Process for ultra-sensitive quantification of target analytes in complex biological systems

Shi, Tujin; Qian, Weijun; Fillmore, Thomas L.; Sun, Xuefei; Smith, Richard D.

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Title: Process for ultra-sensitive quantification of target analytes in complex biological systems

Abstract

Antibody-free processes are disclosed that provide accurate quantification of a wide variety of low-abundance target analytes in complex samples. The processes can employ high-pressure, high-resolution chromatographic separations for analyte enrichment. Intelligent selection of target fractions may be performed via on-line Selected Reaction Monitoring (SRM) or off-line rapid screening of internal standards. Quantification may be performed on individual or multiplexed fractions. Applications include analyses of, e.g., very low abundance proteins or candidate biomarkers in plasma, cell, or tissue samples without the need for affinity-specific reagents.

Inventors:: Shi, Tujin; Qian, Weijun; Fillmore, Thomas L.; Sun, Xuefei; Smith, Richard D.

Issue Date:: 2023-04-04

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

Sponsoring Org.:: USDOE; National Institutes of Health (NIH)

OSTI Identifier:: 1998260

Patent Number(s):: 11619635

Application Number:: 14/949,385

Assignee:: Battelle Memorial Institute (Richland, WA)

DOE Contract Number:: AC06-76RL01830; 5P41-RR018522; 8P41-GM103493; CA111244; DP2OD006668; U24-CA-160019; Y01-CN-05013-29

Resource Type:: Patent

Resource Relation:: Patent File Date: 11/23/2015

Country of Publication:: United States

Language:: English

Citation Formats


                    Shi, Tujin, Qian, Weijun, Fillmore, Thomas L., Sun, Xuefei, and Smith, Richard D. Process for ultra-sensitive quantification of target analytes in complex biological systems.  United States: N. p., 2023. 
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                    Shi, Tujin, Qian, Weijun, Fillmore, Thomas L., Sun, Xuefei, & Smith, Richard D. Process for ultra-sensitive quantification of target analytes in complex biological systems.  United States.

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                    Shi, Tujin, Qian, Weijun, Fillmore, Thomas L., Sun, Xuefei, and Smith, Richard D. Tue .  
        "Process for ultra-sensitive quantification of target analytes in complex biological systems".  United States.  https://www.osti.gov/servlets/purl/1998260.

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@article{osti_1998260,

  title        = {Process for ultra-sensitive quantification of target analytes in complex biological systems},

  author       = {Shi, Tujin and Qian, Weijun and Fillmore, Thomas L. and Sun, Xuefei and Smith, Richard D.},

  abstractNote = {Antibody-free processes are disclosed that provide accurate quantification of a wide variety of low-abundance target analytes in complex samples. The processes can employ high-pressure, high-resolution chromatographic separations for analyte enrichment. Intelligent selection of target fractions may be performed via on-line Selected Reaction Monitoring (SRM) or off-line rapid screening of internal standards. Quantification may be performed on individual or multiplexed fractions. Applications include analyses of, e.g., very low abundance proteins or candidate biomarkers in plasma, cell, or tissue samples without the need for affinity-specific reagents.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2023},

  month        = {4}

}

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Title: Process for ultra-sensitive quantification of target analytes in complex biological systems

Abstract

Citation Formats

Quantitative Mass Spectrometric Multiple Reaction Monitoring Assays for Major Plasma Proteins journal, December 2005

Molecular forms of prostate-specific antigen and the human kallikrein gene family: A new era journal, May 1995

Detection of Oxidized Polypeptides patent-application, December 2012

Analysis of serum total and free PSA using immunoaffinity depletion coupled to SRM: correlation with clinical immunoassay tests journal, August 2012

Protein biomarker discovery and validation: the long and uncertain path to clinical utility journal, August 2006

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments journal, February 2010

Separation of the Components of the Gentamicin Complex patent, March 1972

A-Priori Biomarker Knowledge Based Mass Filtering for Enhanced Biomarker Detection patent-application, January 2006

Evaluation of Large Scale Quantitative Proteomic Assay Development Using Peptide Affinity-based Mass Spectrometry journal, January 2011

Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions journal, September 2005

An Automated and Multiplexed Method for High Throughput Peptide Immunoaffinity Enrichment and Multiple Reaction Monitoring Mass Spectrometry-based Quantification of Protein Biomarkers journal, October 2009

Clinical Quantitation of Prostate-specific Antigen Biomarker in the Low Nanogram/Milliliter Range by Conventional Bore Liquid Chromatography-Tandem Mass Spectrometry (Multiple Reaction Monitoring) Coupling and Correlation with ELISA Tests journal, May 2009

Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks journal, March 2007

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics journal, August 2009

Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics journal, April 2012

Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells journal, April 2011

Nanoporous Substrates for the Analytical Methods patent-application, November 2008

Contributions of mass spectrometry to peptide and protein structure journal, October 1988

Methods and Systems for the Quantitative Analysis of Biomarkers patent-application, October 2011

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma journal, June 2009

Targeted Quantitation of Site-Specific Cysteine Oxidation in Endogenous Proteins Using a Differential Alkylation and Multiple Reaction Monitoring Mass Spectrometry Approach journal, March 2010

Techniques for Mass Spectrometry Peak List Computation Using Parallel Processing patent-application, March 2013

A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans journal, September 2010

Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum journal, September 2012

Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS journal, May 2003

Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor journal, June 2011

A targeted proteomics–based pipeline for verification of biomarkers in plasma journal, June 2011

Moving towards high density clinical signature studies with a human proteome catalogue developing multiplexing mass spectrometry assay panels journal, January 2011

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans journal, July 2009

Mass Spectrometric Quantitation of Peptides and Proteins Using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA) journal, April 2004

Enhanced Sensitivity for Selected Reaction Monitoring Mass Spectrometry-based Targeted Proteomics Using a Dual Stage Electrodynamic Ion Funnel Interface journal, April 2010

Biomarkers for the Detection and Screening of Down Syndrome patent-application, November 2012

Recurrent Fusion of TMPRSS2 and ETS Transcription Factor Genes in Prostate Cancer journal, October 2005

Quantification of Thyroglobulin, a Low-Abundance Serum Protein, by Immunoaffinity Peptide Enrichment and Tandem Mass Spectrometry journal, November 2008

Clinical usefulness of free and complexed PSA journal, January 1995

Verification of a biomarker discovery approach for detection of Down syndrome in amniotic fluid via multiplex selected reaction monitoring (SRM) assay journal, September 2011

Evaluation of Multiprotein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomarker Discovery Using Mass Spectrometry journal, July 2006

Selected reaction monitoring applied to proteomics journal, March 2011

A method for isolation and identification of urinary biomarkers in patients with diabetic nephropathy journal, December 2011

High Sensitivity Detection of Plasma Proteins by Multiple Reaction Monitoring of N-Glycosites journal, October 2007

Frequent overexpression of ETS-related gene-1 (ERG1) in prostate cancer transcriptome journal, March 2005

A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease journal, June 2011

Selected reaction monitoring for quantitative proteomics: a tutorial journal, January 2008

Reference Reagents for Prostate-specific Antigen (PSA): Establishment of the First International Standards for Free PSA and PSA (90:10) journal, September 2000

Mutant proteins as cancer-specific biomarkers journal, January 2011

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions journal, May 2012

Functional Check and Variance Compensation in Mass Spectrometry patent-application, July 2012

Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development journal, June 2009

Quantification of Cardiovascular Biomarkers in Patient Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution journal, October 2009

Enhanced Detection of Low Abundance Human Plasma Proteins Using a Tandem IgY12-SuperMix Immunoaffinity Separation Strategy journal, July 2008

Use of an Immunoaffinity-Mass Spectrometry-based Approach for the Quantification of Protein Biomarkers from Serum Samples of Lung Cancer Patients journal, October 2008

Quantitative Mass Spectrometric Multiple Reaction Monitoring Assays for Major Plasma Proteins
journal, December 2005

Molecular forms of prostate-specific antigen and the human kallikrein gene family: A new era
journal, May 1995

Detection of Oxidized Polypeptides
patent-application, December 2012

Analysis of serum total and free PSA using immunoaffinity depletion coupled to SRM: correlation with clinical immunoassay tests
journal, August 2012

Protein biomarker discovery and validation: the long and uncertain path to clinical utility
journal, August 2006

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
journal, February 2010

Separation of the Components of the Gentamicin Complex
patent, March 1972

A-Priori Biomarker Knowledge Based Mass Filtering for Enhanced Biomarker Detection
patent-application, January 2006

Evaluation of Large Scale Quantitative Proteomic Assay Development Using Peptide Affinity-based Mass Spectrometry
journal, January 2011

Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions
journal, September 2005

An Automated and Multiplexed Method for High Throughput Peptide Immunoaffinity Enrichment and Multiple Reaction Monitoring Mass Spectrometry-based Quantification of Protein Biomarkers
journal, October 2009

Clinical Quantitation of Prostate-specific Antigen Biomarker in the Low Nanogram/Milliliter Range by Conventional Bore Liquid Chromatography-Tandem Mass Spectrometry (Multiple Reaction Monitoring) Coupling and Correlation with ELISA Tests
journal, May 2009

Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks
journal, March 2007

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics
journal, August 2009

Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics
journal, April 2012

Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells
journal, April 2011

Nanoporous Substrates for the Analytical Methods
patent-application, November 2008

Contributions of mass spectrometry to peptide and protein structure
journal, October 1988

Methods and Systems for the Quantitative Analysis of Biomarkers
patent-application, October 2011

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma
journal, June 2009

Targeted Quantitation of Site-Specific Cysteine Oxidation in Endogenous Proteins Using a Differential Alkylation and Multiple Reaction Monitoring Mass Spectrometry Approach
journal, March 2010

Techniques for Mass Spectrometry Peak List Computation Using Parallel Processing
patent-application, March 2013

A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans
journal, September 2010

Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum
journal, September 2012

Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
journal, May 2003

Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor
journal, June 2011

A targeted proteomics–based pipeline for verification of biomarkers in plasma
journal, June 2011

Moving towards high density clinical signature studies with a human proteome catalogue developing multiplexing mass spectrometry assay panels
journal, January 2011

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans
journal, July 2009

Mass Spectrometric Quantitation of Peptides and Proteins Using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA)
journal, April 2004

Enhanced Sensitivity for Selected Reaction Monitoring Mass Spectrometry-based Targeted Proteomics Using a Dual Stage Electrodynamic Ion Funnel Interface
journal, April 2010

Biomarkers for the Detection and Screening of Down Syndrome
patent-application, November 2012

Recurrent Fusion of TMPRSS2 and ETS Transcription Factor Genes in Prostate Cancer
journal, October 2005

Quantification of Thyroglobulin, a Low-Abundance Serum Protein, by Immunoaffinity Peptide Enrichment and Tandem Mass Spectrometry
journal, November 2008

Clinical usefulness of free and complexed PSA
journal, January 1995

Verification of a biomarker discovery approach for detection of Down syndrome in amniotic fluid via multiplex selected reaction monitoring (SRM) assay
journal, September 2011

Evaluation of Multiprotein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomarker Discovery Using Mass Spectrometry
journal, July 2006

Selected reaction monitoring applied to proteomics
journal, March 2011

A method for isolation and identification of urinary biomarkers in patients with diabetic nephropathy
journal, December 2011

High Sensitivity Detection of Plasma Proteins by Multiple Reaction Monitoring of N-Glycosites
journal, October 2007

Frequent overexpression of ETS-related gene-1 (ERG1) in prostate cancer transcriptome
journal, March 2005

A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease
journal, June 2011

Selected reaction monitoring for quantitative proteomics: a tutorial
journal, January 2008

Reference Reagents for Prostate-specific Antigen (PSA): Establishment of the First International Standards for Free PSA and PSA (90:10)
journal, September 2000

Mutant proteins as cancer-specific biomarkers
journal, January 2011

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions
journal, May 2012

Functional Check and Variance Compensation in Mass Spectrometry
patent-application, July 2012

Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development
journal, June 2009

Quantification of Cardiovascular Biomarkers in Patient Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution
journal, October 2009

Enhanced Detection of Low Abundance Human Plasma Proteins Using a Tandem IgY12-SuperMix Immunoaffinity Separation Strategy
journal, July 2008

Use of an Immunoaffinity-Mass Spectrometry-based Approach for the Quantification of Protein Biomarkers from Serum Samples of Lung Cancer Patients
journal, October 2008