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Kim H, Cheon DH, Yang WS, Baek JH. Simultaneous Quantification of Apolipoprotein C-III O-Glycoforms by Protein-MRM. J Proteome Res 2023; 22:91-100. [PMID: 36412001 DOI: 10.1021/acs.jproteome.2c00490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Apolipoprotein C-III (APOC-III) regulates triglyceride levels, associated with a risk of cardiovascular disease. One gene generates several proteoforms, each with a different molecular mass and a unique function. Unlike peptide multiple reaction monitoring (MRM), protein-MRM without digestion is required to analyze clinically relevant individual proteoforms. We developed a protein-MRM method without digestion to individually quantify APOC-III proteoforms in human serum. We optimized the protein-MRM method following 60% acetonitrile extraction with C18 filtration. Bovine serum and myoglobin served as supporting cushions and the internal standard during sample preparation, respectively. Furthermore, we evaluated the LOD, lower limit of quantification, linearity, accuracy, and precision. Good correlation compared with turbidimetric immunoassay (TIA) and peptide-MRM was observed using 30 clinical sera. Individual APOC-III O-glycoforms were identified by top-down proteomics and simultaneously quantified using the protein-MRM method. The sum abundance of APOC-III proteoforms was significantly correlated with TIA and peptide-MRM. Our protein-MRM method provides an affordable and rapid quantification of potential disease-specific proteoforms. Precise quantification of each proteoform allows investigators to identify novel biological roles potentially related to cardiovascular disease or novel biomarkers. We expect our protein-oriented method to be more clinically useful than antibody-based immunoassays and peptide-oriented MRM analysis, especially for quantification of a biomarker proteoform with certain post-translational modifications.
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Affiliation(s)
- Hyojin Kim
- R&D Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seongdong-gu, Seoul 04805, Korea
| | - Dong Huey Cheon
- R&D Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seongdong-gu, Seoul 04805, Korea
| | - Won Suk Yang
- R&D Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seongdong-gu, Seoul 04805, Korea
| | - Je-Hyun Baek
- R&D Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seongdong-gu, Seoul 04805, Korea
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2
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Abstract
While human plasma has a wealth of diagnostic information regarding the state of the human body in heath and disease, low molecular weight (LMW) proteome (<30 kDa) has been shown to contain a rich source of diagnostic biomarkers. Here we describe a protocol for top-down proteomic analysis to identify and characterize the LMW proteoforms present in four types of human plasma samples without immunoaffinity depletion and with depletion of the top two, six, and seven high-abundance proteins. Each type of plasma sample was first fractionated based on molecular weight using gel-eluted liquid fraction entrapment electrophoresis (GELFrEE). Then, the GELFrEE fractions containing up to 30 kDa were subjected to nanocapillary-LC-MS/MS, and the high-resolution MS and MS/MS data were processed using ProSightPC software. As a result, a total of 442 LMW proteins and cleaved products, including those with posttranslational modifications (PTMs) and single amino acid variations (SAAVs), were identified with a threshold E-value of 1 × 10-4 from the four types of plasma samples.
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3
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Del Ben M, Overi D, Polimeni L, Carpino G, Labbadia G, Baratta F, Pastori D, Noce V, Gaudio E, Angelico F, Mancone C. Overexpression of the Vitronectin V10 Subunit in Patients with Nonalcoholic Steatohepatitis: Implications for Noninvasive Diagnosis of NASH. Int J Mol Sci 2018; 19:ijms19020603. [PMID: 29463024 PMCID: PMC5855825 DOI: 10.3390/ijms19020603] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/13/2018] [Accepted: 02/16/2018] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic steatohepatitis (NASH) is the critical stage of nonalcoholic fatty liver disease (NAFLD). The persistence of necroinflammatory lesions and fibrogenesis in NASH is the leading cause of liver cirrhosis and, ultimately, hepatocellular carcinoma. To date, the histological examination of liver biopsies, albeit invasive, remains the means to distinguish NASH from simple steatosis (NAFL). Therefore, a noninvasive diagnosis by serum biomarkers is eagerly needed. Here, by a proteomic approach, we analysed the soluble low-molecular-weight protein fragments flushed out from the liver tissue of NAFL and NASH patients. On the basis of the assumption that steatohepatitis leads to the remodelling of the liver extracellular matrix (ECM), NASH-specific fragments were in silico analysed for their involvement in the ECM molecular composition. The 10 kDa C-terminal fragment of the ECM protein vitronectin (VTN) was then selected as a promising circulating biomarker in discriminating NASH. The analysis of sera of patients provided these major findings: the circulating VTN fragment (i) is overexpressed in NASH patients and positively correlates with the NASH activity score (NAS); (ii) originates from the disulfide bond reduction between the V10 and the V65 subunits. In conclusion, V10 determination in the serum could represent a reliable tool for the noninvasive discrimination of NASH from simple steatosis.
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Affiliation(s)
- Maria Del Ben
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
| | - Diletta Overi
- Department of Anatomical, Histological, Forensic Medicine and Orthopedics Sciences, Sapienza University of Rome, Via Borelli 50, 00161 Rome, Italy.
| | - Licia Polimeni
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
| | - Guido Carpino
- Department of Movement, Human and Health Sciences, Division of Health Sciences, University of Rome "Foro Italico", Piazza Lauro De Bosis 6, 00135 Rome, Italy.
| | - Giancarlo Labbadia
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
| | - Francesco Baratta
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
- Department of Anatomical, Histological, Forensic Medicine and Orthopedics Sciences, Sapienza University of Rome, Via Borelli 50, 00161 Rome, Italy.
| | - Daniele Pastori
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
- Department of Anatomical, Histological, Forensic Medicine and Orthopedics Sciences, Sapienza University of Rome, Via Borelli 50, 00161 Rome, Italy.
| | - Valeria Noce
- Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
| | - Eugenio Gaudio
- Department of Anatomical, Histological, Forensic Medicine and Orthopedics Sciences, Sapienza University of Rome, Via Borelli 50, 00161 Rome, Italy.
| | - Francesco Angelico
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
| | - Carmine Mancone
- Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
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4
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Candidate Urine Peptide Biomarkers for IgA Nephropathy: Where Are We Now? DISEASE MARKERS 2018; 2018:5205831. [PMID: 29606986 PMCID: PMC5827886 DOI: 10.1155/2018/5205831] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 11/29/2017] [Accepted: 12/12/2017] [Indexed: 12/24/2022]
Abstract
Early detection, prognosis, and management of IgA nephropathy (IgAN) remain a challenge. Histological examination of renal tissue still comprises the only way to confirm an IgAN diagnosis. It is of great importance to establish noninvasive diagnostic, prognostic, and predictive biomarkers that would improve the clinical care and outcome of patients suffering from IgAN. This review summarises the findings from previous mass spectrometry- (MS-) based studies dedicated to the discovery of urinary peptide profiles specific to IgAN. There is a substantial number of urinary peptides that have been discovered to date, which show promise as biomarkers of IgAN; however, all of them require further, rigorous validation in well-planned studies, involving a large number of subjects who represent diverse and numerous populations.
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5
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Ciasca G, Papi M, Businaro L, Campi G, Ortolani M, Palmieri V, Cedola A, De Ninno A, Gerardino A, Maulucci G, De Spirito M. Recent advances in superhydrophobic surfaces and their relevance to biology and medicine. BIOINSPIRATION & BIOMIMETICS 2016; 11:011001. [PMID: 26844980 DOI: 10.1088/1748-3190/11/1/011001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
By mimicking naturally occurring superhydrophobic surfaces, scientists can now realize artificial surfaces on which droplets of a few microliters of water are forced to assume an almost spherical shape and an extremely high contact angle. In recent decades, these surfaces have attracted much attention due to their technological applications for anti-wetting and self-cleaning materials. Very recently, researchers have shifted their interest to investigate whether superhydrophobic surfaces can be exploited to study biological systems. This research effort has stimulated the design and realization of new devices that allow us to actively organize, visualize and manipulate matter at both the microscale and nanoscale levels. Such precise control opens up wide applications in biomedicine, as it allows us to directly manipulate objects at the typical length scale of cells and macromolecules. This progress report focuses on recent biological and medical applications of superhydrophobicity. Particular regard is paid to those applications that involve the detection, manipulation and study of extremely small quantities of molecules, and to those that allow high throughput cell and biomaterial screening.
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Affiliation(s)
- G Ciasca
- Istituto di Fisica, Università Cattolica del Sacro Cuore, Largo F Vito 1, 00168 Rome, Italy
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6
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Cheon DH, Nam EJ, Park KH, Woo SJ, Lee HJ, Kim HC, Yang EG, Lee C, Lee JE. Comprehensive Analysis of Low-Molecular-Weight Human Plasma Proteome Using Top-Down Mass Spectrometry. J Proteome Res 2015; 15:229-44. [DOI: 10.1021/acs.jproteome.5b00773] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Dong Huey Cheon
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
- Interdisciplinary
Program of Integrated Biotechnology, Sogang University, Seoul 121-742, Republic of Korea
| | - Eun Ji Nam
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
- Department
of Chemistry, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Kyu Hyung Park
- Department
of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 463-707, Republic of Korea
| | - Se Joon Woo
- Department
of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 463-707, Republic of Korea
| | - Hye Jin Lee
- Department
of Chemistry, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Hee Cheol Kim
- Department
of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Republic of Korea
| | - Eun Gyeong Yang
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
| | - Cheolju Lee
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
- Department
of Biological Chemistry, University of Science and Technology, Daejeon 305-333, Republic of Korea
| | - Ji Eun Lee
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
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7
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Chen L, Zhai L, Li Y, Li N, Zhang C, Ping L, Chang L, Wu J, Li X, Shi D, Xu P. Development of gel-filter method for high enrichment of low-molecular weight proteins from serum. PLoS One 2015; 10:e0115862. [PMID: 25723528 PMCID: PMC4344347 DOI: 10.1371/journal.pone.0115862] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 12/02/2014] [Indexed: 11/18/2022] Open
Abstract
The human serum proteome has been extensively screened for biomarkers. However, the large dynamic range of protein concentrations in serum and the presence of highly abundant and large molecular weight proteins, make identification and detection changes in the amount of low-molecular weight proteins (LMW, molecular weight ≤ 30kDa) difficult. Here, we developed a gel-filter method including four layers of different concentration of tricine SDS-PAGE-based gels to block high-molecular weight proteins and enrich LMW proteins. By utilizing this method, we identified 1,576 proteins (n = 2) from 10 μL serum. Among them, 559 (n = 2) proteins belonged to LMW proteins. Furthermore, this gel-filter method could identify 67.4% and 39.8% more LMW proteins than that in representative methods of glycine SDS-PAGE and optimized-DS, respectively. By utilizing SILAC-AQUA approach with labeled recombinant protein as internal standard, the recovery rate for GST spiked in serum during the treatment of gel-filter, optimized-DS, and ProteoMiner was 33.1 ± 0.01%, 18.7 ± 0.01% and 9.6 ± 0.03%, respectively. These results demonstrate that the gel-filter method offers a rapid, highly reproducible and efficient approach for screening biomarkers from serum through proteomic analyses.
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Affiliation(s)
- Lingsheng Chen
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 102206, P. R. China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, P. R. China
| | - Linhui Zhai
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 102206, P. R. China
| | - Yanchang Li
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 102206, P. R. China
| | - Ning Li
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 102206, P. R. China
| | - Chengpu Zhang
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 102206, P. R. China
| | - Lingyan Ping
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 102206, P. R. China
| | - Lei Chang
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 102206, P. R. China
| | - Junzhu Wu
- Department of Biochemistry, School of Medicine, Wuhan University, Wuhan, 430071, P. R. China
| | - Xiangping Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, P. R. China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, P. R. China
- * E-mail: (DSS); (PX)
| | - Ping Xu
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 102206, P. R. China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, P. R. China
- * E-mail: (DSS); (PX)
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8
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Waybright TJ, Chan KC, Veenstra TD, Xiao Z. Preparation of the low molecular weight serum proteome for mass spectrometry analysis. Methods Mol Biol 2014; 1061:279-89. [PMID: 23963944 DOI: 10.1007/978-1-62703-589-7_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The discovery of viable biomarkers or indicators of disease states is complicated by the inherent complexity of the chosen biological specimen. Every sample, whether it is serum, plasma, urine, tissue, cells, or a host of others, contains thousands of large and small components, each interacting in multiple ways. The need to concentrate on a group of these components to narrow the focus on a potential biomarker candidate becomes, out of necessity, a priority, especially in the search for immune-related low molecular weight serum biomarkers. One such method in the field of proteomics is to divide the sample proteome into groups based on the size of the protein, analyze each group, and mine the data for statistically significant items. This chapter details a portion of this method, concentrating on a method for fractionating and analyzing the low molecular weight proteome of human serum.
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Affiliation(s)
- Timothy J Waybright
- Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, Frederick National Laboratory for Cancer Research, SAIC-Frederick, Frederick, MD, USA
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9
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Ahmed FE. Utility of mass spectrometry for proteome ana lysis: part I. Conceptual and experimental approaches. Expert Rev Proteomics 2014; 5:841-64. [DOI: 10.1586/14789450.5.6.841] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Ahmad-Tajudin A, Adler B, Ekström S, Marko-Varga G, Malm J, Lilja H, Laurell T. MALDI-target integrated platform for affinity-captured protein digestion. Anal Chim Acta 2013; 807:1-8. [PMID: 24356215 DOI: 10.1016/j.aca.2013.08.051] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 08/30/2013] [Indexed: 12/13/2022]
Abstract
To address immunocapture of proteins in large cohorts of clinical samples high throughput sample processing is required. Here a method using the proteomic sample platform, ISET (integrated selective enrichment target) that integrates highly specific immunoaffinity capture of protein biomarker, digestion and sample cleanup with a direct interface to mass spectrometry is presented. The robustness of the on-ISET protein digestion protocol was validated by MALDI MS analysis of model proteins, ranging from 40 fmol to 1 pmol per nanovial. On-ISET digestion and MALDI MS/MS analysis of immunoaffinity captured disease-associated biomarker PSA (prostate specific antigen) from human seminal plasma are presented.
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Affiliation(s)
- Asilah Ahmad-Tajudin
- Department of Measurement Technology and Industrial Electrical Engineering, Lund University, Box 118, 22100 Lund, Sweden; CREATE Health, Lund University, Medicon Village, Bldn 406, 22381 Lund, Sweden; Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Belinda Adler
- Department of Measurement Technology and Industrial Electrical Engineering, Lund University, Box 118, 22100 Lund, Sweden; CREATE Health, Lund University, Medicon Village, Bldn 406, 22381 Lund, Sweden.
| | - Simon Ekström
- Department of Measurement Technology and Industrial Electrical Engineering, Lund University, Box 118, 22100 Lund, Sweden; CREATE Health, Lund University, Medicon Village, Bldn 406, 22381 Lund, Sweden
| | - György Marko-Varga
- Department of Measurement Technology and Industrial Electrical Engineering, Lund University, Box 118, 22100 Lund, Sweden
| | - Johan Malm
- Department of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Skåne University Hospital, 20502 Skåne, Sweden
| | - Hans Lilja
- Department of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Skåne University Hospital, 20502 Skåne, Sweden; Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Surgery (Urology Service), Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine (GU Oncology Service), Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; Institute of Biomedical Technology, University of Tampere, Tampere 33520, Finland
| | - Thomas Laurell
- Department of Measurement Technology and Industrial Electrical Engineering, Lund University, Box 118, 22100 Lund, Sweden; CREATE Health, Lund University, Medicon Village, Bldn 406, 22381 Lund, Sweden; Department of Biomedical Engineering, Dongguk University, Seoul, Republic of Korea
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11
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Tajudin AA, Petersson K, Lenshof A, Swärd-Nilsson AM, Aberg L, Marko-Varga G, Malm J, Lilja H, Laurell T. Integrated acoustic immunoaffinity-capture (IAI) platform for detection of PSA from whole blood samples. LAB ON A CHIP 2013; 13:1790-6. [PMID: 23515524 PMCID: PMC4207374 DOI: 10.1039/c3lc41269e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
On-chip detection of low abundant protein biomarkers is of interest to enable point-of-care diagnostics. Using a simple form of integration, we have realized an integrated microfluidic platform for the detection of prostate specific antigen (PSA), directly in anti-coagulated whole blood. We combine acoustophoresis-based separation of plasma from undiluted whole blood with a miniaturized immunoassay system in a polymer manifold, demonstrating improved assay speed on our Integrated Acoustic Immunoaffinity-capture (IAI) platform. The IAI platform separates plasma from undiluted whole blood by means of acoustophoresis and provides cell free plasma of clinical quality at a rate of 10 uL/min for an online immunoaffinity-capture of PSA on a porous silicon antibody microarray. The whole blood input (hematocrit 38-40%) rate was 50 μl min(-1) giving a plasma volume fraction yield of ≈33%. PSA was immunoaffinity-captured directly from spiked female whole blood samples at clinically significant levels of 1.7-100 ng ml(-1) within 15 min and was subsequently detected via fluorescence readout, showing a linear response over the entire range with a coefficient of variation of 13%.
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Affiliation(s)
- A Ahmad Tajudin
- Department of Measurement Technology and Industrial Electrical Engineering, Lund University, Lund, Sweden
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12
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Tan J, Zhao WJ, Yu JK, Ma S, Sailor MJ, Wu JM. Capture, enrichment, and mass spectrometric detection of low-molecular-weight biomarkers with nanoporous silicon microparticles. Adv Healthc Mater 2012. [PMID: 23184826 DOI: 10.1002/adhm.201200161] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mining the disease information contained in the low-molecular-weight range of a proteomic profile is becoming of increasing interest in cancer research. This work evaluates the ability of nanoporous silicon microparticles (NPSMPs) to capture, enrich, protect, and detect low-molecular-weight peptides (LMWPs) sieved from a pool of highly abundant plasma proteins. The average pore size and porosity of NPSMPs are controlled by the electrochemical preparation conditions, and the critical parameters for admission or exclusion of protein with a definite molecular weight are determined by reflectometric-interference Fourier transform spectroscopy (RIFTS). Sodium dodecyl sulfate polyacrylamide-gel electrophoresis (SDS-PAGE) and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) analysis of the proteins captured by the NPSMPs show that the chemical nature of the NPSMPs surface and the solution pH also play vital roles in determining the affinity of NPSMPs for target analytes. It is found that carboxyl-terminated porous microparticles with a porosity of 26% (pore diameter around 9.0 nm) specifically fractionate, enrich and protect LMWPs sieved from either simulated samples or human serum samples. Moreover, NPSMPs containing captured peptides can be directly spotted onto a MALDI plate. When placed in a conventional MALDI matrix, laser irradiation of the particles results in the release of the target peptides confined in the nanopores, which are then ionized and detected in the MALDI experiment. As a proof-of-principle test case, mass spectra of NPSMPs prepared using serum from colorectal cancer patients and from control patients can be clearly distinguished by statistical analysis. The work demonstrates the utility of the method for discovery of biomarkers in the untapped LMWP fraction of human serum, which can be of significant value in the early diagnosis and management of diseases.
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Affiliation(s)
- Jie Tan
- Department of Chemistry, Zhejiang University, Hangzhou, China
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13
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Greening DW, Simpson RJ. Low-molecular weight plasma proteome analysis using centrifugal ultrafiltration. Methods Mol Biol 2011; 728:109-124. [PMID: 21468943 DOI: 10.1007/978-1-61779-068-3_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The low-molecular weight fraction (LMF) of the human plasma proteome is an invaluable source of biological information, especially in the context of identifying plasma-based biomarkers of disease. This protocol outlines a standardized procedure for the rapid/reproducible LMF profiling of human plasma samples using centrifugal ultrafiltration fractionation, followed by 1D-SDS-PAGE separation and nano-LC-MS/MS. Ultrafiltration is a convective process that uses anisotropic semipermeable membranes to separate macromolecular species on the basis of size. We have optimized centrifugal ultrafiltration for plasma fractionation with respect to buffer and solvent composition, centrifugal force, duration and temperature to facilitate >95% recovery, and enrichment of low-M (r) components from human plasma. Using this protocol, >260 unique peptides can be identified from a single plasma profiling experiment using 100 μL of plasma (Greening and Simpson, J Proteomics 73:637-648, 2010). The efficacy of this method is demonstrated by the identification, for the first time, of several plasma proteins (e.g., protein KIAA0649 (Q9Y4D3), rheumatoid factor D5, serine protease inhibitor A3, and transmembrane adapter protein PAG) previously not reported in extant high-confidence Human Proteome Organization Plasma Proteome Project datasets.
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Affiliation(s)
- David W Greening
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Australia
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14
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Randall SA, McKay MJ, Molloy MP. Evaluation of blood collection tubes using selected reaction monitoring MS: Implications for proteomic biomarker studies. Proteomics 2010; 10:2050-6. [DOI: 10.1002/pmic.200900517] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Richens JL, Lunt EAM, Sanger D, McKenzie G, O'Shea P. Avoiding nonspecific interactions in studies of the plasma proteome: practical solutions to prevention of nonspecific interactions for label-free detection of low-abundance plasma proteins. J Proteome Res 2010; 8:5103-10. [PMID: 19817376 DOI: 10.1021/pr900487y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The molecular constitution of blood can be highly representative of the physiological state of an individual and offers an ideal target for studies of biomarkers. High-abundance plasma proteins, particularly albumin, dominate the plasma proteome, but it is the low-abundance proteins (such as cytokines) that are commonly associated with many pathophysiological states. Several detection strategies, and particularly those that involve label-free detection, are available for low-abundance protein detection in plasma, but all can be severely compromised by the high-abundance of serum albumin. In the present study, we examine the effect of albumin interference on accurate label-free detection by protein microarrays. Albumin was found to disrupt specific antigen-antibody binding interactions of low-abundance proteins. In clinical analysis, where it is imperative to preserve the integrity of samples, depletion of albumin may further undermine quantitative measurements. We have optimized procedures that permit accurate analysis to be undertaken without the need for prior treatment of samples. The emphasis is placed on disrupting nonspecific interactions including both electrostatic (i.e., Colulombic) and electrodynamic (hydrophobic and other nonpolar based) interactions. These protocols appear to be generic with potential applications in several areas of analytical biotechnology.
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Affiliation(s)
- Joanna L Richens
- Cell Biophysics Group, School of Biology, University of Nottingham, Nottingham, England, NG7 2RD, UK
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A centrifugal ultrafiltration strategy for isolating the low-molecular weight (≤25K) component of human plasma proteome. J Proteomics 2010; 73:637-48. [DOI: 10.1016/j.jprot.2009.09.013] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 09/14/2009] [Accepted: 09/16/2009] [Indexed: 02/03/2023]
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Bakun M, Karczmarski J, Poznanski J, Rubel T, Rozga M, Malinowska A, Sands D, Hennig E, Oledzki J, Ostrowski J, Dadlez M. An integrated LC-ESI-MS platform for quantitation of serum peptide ladders. Application for colon carcinoma study. Proteomics Clin Appl 2009; 3:932-46. [PMID: 21136997 DOI: 10.1002/prca.200800111] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 02/23/2009] [Accepted: 03/06/2009] [Indexed: 11/07/2022]
Abstract
Mounting evidence indicates that MS analysis of the human blood peptidome allows to distinguish between cancer and non-cancer samples, giving promise for a new MS-based diagnostic tool. However, several aspects of already published work have been criticized and demand for more methodical approach has been formulated. Motivated by this we undertook a systematic study of the plasma and serum peptidome using an integrated ESI-LC-MS-based platform, equipped with new data analysis tools for relative and absolute peptide quantitation. We used a high resolution LC-ESI-MS to analyze well-separated MS signals corresponding to peptides, and measured the variability of >1000 peptide signal amplitudes across a set of plasma and serum samples from healthy individuals. By spiking serum samples with known amounts of isotopically labeled versions of a selected set of peptides we measured the variability of their absolute concentration in this sample set and demonstrated a strong influence of clotting time on the concentration of these peptides in serum. Finally, we used this new LC-ESI-MS analytical platform for the differential analysis of healthy versus colon cancer serum samples and found that it was possible to distinguish the two groups with 89.8% sensitivity and 94.6% specificity.
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Affiliation(s)
- Magda Bakun
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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Karbassi ID, Nyalwidhe JO, Wilkins CE, Cazares LH, Lance RS, Semmes OJ, Drake RR. Proteomic Expression Profiling and Identification of Serum Proteins Using Immobilized Trypsin Beads with MALDI-TOF/TOF. J Proteome Res 2009; 8:4182-92. [DOI: 10.1021/pr800836c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Izabela D. Karbassi
- George L. Wright, Jr. Center for Biomedical Proteomics, Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - Julius O. Nyalwidhe
- George L. Wright, Jr. Center for Biomedical Proteomics, Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - Christopher E. Wilkins
- George L. Wright, Jr. Center for Biomedical Proteomics, Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - Lisa H. Cazares
- George L. Wright, Jr. Center for Biomedical Proteomics, Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - Raymond S. Lance
- George L. Wright, Jr. Center for Biomedical Proteomics, Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - O. John Semmes
- George L. Wright, Jr. Center for Biomedical Proteomics, Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507
| | - Richard R. Drake
- George L. Wright, Jr. Center for Biomedical Proteomics, Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507
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Manuel González-Buitrago J, Ferreira L, Del Carmen Muñiz M. Proteómica clínica y nuevos biomarcadores en los líquidos biológicos. Med Clin (Barc) 2008; 131:426-34. [DOI: 10.1157/13126219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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