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Zhuang YJ, Mangwiro Y, Wake M, Saffery R, Greaves RF. Multi-omics analysis from archival neonatal dried blood spots: limitations and opportunities. Clin Chem Lab Med 2022; 60:1318-1341. [PMID: 35670573 DOI: 10.1515/cclm-2022-0311] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/25/2022] [Indexed: 02/07/2023]
Abstract
Newborn screening (NBS) programs operate in many countries, processing millions of dried bloodspot (DBS) samples annually. In addition to early identification of various adverse health outcomes, these samples have considerable potential as a resource for population-based research that could address key questions related to child health. The feasibility of archival DBS samples for emerging targeted and untargeted multi-omics analysis has not been previously explored in the literature. This review aims to critically evaluate the latest advances to identify opportunities and challenges of applying omics analyses to NBS cards in a research setting. Medline, Embase and PubMed databases were searched to identify studies utilizing DBS for genomic, proteomic and metabolomic assays. A total of 800 records were identified after removing duplicates, of which 23 records were included in this review. These papers consisted of one combined genomic/metabolomic, four genomic, three epigenomic, four proteomic and 11 metabolomic studies. Together they demonstrate that the increasing sensitivity of multi-omic analytical techniques makes the broad use of NBS samples achievable for large cohort studies. Maintaining the pre-analytical integrity of the DBS sample through storage at temperatures below -20 °C will enable this important resource to be fully realized in a research capacity.
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Affiliation(s)
- Yuan-Jessica Zhuang
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Yeukai Mangwiro
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Melissa Wake
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Richard Saffery
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Ronda F Greaves
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
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2
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Nguyen MT, Halvorsen TG, Thiede B, Reubsaet L. Smart proteolysis samplers for pre‐lab bottom‐up protein analysis – Performance of on‐paper digestion compared to conventional digestion. Separation Science Plus 2022. [DOI: 10.1002/sscp.202100062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Minh Thao Nguyen
- Section of Pharmaceutical Chemistry, Department of Pharmacy University of Oslo Oslo Norway
| | | | - Bernd Thiede
- Section of Biochemistry and Molecular Biology, Department of Biosciences University of Oslo Oslo Norway
| | - Léon Reubsaet
- Section of Pharmaceutical Chemistry, Department of Pharmacy University of Oslo Oslo Norway
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3
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Pollard S, Anderson JC, Bah F, Mateus M, Sidhu M, Simmons D. Non-Lethal Blood Sampling of Fish in the lab and Field With Methods for Dried Blood Plasma Spot Omic Analyses. Front Genet 2022; 13:795348. [PMID: 35401689 PMCID: PMC8988233 DOI: 10.3389/fgene.2022.795348] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
There is global acknowledgment that humane methods in animal research are a priority, but few environmental effects monitoring programs use nonlethal methods for fish. The goal of the present study was to determine the impacts of sampling small volumes of blood in larger-bodied fish on survival and healing. In addition to evaluating survival following blood sampling, we evaluated the utility of dried blood spots as an alternative for sample processing and storage in the field. In our approach, we housed 80 rainbow trout (Oncorhynchus mykiss) in our flow-through aquatic facility. We then anaesthetized using MS-222 and sampled 1 μl/g bw of blood via puncture of the caudal vasculature. We tested four different post-blood sampling treatments on the puncture wound: 1. application of liquid bandage; 2. a swab of betadine; 3. a swab of fish mucous; and 4. compared survival outcomes to a group where no post-treatment was performed (negative control). Overall, we observed 90% survival among all treatments, with the most effective approach being the negative control (100% survival). Based upon these results, we repeated the blood sampling with no-post treatment by housing 20 rainbow trout (not previously tested upon) in cages at a nearby creek and monitored survival for 2 weeks post sampling. The survival rate was 95% with full healing of the puncture site in all subjects. In addition to this, we tested the efficacy of dry blood spotting on proteomic, lipidomic and amino acid analysis as an alternative method for blood sample processing and storage. It was found that dried plasma spotting using parafilm in conjunction with a modified Bligh-Dyer extraction offered the best balance for good recovery of protein, lipid and amino acids relative to wet plasma and Noviplex dried plasma spot cards. In this article, we will present the detailed results of these combined studies and describe what we have determined to be the safest non-lethal blood sampling protocol.
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Affiliation(s)
- S Pollard
- Aquatic Omics Laboratory, Department of Biology, Ontario Tech University, Oshawa, ON, Canada
| | - J C Anderson
- Aquatic Omics Laboratory, Department of Biology, Ontario Tech University, Oshawa, ON, Canada
| | - F Bah
- Aquatic Omics Laboratory, Department of Biology, Ontario Tech University, Oshawa, ON, Canada
| | - M Mateus
- Aquatic Omics Laboratory, Department of Biology, Ontario Tech University, Oshawa, ON, Canada
| | - M Sidhu
- Aquatic Omics Laboratory, Department of Biology, Ontario Tech University, Oshawa, ON, Canada
| | - Dbd Simmons
- Aquatic Omics Laboratory, Department of Biology, Ontario Tech University, Oshawa, ON, Canada
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Molloy MP, Hill C, O'Rourke MB, Chandra J, Steffen P, McKay MJ, Pascovici D, Herbert BR. Proteomic Analysis of Whole Blood Using Volumetric Absorptive Microsampling for Precision Medicine Biomarker Studies. J Proteome Res 2022; 21:1196-1203. [PMID: 35166117 DOI: 10.1021/acs.jproteome.1c00971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microsampling of patient blood promises several benefits over conventional phlebotomy practices to facilitate precision medicine studies. These include at-home patient blood collection, supporting telehealth monitoring, minimal postcollection processing, and compatibility with nonrefrigerated transport and storage. However, for proteomic biomarker studies, mass spectrometry of whole blood has generally been avoided in favor of using plasma or serum obtained from venepuncture. We evaluated the use of a volumetric absorptive microsampling (VAMS) device as a sample preparation matrix to enable LC-MS proteomic analyses of dried whole blood. We demonstrated the detection and robust quantitation of up to 1600 proteins from single-shot shotgun-LC-MS analysis of dried whole blood, greatly enhancing proteome depth compared with conventional single-shot LC-MS analyses of undepleted plasma. Some proteins not previously reported in blood were detected using this approach. Various washing reagents were used to demonstrate that proteins can be preferentially removed from VAMS devices prior to downstream analyses. We provide a demonstration that archival frozen blood cell pellets housed under long-term storage (exceeding 5 years) are compatible with VAMS to enable quantitation of potential biomarker proteins from biobank repositories. These demonstrations are important steps in establishing viable analysis workflows to underpin large-scale precision medicine studies. Data are available via ProteomeXchange with the identifier PXD028605.
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Affiliation(s)
- Mark P Molloy
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
| | | | - Matthew B O'Rourke
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
| | - Jason Chandra
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
| | - Pascal Steffen
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
| | - Matthew J McKay
- Bowel Cancer and Biomarker Research Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia
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Nakajima D, Ohara O, Kawashima Y. Toward proteome-wide exploration of proteins in dried blood spots using liquid chromatography-coupled mass spectrometry. Proteomics 2021; 21:e2100019. [PMID: 34379369 DOI: 10.1002/pmic.202100019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 08/07/2021] [Accepted: 08/09/2021] [Indexed: 11/12/2022]
Abstract
Dried blood spot (DBS) sampling is a method with advantages over conventional blood sampling in relation to collection, cost, storage, and transportation. Such advantages have led to its wide use in newborn screening (NBS). Although target analysis of various biomolecules is conducted in NBS, protein quantification-based NBS is still in its infancy. Thus, it is important to clarify how many proteins could be quantitatively detected in DBS samples using advanced liquid chromatography-mass spectrometry (LC-MS/MS) technologies; a catalog of proteins detectable in DBSs by LC-MS/MS will enable us to judge which causative proteins in genetic diseases can be monitored at the protein level in NBS. In this review, we outline conventional proteome analyses of DBSs with a distinction between target and nontarget approaches. Additionally, we discuss the future perspectives for proteome analysis of DBSs in NBS of genetic diseases. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Daisuke Nakajima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
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Okai CA, Wölter M, Russ M, Koy C, Petre BA, Rath W, Pecks U, Glocker MO. Profiling of intact blood proteins by matrix-assisted laser desorption/ionization mass spectrometry without the need for freezing - Dried serum spots as future clinical tools for patient screening. Rapid Commun Mass Spectrom 2021; 35:e9121. [PMID: 33955049 DOI: 10.1002/rcm.9121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/30/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE To open up new ways for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS)-based patient screening, blood serum is the most preferred specimen because of its richness in patho-physiological information and due to ease of collection. To overcome deleterious freeze/thaw cycles and to reduce high costs for shipping and storage, we sought to develop a procedure which enables MALDI-MS protein profiling of blood serum proteins without the need for serum freezing. METHODS Blood sera from patients/donors were divided into portions which after pre-incubation were fast frozen. Thawed aliquots were deposited on filter paper discs and air-dried at room temperature. Intact serum proteins were eluted with acid-labile detergent-containing solutions and were desalted by employing a reversed-phase bead system. Purified protein solutions were screened by MALDI-MS using standardized instrument settings. RESULTS MALDI mass spectra from protein solutions which were eluted from filter paper discs and desalted showed on average 25 strong ion signals (mass range m/z 6000 to 10,000) from intact serum proteins (apolipoproteins, complement proteins, transthyretin and hemoglobin) and from proteolytic processing products. Semi-quantitative analysis of three ion pairs: m/z 6433 and 6631, m/z 8205 and 8916, as well as m/z 9275 and 9422, indicated that the mass spectra from either pre-incubated fast-frozen serum or pre-incubated dried serum spot eluted serum contained the same information on protein composition. CONCLUSIONS A workflow that avoids the conventional cold-chain and yet enables the investigation of intact serum proteins and/or serum proteolysis products by MALDI-MS profiling was developed. The presented protocol tremendously broadens the clinical application of MALDI-MS and simultaneously allows a reduction in the costs for storage and shipping of serum samples. This will pave the way for clinical screening of patients also in areas with limited access to health care systems, and/or specialized laboratories.
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Affiliation(s)
- Charles A Okai
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
| | - Manja Wölter
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
- Department of Obstetrics and Gynecology, Medical Faculty, University of Rostock, Clinic Südstadt, Rostock, 18059, Germany
| | - Manuela Russ
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
| | - Cornelia Koy
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
| | - Brindusa A Petre
- Department of Chemistry, Alexandru Ioan Cuza University, Bd. Carol I, No.11, Iasi, 700506, Romania
- Transcend Research Center, Regional Institute of Oncology, General Henri Mathias, No.2-4, Iasi, 700483, Romania
| | - Werner Rath
- Department of Obstetrics and Gynecology, Medical Faculty, RWTH Aachen University, Aachen, 52062, Germany
| | - Ulrich Pecks
- Department of Obstetrics and Gynecology, Medical Faculty, University of Schleswig-Holstein, Campus Kiel, Arnold-Heller-Straße 3, Kiel, 24105, Germany
| | - Michael O Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
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Abstract
Early disease diagnosis is necessary to enable timely interventions. Implementation of this vital task in the developing world is challenging owing to limited resources. Diagnostic approaches developed for resource-limited settings have often involved colorimetric tests (based on immunoassays) due to their low cost. Unfortunately, the performance/sensitivity of such simplistic tests are often limited and significantly hinder opportunities for early disease detection. A new criterion for selecting diagnostic tests in low- and middle-income countries is proposed here that is based on performance-to-cost ratio. For example, modern mass spectrometry (MS) now involves analysis of the native sample in the open laboratory environment, enabling applications in many fields, including clinical research, forensic science, environmental analysis, and agriculture. In this critical review, we summarize recent developments in chemistry that enable MS to be applied effectively in developing countries. In particular, we argue that closed automated analytical systems may not offer the analytical flexibility needed in resource-limited settings. Alternative strategies proposed here have potential to be widely accepted in low- and middle-income countries through the utilization of the open-source ambient MS platform that enables microsampling techniques such as dried blood spot to be coupled with miniature mass spectrometers in a centralized analytical platform. Consequently, costs associated with sample handling and maintenance can be reduced by >50% of the total ownership cost, permitting analytical measurements to be operated at high performance-to-cost ratios in the developing world.
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Affiliation(s)
- Suji Lee
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA;
| | - Kavyasree Chintalapudi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA;
| | - Abraham K Badu-Tawiah
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA;
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8
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Friedrich C, Schallenberg S, Kirchner M, Ziehm M, Niquet S, Haji M, Beier C, Neudecker J, Klauschen F, Mertins P. Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories. Nat Commun 2021; 12:3576. [PMID: 34117251 PMCID: PMC8196151 DOI: 10.1038/s41467-021-23855-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are a valuable resource for retrospective clinical studies. Here, we evaluate the feasibility of (phospho-)proteomics on FFPE lung tissue regarding protein extraction, quantification, pre-analytics, and sample size. After comparing protein extraction protocols, we use the best-performing protocol for the acquisition of deep (phospho-)proteomes from lung squamous cell and adenocarcinoma with >8,000 quantified proteins and >14,000 phosphosites with a tandem mass tag (TMT) approach. With a microscaled approach, we quantify 7,000 phosphosites, enabling the analysis of FFPE biopsies with limited tissue amounts. We also investigate the influence of pre-analytical variables including fixation time and heat-assisted de-crosslinking on protein extraction efficiency and proteome coverage. Our improved workflows provide quantitative information on protein abundance and phosphosite regulation for the most relevant oncogenes, tumor suppressors, and signaling pathways in lung cancer. Finally, we present general guidelines to which methods are best suited for different applications, highlighting TMT methods for comprehensive (phospho-)proteome profiling for focused clinical studies and label-free methods for large cohorts.
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Affiliation(s)
- Corinna Friedrich
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany ,grid.419491.00000 0001 1014 0849Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), MDC graduate school, Berlin, Germany ,grid.7468.d0000 0001 2248 7639Humboldt Universität zu Berlin, Institute of Chemistry, Berlin, Germany
| | - Simon Schallenberg
- grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marieluise Kirchner
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Ziehm
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Sylvia Niquet
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Mohamed Haji
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany
| | - Christin Beier
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany
| | - Jens Neudecker
- grid.6363.00000 0001 2218 4662Department of Surgery - Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Frederick Klauschen
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany ,grid.5252.00000 0004 1936 973XInstitute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Philipp Mertins
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
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Nakajima D, Kawashima Y, Shibata H, Yasumi T, Isa M, Izawa K, Nishikomori R, Heike T, Ohara O. Simple and Sensitive Analysis for Dried Blood Spot Proteins by Sodium Carbonate Precipitation for Clinical Proteomics. J Proteome Res 2020; 19:2821-2827. [PMID: 32343581 DOI: 10.1021/acs.jproteome.0c00271] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Dried blood spots (DBS) are widely used for screening biomolecular profiles, including enzymatic activities. However, detection of minor proteins in DBS by liquid chromatography-mass spectrometry (LC-MS/MS) without pre-enrichment remains challenging because of the coexistence of large quantities of hydrophilic proteins. In this study, we address this problem by developing a simple method using sodium carbonate precipitation (SCP). SCP enriches hydrophobic proteins from DBS, allowing substantial removal of soluble proteins. In combination with SCP, we used quantitative LC-MS/MS proteome analysis in a data-independent acquisition mode (DIA) to enhance the sensitivity and quantification limits of proteome analysis. As a result, identification of 1977 proteins in DBS is possible, including 585 disease-related proteins listed in the Online Mendelian Inheritance in Man.
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Affiliation(s)
| | | | - Hirofumi Shibata
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Takahiro Yasumi
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Masahiko Isa
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Kazushi Izawa
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Ryuta Nishikomori
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, Fukuoka 830-0111, Japan
| | - Toshio Heike
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.,Hyogo Prefectural Amagasaki General Medical Center, Hyogo 660-8550, Japan
| | - Osamu Ohara
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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10
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Lombardi V, Carassiti D, Giovannoni G, Lu CH, Adiutori R, Malaspina A. The potential of neurofilaments analysis using dry-blood and plasma spots. Sci Rep 2020; 10:97. [PMID: 31919375 DOI: 10.1038/s41598-019-54310-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022] Open
Abstract
The lack of biomarkers for an early diagnosis of neurodegenerative disorders (NDs) has hampered the development of therapeutics whose effect would be enhanced by a timely intervention. Neurofilaments light chain (Nf-L), an integral part of the axonal structure, has emerged as a robust fluid biomarker for fatal neurodegenerative disorders like amyotrophic lateral sclerosis (ALS). To facilitate large-scale studies into early-stage neurodegeneration, reduce costs of samples collection/processing and cold-chain storage, we describe the measurement of Nf-L in blood fractions obtained from dry blood spots (DBS) and dry plasma spots (DPS), two filter paper-based remote blood collection tools. To test the feasibility of using this approach, Nf-L analysis in DBS/DPS is compared to that in plasma obtained from the same blood sample, looking at Nf-L discriminatory power in the clinical stratification of ALS compared to healthy controls. With the best pre-analytical treatment for total protein recovery and using highly sensitive immunoassays, we report the detection of different Nf-L levels in DBS elute compared to reference plasma and DPS from the same blood samples. However, Nf-L measurement in DBS elutes provides a very good discrimination of ALS from healthy controls which is comparable to that obtained using plasma Nf-L assays. With the available immunodetection methods, we show that Nf-L measurement based on DPS microsampling is similar to that in plasma. The filter-paper biophysical characteristics and the interference of high haemoglobin concentration released by erythrocyte lysis is likely to perturb Nf-L detection in DBS elute. Further studies into DBS-based Nf-L detection and its analytical optimization are needed to make this method suitable for routine Nf-L blood analyses in neurodegeneration.
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11
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Skjærvø Ø, Halvorsen TG, Reubsaet L. All-in-one paper-based sampling chip for targeted protein analysis. Anal Chim Acta 2019; 1089:56-65. [DOI: 10.1016/j.aca.2019.08.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022]
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12
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Kumar P, Agrawal P, Chatterjee K. Challenges and opportunities in blood flow through porous substrate: A design and interface perspective of dried blood spot. J Pharm Biomed Anal 2019; 175:112772. [DOI: 10.1016/j.jpba.2019.07.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/13/2022]
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Abstract
Background and Objectives Latinos residing in the United States exhibit an increased risk for cardiovascular and metabolic diseases compared to non-Latino whites. This elevated risk contributes to a significantly higher prevalence of diabetes and hypertension among Latino adults. Examining biological risk profiles of older Latinos as a “pan-ethnic group” and by Latino subpopulations may help to explain the increased burden of disease in later life among this population. The objective of this study is to document biological risk profiles among a nationally representative sample of older U.S. Latinos by nativity and country of origin. Research Design and Methods We use the 2006–2012 Health and Retirement Study to compare cardiovascular, metabolic, inflammatory and cumulative biological risk among U.S.-born Mexicans, foreign-born Mexicans, U.S.-born Puerto Ricans, island-born Puerto Ricans, U.S.-born “other” Latinos, foreign-born “other” Latinos, and non-Latino whites. Results Older Latinos exhibit heterogeneous biological risk profiles. U.S.-born Mexicans, foreign-born Mexicans, U.S.-born “other” Latinos, and foreign-born “other” Latinos exhibited a higher rate of cardiovascular risk relative to non-Latino whites. In addition, U.S.-born Mexicans, foreign-born Mexicans, island-born Puerto Ricans, and foreign-born “other” Latinos had a higher rate of metabolic risk than non-Latino whites. Island-born Puerto Ricans were the only group to exhibit higher inflammation than non-Latino whites. The observed differences were largely attenuated by socioeconomic status, indicating that high levels of risk among older Latino subpopulations compared to non-Latino whites are associated with lower socioeconomic status. Discussion and Implications Older U.S. Latinos are a demographically diverse population with unique sociocultural characteristics which may contribute to differences in biological risk across the life course that influence disease progression. Examining Latinos by nativity and country of origin may help identify risks specific to individual subpopulations that can lead to culturally appropriate interventions which help prevent and reduce the burden of cardiovascular and metabolic diseases.
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Affiliation(s)
- Catherine García
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California
| | - Jennifer A Ailshire
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California
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14
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Rifflet A, Filali S, Chenau J, Simon S, Fenaille F, Junot C, Carniel E, Becher F. Quantification of low abundance Yersinia pestis markers in dried blood spots by immuno-capture and quantitative high-resolution targeted mass spectrometry. Eur J Mass Spectrom (Chichester) 2019; 25:268-277. [PMID: 31096787 DOI: 10.1177/1469066718795978] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Plague, caused by the bacterium Yersinia pestis, is still present in several countries worldwide. Besides, Y. pestis has been designated as Tier 1 agent, the highest rank of bioterrorism agents. In this context, reliable diagnostic methods are of great importance. Here, we have developed an original workflow based upon dried blood spot for simplified sampling of clinical specimens, and specific immuno-mass spectrometry monitoring of Y. pestis biomarkers. Targeted proteins were selectively enriched from dried blood spot extracts by multiplex immunocapture using antibody-coated magnetic beads. After accelerated on-beads digestion, proteotypic peptides were monitored by multiplex LC-MS/MS through the parallel reaction monitoring mode. The DBS-IC-MS assay was designed to quantify both F1 and LcrV antigens, although 10-fold lower sensitivity was observed with LcrV. The assay was successfully validated for F1 with a lower limit of quantification at 5 ng·mL-1 in spiked blood, corresponding to only 0.1 ng on spots. In vivo quantification of F1 in blood and organ samples was demonstrated in the mouse model of pneumonic plague. The new assay could help to simplify the laboratory confirmation of positive point of care F1 dipstick.
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Affiliation(s)
- Aline Rifflet
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | - Sofia Filali
- 2 Yersinia Research Unit, Institut Pasteur, Paris, France
| | - Jérôme Chenau
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | - Stéphanie Simon
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | - François Fenaille
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | - Christophe Junot
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | | | - François Becher
- 1 Service de Pharmacologie et d'Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, Gif sur Yvette, France
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15
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Affiliation(s)
- Carol E Parker
- University of Victoria - Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Christoph H Borchers
- University of Victoria - Genome British Columbia Proteomics Centre, Victoria, BC, Canada
- Jewish General Hospital Proteomics Laboratory, McGill University, Lady Davis Institute, Montréal, QC, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- Department of Oncology, Jewish General Hospital Proteomics Centre, McGill University, Montreal, QC, Canada
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16
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Yano Y, Grigoryan H, Schiffman C, Edmands W, Petrick L, Hall K, Whitehead T, Metayer C, Dudoit S, Rappaport S. Untargeted adductomics of Cys34 modifications to human serum albumin in newborn dried blood spots. Anal Bioanal Chem 2019; 411:2351-2362. [PMID: 30783713 PMCID: PMC6461474 DOI: 10.1007/s00216-019-01675-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/06/2018] [Accepted: 02/06/2019] [Indexed: 02/06/2023]
Abstract
Metabolism of chemicals from the diet, exposures to xenobiotics, the microbiome, and lifestyle factors (e.g., smoking, alcohol intake) produce electrophiles that react with nucleophilic sites in circulating proteins, notably Cys34 of human serum albumin (HSA). To discover potential risk factors resulting from in utero exposures, we are investigating HSA-Cys34 adducts in archived newborn dried blood spots (DBS) that reflect systemic exposures during the last month of gestation. The workflow includes extraction of proteins from DBS, measurement of hemoglobin (Hb) to normalize for blood volume, addition of methanol to enrich HSA by precipitation of Hb and other interfering proteins, digestion with trypsin, and detection of HSA-Cys34 adducts via nanoflow liquid chromatography-high-resolution mass spectrometry. As proof-of-principle, we applied the method to 49 archived DBS collected from newborns whose mothers either actively smoked during pregnancy or were nonsmokers. Twenty-six HSA-Cys34 adducts were detected, including Cys34 oxidation products, mixed disulfides with low molecular weight thiols (e.g., cysteine, homocysteine, glutathione, cysteinylglycine), and other modifications. Data were normalized with a novel method ("scone") to remove unwanted technical variation arising from HSA digestion, blood volume, DBS age, mass spectrometry analysis, and batch effects. Using an ensemble of linear and nonlinear models, the Cys34 adduct of cyanide was found to consistently discriminate between newborns of smoking and nonsmoking mothers with a mean fold change (smoking/nonsmoking) of 1.31. These results indicate that DBS adductomics is suitable for investigating in utero exposures to reactive chemicals and metabolites that may influence disease risks later in life.
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Affiliation(s)
- Yukiko Yano
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Hasmik Grigoryan
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Courtney Schiffman
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - William Edmands
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Lauren Petrick
- The Senator Frank R. Lautenberg Environmental Health Sciences Laboratory, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Katie Hall
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Todd Whitehead
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, 94720, USA
- Center for Integrative Research on Childhood Leukemia and the Environment, University of California, Berkeley, CA, 94720, USA
| | - Catherine Metayer
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, 94720, USA
- Center for Integrative Research on Childhood Leukemia and the Environment, University of California, Berkeley, CA, 94720, USA
| | - Sandrine Dudoit
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Stephen Rappaport
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, 94720, USA.
- Center for Integrative Research on Childhood Leukemia and the Environment, University of California, Berkeley, CA, 94720, USA.
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17
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Rosting C, Yu J, Cooper HJ. High Field Asymmetric Waveform Ion Mobility Spectrometry in Nontargeted Bottom-up Proteomics of Dried Blood Spots. J Proteome Res 2018; 17:1997-2004. [DOI: 10.1021/acs.jproteome.7b00746] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Jinglei Yu
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Helen J. Cooper
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
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18
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Nys G, Kok MG, Servais AC, Fillet M. Beyond dried blood spot: Current microsampling techniques in the context of biomedical applications. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.10.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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19
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Choi NY, Hwang H, Ji ES, Park GW, Lee JY, Lee HK, Kim JY, Yoo JS. Direct analysis of site-specific N-glycopeptides of serological proteins in dried blood spot samples. Anal Bioanal Chem 2017; 409:4971-81. [DOI: 10.1007/s00216-017-0438-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/22/2017] [Accepted: 05/29/2017] [Indexed: 10/19/2022]
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20
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Lehmann S, Picas A, Tiers L, Vialaret J, Hirtz C. Clinical perspectives of dried blood spot protein quantification using mass spectrometry methods. Crit Rev Clin Lab Sci 2017; 54:173-184. [DOI: 10.1080/10408363.2017.1297358] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Sylvain Lehmann
- Laboratory of Biochemistry and Clinical Proteomics, CHU Montpellier, Institute of Regenerative Medicine & Biotherapy, Montpellier, France
| | - Alexia Picas
- Laboratory of Biochemistry and Clinical Proteomics, CHU Montpellier, Institute of Regenerative Medicine & Biotherapy, Montpellier, France
| | - Laurent Tiers
- Laboratory of Biochemistry and Clinical Proteomics, CHU Montpellier, Institute of Regenerative Medicine & Biotherapy, Montpellier, France
| | - Jerome Vialaret
- Laboratory of Biochemistry and Clinical Proteomics, CHU Montpellier, Institute of Regenerative Medicine & Biotherapy, Montpellier, France
| | - Christophe Hirtz
- Laboratory of Biochemistry and Clinical Proteomics, CHU Montpellier, Institute of Regenerative Medicine & Biotherapy, Montpellier, France
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21
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Ozcan S, Cooper JD, Lago SG, Kenny D, Rustogi N, Stocki P, Bahn S. Towards reproducible MRM based biomarker discovery using dried blood spots. Sci Rep 2017; 7:45178. [PMID: 28345601 PMCID: PMC5366927 DOI: 10.1038/srep45178] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/17/2017] [Indexed: 12/14/2022] Open
Abstract
There is an increasing interest in the use of dried blood spot (DBS) sampling and multiple reaction monitoring in proteomics. Although several groups have explored the utility of DBS by focusing on protein detection, the reproducibility of the approach and whether it can be used for biomarker discovery in high throughput studies is yet to be determined. We assessed the reproducibility of multiplexed targeted protein measurements in DBS compared to serum. Eighty-two medium to high abundance proteins were monitored in a number of technical and biological replicates. Importantly, as part of the data analysis, several statistical quality control approaches were evaluated to detect inaccurate transitions. After implementing statistical quality control measures, the median CV on the original scale for all detected peptides in DBS was 13.2% and in Serum 8.8%. We also found a strong correlation (r = 0.72) between relative peptide abundance measured in DBS and serum. The combination of minimally invasive sample collection with a highly specific and sensitive mass spectrometry (MS) technique allows for targeted quantification of multiple proteins in a single MS run. This approach has the potential to fundamentally change clinical proteomics and personalized medicine by facilitating large-scale studies.
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Affiliation(s)
- Sureyya Ozcan
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Jason D Cooper
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Santiago G Lago
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Diarmuid Kenny
- Department of Chemical Engineering and Biotechnology, Psynova Neurotech Ltd, Cambridge, United Kingdom
| | - Nitin Rustogi
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Pawel Stocki
- Department of Chemical Engineering and Biotechnology, Psynova Neurotech Ltd, Cambridge, United Kingdom
| | - Sabine Bahn
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
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22
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Rosting C, Gjelstad A, Halvorsen TG. Expanding the knowledge on dried blood spots and LC-MS-based protein analysis: two different sampling materials and six protein targets. Anal Bioanal Chem 2017; 409:3383-3392. [PMID: 28299418 DOI: 10.1007/s00216-017-0280-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/03/2017] [Accepted: 02/24/2017] [Indexed: 12/19/2022]
Abstract
The combination of dried blood spots (DBS) and bottom-up LC-MS-based protein analysis was investigated in the present paper using six model proteins (1 mg/mL of each protein) with different physicochemical properties. Two different materials for DBS were examined: a water-soluble DBS material (carboxymethyl cellulose, (CMC)) and a commercially available (non-soluble) material (DMPK-C). The sample preparation was optimised regarding the water-soluble material and achieving acceptable repeatability of the signal was emphasised. Five microlitres of whole blood were deposited and dried on either CMC or DMPK-C. The samples were dissolved (CMC) or extracted (DMPK-C) prior to tryptic digest and matrix precipitation. The optimization of the sample preparation showed that an increased buffer concentration (100 mM ammonium bicarbonate) for dissolving the DBS samples gave better repeatability combined with a decrease in analyte signal. CMC seemed to add extra variability (RSD 8-60%) into the analysis compared to sample prepared without CMC (RSD 6-36%), although equal performance compared to DMPK-C material (RSD 13-60%) was demonstrated. The stability of the analytes was examined for different storage periods (1 and 4 weeks) and different storage temperatures (-25, 25, and 40 °C). The stability on both CMC (> 70% compared to reference) and DMPK-C (> 50% compared to reference) was acceptable for most of the peptides. This paper shows that both DBS materials can be used in targeted LC-MS-based protein analysis of proteins with different physicochemical properties. Graphical Abstract Overview of the experimental set-up for expanding the knowledge of dried blood spots in LC-MS-based protein anaysis.
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Affiliation(s)
- Cecilie Rosting
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, 0316, Oslo, Norway
| | - Astrid Gjelstad
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, 0316, Oslo, Norway
| | - Trine Grønhaug Halvorsen
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, 0316, Oslo, Norway.
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23
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Henderson CM, Bollinger JG, Becker JO, Wallace JM, Laha TJ, MacCoss MJ, Hoofnagle AN. Quantification by nano liquid chromatography parallel reaction monitoring mass spectrometry of human apolipoprotein A-I, apolipoprotein B, and hemoglobin A1c in dried blood spots. Proteomics Clin Appl 2017; 11. [PMID: 28112871 DOI: 10.1002/prca.201600103] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 12/20/2016] [Accepted: 01/19/2017] [Indexed: 12/21/2022]
Abstract
PURPOSE Proteomic analysis of blood proteins in dried blood spots (DBS) is gaining attention as a possible replacement for measurements in plasma/serum collected by venipuncture. We aimed to develop and provisionally validate a nanoflow LC-PRM-MS method for clinical use. EXPERIMENTAL DESIGN We used Skyline to develop a nanoflow LC-PRM-MS method to quantify glycated hemoglobin-β, apolipoprotein A-I, and apolipoprotein B in DBS. Precision, linearity, interferences, and stability were determined and the method was used to analyze samples from 36 human volunteers. The method was compared with clinically validated measurements in paired blood collected via venipuncture. RESULTS The method was relatively precise for these proteins (10-11% CV) and linear across the normal concentration ranges of these proteins. Interference from high total serum protein concentration (>8 g/dL) was noted for apolipoprotein A-I and apolipoprotein B. Proteins in DBS were stable for 14 days at temperatures below 25°C and trypsinized samples were stable for 48 h at 7°C. There was moderate correlation with clinical methods (r = 0.783-0.858) and significant bias in individual samples. CONCLUSIONS AND CLINICAL RELEVANCE Although the method had adequate precision and linearity for a biomarker, the accuracy compared with clinically validated assays raises concerns regarding the use of DBS compared with venipuncture for clinical use.
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Affiliation(s)
- Clark M Henderson
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - James G Bollinger
- Departments of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jessica O Becker
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer M Wallace
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Thomas J Laha
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Michael J MacCoss
- Departments of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
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24
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Abstract
A concept integrating sampling and protein digestion is introduced here combining fast and simple fabrication by wax printing on filter paper with trypsin immobilized polymer beads.
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Affiliation(s)
- Øystein Skjærvø
- Department of Pharmaceutical Chemistry
- School of Pharmacy
- University of Oslo
- NO-0316 Oslo
- Norway
| | - Cecilie Rosting
- Department of Pharmaceutical Chemistry
- School of Pharmacy
- University of Oslo
- NO-0316 Oslo
- Norway
| | | | - Léon Reubsaet
- Department of Pharmaceutical Chemistry
- School of Pharmacy
- University of Oslo
- NO-0316 Oslo
- Norway
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25
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Fernández-Puente P, Calamia V, González-Rodríguez L, Lourido L, Camacho-Encina M, Oreiro N, Ruiz-Romero C, Blanco FJ. Multiplexed mass spectrometry monitoring of biomarker candidates for osteoarthritis. J Proteomics 2017; 152:216-25. [PMID: 27865793 DOI: 10.1016/j.jprot.2016.11.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/10/2016] [Accepted: 11/14/2016] [Indexed: 12/22/2022]
Abstract
The methods currently available for the diagnosis and monitoring of osteoarthritis (OA) are very limited and lack sensitivity. Being the most prevalent rheumatic disease, one of the most disabling pathologies worldwide and currently untreatable, there is a considerable interest pointed in the verification of specific biological markers for improving its diagnosis and disease progression studies. Considering the remarkable development of targeted proteomics methodologies in the frame of the Human Proteome Project, the aim of this work was to develop and apply a MRM-based method for the multiplexed analysis of a panel of 6 biomarker candidates for OA encoded by the Chromosome 16, and another 8 proteins identified in previous shotgun studies as related with this pathology, in specimens derived from the human joint and serum. The method, targeting 35 different peptides, was applied to samples from human articular chondrocytes, healthy and osteoarthritic cartilage, synovial fluid and serum. Subsequently, a verification analysis of the biomarker value of these proteins was performed by single point measurements on a set of 116 serum samples, leading to the identification of increased amounts of Haptoglobin and von Willebrand Factor in OA patients. Altogether, the present work provides a tool for the multiplexed monitoring of 14 biomarker candidates for OA, and verifies for the first time the increased amount of two of these circulating markers in patients diagnosed with this disease. SIGNIFICANCE We have developed an MRM method for the identification and relative quantification of a panel of 14 protein biomarker candidates for osteoarthritis. This method has been applied to analyze human articular chondrocytes, articular cartilage, synovial fluid, and finally a collection of 116 serum samples from healthy controls and patients suffering different degrees of osteoarthritis, in order to verify the biomarker usefulness of the candidates. HPT and VWF were validated as increased in OA patients.
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26
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Abstract
Protein denaturation is the common basis for enzyme inactivation and inactivation of pathogens, necessary for preservation and safe handling of biosamples for downstream analysis. While heat-stabilization technology has been used in proteomic and peptidomic research since its introduction in 2009, the advantages of using the technique for simultaneous pathogen inactivation have only recently been addressed. The time required for enzyme inactivation by heat (≈1 min) is short compared with chemical treatments, and inactivation is irreversible in contrast to freezing. Heat stabilization thus facilitates mass spectrometric studies of biomolecules with a fast conversion rate, and expands the chemical space of potential biomarkers to include more short-lived entities, such as phosphorylated proteins, in tissue samples as well as whole-blood (dried blood sample) samples.
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27
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Affiliation(s)
- Cecilie Rosting
- Department of Pharmaceutical
Chemistry, School of Pharmacy, University of Oslo, 0316 Oslo, Norway
| | - Astrid Gjelstad
- Department of Pharmaceutical
Chemistry, School of Pharmacy, University of Oslo, 0316 Oslo, Norway
| | - Trine Grønhaug Halvorsen
- Department of Pharmaceutical
Chemistry, School of Pharmacy, University of Oslo, 0316 Oslo, Norway
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28
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Milosheska D, Grabnar I, Vovk T. Dried blood spots for monitoring and individualization of antiepileptic drug treatment. Eur J Pharm Sci 2015; 75:25-39. [DOI: 10.1016/j.ejps.2015.04.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 11/21/2022]
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29
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Sakhi AK, Bastani NE, Ellingjord-Dale M, Gundersen TE, Blomhoff R, Ursin G. Feasibility of self-sampled dried blood spot and saliva samples sent by mail in a population-based study. BMC Cancer 2015; 15:265. [PMID: 25886002 PMCID: PMC4428002 DOI: 10.1186/s12885-015-1275-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 03/26/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND In large epidemiological studies it is often challenging to obtain biological samples. Self-sampling by study participants using dried blood spots (DBS) technique has been suggested to overcome this challenge. DBS is a type of biosampling where blood samples are obtained by a finger-prick lancet, blotted and dried on filter paper. However, the feasibility and efficacy of collecting DBS samples from study participants in large-scale epidemiological studies is not known. The aim of the present study was to test the feasibility and response rate of collecting self-sampled DBS and saliva samples in a population-based study of women above 50 years of age. METHODS We determined response proportions, number of phone calls to the study center with questions about sampling, and quality of the DBS. We recruited women through a study conducted within the Norwegian Breast Cancer Screening Program. Invitations, instructions and materials were sent to 4,597 women. The data collection took place over a 3 month period in the spring of 2009. RESULTS Response proportions for the collection of DBS and saliva samples were 71.0% (3,263) and 70.9% (3,258), respectively. We received 312 phone calls (7% of the 4,597 women) with questions regarding sampling. Of the 3,263 individuals that returned DBS cards, 3,038 (93.1%) had been packaged and shipped according to instructions. A total of 3,032 DBS samples were sufficient for at least one biomarker analysis (i.e. 92.9% of DBS samples received by the laboratory). 2,418 (74.1%) of the DBS cards received by the laboratory were filled with blood according to the instructions (i.e. 10 completely filled spots with up to 7 punches per spot for up to 70 separate analyses). To assess the quality of the samples, we selected and measured two biomarkers (carotenoids and vitamin D). The biomarker levels were consistent with previous reports. CONCLUSION Collecting self-sampled DBS and saliva samples through the postal services provides a low cost, effective and feasible alternative in epidemiological studies.
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Affiliation(s)
- Amrit Kaur Sakhi
- Norwegian Institute of Public Health, 0456, Oslo, Norway.
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, 0316, Oslo, Norway.
| | - Nasser Ezzatkhah Bastani
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, 0316, Oslo, Norway.
| | - Merete Ellingjord-Dale
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, 0316, Oslo, Norway.
| | | | - Rune Blomhoff
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, 0316, Oslo, Norway.
- Department of Clinical Service, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, 0424, Oslo, Norway.
| | - Giske Ursin
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, 0316, Oslo, Norway.
- Cancer Registry of Norway, P.O. Box 5313, 0304, Oslo, Norway.
- Department of Preventive Medicine, University of Southern California, 90032-3628, Los Angeles, CA, USA.
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30
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Mohammed Y, Percy AJ, Chambers AG, Borchers CH. Qualis-SIS: automated standard curve generation and quality assessment for multiplexed targeted quantitative proteomic experiments with labeled standards. J Proteome Res 2015; 14:1137-46. [PMID: 25546269 DOI: 10.1021/pr5010955] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multiplexed targeted quantitative proteomics typically utilizes multiple reaction monitoring and allows the optimized quantification of a large number of proteins. One challenge, however, is the large amount of data that needs to be reviewed, analyzed, and interpreted. Different vendors provide software for their instruments, which determine the recorded responses of the heavy and endogenous peptides and perform the response-curve integration. Bringing multiplexed data together and generating standard curves is often an off-line step accomplished, for example, with spreadsheet software. This can be laborious, as it requires determining the concentration levels that meet the required accuracy and precision criteria in an iterative process. We present here a computer program, Qualis-SIS, that generates standard curves from multiplexed MRM experiments and determines analyte concentrations in biological samples. Multiple level-removal algorithms and acceptance criteria for concentration levels are implemented. When used to apply the standard curve to new samples, the software flags each measurement according to its quality. From the user's perspective, the data processing is instantaneous due to the reactivity paradigm used, and the user can download the results of the stepwise calculations for further processing, if necessary. This allows for more consistent data analysis and can dramatically accelerate the downstream data analysis.
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Affiliation(s)
- Yassene Mohammed
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria , Vancouver Island Technology Park, #3101-4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
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31
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Ignjatovic V, Pitt J, Monagle P, Craig JM. The utility of dried blood spots for proteomic studies: looking forward to looking back. Proteomics Clin Appl 2014; 8:896-900. [PMID: 25220422 DOI: 10.1002/prca.201400042] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 08/04/2014] [Accepted: 09/03/2014] [Indexed: 11/12/2022]
Abstract
The possibility to detect biomarkers of adult disease in early life and particularly in newborns holds enormous promise for early disease detection and prevention. Early detection of disease or potential for future disease would allow for prevention or amelioration of disease before overt symptoms develop, by lifestyle modifications, appropriate medication and monitoring. It is now increasingly important to develop the technologies that allow dried blood spots (DBS) to be utilized for protein-based studies. The use of DBS in proteome wide association studies (PWAS) may in turn allow for detection of major diseases of adulthood at the earliest possible time. This review focuses on the utility of DBS in proteomics, the main challenges, as well as the latest approaches for overcoming those, facilitating the use of DBS for detection of major diseases of adulthood at the earliest possible time.
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Affiliation(s)
- Vera Ignjatovic
- Murdoch Childrens Research Institute, Royal Children's Hospital, Victoria, Australia; Department of Paediatrics, The University of Melbourne, Victoria, Australia
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Martin NJ, Cooper HJ. Challenges and opportunities in mass spectrometric analysis of proteins from dried blood spots. Expert Rev Proteomics 2014; 11:685-95. [DOI: 10.1586/14789450.2014.965158] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Abstract
Background: Dried blood spot sample collection could improve detection of the misuse of IGF-1, its analogs and growth hormone. An LC–MS/MS method was developed to measure two IGF-1 peptides and one analog peptide after trypsin digestion. In addition to standard method validation parameters, the effect of hematocrit on cysteine alkylation, trypsin digestion and the selection of internal standard were evaluated. Results: Quantification of IGF-1 peptides was possible with an LLOQ of 25 ng/ml and imprecision of less than 15%. Conclusion: While the effects of hematocrit must be evaluated empirically for each method, dried blood spots are a suitable matrix for the measurement of IGF-1 and its analogs by MS.
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