1
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Sobsey CA, Froehlich B, Batist G, Borchers CH. Immuno-MALDI-MS for Accurate Quantitation of Targeted Peptides from Volume-Restricted Samples. Methods Mol Biol 2022; 2515:203-225. [PMID: 35776354 DOI: 10.1007/978-1-0716-2409-8_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The immuno-MALDI-MS method can be used to quantify low-abundance proteins from clinical samples that offer only a limited amount of material for analysis. An internal standard, in the form of a stable isotope-labeled peptide, is used to ensure reproducible and absolute quantitation. The protocol described here was optimized for the quantitation of AKT1 and AKT2, but we offer instructions on how to adapt the method to target other proteins. The described workflow is compatible with automation via a liquid handling robot for high-throughput applications.
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Affiliation(s)
- Constance A Sobsey
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Bjoern Froehlich
- University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Gerald Batist
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Exactis Innovation, Montreal, QC, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC, Canada.
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2
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Ibrahim S, Froehlich BC, Aguilar-Mahecha A, Aloyz R, Poetz O, Basik M, Batist G, Zahedi RP, Borchers CH. Using Two Peptide Isotopologues as Internal Standards for the Streamlined Quantification of Low-Abundance Proteins by Immuno-MRM and Immuno-MALDI. Anal Chem 2020; 92:12407-12414. [DOI: 10.1021/acs.analchem.0c02157] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Sahar Ibrahim
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Bjoern C. Froehlich
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria V8Z 7X8, Canada
| | - Adriana Aguilar-Mahecha
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Raquel Aloyz
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Oliver Poetz
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
- SIGNATOPE GmbH, Reutlingen 72770, Germany
| | - Mark Basik
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Gerald Batist
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - René P. Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Christoph H. Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria V8Z 7X8, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
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3
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Zhang C, Glaros T, Manicke NE. Targeted Protein Detection Using an All-in-One Mass Spectrometry Cartridge. J Am Chem Soc 2017; 139:10996-10999. [DOI: 10.1021/jacs.7b05571] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Chengsen Zhang
- Department
of Chemistry and Chemical Biology, Indiana University—Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Trevor Glaros
- BioSciences
Division, BioDefense Branch, US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
| | - Nicholas E. Manicke
- Department
of Chemistry and Chemical Biology, Indiana University—Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
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4
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Li H, Popp R, Borchers CH. Affinity-mass spectrometric technologies for quantitative proteomics in biological fluids. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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5
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Li H, Popp R, Chen M, MacNamara EM, Juncker D, Borchers CH. Bead-Extractor Assisted Ready-to-Use Reagent System (BEARS) for Immunoprecipitation Coupled to MALDI-MS. Anal Chem 2017; 89:3834-3839. [DOI: 10.1021/acs.analchem.6b04169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huiyan Li
- University of Victoria - Genome BC Proteomics Centre, #3101-4464 Markham Street, Vancouver
Island Technology Park, Victoria, British Columbia V8Z 7X8, Canada
- Biomedical
Engineering Department, McGill University, Duff Medical Building, McGill University,
3775, rue University, Room 316, Montreal, Quebec H3A 2B4, Canada
- McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Avenue, Room 6206, Montreal, Quebec H3A 1A4, Canada
| | - Robert Popp
- University of Victoria - Genome BC Proteomics Centre, #3101-4464 Markham Street, Vancouver
Island Technology Park, Victoria, British Columbia V8Z 7X8, Canada
| | - Michael Chen
- Jewish General Hospital, 3755
Côte-Ste-Catherine Road, Montreal, Quebec H3T 1E2, Canada
| | | | - David Juncker
- Biomedical
Engineering Department, McGill University, Duff Medical Building, McGill University,
3775, rue University, Room 316, Montreal, Quebec H3A 2B4, Canada
- McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Avenue, Room 6206, Montreal, Quebec H3A 1A4, Canada
| | - Christoph H. Borchers
- University of Victoria - Genome BC Proteomics Centre, #3101-4464 Markham Street, Vancouver
Island Technology Park, Victoria, British Columbia V8Z 7X8, Canada
- Department
of Biochemistry and Microbiology, University of Victoria, Petch Building
Room 207, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada
- Gerald Bronfman
Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada
- Proteomics
Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General
Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada
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6
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Torres VM, Popovic L, Vaz F, Penque D. Proteomics in the Assessment of the Therapeutic Response of Antineoplastic Drugs: Strategies and Practical Applications. Methods Mol Biol 2016; 1395:281-298. [PMID: 26910080 DOI: 10.1007/978-1-4939-3347-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Uncovering unknown pathological mechanisms and body response to applied medication are the driving forces toward personalized medicine. In this post-genomic era, all eyes are turned to the proteomics field, searching for answers and explanations by investigating the gene end point functional units-proteins and their proteoforms. The development of cutting-edge mass spectrometric technologies and bioinformatics tools have allowed the life-science community to discover disease-specific proteins as biomarkers, which are often concealed by high sample complexity and dynamic range of abundance. Currently, there are several proteomics-based approaches to investigate the proteome. This chapter focuses on gold standard proteomics strategies and related issues toward candidate biomarker discovery, which may have diagnostic/prognostic as well as mechanistic utility in cancer drug resistance.
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Affiliation(s)
- Vukosava Milic Torres
- Laboratory of Proteomics, Human Genetics Departament, Instituto Nacional de Saúde Dr Ricardo Jorge, Av. Padre Cruz, Lisbon, 1649-016, Portugal
- ToxOmics-Centre of Toxicogenomics and Human Health, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Lazar Popovic
- Medical Oncology Department, Oncology Institute of Vojvodina, Sremska Kamenica, Serbia
- Medical Faculty, University of Novi Sad, Novi Sad, Serbia
| | - Fátima Vaz
- Laboratory of Proteomics, Human Genetics Departament, Instituto Nacional de Saúde Dr Ricardo Jorge, Av. Padre Cruz, Lisbon, 1649-016, Portugal
- ToxOmics-Centre of Toxicogenomics and Human Health, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Deborah Penque
- Laboratory of Proteomics, Human Genetics Departament, Instituto Nacional de Saúde Dr Ricardo Jorge, Av. Padre Cruz, Lisbon, 1649-016, Portugal.
- ToxOmics-Centre of Toxicogenomics and Human Health, Universidade Nova de Lisboa, Lisboa, Portugal.
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7
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Pompach P, Nováková J, Kavan D, Benada O, Růžička V, Volný M, Novák P. Planar Functionalized Surfaces for Direct Immunoaffinity Desorption/Ionization Mass Spectrometry. Clin Chem 2016; 62:270-8. [DOI: 10.1373/clinchem.2015.244004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/25/2015] [Indexed: 01/21/2023]
Abstract
Abstract
BACKGROUND
Recent studies show that the haptoglobin phenotype in individuals with diabetes mellitus is an important factor for predicting the risk of myocardial infarction, cardiovascular death, and stroke. Current methods for haptoglobin phenotyping include PCR and gel electrophoresis. A need exists for a reliable method for high-throughput clinical applications. Mass spectrometry (MS) can in principle provide fast phenotyping because haptoglobin α 1 and α 2, which define the phenotype, have different molecular masses. Because of the complexity of the serum matrix, an efficient and fast enrichment technique is necessary for an MS-based assay.
METHODS
MALDI plates were functionalized by ambient ion landing of electrosprayed antihaptoglobin antibody. The array was deposited on standard indium tin oxide slides. Fast immunoaffinity enrichment was performed in situ on the plate, which was further analyzed by MALDI-TOF MS. The haptoglobin phenotype was determined from the spectra by embedded software script.
RESULTS
The MALDI mass spectra showed ion signals of haptoglobin α subunits at m/z 9192 and at m/z 15 945. A cohort of 116 sera was analyzed and the reliability of the method was confirmed by analyzing the identical samples by Western blot. One hundred percent overlap of results between the direct immunoaffinity desorption/ionization MS and Western Blot analysis was found.
CONCLUSIONS
MALDI plates modified by antihaptoglobin antibody using ambient ion landing achieve low nonspecific interactions and efficient MALDI ionization and are usable for quick haptoglobin phenotyping.
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Affiliation(s)
- Petr Pompach
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
- AffiPro, s.r.o., Mratin, Czech Republic
| | - Jana Nováková
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Oldřich Benada
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
| | | | - Michael Volný
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
- AffiPro, s.r.o., Mratin, Czech Republic
| | - Petr Novák
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
- AffiPro, s.r.o., Mratin, Czech Republic
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8
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Kwon SR, Jeon CS, Hong NY, Kim KP, Hwang I, Chung TD. Gold-plated magnetic polymers for highly specific enrichment and label-free detection of blood biomarkers under physiological conditions. Chem Commun (Camb) 2015; 50:10066-9. [PMID: 25036285 DOI: 10.1039/c4cc04281f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mass-based label-free detection of blood biomarkers under physiological conditions is realised using gold-plated magnetic polymer microspheres covered with self-assembled monolayers of polyethylene glycol alkanethiolates that effectively prevent heavy nonspecific binding of serum proteins.
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Affiliation(s)
- Seung-Ryong Kwon
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea.
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9
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Borrebaeck CAK, Wingren C. High-throughput proteomics using antibody microarrays: an update. Expert Rev Mol Diagn 2014; 7:673-86. [PMID: 17892372 DOI: 10.1586/14737159.7.5.673] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Antibody-based microarrays are a rapidly emerging technology that has advanced from the first proof-of-concept studies to demanding serum protein profiling applications during recent years, displaying great promise within disease proteomics. Miniaturized micro- and nanoarrays can be fabricated with an almost infinite number of antibodies carrying the desired specificities. While consuming only minute amounts of reagents, multiplexed and ultrasensitive assays can be performed targeting high- as well as low-abundance analytes in complex nonfractionated proteomes. The microarray images generated can then be converted into protein expression profiles or protein atlases, revealing a detailed composition of the sample. The technology will provide unique opportunities for fields such as disease diagnostics, biomarker discovery, patient stratification, predicting disease recurrence and drug target discovery. This review describes an update of high-throughput proteomics, using antibody-based microarrays, focusing on key technological advances and novel applications that have emerged over the last 3 years.
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Affiliation(s)
- Carl A K Borrebaeck
- Lund University, Department of Immunotechnology & CREATE Health, BMC D13, SE-221 84 Lund, Sweden.
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10
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Yassine H, Borges CR, Schaab MR, Billheimer D, Stump C, Reaven P, Lau SS, Nelson R. Mass spectrometric immunoassay and MRM as targeted MS-based quantitative approaches in biomarker development: potential applications to cardiovascular disease and diabetes. Proteomics Clin Appl 2013; 7:528-40. [PMID: 23696124 DOI: 10.1002/prca.201200028] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 02/04/2013] [Accepted: 03/30/2013] [Indexed: 12/29/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is an important risk factor for cardiovascular disease (CVD)--the leading cause of death in the United States. Yet not all subjects with T2DM are at equal risk for CVD complications; the challenge lies in identifying those at greatest risk. Therapies directed toward treating conventional risk factors have failed to significantly reduce this residual risk in T2DM patients. Thus newer targets and markers are needed for the development and testing of novel therapies. Herein we review two complementary MS-based approaches--mass spectrometric immunoassay (MSIA) and MS/MS as MRM--for the analysis of plasma proteins and PTMs of relevance to T2DM and CVD. Together, these complementary approaches allow for high-throughput monitoring of many PTMs and the absolute quantification of proteins near the low picomolar range. In this review article, we discuss the clinical relevance of the high density lipoprotein (HDL) proteome and Apolipoprotein A-I PTMs to T2DM and CVD as well as provide illustrative MSIA and MRM data on HDL proteins from T2DM patients to provide examples of how these MS approaches can be applied to gain new insight regarding cardiovascular risk factors. Also discussed are the reproducibility, interpretation, and limitations of each technique with an emphasis on their capacities to facilitate the translation of new biomarkers into clinical practice.
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Affiliation(s)
- Hussein Yassine
- Department of Medicine, University of Southern California, Los Angeles, CA, USA
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11
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Zhang X, Zhu S, Xiong Y, Deng C, Zhang X. Development of a MALDI-TOF MS Strategy for the High-Throughput Analysis of Biomarkers: On-Target Aptamer Immobilization and Laser-Accelerated Proteolysis. Angew Chem Int Ed Engl 2013; 52:6055-8. [DOI: 10.1002/anie.201300566] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/04/2013] [Indexed: 01/18/2023]
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12
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Zhang X, Zhu S, Xiong Y, Deng C, Zhang X. Development of a MALDI-TOF MS Strategy for the High-Throughput Analysis of Biomarkers: On-Target Aptamer Immobilization and Laser-Accelerated Proteolysis. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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13
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Stolowitz ML. On-target and nanoparticle-facilitated selective enrichment of peptides and proteins for analysis by MALDI-MS. Proteomics 2012; 12:3438-50. [DOI: 10.1002/pmic.201200252] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 08/27/2012] [Accepted: 09/20/2012] [Indexed: 01/09/2023]
Affiliation(s)
- Mark L. Stolowitz
- Canary Center at Stanford for Cancer Early Detection; Department of Radiology; Stanford University School of Medicine; Palo Alto CA USA
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14
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Whiteaker JR, Paulovich AG. Peptide immunoaffinity enrichment coupled with mass spectrometry for peptide and protein quantification. Clin Lab Med 2012; 31:385-96. [PMID: 21907104 DOI: 10.1016/j.cll.2011.07.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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15
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Jiang J, Parker CE, Hoadley KA, Perou CM, Boysen G, Borchers CH. Development of an immuno tandem mass spectrometry (iMALDI) assay for EGFR diagnosis. Proteomics Clin Appl 2012; 1:1651-9. [PMID: 21136662 DOI: 10.1002/prca.200700009] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The epidermal growth factor receptor (EGFR) is highly expressed in a variety of tumors, and is therefore an important biomarker for cancer diagnosis and a target for cancer therapy. We have developed a novel peptide-based immuno tandem mass spectrometry (iMALDI) diagnostic assay for highly sensitive, highly specific, and quantitative analysis of EGFR, which we have applied to the detection of the EGFR peptide in three cell lines and in a tumor biopsy sample. This assay is capable of detecting the EGFR target peptide bound to the antibody beads at attomole levels. The ability to directly obtain amino acid sequence data by MS/MS on any affinity-captured peptides provides specificity to this diagnostic technique. This avoids the problem of "false positives" which can result from the nonspecific binding that can occur with any affinity-based technique. The addition of stable-labeled versions of the target peptide (synthesized from stable-isotope coded amino acids) as internal standards allows absolute quantitation of the target protein.
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Affiliation(s)
- Jian Jiang
- Curriculum in Applied and Materials Sciences, UNC-CH, Chapel Hill, NC, USA
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16
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Duplexed iMALDI for the detection of angiotensin I and angiotensin II. Methods 2012; 56:213-22. [DOI: 10.1016/j.ymeth.2012.02.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 02/11/2012] [Accepted: 02/15/2012] [Indexed: 11/23/2022] Open
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Reid JD, Holmes DT, Mason DR, Shah B, Borchers CH. Towards the development of an immuno MALDI (iMALDI) mass spectrometry assay for the diagnosis of hypertension. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1680-6. [PMID: 20199871 DOI: 10.1016/j.jasms.2010.01.024] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 01/15/2010] [Accepted: 01/25/2010] [Indexed: 05/12/2023]
Abstract
The renin-angiotensin-aldosterone system (RAAS) plays an essential role in the regulation of plasma volume and arterial blood pressure. One of the most common diseases of the RAAS is the autonomous production of aldosterone by the adrenal glands, caused by either bilateral adrenal hyperplasia or an aldosterone-producing adenoma. This condition, known as primary aldosteronism, is a treatable and often curable form of hypertension. The measurement of plasma renin activity (PRA), as determined by radioimmunoassay for angiotensin I is essential to the diagnosis of primary aldosteronism. However, accurate determination of PRA is often hampered by low plasma concentrations of angiotensin I. Here, we report the use of immuno-MALDI (iMALDI) as a highly sensitive and specific method for the absolute quantitation of angiotensin I in plasma. iMALDI permits concentration determination by affinity-capture of angiotensin I and a stable-isotopically labeled standard (SIS) peptide on immobilized anti-peptide antibodies. The affinity beads are placed on the MALDI target, permitting automated analysis of large numbers of patient samples. Pretreatment of the plasma is not required, and this method is suitable for the accurate determination of angiotensin I in whole plasma. The calibration curve generated using this method was linear over a 50-fold concentration range in plasma, with a correlation coefficient of 0.984. MS/MS sequence confirmation provides absolute specificity. The iMALDI angiotensin I assay, therefore, has the potential to be developed into a method for determining PRA that has advantages in time, in specificity, and in safety.
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Affiliation(s)
- Jennifer D Reid
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
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18
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Planatscher H, Supper J, Poetz O, Stoll D, Joos T, Templin MF, Zell A. Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry. Algorithms Mol Biol 2010; 5:28. [PMID: 20579369 PMCID: PMC2911453 DOI: 10.1186/1748-7188-5-28] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 06/25/2010] [Indexed: 11/16/2022] Open
Abstract
Background Mass spectrometry (MS) based protein profiling has become one of the key technologies in biomedical research and biomarker discovery. One bottleneck in MS-based protein analysis is sample preparation and an efficient fractionation step to reduce the complexity of the biological samples, which are too complex to be analyzed directly with MS. Sample preparation strategies that reduce the complexity of tryptic digests by using immunoaffinity based methods have shown to lead to a substantial increase in throughput and sensitivity in the proteomic mass spectrometry approach. The limitation of using such immunoaffinity-based approaches is the availability of the appropriate peptide specific capture antibodies. Recent developments in these approaches, where subsets of peptides with short identical terminal sequences can be enriched using antibodies directed against short terminal epitopes, promise a significant gain in efficiency. Results We show that the minimal set of terminal epitopes for the coverage of a target protein list can be found by the formulation as a set cover problem, preceded by a filtering pipeline for the exclusion of peptides and target epitopes with undesirable properties. Conclusions For small datasets (a few hundred proteins) it is possible to solve the problem to optimality with moderate computational effort using commercial or free solvers. Larger datasets, like full proteomes require the use of heuristics.
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19
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Quantification of target proteins using hydrogel antibody arrays and MALDI time-of-flight mass spectrometry (A2M2S). N Biotechnol 2009; 25:404-16. [DOI: 10.1016/j.nbt.2009.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 02/22/2009] [Accepted: 03/01/2009] [Indexed: 11/18/2022]
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Abstract
Antibody-based microarrays are a new powerful proteomic technology that can be used to generate rapid and detailed expression profiles of defined sets of protein analytes in complex samples as well as high-resolution portraits of entire proteomes. Miniaturized micro- and nanoarrays can be printed with numerous antibodies carrying the desired specificities. Multiplexed and ultra-sensitive assays, specifically targeting several analytes in a single experiment, can be performed, while consuming only minute amounts of the sample. The array images generated can then be converted into protein expression profiles, or maps, revealing the detailed composition of the sample. This promising proteomic research tool will thus provide unique opportunities for e.g. disease proteomics, biomarker discovery, disease diagnostics, and patient stratification. This review describes the antibody-based microarray technology and applications thereof.
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Wang KY, Chuang SA, Lin PC, Huang LS, Chen SH, Ouarda S, Pan WH, Lee PY, Lin CC, Chen YJ. Multiplexed Immunoassay: Quantitation and Profiling of Serum Biomarkers Using Magnetic Nanoprobes and MALDI-TOF MS. Anal Chem 2008; 80:6159-67. [DOI: 10.1021/ac800354u] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kai-Yi Wang
- Institute of Chemistry, Institute of Biomedical Sciences, and Genomic Research Center and Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, Department of Chemistry, National Central University, Taoyuan County, Department of Chemistry, National Tsing Hua University, Hsinchu, Department of Chemistry, National Taiwan University, Taipei, and Division of Cardiology, Department of Internal Medicine, Mackay Memorial Hospital, Mackay Medicine, Nursing and
| | - Szu-An Chuang
- Institute of Chemistry, Institute of Biomedical Sciences, and Genomic Research Center and Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, Department of Chemistry, National Central University, Taoyuan County, Department of Chemistry, National Tsing Hua University, Hsinchu, Department of Chemistry, National Taiwan University, Taipei, and Division of Cardiology, Department of Internal Medicine, Mackay Memorial Hospital, Mackay Medicine, Nursing and
| | - Po-Chiao Lin
- Institute of Chemistry, Institute of Biomedical Sciences, and Genomic Research Center and Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, Department of Chemistry, National Central University, Taoyuan County, Department of Chemistry, National Tsing Hua University, Hsinchu, Department of Chemistry, National Taiwan University, Taipei, and Division of Cardiology, Department of Internal Medicine, Mackay Memorial Hospital, Mackay Medicine, Nursing and
| | - Li-Shing Huang
- Institute of Chemistry, Institute of Biomedical Sciences, and Genomic Research Center and Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, Department of Chemistry, National Central University, Taoyuan County, Department of Chemistry, National Tsing Hua University, Hsinchu, Department of Chemistry, National Taiwan University, Taipei, and Division of Cardiology, Department of Internal Medicine, Mackay Memorial Hospital, Mackay Medicine, Nursing and
| | - Shu-Hua Chen
- Institute of Chemistry, Institute of Biomedical Sciences, and Genomic Research Center and Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, Department of Chemistry, National Central University, Taoyuan County, Department of Chemistry, National Tsing Hua University, Hsinchu, Department of Chemistry, National Taiwan University, Taipei, and Division of Cardiology, Department of Internal Medicine, Mackay Memorial Hospital, Mackay Medicine, Nursing and
| | - Saib Ouarda
- Institute of Chemistry, Institute of Biomedical Sciences, and Genomic Research Center and Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, Department of Chemistry, National Central University, Taoyuan County, Department of Chemistry, National Tsing Hua University, Hsinchu, Department of Chemistry, National Taiwan University, Taipei, and Division of Cardiology, Department of Internal Medicine, Mackay Memorial Hospital, Mackay Medicine, Nursing and
| | - Wen-Harn Pan
- Institute of Chemistry, Institute of Biomedical Sciences, and Genomic Research Center and Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, Department of Chemistry, National Central University, Taoyuan County, Department of Chemistry, National Tsing Hua University, Hsinchu, Department of Chemistry, National Taiwan University, Taipei, and Division of Cardiology, Department of Internal Medicine, Mackay Memorial Hospital, Mackay Medicine, Nursing and
| | - Ping-Ying Lee
- Institute of Chemistry, Institute of Biomedical Sciences, and Genomic Research Center and Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, Department of Chemistry, National Central University, Taoyuan County, Department of Chemistry, National Tsing Hua University, Hsinchu, Department of Chemistry, National Taiwan University, Taipei, and Division of Cardiology, Department of Internal Medicine, Mackay Memorial Hospital, Mackay Medicine, Nursing and
| | - Chun-Cheng Lin
- Institute of Chemistry, Institute of Biomedical Sciences, and Genomic Research Center and Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, Department of Chemistry, National Central University, Taoyuan County, Department of Chemistry, National Tsing Hua University, Hsinchu, Department of Chemistry, National Taiwan University, Taipei, and Division of Cardiology, Department of Internal Medicine, Mackay Memorial Hospital, Mackay Medicine, Nursing and
| | - Yu-Ju Chen
- Institute of Chemistry, Institute of Biomedical Sciences, and Genomic Research Center and Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, Department of Chemistry, National Central University, Taoyuan County, Department of Chemistry, National Tsing Hua University, Hsinchu, Department of Chemistry, National Taiwan University, Taipei, and Division of Cardiology, Department of Internal Medicine, Mackay Memorial Hospital, Mackay Medicine, Nursing and
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22
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Jiang J, Parker CE, Fuller JR, Kawula TH, Borchers CH. An immunoaffinity tandem mass spectrometry (iMALDI) assay for detection of Francisella tularensis. Anal Chim Acta 2007; 605:70-9. [PMID: 18022413 PMCID: PMC2135554 DOI: 10.1016/j.aca.2007.10.025] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 10/02/2007] [Accepted: 10/12/2007] [Indexed: 11/25/2022]
Abstract
Francisella tularensis (F. tularensis) has been designated by the CDC as 1 of the 10 organisms most likely to be engineered for bioterrorism. Symptoms of tularemia in humans are non-specific, thus making the disease difficult to diagnose. If not quickly diagnosed and treated, the disease has a high mortality rate--thus methods for early and specific diagnosis are of critical importance. This immunoaffinity MALDI MS/MS (iMALDI) assay provides unambiguous detection of F. tularensis peptides at attomole levels from peptide solutions, and at low CFU levels from bacteria. The addition of stable-labeled versions of the peptide as internal standards allows absolute quantitation of F. tularensis peptides with a linear dynamic range spanning two orders of magnitude. The ability of mass spectrometry to obtain amino acid sequence data on affinity-captured peptides provides absolute specificity and avoids "false positives" from the non-specific binding. The F. tularensis iMALDI assay has been applied to different samples, such as nasal swabs. This novel quantitative diagnostic F. tularensis iMALDI assay allows the safe, sensitive, and specific detection of F. tularensis. The assay can be easily adapted to other target peptides and therefore has broad application potential in clinical diagnosis of other pathogens and diseases.
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Affiliation(s)
- Jian Jiang
- Curriculum in Applied and Materials Sciences, UNC-CH, Chapel Hill, NC, United States
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23
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Chen SH, Liao HK, Chang CY, Juo CG, Chen JH, Chan SI, Chen YJ. Targeted protein quantitation and profiling using PVDF affinity probe and MALDI-TOF MS. Proteomics 2007; 7:3038-50. [PMID: 17676666 DOI: 10.1002/pmic.200700393] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Development of a rapid, effective, and highly specific platform for target identification in complex biofluids is one of the most important tasks in proteomic research. Taking advantage of the natural hydrophobic interaction of PVDF with probe protein, a simple and effective method was developed for protein quantitation and profiling. Using antibody-antigen interactions as a proof-of-concept system, the targeted plasma proteins, serum amyloid P (SAP), serum amyloid A (SAA), and C-reactive protein (CRP), could be selectively isolated and enriched from human plasma by antibody-immobilized PVDF membrane and directly identified by MALDI-TOF MS without additional elution step. The approach was successfully applied to human plasma for rapid quantitation and variant screening of SAP, SAA, and CRP in healthy individuals and patients with gastric cancer. The triplexed on-probe quantitative analysis revealed significant overexpression of CRP and SAA in gastric cancer group, consistent with parallel ELISA measurements and pathological progression and prognostic significance reported in previous literatures. Furthermore, the variant mass profiling of the post-translationally modified forms revealed a high occurrence of de-sialic acid SAP in patients with gastric cancer. Due to the versatile assay design, ease of probe preparation without chemical synthesis, and compatibility with MALDI-TOF MS analysis, the methodology may be useful for target protein characterization, functional proteomics, and screening in clinical proteomics.
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Affiliation(s)
- Shu-Hua Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, ROC
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24
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Wingren C, Borrebaeck CAK. Antibody microarrays: current status and key technological advances. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2006; 10:411-27. [PMID: 17069517 DOI: 10.1089/omi.2006.10.411] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Antibody-based microarrays are among the novel classes of rapidly evolving proteomic technologies that holds great promise in biomedicine. Miniaturized microarrays (< 1 cm2) can be printed with thousands of individual antibodies carrying the desired specificities, and with biological sample (e.g., an entire proteome) added, virtually any specifically bound analytes can be detected. While consuming only minute amounts (< microL scale) of reagents, ultra- sensitive assays (zeptomol range) can readily be performed in a highly multiplexed manner. The microarray patterns generated can then be transformed into proteomic maps, or detailed molecular fingerprints, revealing the composition of the proteome. Thus, protein expression profiling and global proteome analysis using this tool will offer new opportunities for drug target and biomarker discovery, disease diagnostics, and insights into disease biology. Adopting the antibody microarray technology platform, several biomedical applications, ranging from focused assays to proteome-scale analysis will be rapidly emerging in the coming years. This review will discuss the current status of the antibody microarray technology focusing on recent technological advances and key issues in the process of evolving the methodology into a high-performing proteomic research tool.
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25
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Weber A, Hengge UR, Stricker I, Tischoff I, Markwart A, Anhalt K, Dietz A, Wittekind C, Tannapfel A. Protein microarrays for the detection of biomarkers in head and neck squamous cell carcinomas. Hum Pathol 2006; 38:228-38. [PMID: 17020778 DOI: 10.1016/j.humpath.2006.07.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 07/18/2006] [Accepted: 07/25/2006] [Indexed: 11/17/2022]
Abstract
Protein microarrays are of increasing importance for high-throughput screening of fresh tissues. In our study, protein microarrays were generated by printing antibodies onto membranes to characterize protein profiles expressed by head and neck squamous cell carcinomas (HNSCCs). Cellular proteomes of 30 matched normal squamous epithelial cells and carcinoma specimens were analyzed after tissue microdissection using microarrays composed of 83 different antibodies. As controls, Western blot analysis and tissue microarrays (TMAs) containing 98 HNSCC specimens were used. Of the 83 proteins examined, 14 showed differential expression between HNSCCs and normal epithelium. The protein microarray approach revealed an upregulation of 8 proteins and a downregulation of 6 proteins. Bag-1, Cox-2, Hsp-70, Stat3, pescadillo, MMP-7 (matrilysin), IGF-2, and cyclin D1 were identified to be significantly upregulated, whereas suppressor of cytokine signaling 1, thrombospondin, TGF-beta1, Jun, Fos, and Fra-2 were downregulated. The differential expression of these proteins was confirmed using Western blot and TMA. Upon correlation of differentially regulated proteins with the clinicopathologic data of our patients, MMP-7 (matrilysin) was found to be associated with survival in univariate, but not multivariate, analysis. These data indicate that our protein arrays provide protein information in a systematic, reproducible, and also high-throughput fashion.
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Affiliation(s)
- Anette Weber
- Department of ENT, University of Leipzig, 04103 Leipzig, Germany
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26
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Brönstrup M. Absolute quantification strategies in proteomics based on mass spectrometry. Expert Rev Proteomics 2006; 1:503-12. [PMID: 15966845 DOI: 10.1586/14789450.1.4.503] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The strong need for quantitative information in proteomics has fueled the development of mass spectrometry-based analytical methods that are able to determine protein abundances. This article reviews mass spectrometry experiments aimed at providing an absolute quantification of proteins. The experiments make use of the isotope-dilution concept by spiking a known amount of synthetic, isotope-labeled reference peptide into the analyte sample. Quantification is achieved by comparing the mass spectrometry signal intensities of the reference with an endogenous peptide that is generated upon proteolytic cleavage of the target protein. In an analogous manner, the level of post-translational modification at a distinct residue within a target protein can be determined. Among the strengths of absolute quantification are low detection limits reaching subfemtomole levels, a high dynamic range spanning approximately five orders of magnitude, low requirements for sample clean-up, and a fast and straightforward method development. Recent studies have demonstrated the compatibility of absolute quantification with various mass spectrometry readout techniques and sample purification steps such as 1D gel electrophoresis, size-exclusion chromatography, isoelectric peptide focusing, strong cation exchange and reversed phase or affinity chromatography. Under ideal conditions, quantification errors and coefficients of variation below 5% have been reported. However, the fact that at the start of the experiment the analyte is a protein and the internal standard is a peptide, severe quantification errors may result due to the selection of unsuitable reference peptides and/or imperfect protein proteolysis. Within the ensemble of mass spectrometry-based quantification methods, absolute quantification is the method of choice in cases where absolute numbers, many repetitive experiments or precise levels of post-translational modifications are required for a few, preselected species of interest. Consequently, prominent application areas include biomarker quantification, the study of post-translational modifications such as phosphorylation or ubiquitination and the comparison of concentrations of interacting proteins.
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Affiliation(s)
- Mark Brönstrup
- Sanofi-Aventis, Building G878, D-65926 Frankfurt, Germany.
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27
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Chou PH, Chen SH, Liao HK, Lin PC, Her GR, Lai ACY, Chen JH, Lin CC, Chen YJ. Nanoprobe-Based Affinity Mass Spectrometry for Selected Protein Profiling in Human Plasma. Anal Chem 2005; 77:5990-7. [PMID: 16159132 DOI: 10.1021/ac050655o] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In recent decades, magnetic nanoparticles have emerged as a promising new platform in biomedical applications, particularly bioseparations. We have developed an immunoassay using antibody-conjugated magnetic nanoparticles as an efficient affinity probe to simultaneously preconcentrate and isolate targeted antigens from biological media. We combined this probe with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI MS) to profile proteins in diluted human plasma. The nanoparticles were designed to detect several disease-associated proteins and could be used directly in MALDI MS without an elution step, thereby facilitating multiple antigen screening and the characterization of antigen variants. Plasma antigens bound rapidly (approximately 10 min) to the antibody-conjugated nanoparticles, allowing the assay to be performed within 20 min. With sensitivity of detection in the femtomole range, the nanoscale immunoassay is superior to assays using microscale particles. We applied our method to comparative protein profiling of patients with gastric cancer and healthy individuals and found differential protein expression levels associated with the disease as well as individuals. Given the flexibility of manipulating functional groups on the nanoprobes, their low cost, robustness, and simplicity of the assay, our approach shows promise for targeted proteome profiling in clinical settings.
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Affiliation(s)
- Po-Hung Chou
- Institute of Chemistry and Genomic Research Center, Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
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28
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Warren EN, Jiang J, Parker CE, Borchers CH. Absolute quantitation of cancer-related proteins using an MS-based peptide chip. Biotechniques 2005; Suppl:7-11. [PMID: 16528910 DOI: 10.2144/05386su01] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
New technologies are needed that can diagnose cancer more rapidly and accurately. These technologies must also have the ability to identify the particular cellular abnormalities contributing to the malignancy, thus directing the appropriate treatments. Such technologies should permit absolute quantitation of specific tumor biomarkers and their level of posttranslational modifications. Quantitative molecular profiling of cancer signaling networks would provide a more detailed understanding of the contribution of protein expression and posttranslational modification levels to tumorigenesis. We have developed a unique approach for absolute quantitation of protein expression that integrates affinity capture of proteolytic peptides with mass spectrometry and thus provides detection, identification, and quantitation of their cognate proteins. We have previously shown the high sensitivity and specificity of this approach. Here we demonstrate the absolute quantitation of a model peptide using our technology. We have used this approach to capture epitope-containing peptides from proteolytically digested target proteins, including p53, epidermal growth factor receptor (EGFR), and prostate-specific antigen (PSA). Our technology can easily be extended to the absolute quantitation of protein modification levels, in addition to the determination of protein expression levels, and can be readily adapted for use in a microarray format. This method offers an improved approach to protein chip technology that should prove useful for clinical diagnosis and drug development applications.
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Affiliation(s)
- Erin N Warren
- University of North Carolina Medical School, Chapel Hill, NC 27599, USA
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