutionize whole-organism science
journal, July 2013

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics
journal, October 2016

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum
journal, May 2011

Quantitative Studies on Cell Proteins in Suspension Cultures
journal, January 1970

Ultrasensitive nanoelectrospray ionization-mass spectrometry using poly(dimethylsiloxane) microchips with monolithically integrated emitters
journal, January 2010

NIH Image to ImageJ: 25 years of image analysis
journal, June 2012

Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module
journal, August 2016

Ultrasensitive and Fast Bottom-up Analysis of Femtogram Amounts of Complex Proteome Digests
journal, October 2013

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells
journal, February 2018

Getting intimate with trypsin, the leading protease in proteomics: TRYPSIN IN PROTEOMICS
journal, June 2013

A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards
journal, September 2014

Printing 2-Dimentional Droplet Array for Single-Cell Reverse Transcription Quantitative PCR Assay with a Microfluidic Robot
journal, April 2015

Virtual wells for use in high throughput screening assays
patent, May 2003

Sequential Operation Droplet Array: An Automated Microfluidic Platform for Picoliter-Scale Liquid Handling, Analysis, and Screening
journal, June 2013

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin
journal, April 2015

Quantification of islet size and architecture
journal, March 2012

Quantitative proteomic analysis of single pancreatic islets
journal, October 2009

The ion funnel: Theory, implementations, and applications
journal, April 2009

High Throughput Miniaturized Assay System and Methods
patent-application, August 2014

SNaPP: Simplified Nanoproteomics Platform for Reproducible Global Proteomic Analysis of Nanogram Protein Quantities
journal, March 2016

Integrated Droplet Analysis System with Electrospray Ionization-Mass Spectrometry Using a Hydrophilic Tongue-Based Droplet Extraction Interface
journal, October 2010

Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples
journal, December 2016

Apparatus for Assay, Synthesis and Storage, and Methods of Manufacture, Use, and Manipulation Thereof
patent-application, October 2010

Development and Evaluation of a Micro- and Nanoscale Proteomic Sample Preparation Method
journal, December 2005

Enzyme-Friendly, Mass Spectrometry-Compatible Surfactant for In-Solution Enzymatic Digestion of Proteins
journal, November 2003

Proteomic profiling of human islets collected from frozen pancreata using laser capture microdissection
journal, January 2017

Nanoliter-Scale Protein Crystallization and Screening with a Microfluidic Droplet Robot
journal, May 2014

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types
journal, February 2014

An Integrated Platform for Isolation, Processing, and Mass Spectrometry-based Proteomic Profiling of Rare Cells in Whole Blood
journal, March 2015

Methods for processing biological tissue
patent-application, July 2006

Apparatus and method for analyzing a metabolite profile
patent-application, January 2007

High-throughput microfluidic single-cell RT-qPCR
journal, August 2011

The importance of using the optimal plasticware and glassware in studies involving peptides
journal, July 2011

Development of Mass Spectrometry-Based Shotgun Method for Proteome Analysis of 500 to 5000 Cancer Cells
journal, March 2010

Heterogeneity and Lobularity of Pancreatic Pathology in Type 1 Diabetes during the Prediabetic Phase
journal, July 2015

Automatic Combination of Microfluidic Nanoliter-Scale Droplet Array with High-Speed Capillary Electrophoresis
journal, May 2016

High Recovery FASP Applied to the Proteomic Analysis of Microdissected Formalin Fixed Paraffin Embedded Cancer Tissues Retrieves Known Colon Cancer Markers
journal, July 2011

A Protein Epitope Signature Tag (PrEST) Library Allows SILAC-based Absolute Quantification and Multiplexed Determination of Protein Copy Numbers in Cell Lines
journal, September 2011

High-Precision Dispensing of Nanoliter Biofluids on Glass Pedestal Arrays for Ultrasensitive Biomolecule Detection
journal, April 2016

Tissue preparation for laser capture microdissection and RNA extraction from fresh frozen breast tissue
journal, July 2007

Single-Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16-Cell Frog ( Xenopus ) Embryo
journal, January 2016

Ultrasensitive Proteomics Using High-Efficiency On-Line Micro-SPE-NanoLC-NanoESI MS and MS/MS
journal, January 2004

BoxPlotR: a web tool for generation of box plots
journal, January 2014

The Perseus computational platform for comprehensive analysis of (prote)omics data
journal, June 2016

New Mass-Spectrometry-Compatible Degradable Surfactant for Tissue Proteomics
journal, January 2015

Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling
journal, April 2016

Ultrasensitive and Quantitative Analyses from Combined Separations−Mass Spectrometry for the Characterization of Proteomes
journal, April 2004

Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics
journal, November 2014

Single Cell Proteomics Using Frog ( Xenopus laevis ) Blastomeres Isolated from Early Stage Embryos, Which Form a Geometric Progression in Protein Content
journal, June 2016

Ultrasensitive Proteome Profiling for 100 Living Cells by Direct Cell Injection, Online Digestion and Nano-LC-MS/MS Analysis
journal, June 2015

Quantitative analysis of cell composition and purity of human pancreatic islet preparations
journal, August 2010

Islet cell hyperexpression of HLA class I antigens: a defining feature in type 1 diabetes
journal, August 2016