skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids

Journal Article · · Journal of Chromatography. B

Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methods are also discussed.

Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC05-76RL01830
OSTI ID:
1251560
Report Number(s):
PNNL-SA-112289; PII: S1570023216300150
Journal Information:
Journal of Chromatography. B, Vol. 1021, Issue C; ISSN 1570-0232
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 37 works
Citation information provided by
Web of Science

References (153)

Human body fluid proteome analysis journal December 2006
The Clinical Plasma Proteome: A Survey of Clinical Assays for Proteins in Plasma and Serum journal November 2009
The Human Plasma Proteome: History, Character, and Diagnostic Prospects journal October 2002
Utilizing Human Blood Plasma for Proteomic Biomarker Discovery journal August 2005
Mining the plasma proteome for cancer biomarkers journal April 2008
Protein biomarker discovery and validation: the long and uncertain path to clinical utility journal August 2006
Body Fluid Proteomics for Biomarker Discovery: Lessons from the Past Hold the Key to Success in the Future journal October 2007
Advances in Urinary Proteome Analysis and Biomarker Discovery journal February 2007
Recommendations for Biomarker Identification and Qualification in Clinical Proteomics journal August 2010
Advances in urinary proteome analysis and biomarker discovery in pediatric renal disease journal January 2010
Urine as a source for clinical proteome analysis: From discovery to clinical application journal May 2014
Urine Collection and Processing for Protein Biomarker Discovery and Quantification journal March 2010
Salivary diagnostics powered by nanotechnologies, proteomics and genomics journal March 2006
Label-Free Biochemical Analytic Method for the Early Detection of Adenoviral Conjunctivitis Using Human Tear Biofluids journal October 2014
Cerebrospinal Fluid Biomarkers for Alzheimer's Disease journal August 2009
Immunoaffinity chromatography: an introduction to applications and recent developments journal April 2010
Affinity separation and enrichment methods in proteomic analysis journal August 2008
Advances and Challenges in Liquid Chromatography-Mass Spectrometry-based Proteomics Profiling for Clinical Applications journal October 2006
Enhanced Detection of Low Abundance Human Plasma Proteins Using a Tandem IgY12-SuperMix Immunoaffinity Separation Strategy journal July 2008
Immunoaffinity Enrichment and Liquid Chromatography-Selected Reaction Monitoring Mass Spectrometry for Quantitation of Carbonic Anhydrase 12 in Cultured Renal Carcinoma Cells journal November 2010
Affinity Depletion of Plasma and Serum for Mass Spectrometry-Based Proteome Analysis book January 2013
Mass Spectrometric Quantitation of Peptides and Proteins Using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA) journal April 2004
Interlaboratory Evaluation of Automated, Multiplexed Peptide Immunoaffinity Enrichment Coupled to Multiple Reaction Monitoring Mass Spectrometry for Quantifying Proteins in Plasma journal December 2011
Critical Steps in the Production of Polyclonal and Monoclonal Antibodies: Evaluation and Recommendations journal January 2005
SISCAPA Peptide Enrichment on Magnetic Beads Using an In-line Bead Trap Device journal May 2009
Latest technologies for the enhancement of antibody affinity journal August 2006
Automated screening of monoclonal antibodies for SISCAPA assays using a magnetic bead processor and liquid chromatography-selected reaction monitoring-mass spectrometry journal February 2010
Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae journal March 2002
Phosphopeptide enrichment using metal oxide affinity chromatography journal February 2010
Combination of Abundant Protein Depletion and Multi-Lectin Affinity Chromatography (M-LAC) for Plasma Protein Biomarker Discovery journal February 2007
Aptamer affinity chromatography: journal August 1999
Immunoaffinity separation of plasma proteins by IgY microbeads: Meeting the needs of proteomic sample preparation and analysis journal August 2005
Differences among techniques for high-abundant protein depletion journal August 2005
Multi-component immunoaffinity subtraction chromatography: An innovative step towards a comprehensive survey of the human plasma proteome journal April 2003
Evaluation of Multiprotein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomarker Discovery Using Mass Spectrometry journal July 2006
IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography–mass spectrometry for human plasma proteomics biomarker discovery journal February 2012
Depletion efficiency and recovery of trace markers from a multiparameter immunodepletion column journal June 2006
Effect of Immunoaffinity Depletion of Human Serum during Proteomic Investigations journal October 2005
Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma journal August 2005
Sepsis Plasma Protein Profiling with Immunodepletion, Three-Dimensional Liquid Chromatography Tandem Mass Spectrometry, and Spectrum Counting journal November 2006
Intact-protein-based High-resolution Three-dimensional Quantitative Analysis System for Proteome Profiling of Biological Fluids journal May 2005
Depletion of Abundant Plasma Proteins and Limitations of Plasma Proteomics journal October 2010
Combination of affinity depletion of abundant proteins and reversed-phase fractionation in proteomic analysis of human plasma/serum journal May 2008
A Proteomic Approach for Plasma Biomarker Discovery with iTRAQ Labelling and OFFGEL Fractionation journal January 2010
Additions to the Human Plasma Proteome via a Tandem MARS Depletion iTRAQ-Based Workflow journal February 2013
Optimizing Performance of Glycopeptide Capture for Plasma Proteomics journal March 2010
Prediction of high-responding peptides for targeted protein assays by mass spectrometry journal January 2009
Plasma proteome changes associated with refractory cytopenia with multilineage dysplasia journal January 2011
Variation and quantification among a target set of phosphopeptides in human plasma by multiple reaction monitoring and SWATH-MS2 data-independent acquisition: Proteomics and 2DE journal July 2014
High Abundance Proteins Depletion vs Low Abundance Proteins Enrichment: Comparison of Methods to Reduce the Plasma Proteome Complexity journal May 2011
Identification of potential bladder cancer markers in urine by abundant-protein depletion coupled with quantitative proteomics journal June 2013
Proteomic Changes in Cerebrospinal Fluid of Presymptomatic and Affected Persons Carrying Familial Alzheimer Disease Mutations journal January 2012
In-depth Characterization of the Cerebrospinal Fluid (CSF) Proteome Displayed Through the CSF Proteome Resource (CSF-PR) journal November 2014
Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM journal January 2013
Proteomic Analysis of Ovarian Cancer Proximal Fluids: Validation of Elevated Peroxiredoxin 1 in Patient Peripheral Circulation journal September 2011
Quantitative, Multiplexed Assays for Low Abundance Proteins in Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution journal October 2007
Comparison of protein enrichment strategies for proteome analysis of plasma journal February 2010
Spectral counting assessment of protein dynamic range in cerebrospinal fluid following depletion with plasma-designed immunoaffinity columns journal June 2011
Assessment of Two Immunodepletion Methods: Off-Target Effects and Variations in Immunodepletion Efficiency May Confound Plasma Proteomics journal October 2012
Comparison of the performance of two affinity depletion spin filters for quantitative proteomics of CSF: Evaluation of sensitivity and reproducibility of CSF analysis using GeLC-MS/MS and spectral counting journal June 2010
Quantitative assessment of human serum high-abundance protein depletion journal November 2008
Identification of ovarian cancer-associated proteins in symptomatic women: A novel method for semi-quantitative plasma proteomics journal April 2012
iTRAQ Identification of Candidate Serum Biomarkers Associated with Metastatic Progression of Human Prostate Cancer journal February 2012
Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum journal September 2012
Glycoprotein Biomarker Panel for Pancreatic Cancer Discovered by Quantitative Proteomics Analysis journal March 2014
Alterations in Protein Regulators of Neurodevelopment in the Cerebrospinal Fluid of Infants with Posthemorrhagic Hydrocephalus of Prematurity journal June 2012
Proteome Profiling of Human Cerebrospinal Fluid: Exploring the Potential of Capillary Electrophoresis with Surface Modified Capillaries for Analysis of Complex Biological Samples journal April 2008
Mouse-Specific Tandem IgY7-SuperMix Immunoaffinity Separations for Improved LC-MS/MS Coverage of the Plasma Proteome journal November 2009
Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: analysis of human plasma and cerebrospinal fluid journal September 2014
Protein Equalizer™ Technology: The quest for a “democratic proteome” journal July 2006
Combinatorial Peptide Ligand Libraries as a “Trojan Horse” in Deep Discovery Proteomics journal August 2014
Inside human aortic stenosis: A proteomic analysis of plasma journal February 2012
Biomarker Discovery for Early Detection of Hepatocellular Carcinoma in Hepatitis C–infected Patients journal December 2013
SAA1 is over-expressed in plasma of non small cell lung cancer patients with poor outcome after treatment with epidermal growth factor receptor tyrosine-kinase inhibitors journal December 2012
Enrichment strategies in glycomics-based lung cancer biomarker development journal August 2013
Improvements in Proteomic Metrics of Low Abundance Proteins through Proteome Equalization Using ProteoMiner Prior to MudPIT journal August 2011
Rapid development of sensitive, high-throughput, quantitative and highly selective mass spectrometric targeted immunoassays for clinically important proteins in human plasma and serum journal April 2013
Mass-Linked Immuno-Selective Assays in Targeted Proteomics journal November 2012
Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry journal May 2003
Modification-specific proteomics: Strategies for characterization of post-translational modifications using enrichment techniques journal October 2009
Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications journal December 2013
High-Throughput Comparative Proteome Analysis Using a Quantitative Cysteinyl-peptide Enrichment Technology journal September 2004
Structure of the IgG-binding regions of streptococcal protein G. journal July 1986
Affibody-mediated transferrin depletion for proteomics applications journal November 2007
Affibody molecules: Engineered proteins for therapeutic, diagnostic and biotechnological applications journal April 2010
Lectins: Proteins That Interpret the Sugar Code journal August 2003
A Proteomics Platform Combining Depletion, Multi-lectin Affinity Chromatography (M-LAC), and Isoelectric Focusing to Study the Breast Cancer Proteome journal June 2011
Development of an improved fractionation of the human plasma proteome by a combination of abundant proteins depletion and multi-lectin affinity chromatography journal October 2014
Intracellular antibodies and challenges facing their use as therapeutic agents journal September 2003
Intracellular antibodies and cancer: New technologies offer therapeutic opportunities journal June 2010
Single-chain antibodies as diagnostic tools and therapeutic agents journal January 2009
scFv Antibody: Principles and Clinical Application journal January 2012
A human scFv antibody generation pipeline for proteome research journal April 2011
Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface journal June 1985
Selection of human antibody fragments by phage display journal November 2007
Use of a Single-Chain Antibody Library for Ovarian Cancer Biomarker Discovery journal July 2010
Dual-color Proteomic Profiling of Complex Samples with a Microarray of 810 Cancer-related Antibodies journal June 2010
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
Sequential Multiplexed Analyte Quantification Using Peptide Immunoaffinity Enrichment Coupled to Mass Spectrometry journal December 2011
Global Proteomic Assessment of the Classical Protein-Tyrosine Phosphatome and “Redoxome” journal September 2011
Temporal Perturbation of Tyrosine Phosphoproteome Dynamics Reveals the System-wide Regulatory Networks journal February 2009
Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling journal July 2010
Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions journal July 2009
Generation of acetyllysine antibodies and affinity enrichment of acetylated peptides journal September 2010
Different techniques for urinary protein analysis of normal and lung cancer patients journal March 2005
Different Immunoaffinity Fractionation Strategies to Characterize the Human Plasma Proteome journal June 2006
High-abundance protein depletion: Comparison of methods for human plasma biomarker discovery journal January 2010
High Dynamic Range Characterization of the Trauma Patient Plasma Proteome journal October 2006
Human Plasma N -Glycoproteome Analysis by Immunoaffinity Subtraction, Hydrazide Chemistry, and Mass Spectrometry journal December 2005
Two-stage Off-Gel? isoelectric focusing: Protein followed by peptide fractionation and application to proteome analysis of human plasma journal March 2005
Analysis of serum total and free PSA using immunoaffinity depletion coupled to SRM: correlation with clinical immunoassay tests journal August 2012
Quantification of Cardiovascular Biomarkers in Patient Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution journal October 2009
Reproducible Quantification of Cancer-Associated Proteins in Body Fluids Using Targeted Proteomics journal July 2012
Quantitative Mass Spectrometric Multiple Reaction Monitoring Assays for Major Plasma Proteins journal December 2005
Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry journal December 2012
Protein Alterations Associated with Pancreatic Cancer and Chronic Pancreatitis Found in Human Plasma using Global Quantitative Proteomics Profiling journal May 2011
A Systematic Analysis of Eluted Fraction of Plasma Post Immunoaffinity Depletion: Implications in Biomarker Discovery journal September 2011
Mass Spectrometric Immunoassay journal April 1995
Developing Multiplexed Assays for Troponin I and Interleukin-33 in Plasma by Peptide Immunoaffinity Enrichment and Targeted Mass Spectrometry journal June 2009
Proteomic technologies for the identification of disease biomarkers in serum: Advances and challenges ahead journal May 2011
Discovery of serum biomarkers of ovarian cancer using complementary proteomic profiling strategies journal November 2014
Deep depletion of abundant serum proteins reveals low-abundant proteins as potential biomarkers for human ovarian cancer journal July 2009
A mass spectrometry-based plasma protein panel targeting the tumor microenvironment in patients with breast cancer journal April 2013
Serum Soluble CD14 Is a Potential Prognostic Indicator of Recurrence of Human Breast Invasive Ductal Carcinoma with Her2-Enriched Subtype journal September 2013
Mass spectrometry in cancer biomarker research: a case for immunodepletion of abundant blood-derived proteins from clinical tissue specimens journal February 2014
Identification and validation of novel candidate protein biomarkers for the detection of human gastric cancer journal May 2014
2D-DIGE as a Strategy To Identify Serum Markers for the Progression of Prostate Cancer journal December 2008
A Highly Sensitive Targeted Mass Spectrometric Assay for Quantification of AGR2 Protein in Human Urine and Serum journal December 2013
Sequential depletion of human serum for the search of osteoarthritis biomarkers journal January 2012
Identification of a Panel of Novel Serum Osteoarthritis Biomarkers journal November 2011
Identification of Potential Prognostic Markers for Knee Osteoarthritis by Serum Proteomic Analysis journal January 2013
A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease journal June 2011
Advances in urinary protein biomarkers for urogenital and non-urogenital pathologies journal January 2015
Identification of a urine metabolomic signature in patients with advanced-stage chronic kidney disease journal January 2014
A stable panel comprising 18 urinary proteins in the human healthy population journal April 2012
Urine 2DE proteome analysis in healthy condition and kidney disease: Proteomics and 2DE journal August 2014
Comparison of different depletion strategies for improving resolution of the human urine proteome journal January 2010
Clinical validation of an immunoaffinity LC–MS/MS assay for the quantification of a collagen type II neoepitope peptide: A biomarker of matrix metalloproteinase activity and osteoarthritis in human urine journal October 2007
A method for isolation and identification of urinary biomarkers in patients with diabetic nephropathy journal December 2011
Proteomic Identification of Urinary Biomarkers of Diabetic Nephropathy journal February 2007
Urinary proteomic shotgun approach for identification of potential acute rejection biomarkers in renal transplant recipients journal January 2012
Recent cerebrospinal fluid biomarker studies of Alzheimer’s disease journal December 2010
Proteomics of human cerebrospinal fluid: Discovery and verification of biomarker candidates in neurodegenerative diseases using quantitative proteomics journal April 2011
Protein Changes in Immunodepleted Cerebrospinal Fluid from a Transgenic Mouse Model of Alexander Disease Detected Using Mass Spectrometry journal January 2013
Establishing the Proteome of Normal Human Cerebrospinal Fluid journal June 2010
Distinct Cerebrospinal Fluid Proteomes Differentiate Post-Treatment Lyme Disease from Chronic Fatigue Syndrome journal February 2011
A comprehensive map and functional annotation of the normal human cerebrospinal fluid proteome journal April 2015
iTRAQ and multiple reaction monitoring as proteomic tools for biomarker search in cerebrospinal fluid of patients with Parkinson's disease dementia journal April 2012
Brain-specific Proteins Decline in the Cerebrospinal Fluid of Humans with Huntington Disease journal March 2009
Differential protein profiling of synovial fluid from rheumatoid arthritis and osteoarthritis patients using LC–MALDI TOF/TOF journal June 2012
Proteomic analysis of human osteoarthritis synovial fluid journal January 2014
Microfluidic integration for automated targeted proteomic assays journal April 2012
A comprehensive and non-prefractionation on the protein level approach for the human urinary proteome: touching phosphorylation in urine: Human urinary proteome: touching phosphorylation in urine journal February 2010

Cited By (8)

Affinity depletion versus relative protein enrichment: a side-by-side comparison of two major strategies for increasing human cerebrospinal fluid proteome coverage journal February 2019
Needle lost in the haystack: multiple reaction monitoring fails to detect Treponema pallidum candidate protein biomarkers in plasma and urine samples from individuals with syphilis journal January 2018
Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery journal October 2019
The role of proteomics in assessing beta-cell dysfunction and death in type 1 diabetes journal June 2019
Sample preparation in foodomic analyses journal May 2018
Two-Dimensional Gel Electrophoresis and 2D-DIGE book October 2017
Assessment of the Utility of the Oral Fluid and Plasma Proteomes for Hydrocodone Exposure journal November 2019
Needle lost in the haystack: multiple reaction monitoring fails to detect Treponema pallidum candidate protein biomarkers in plasma and urine samples from individuals with syphilis journal January 2018