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Zhang N, An J, Qin H, Wang Y, Fang Z, Ji Y, Ye M. A Mass-Spectrometry-Based Antibody-Free Approach Enables the Quantification of D-Dimer in Plasma. J Proteome Res 2020; 19:3143-3152. [PMID: 32519545 DOI: 10.1021/acs.jproteome.0c00148] [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: 11/30/2022]
Abstract
D-dimer is an important marker of different coagulation diseases, such as venous thromboembolism (including deep vein thrombosis and pulmonary embolism) and disseminated intravascular coagulation. Though it is frequently used in many clinical diagnostic situations, the D-dimer assays currently lack standardization due to its inherent heterogeneity which makes the antibody-based methods have different quantitative results and cutoffs to define an abnormal value. In this study, we report the first antibody-free D-dimer quantification method. In the method, a cross-linked peptide of fibrin D domain carboxyl terminal cross-linked by the factor XIIIa was used to represent the D-dimer. By using a filter-aided sample preparation and a nickel immobilized metal affinity chromatography enrichment strategy, the complexity of the plasma sample was significantly reduced, and the cross-linked peptide was enriched effectively for analysis with parallel reaction monitoring in mass spectrometry. The linear range of this method was 3.125-400 nmol/L which spans over two magnitudes. Recovery and reproducibility of the method were found to be good. To further demonstrate the performance of our method, D-dimer concentrations of 25 human plasma samples were analyzed, and the results had a good correlation between with the commercial D-dimer assay kit used in hospitals. This method was completely antibody-free and has the potential to promote the standardization of D-dimer analysis.
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Affiliation(s)
- Na Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun An
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital, Dalian Medical University, Dalian 116011, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinqun Ji
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital, Dalian Medical University, Dailan 116011, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
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Peng H, Yan Z, Zeng X, Zhang S, Jiang H, Huang H, Zhuo H. Serum and tissue proteomic signatures of patients with hepatocellular carcinoma using 2‑D gel electrophoresis. Mol Med Rep 2019; 20:1025-1038. [PMID: 31173207 PMCID: PMC6625405 DOI: 10.3892/mmr.2019.10311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 04/24/2019] [Indexed: 12/23/2022] Open
Abstract
Hepatocellular carcinoma (HCC) accounts for ~85% of primary liver cancer cases and is a leading cause of mortality worldwide. Effective early diagnosis is difficult for HCC; however, effective biomarkers may be beneficial for diagnosis. In the current study, serum samples, and HCC and adjacent tissue samples were obtained from patients with HCC for the detection of biomarkers using 2-D gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization-time of flight (TOF)/TOF mass spectrometry. The crude serum samples did not need to be prepared for removal of high abundance proteins. The mRNA expression levels of HCC-associated proteins were detected in tissues using reverse transcription-quantitative PCR. Statistical analysis and database matching were used to identify the differentially expressed proteins detected in the serum and tissue groups. Immunohistochemistry (IHC) was performed to detect the expression of significant proteins in HCC and adjacent tissues. The results revealed ~800 protein spots on a 2-DE gel that were detected in serum samples, and 1,200 spots were identified in the tissue samples. The protein and mRNA expression levels of oxysterol binding protein-like 11 (OSBPL11) in HCC serum and tissue samples were consistent. Pathway analysis demonstrated that members of the apolipoprotein family, particularly apolipoprotein E (APOE), and RAS family members were closely associated in HCC, either directly or via ferratin heavy polypeptide 1. IHC results demonstrated that the APOE protein serves an important role in liver cancer development. The lysis buffer used in the current study was effective for serum protein separation in 2-DE sample preparation. In addition, the present study revealed that downregulated OSBPL11 may be a potential indicator for HCC, and the apolipoprotein family, particularly APOE, and the RAS family may cooperatively serve an important role.
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Affiliation(s)
- Huifang Peng
- Department of Endocrinology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471000, P.R. China
| | - Zhijian Yan
- Department of Urology, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Xinhua Zeng
- State Key Laboratory of Stress Cell Biology, School of Life Science, Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Sheng Zhang
- Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Hongwei Jiang
- Department of Endocrinology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471000, P.R. China
| | - Heqing Huang
- State Key Laboratory of Stress Cell Biology, School of Life Science, Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Huiqin Zhuo
- Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, P.R. China
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Kontostathi G, Makridakis M, Zoidakis J, Vlahou A. Applications of multiple reaction monitoring targeted proteomics assays in human plasma. Expert Rev Mol Diagn 2019; 19:499-515. [PMID: 31057016 DOI: 10.1080/14737159.2019.1615448] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Introduction: Multiple (or selected) reaction monitoring-mass spectrometry (MRM/SRM) is a targeted proteomic method that can be used for relative and absolute quantification. Multiple reports exist supporting the potential of the approach in proteomic biomarker validation. Areas covered: To get an overview of the applications of MRM in protein quantification in plasma, a search in MedLine/PubMed was performed using the keywords: 'MRM/SRM plasma proteomic/proteomics/proteome'. The retrieved studies were further filtered to focus on disease biomarkers and the main results are summarized. Expert opinion: MRM is increasingly employed for the quantification of both well-established but also newly discovered putative biomarkers and occasionally their post-translationally modified forms in plasma. Fractionation is regularly required for the detection of low abundance proteins. Standardized procedures to facilitate assay establishment and marker quantification have been proposed and, in few cases, implemented. Nevertheless, in most cases, absolute quantification is not performed. To advance, multiple technical issues including the regular use of standard labeled peptides and appropriate quality controls to monitor assay performance should be considered. Additionally, clinical aspects involving careful study design to address biomarker clinical use should also be considered.
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Affiliation(s)
- Georgia Kontostathi
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Manousos Makridakis
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Jerome Zoidakis
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Antonia Vlahou
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
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Katahira T, Kanazawa A, Shinohara M, Koshibu M, Kaga H, Mita T, Tosaka Y, Komiya K, Miyatsuka T, Ikeda F, Azuma K, Takayanagi N, Ogihara T, Ohmura C, Miyachi A, Mieno E, Yamashita S, Watada H. Postprandial Plasma Glucagon Kinetics in Type 2 Diabetes Mellitus: Comparison of Immunoassay and Mass Spectrometry. J Endocr Soc 2019; 3:42-51. [PMID: 30560227 PMCID: PMC6293234 DOI: 10.1210/js.2018-00142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/23/2018] [Indexed: 01/20/2023] Open
Abstract
CONTEXT Accurate glucagon level measurements are necessary for investigation of mechanisms for postprandial hyperglycemia in type 2 diabetes. OBJECTIVE To evaluate the accuracy of postprandial glucagon level measurements using a sandwich ELISA vs a recently established liquid chromatography-high resolution mass spectrometry (LC-HRMS) method in type 2 diabetes mellitus. DESIGN AND PARTICIPANTS Twenty patients with type 2 diabetes treated with insulin underwent a meal test before and after administration of the dipeptidyl peptidase-4 inhibitor anagliptin for 4 weeks. Blood samples were taken serially after the meal, and glucagon levels were measured using both ELISA and LC-HRMS. We compared the change from baseline to 4 weeks (Δ0-4W) using the area under the curve for plasma glucagon during the meal test [area under the curve (AUC)0-3h] measured using ELISA and LC-HRMS. RESULTS ELISA-based glucagon AUC0-3h was higher than LC-HRMS-based AUC0-3h at baseline and 4 weeks. However, differences in Δ0-4W-AUC0-3h measured using ELISA and LC-HRMS were not statistically significant. Additionally, Δ0-4W-AUC0-3h measured using ELISA and LC-HRMS were strongly correlated (r = 0.87, P < 0.001). CONCLUSIONS Plasma glucagon levels during a meal test in patients with type 2 diabetes measured using ELISA were consistently higher than those measured using LC-HRMS. However, given that the changes in glucagon levels measured using ELISA before and after dipeptidyl peptidase-4 inhibitor therapy were similar to those based on LC-HRMS, this ELISA seems to be useful for evaluating the effect of the drug interventions on postprandial glucagon levels.
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Affiliation(s)
- Takehiro Katahira
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Akio Kanazawa
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mai Shinohara
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mami Koshibu
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hideyoshi Kaga
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomoya Mita
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuka Tosaka
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Koji Komiya
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takeshi Miyatsuka
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Center for Identification of Diabetic Therapeutic Targets, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Fuki Ikeda
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kosuke Azuma
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Naoko Takayanagi
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takeshi Ogihara
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Chie Ohmura
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Atsushi Miyachi
- Radioisotope and Chemical Analysis Center, Sanwa Kagaku Kenkyusho Co., Ltd., Inabe, Mie, Japan
| | - Eri Mieno
- Radioisotope and Chemical Analysis Center, Sanwa Kagaku Kenkyusho Co., Ltd., Inabe, Mie, Japan
| | - Satoko Yamashita
- Pharmaceutical Research Laboratories, Sanwa Kagaku Kenkyusho Co., Ltd., Inabe, Mie, Japan
| | - Hirotaka Watada
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Center for Identification of Diabetic Therapeutic Targets, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Center for Therapeutic Innovations in Diabetes, Juntendo University Graduate School of Medicine, Tokyo, Japan
- 6Sportology Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
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5
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Absolute quantification of two antimicrobial peptides α S2 -casein 182–207 and α S2 -casein 151–181 in bovine milk by UHPLC–ESI–MS/MS in sMRM mode. Food Chem 2018; 261:15-20. [DOI: 10.1016/j.foodchem.2018.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 12/01/2017] [Accepted: 04/01/2018] [Indexed: 11/21/2022]
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Tanaka-Okamoto M, Hanzawa K, Mukai M, Takahashi H, Ohue M, Miyamoto Y. Correlation of serum sialyl Tn antigen values determined by immunoassay and SRM based method. Anal Biochem 2017; 544:42-48. [PMID: 29273237 DOI: 10.1016/j.ab.2017.12.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/11/2017] [Accepted: 12/18/2017] [Indexed: 01/02/2023]
Abstract
We previously identified four glycan tumor marker candidates using a HPLC-based method. One candidate was sialyl Tn (STN), NeuAcα2-6-GalNAc. In this study, glycans were prepared from sera by hydrazine treatment followed by fluorescent labeling with aminopyridine. Pyridylaminated-STN levels of 147 gastric cancer, 85 pancreatic cancer and 10 cholangiocarcinoma patients together with 102 normal controls were accurately quantified using HPLC separation followed by selected reaction monitoring (SRM) assay, which used a stable isotope, tetradeuterium-labeled pyridylamino glycan as an internal standard. Additionally, STN values were also quantified using conventional competitive inhibition radioimmunoassay (RIA). The two STN levels determined by RIA and SRM gave a similar distribution pattern in sera. STN levels were increased in sera from cancer patients compared to those from normal controls. Moreover, the STN levels in sera of cancer patients determined by the two different assay procedures showed a good correlation (i.e., correlation coefficient >0.9). Our results suggest it may be better to determine STN levels using SRM instead of RIA.
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Affiliation(s)
- Miki Tanaka-Okamoto
- Department of Molecular Biology, Osaka International Cancer Institute, 3-1-69, Otemae, Chuo-ku, Osaka 541-8567, Japan
| | - Ken Hanzawa
- Department of Molecular Biology, Osaka International Cancer Institute, 3-1-69, Otemae, Chuo-ku, Osaka 541-8567, Japan
| | - Mikio Mukai
- Department of Medical Checkup, Osaka International Cancer Institute, 3-1-69, Otemae, Chuo-ku, Osaka 541-8567, Japan
| | - Hidenori Takahashi
- Department of Gastroenterological Surgery, Osaka International Cancer Institute, 3-1-69, Otemae, Chuo-ku, Osaka 541-8567, Japan
| | - Masayuki Ohue
- Department of Gastroenterological Surgery, Osaka International Cancer Institute, 3-1-69, Otemae, Chuo-ku, Osaka 541-8567, Japan
| | - Yasuhide Miyamoto
- Department of Molecular Biology, Osaka International Cancer Institute, 3-1-69, Otemae, Chuo-ku, Osaka 541-8567, Japan.
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2D-LC–MS/MS to measure cleaved high-molecular-weight kininogen in human plasma as a biomarker for C1-INH-HAE. Bioanalysis 2017; 9:1477-1491. [DOI: 10.4155/bio-2017-0105] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: C1-INH-HAE is caused by activation of plasma kallikrein which subsequently cleaves high-molecular-weight kininogen (HMWK) to generate bradykinin and cHMWK. Materials & methods: A novel ion-pair 2D LC–MS/MS assay was developed to measure the 46 kDa cHMWK in plasma as a biomarker for C1-INH-HAE. The sample preparation included sodium dodecyl sulfate denaturation, methanol crash, chymotryptic digestion and peptide enrichment by solid phase extraction. Results: The LLOQ was 200 ng/ml. The overall cHMWK recovery combining crash and digestion was 57.5%. The precision of the method was ≤12.7% and accuracy ≤-13.8%. Conclusion: A reagent-free LC–MS assay has been developed for the quantitation of 46 kDa cHMWK, which was shown to be elevated in plasma of C1-INH-HAE patients due to C1-INH deficiency relative to that of healthy subjects.
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8
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Accurate analytical method for human plasma glucagon levels using liquid chromatography-high resolution mass spectrometry: comparison with commercially available immunoassays. Anal Bioanal Chem 2017; 409:5911-5918. [DOI: 10.1007/s00216-017-0534-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/26/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
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9
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Li H, Han J, Pan J, Liu T, Parker CE, Borchers CH. Current trends in quantitative proteomics - an update. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:319-341. [PMID: 28418607 DOI: 10.1002/jms.3932] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/28/2017] [Accepted: 04/06/2017] [Indexed: 05/11/2023]
Abstract
Proteins can provide insights into biological processes at the functional level, so they are very promising biomarker candidates. The quantification of proteins in biological samples has been routinely used for the diagnosis of diseases and monitoring the treatment. Although large-scale protein quantification in complex samples is still a challenging task, a great amount of effort has been made to advance the technologies that enable quantitative proteomics. Seven years ago, in 2009, we wrote an article about the current trends in quantitative proteomics. In writing this current paper, we realized that, today, we have an even wider selection of potential tools for quantitative proteomics. These tools include new derivatization reagents, novel sampling formats, new types of analyzers and scanning techniques, and recently developed software to assist in assay development and data analysis. In this review article, we will discuss these innovative methods, and their current and potential applications in proteomics. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- H Li
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - J Han
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - J Pan
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - T Liu
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - C E Parker
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - C H Borchers
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8P 5C2, Canada
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada
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Mizuta N, Yanagida K, Kodama T, Tomonaga T, Takami M, Oyama H, Kudo T, Ikeda M, Takeda M, Tagami S, Okochi M. Identification of Small Peptides in Human Cerebrospinal Fluid upon Amyloid-β Degradation. NEURODEGENER DIS 2017; 17:103-109. [PMID: 28103595 DOI: 10.1159/000453358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 11/10/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Amyloid-β (Aβ) degradation in brains of Alzheimer disease patients is a crucial focus for the clarification of disease pathogenesis. Nevertheless, the mechanisms underlying Aβ degradation in the human brain remain unclear. OBJECTIVE This study aimed to quantify the levels of small C-terminal Aβ fragments generated upon Aβ degradation in human cerebrospinal fluid (CSF). METHODS A fraction containing small peptides was isolated and purified from human CSF by high-pressure liquid chromatography. Degradation products of Aβ C termini were identified and measured by liquid chromatography-tandem mass spectrometry. The C-terminal fragments of Aβ in the conditioned medium of cultured cells transfected with the Swedish variant of βAPP (sw βAPP) were analyzed. These fragments in brains of PS1 I213T knock-in transgenic mice, overexpressing sw βAPP, were also analyzed. RESULTS The peptide fragments GGVV and GVV, produced by the cleavage of Aβ40, were identified in human CSF as well as in the brains of the transgenic mice and in the conditioned medium of the cultured cells. Relative to Aβ40 levels, GGVV and GVV levels were 7.6 ± 0.81 and 1.5 ± 0.18%, respectively, in human CSF. Levels of the GGVV fragment did not increase by the introduction of genes encoding neprilysin and insulin-degrading enzyme to the cultured cells. CONCLUSION Our results indicate that a substantial amount of Aβ40 in human brains is degraded via a neprilysin- or insulin-degrading enzyme-independent pathway.
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Affiliation(s)
- Naoki Mizuta
- Psychiatry, Department of Integrated Medicine, Division of Internal Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
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11
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Kikuchi W, Nishimura M, Kuga T, Tsuchida S, Saito T, Satoh M, Noda K, Kodera Y, Tomonaga T, Nomura F. Fibrinogen alpha C chain 5.9 kDa fragment (FIC5.9), a biomarker for various pathological conditions, is produced in post-blood collection by fibrinolysis and coagulation factors. Clin Proteomics 2016; 13:27. [PMID: 27761105 PMCID: PMC5055723 DOI: 10.1186/s12014-016-9129-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 09/23/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fibrinogen alpha C chain 5.9 kDa fragment (FIC5.9) is a new serum biomarker for chronic hepatitis that was discovered by proteomics analysis. Previous studies have shown that FIC5.9 is derived from the C-terminal region of fibrinogen alpha chain and the serum levels of FIC5.9 decrease in chronic hepatitis. It also have been reported that FIC5.9 cannot be detected in the blood stream of the systemic circulation and it is released from fibrinogen during blood clotting in collecting tube. However, the mechanism of FIC5.9 releasing from fibrinogen is unclear. METHODS We formulated a hypothesis that FIC5.9 is released by enzymes that are activated by post-blood collection and may be coagulation and fibrinolysis factors. In this study, we analyzed the mechanisms of FIC5.9 releasing from fibrinogen in healthy blood. RESULTS Our analysis showed that thrombin acts as an initiator for FIC5.9 releasing, and that mainly plasmin cleaves N-terminal end of FIC5.9 and neutrophil elastase cleave C-terminal end of FIC5.9. CONCLUSION FIC5.9 reflects minute changes in coagulation and fibrinolysis factors and may be associated with pathological conditions.
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Affiliation(s)
- Wataru Kikuchi
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
- R&D Department, Nittobo Medical Co., Ltd., Koriyama, Japan
| | - Motoi Nishimura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takahisa Kuga
- Department of Biochemistry and Molecular Biology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Sachio Tsuchida
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tatsuya Saito
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa Japan
| | - Mamoru Satoh
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kenta Noda
- R&D Department, Nittobo Medical Co., Ltd., Koriyama, Japan
| | - Yoshio Kodera
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Fumio Nomura
- Division of Clinical Mass Spectrometry and Clinical Genetics, Chiba University Hospital, Chiba, Japan
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12
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Shi T, Song E, Nie S, Rodland KD, Liu T, Qian WJ, Smith RD. Advances in targeted proteomics and applications to biomedical research. Proteomics 2016; 16:2160-82. [PMID: 27302376 PMCID: PMC5051956 DOI: 10.1002/pmic.201500449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/09/2016] [Accepted: 06/10/2016] [Indexed: 12/17/2022]
Abstract
Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074-1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ehwang Song
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Song Nie
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karin D Rodland
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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Percy AJ, Byrns S, Pennington SR, Holmes DT, Anderson NL, Agreste TM, Duffy MA. Clinical translation of MS-based, quantitative plasma proteomics: status, challenges, requirements, and potential. Expert Rev Proteomics 2016; 13:673-84. [DOI: 10.1080/14789450.2016.1205950] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Andrew J. Percy
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
| | - Simon Byrns
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Stephen R. Pennington
- Department of Pathology, School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Daniel T. Holmes
- Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - N. Leigh Anderson
- Department of Clinical Biomarkers, SISCAPA Assay Technologies, Inc., Washington, DC, USA
| | - Tasha M. Agreste
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
| | - Maureen A. Duffy
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
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14
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Yamada K, Watanabe A, Takeshita H, Matsumoto KI. A method for quantification of serum tenascin-X by nano-LC/MS/MS. Clin Chim Acta 2016; 459:94-100. [PMID: 27236034 DOI: 10.1016/j.cca.2016.05.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/21/2016] [Accepted: 05/21/2016] [Indexed: 01/02/2023]
Abstract
BACKGROUND Complete deficiency of an extracellular matrix tenascin-X (TNX) leads to a classical type of Ehlers-Danlos syndrome (EDS). TNX haploinsufficiency is a cause of hypermobility type of EDS. Human TNX is also present in a serum form (sTNX) with a molecular size of 140kDa. In this study, we established a method for quantification of sTNX using nano-liquid chromatography tandem mass spectrometry (LC/MS/MS) with selected/multiple reaction monitoring. METHODS Twelve abundant protein-depleted sera were reduced, alkylated, and digested with Lys-C and trypsin. Subsequently, the digests were fractionated by strong cation exchange chromatography. Optimal and validated transitions of precursor and product ions of the peptides from sTNX were developed on a triple quadrupole mass spectrometer. RESULTS Serum concentrations of sTNX of healthy individuals were quantified as an average of 144ng/ml. However, sTNX was not detected by this method in serum from a patient with a classical type of EDS in whom sTNX was not found by Western blot analysis. The limit of quantification (LOQ) of sTNX by nano-LC/MS/MS method was 2.8pg whereas the detection sensitivity of sTNX by Western blot analysis was 19pg. The nano-LC/MS/MS method is more sensitive than Western blot analysis. CONCLUSIONS The quantification method will be useful for diagnosis and risk stratification of EDS caused by TNX deficiency and haploinsufficiency.
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Affiliation(s)
- Kazuo Yamada
- Department of Biosignaling and Radioisotope Experiment, Interdisciplinary Center for Science Research, Organization for Research and Academic Information, Shimane University, Enya-cho, Izumo, Shimane 693-8501, Japan; Department of Legal Medicine, Faculty of Medicine, Shimane University, Enya-cho, Izumo, Shimane 693-8501, Japan
| | - Atsushi Watanabe
- Division of Clinical Genetics, Nippon Medical School Hospital, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8603, Japan; Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8603, Japan
| | - Haruo Takeshita
- Department of Legal Medicine, Faculty of Medicine, Shimane University, Enya-cho, Izumo, Shimane 693-8501, Japan
| | - Ken-Ichi Matsumoto
- Department of Biosignaling and Radioisotope Experiment, Interdisciplinary Center for Science Research, Organization for Research and Academic Information, Shimane University, Enya-cho, Izumo, Shimane 693-8501, Japan.
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15
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Ponomarenko EA, Poverennaya EV, Ilgisonis EV, Pyatnitskiy MA, Kopylov AT, Zgoda VG, Lisitsa AV, Archakov AI. The Size of the Human Proteome: The Width and Depth. Int J Anal Chem 2016; 2016:7436849. [PMID: 27298622 PMCID: PMC4889822 DOI: 10.1155/2016/7436849] [Citation(s) in RCA: 280] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/11/2016] [Accepted: 04/19/2016] [Indexed: 01/01/2023] Open
Abstract
This work discusses bioinformatics and experimental approaches to explore the human proteome, a constellation of proteins expressed in different tissues and organs. As the human proteome is not a static entity, it seems necessary to estimate the number of different protein species (proteoforms) and measure the number of copies of the same protein in a specific tissue. Here, meta-analysis of neXtProt knowledge base is proposed for theoretical prediction of the number of different proteoforms that arise from alternative splicing (AS), single amino acid polymorphisms (SAPs), and posttranslational modifications (PTMs). Three possible cases are considered: (1) PTMs and SAPs appear exclusively in the canonical sequences of proteins, but not in splice variants; (2) PTMs and SAPs can occur in both proteins encoded by canonical sequences and in splice variants; (3) all modification types (AS, SAP, and PTM) occur as independent events. Experimental validation of proteoforms is limited by the analytical sensitivity of proteomic technology. A bell-shaped distribution histogram was generated for proteins encoded by a single chromosome, with the estimation of copy numbers in plasma, liver, and HepG2 cell line. The proposed metabioinformatics approaches can be used for estimation of the number of different proteoforms for any group of protein-coding genes.
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16
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Tanaka-Okamoto M, Yabu M, Mukai M, Takahashi H, Fujiwara Y, Ohue M, Kamada Y, Miyoshi E, Miyamoto Y. Elevation of CA19-9-Related Novel Marker, Core 1 Sialyl Lewis A, in Sera of Adenocarcinoma Patients Verified by a SRM-Based Method. J Proteome Res 2015; 15:152-65. [PMID: 26641888 DOI: 10.1021/acs.jproteome.5b00893] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have attempted to identify a novel glycan tumor marker. Pyridylaminated (PA) O-glycans were prepared from sera, and the corresponding O-glycan profiles were constructed by HPLC separation. By comparing the serum O-glycan profiles from healthy controls with those of cancer patients, we identified a marker candidate, core 1 sialyl Lewis A (NeuAcα2-3Galβ1-3(Fucα1-4)GlcNAcβ1-3Gal) (abbreviated C1SLA), whose concentration appeared to be weakly correlated with CA19-9 values. To quantify this glycan, we developed a selected reaction monitoring (SRM) assay that used a stable isotope, tetradeuterium-labeled pyridylamino (d4-PA) glycan, as an internal standard. The analyte (d0-PA-C1SLA) and the internal standard (d4-PA-C1SLA) were subjected to SRM analyses after two types of HPLC separation. Serum levels of C1SLA, determined as the relative ratio to total O-glycans, were then measured. These analyses revealed that (i) C1SLA is a CA19-9-related glycan, (ii) the mean value of C1SLA in normal controls is 3.41 ppm, (iii) the level of C1SLA was significantly higher in samples of stages II-IV stomach cancers (P = 0.0036) as well as pancreatic cancers (P < 0.0001) compared to that of normal controls, (iv) the relationship between C1SLA and CA19-9 varies from poor to weak depending on the cancer, and (v) C1SLA could be valuable as a diagnostic adjunct for cancer.
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Affiliation(s)
- Miki Tanaka-Okamoto
- Department of Molecular Biology, Osaka Medical Center for Cancer and Cardiovascular Diseases , 1-3-2 Nakamichi, Higashinari-ku, Osaka 537-8511, Japan
| | - Masahiko Yabu
- Department of Molecular Biology, Osaka Medical Center for Cancer and Cardiovascular Diseases , 1-3-2 Nakamichi, Higashinari-ku, Osaka 537-8511, Japan
| | | | | | | | | | - Yoshihiro Kamada
- Department of Molecular Biochemistry and Clinical Investigation, Osaka University, Graduate School of Medicine , 1-7 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Eiji Miyoshi
- Department of Molecular Biochemistry and Clinical Investigation, Osaka University, Graduate School of Medicine , 1-7 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yasuhide Miyamoto
- Department of Molecular Biology, Osaka Medical Center for Cancer and Cardiovascular Diseases , 1-3-2 Nakamichi, Higashinari-ku, Osaka 537-8511, Japan
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17
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Kalló G, Chatterjee A, Tóth M, Rajnavölgyi É, Csutak A, Tőzsér J, Csősz É. Relative quantification of human β-defensins by a proteomics approach based on selected reaction monitoring. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1623-1631. [PMID: 26467114 DOI: 10.1002/rcm.7259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 06/16/2015] [Accepted: 06/21/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE A targeted proteomics method based on selected reaction monitoring (SRM) is a relevant approach for the analysis of multiple analytes in biological samples. Defensins are phylogenetically conserved small antimicrobial peptides contributing to innate host defense and exhibiting low immunogenicity, resistance to proteolysis and a broad range of antimicrobial activities. The goal of the present study was to develop and optimize SRM-based targeted proteomics methods for the detection of human β-defensins 1-4 in various biological fluids. METHODS An SRM-based targeted proteomics method was developed and validated for the detection of human β-defensins 1-4. The supernatants of resting and IL-1β-stimulated Caco2, HT-29 and SW-1116 colonic epithelial cells (CEC), cell lysates of CECs and tear samples of human healthy individuals were analyzed and the feasibility of the developed method was validated by ELISA and dot-blot analysis complemented by RT-qPCR. RESULTS Our results demonstrate that the developed SRM method offers an alternative approach for the cost-effective and rapid analysis of human β-defensins in samples with biological relevance. CONCLUSIONS A semi-quantitative targeted mass spectrometry method was developed and validated for the relative quantification of β-defensins 1-4 in cell culture supernatants and body fluid analyses.
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Affiliation(s)
- Gergő Kalló
- Department of Biochemistry and Molecular Biology, Proteomics Core Facility, Faculty of Medicine, University of Debrecen, Egyetem ter. 1, 4010, Debrecen, Hungary
| | - Arunima Chatterjee
- Department of Immunology, Faculty of Medicine, University of Debrecen, Egyetem ter. 1, 4010, Debrecen, Hungary
| | - Márta Tóth
- Department of Immunology, Faculty of Medicine, University of Debrecen, Egyetem ter. 1, 4010, Debrecen, Hungary
| | - Éva Rajnavölgyi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Egyetem ter. 1, 4010, Debrecen, Hungary
| | - Adrienne Csutak
- Department of Ophthalmology, Faculty of Medicine, University of Debrecen, Egyetem ter. 1, 4010, Debrecen, Hungary
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Proteomics Core Facility, Faculty of Medicine, University of Debrecen, Egyetem ter. 1, 4010, Debrecen, Hungary
| | - Éva Csősz
- Department of Biochemistry and Molecular Biology, Proteomics Core Facility, Faculty of Medicine, University of Debrecen, Egyetem ter. 1, 4010, Debrecen, Hungary
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18
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Shen Y, Zhang G, Yang J, Qiu Y, McCauley T, Pan L, Wu J. Online 2D-LC-MS/MS Assay To Quantify Therapeutic Protein in Human Serum in the Presence of Pre-existing Antidrug Antibodies. Anal Chem 2015; 87:8555-63. [DOI: 10.1021/acs.analchem.5b02293] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yinghua Shen
- Bioanalytical and
Biomarker
Development, Research and Nonclinical Development, Shire, Lexington, Massachusetts 02421, United States
| | - Guodong Zhang
- Bioanalytical and
Biomarker
Development, Research and Nonclinical Development, Shire, Lexington, Massachusetts 02421, United States
| | - Jinsong Yang
- Bioanalytical and
Biomarker
Development, Research and Nonclinical Development, Shire, Lexington, Massachusetts 02421, United States
| | - Yongchang Qiu
- Bioanalytical and
Biomarker
Development, Research and Nonclinical Development, Shire, Lexington, Massachusetts 02421, United States
| | - Thomas McCauley
- Bioanalytical and
Biomarker
Development, Research and Nonclinical Development, Shire, Lexington, Massachusetts 02421, United States
| | - Luying Pan
- Bioanalytical and
Biomarker
Development, Research and Nonclinical Development, Shire, Lexington, Massachusetts 02421, United States
| | - Jiang Wu
- Bioanalytical and
Biomarker
Development, Research and Nonclinical Development, Shire, Lexington, Massachusetts 02421, United States
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19
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Looße C, Galozzi S, Debor L, Julsing MK, Bühler B, Schmid A, Barkovits K, Müller T, Marcus K. Direct infusion-SIM as fast and robust method for absolute protein quantification in complex samples. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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20
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Mahboob S, Mohamedali A, Ahn SB, Schulz-Knappe P, Nice E, Baker MS. Is isolation of comprehensive human plasma peptidomes an achievable quest? J Proteomics 2015; 127:300-9. [PMID: 25979773 DOI: 10.1016/j.jprot.2015.05.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/06/2015] [Accepted: 05/09/2015] [Indexed: 01/12/2023]
Abstract
The low molecular weight (LMW; <10kDa)* plasma peptidome has been considered a source of useful diagnostic biomarkers and potentially therapeutic molecules, as it contains many cytokines, peptide hormones, endogenous peptide products and potentially bioactive fragments derived from the parent proteome. The small size of the peptides allows them almost unrestricted vascular and interstitial access, and hence distribution across blood-brain barriers, tumour and other vascular permeability barriers. Therefore, the peptidome may carry specific signatures or fingerprints of an individual's health, wellbeing or disease status. This occurs primarily because of the advantage the peptidome has in being readily accessible in human blood and/or other biofluids. However, the co-expression of highly abundant proteins (>10kDa) and other factors present inherently in human plasma make direct analysis of the blood peptidome one of the most challenging tasks faced in contemporary analytical biochemistry. A comprehensive compendium of extraction and fractionation tools has been collected concerning the isolation and micromanipulation of peptides. However, the search for a reliable, accurate and reproducible single or combinatorial separation process for capturing and analysing the plasma peptidome remains a challenge. This review outlines current techniques used for the separation and detection of plasma peptides and suggests potential avenues for future investigation. This article is part of a Special Issue entitled: HUPO 2014.
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Affiliation(s)
- S Mahboob
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, NSW 2109, Australia
| | - A Mohamedali
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, NSW 2109, Australia
| | - S B Ahn
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, NSW 2109, Australia
| | | | - E Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - M S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, NSW 2109, Australia.
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21
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Dallas DC, Guerrero A, Parker EA, Robinson RC, Gan J, German JB, Barile D, Lebrilla CB. Current peptidomics: applications, purification, identification, quantification, and functional analysis. Proteomics 2015; 15:1026-38. [PMID: 25429922 PMCID: PMC4371869 DOI: 10.1002/pmic.201400310] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/08/2014] [Accepted: 11/24/2014] [Indexed: 12/28/2022]
Abstract
Peptidomics is an emerging field branching from proteomics that targets endogenously produced protein fragments. Endogenous peptides are often functional within the body-and can be both beneficial and detrimental. This review covers the use of peptidomics in understanding digestion, and identifying functional peptides and biomarkers. Various techniques for peptide and glycopeptide extraction, both at analytical and preparative scales, and available options for peptide detection with MS are discussed. Current algorithms for peptide sequence determination, and both analytical and computational techniques for quantification are compared. Techniques for statistical analysis, sequence mapping, enzyme prediction, and peptide function, and structure prediction are explored.
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Affiliation(s)
- David C. Dallas
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Andres Guerrero
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Evan A. Parker
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Randall C. Robinson
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Junai Gan
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - J. Bruce German
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Daniela Barile
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Carlito B. Lebrilla
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
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22
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Archakov A, Lisitsa A, Ponomarenko E, Zgoda V. Recent advances in proteomic profiling of human blood: clinical scope. Expert Rev Proteomics 2015; 12:111-3. [DOI: 10.1586/14789450.2015.1018895] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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23
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Yamaguchi S, Zhang B, Tomonaga T, Seino U, Kanagawa A, Segawa M, Nagasaka H, Suzuki A, Miida T, Yamada S, Sasaguri Y, Doi T, Saku K, Okazaki M, Tochino Y, Hirano KI. Selective evaluation of high density lipoprotein from mouse small intestine by an in situ perfusion technique. J Lipid Res 2014; 55:905-18. [PMID: 24569139 DOI: 10.1194/jlr.m047761] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The small intestine (SI) is the second-greatest source of HDL in mice. However, the selective evaluation of SI-derived HDL (SI-HDL) has been difficult because even the origin of HDL obtained in vivo from the intestinal lymph duct of anesthetized rodents is doubtful. To shed light on this question, we have developed a novel in situ perfusion technique using surgically isolated mouse SI, with which the possible filtration of plasma HDL into the SI lymph duct can be prevented. With the developed method, we studied the characteristics of and mechanism for the production and regulation of SI-HDL. Nascent HDL particles were detected in SI lymph perfusates in WT mice, but not in ABCA1 KO mice. SI-HDL had a high protein content and was smaller than plasma HDL. SI-HDL was rich in TG and apo AIV compared with HDL in liver perfusates. SI-HDL was increased by high-fat diets and reduced in apo E KO mice. In conclusion, with our in situ perfusion model that enables the selective evaluation of SI-HDL, we demonstrated that ABCA1 plays an important role in intestinal HDL production, and SI-HDL is small, dense, rich in apo AIV, and regulated by nutritional and genetic factors.
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Affiliation(s)
- Satoshi Yamaguchi
- Laboratory of Cardiovascular Disease, Novel, Non-invasive and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University, Osaka, Japan
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