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Masuda K, Kasahara K, Narumi R, Shimojo M, Shimizu Y. Versatile and multiplexed mass spectrometry-based absolute quantification with cell-free-synthesized internal standard peptides. J Proteomics 2021; 251:104393. [PMID: 34678518 DOI: 10.1016/j.jprot.2021.104393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 09/01/2021] [Revised: 10/04/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022]
Abstract
Preparation of stable isotope-labeled internal standard peptides is crucial for mass spectrometry (MS)-based targeted proteomics. Herein, we developed versatile and multiplexed absolute protein quantification method using MS. A previously developed method based on the cell-free peptide synthesis system, termed MS-based quantification by isotope-labeled cell-free products (MS-QBiC), was improved for multiple peptide synthesis in one-pot reaction. We pluralized the quantification tags used for the quantification of synthesized peptides and thus, made it possible to use cell-free synthesized isotope-labeled peptides as mixtures for the absolute quantification. The improved multiplexed MS-QBiC method was proved to be applied to clarify ribosomal proteins stoichiometry in the ribosomal subunit, one of the largest cellular complexes. The study demonstrates that the developed method enables the preparation of several dozens and even several hundreds of internal standard peptides within a few days for quantification of multiple proteins with only a single-run of MS analysis. SIGNIFICANCE: The developed method can be applied for the preparation of internal standard peptides without limiting the number of peptides to be synthesized, which may result in more practical screening of quantitatively reliable peptides, one of the fundamental steps in the reliable absolute quantification using MS. Furthermore, the method is highly versatile for proteome analysis of any organisms or species without any cDNA or SIL peptide libraries. The quantification can be finished in a few days including design and preparation of appropriate SIL peptides using small-scale batch cell-free reactions, which has a potential to be a part of the standard methodology in a field of quantitative proteomics.
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Affiliation(s)
- Keiko Masuda
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Keiko Kasahara
- Department of Surgery, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan; Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Ryohei Narumi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Masaru Shimojo
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan.
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Narumi R, Masuda K, Tomonaga T, Adachi J, Ueda HR, Shimizu Y. Cell-free synthesis of stable isotope-labeled internal standards for targeted quantitative proteomics. Synth Syst Biotechnol 2018; 3:97-104. [PMID: 29900422 PMCID: PMC5995455 DOI: 10.1016/j.synbio.2018.02.004] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/16/2018] [Accepted: 02/18/2018] [Indexed: 01/04/2023] Open
Abstract
High-sensitivity mass spectrometry approaches using selected reaction monitoring (SRM) or multiple reaction monitoring (MRM) methods are powerful tools for targeted quantitative proteomics-based investigation of dynamics in specific biological systems. Both high-sensitivity detection of low-abundance proteins and their quantification using this technique employ stable isotope-labeled peptide internal standards. Currently, there are various ways for preparing standards, including chemical peptide synthesis, cellular protein expression, and cell-free protein or peptide synthesis. Cell-free protein synthesis (CFPS) or in vitro translation (IVT) systems in particular provide high-throughput and low-cost preparation methods, and various cell types and reconstituted forms are now commercially available. Herein, we review the use of such systems for precise and reliable protein quantification.
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Affiliation(s)
- Ryohei Narumi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Satio-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Keiko Masuda
- Laboratory for Single Cell Mass Spectrometry, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Satio-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Satio-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Hiroki R. Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Yoshihiro Shimizu
- Laboratory for Single Cell Mass Spectrometry, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
- Laboratory for Cell-Free Protein Synthesis, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
- Corresponding author. Laboratory for Cell-Free Protein Synthesis, RIKEN Quantitative Biology Center (QBiC), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan.
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van Zutphen T, Ciapaite J, Bloks VW, Ackereley C, Gerding A, Jurdzinski A, de Moraes RA, Zhang L, Wolters JC, Bischoff R, Wanders RJ, Houten SM, Bronte-Tinkew D, Shatseva T, Lewis GF, Groen AK, Reijngoud DJ, Bakker BM, Jonker JW, Kim PK, Bandsma RHJ. Malnutrition-associated liver steatosis and ATP depletion is caused by peroxisomal and mitochondrial dysfunction. J Hepatol 2016; 65:1198-1208. [PMID: 27312946 DOI: 10.1016/j.jhep.2016.05.046] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 04/15/2016] [Accepted: 05/30/2016] [Indexed: 12/04/2022]
Abstract
BACKGROUND & AIMS Severe malnutrition in young children is associated with signs of hepatic dysfunction such as steatosis and hypoalbuminemia, but its etiology is unknown. Peroxisomes and mitochondria play key roles in various hepatic metabolic functions including lipid metabolism and energy production. To investigate the involvement of these organelles in the mechanisms underlying malnutrition-induced hepatic dysfunction we developed a rat model of malnutrition. METHODS Weanling rats were placed on a low protein or control diet (5% or 20% of calories from protein, respectively) for four weeks. Peroxisomal and mitochondrial structural features were characterized using immunofluorescence and electron microscopy. Mitochondrial function was assessed using high-resolution respirometry. A novel targeted quantitative proteomics method was applied to analyze 47 mitochondrial proteins involved in oxidative phosphorylation, tricarboxylic acid cycle and fatty acid β-oxidation pathways. RESULTS Low protein diet-fed rats developed hypoalbuminemia and hepatic steatosis, consistent with the human phenotype. Hepatic peroxisome content was decreased and metabolomic analysis indicated peroxisomal dysfunction. This was followed by changes in mitochondrial ultrastructure and increased mitochondrial content. Mitochondrial function was impaired due to multiple defects affecting respiratory chain complex I and IV, pyruvate uptake and several β-oxidation enzymes, leading to strongly reduced hepatic ATP levels. Fenofibrate supplementation restored hepatic peroxisome abundance and increased mitochondrial β-oxidation capacity, resulting in reduced steatosis and normalization of ATP and plasma albumin levels. CONCLUSIONS Malnutrition leads to severe impairments in hepatic peroxisomal and mitochondrial function, and hepatic metabolic dysfunction. We discuss the potential future implications of our findings for the clinical management of malnourished children. LAY SUMMARY Severe malnutrition in children is associated with metabolic disturbances that are poorly understood. In order to study this further, we developed a malnutrition animal model and found that severe malnutrition leads to an impaired function of liver mitochondria which are essential for energy production and a loss of peroxisomes, which are important for normal liver metabolic function.
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Affiliation(s)
- Tim van Zutphen
- Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jolita Ciapaite
- Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Vincent W Bloks
- Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cameron Ackereley
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Albert Gerding
- Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Angelika Jurdzinski
- Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Roberta Allgayer de Moraes
- Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ling Zhang
- Physiology and Experimental Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Justina C Wolters
- Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands; Department of Pharmacy, Analytical Biochemistry, University of Groningen, Groningen, The Netherlands
| | - Rainer Bischoff
- Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands; Department of Pharmacy, Analytical Biochemistry, University of Groningen, Groningen, The Netherlands
| | - Ronald J Wanders
- Laboratory Genetic Metabolic Diseases, Departments of Pediatrics and Clinical Chemistry, Academic Medical Center, Amsterdam, The Netherlands (current address: Icahn Institute for Genomics and Multiscale Biology, New York, USA)
| | - Sander M Houten
- Laboratory Genetic Metabolic Diseases, Departments of Pediatrics and Clinical Chemistry, Academic Medical Center, Amsterdam, The Netherlands (current address: Icahn Institute for Genomics and Multiscale Biology, New York, USA)
| | | | - Tatiana Shatseva
- Program in Cell Biology, Hospital for Sick Children, Toronto, Canada
| | - Gary F Lewis
- The Division of Endocrinology and Metabolism, Department of Medicine and the Banting and Best Diabetes Centre, University of Toronto, Toronto, Canada
| | - Albert K Groen
- Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dirk-Jan Reijngoud
- Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Barbara M Bakker
- Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Johan W Jonker
- Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter K Kim
- Program in Cell Biology, Hospital for Sick Children, Toronto, Canada; Department of Biochemistry, University of Toronto, Toronto, Canada.
| | - Robert H J Bandsma
- Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Physiology and Experimental Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Canada; Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, Canada; Centre for Global Child Health, The Hospital for Sick Children, Toronto, Canada.
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Olkowicz M, Radulska A, Suraj J, Kij A, Walczak M, Chlopicki S, Smolenski RT. Development of a sensitive, accurate and robust liquid chromatography/mass spectrometric method for profiling of angiotensin peptides in plasma and its application for atherosclerotic mice. J Chromatogr A 2015; 1393:37-46. [PMID: 25817477 DOI: 10.1016/j.chroma.2015.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 02/28/2015] [Accepted: 03/06/2015] [Indexed: 02/05/2023]
Abstract
Quantification of angiotensin (Ang) peptides in biological matrices is a challenge due to their low picomolar (pM) concentration and poor analytical performance of current methods. This work aimed to select an optimal strategy for liquid chromatography/mass spectrometry (LC/MS) quantification of major angiotensins in plasma of wild type and atherosclerotic mice. Optimal LC/MS set-up for Ang quantification was chosen, based on analytical performance, from: nanoflow/orbitrap, nanoflow/triple quadrupole and preconcentration nanoflow/triple quadrupole. The best LC/MS configuration (preconcentration nanoflow/triple quadrupole) was validated and used for measurement of angiotensins (Ang I, II, III, IV and (1-7)) in plasma of 6-month-old atherosclerotic apolipoprotein E/LDL receptor double knock-outs (ApoE/LDLR (--/--)) and wild type C57BL/6J (WT) mice. The method established for Ang quantification was selective, accurate and highly sensitive with LLOQ of 5pgmL(-1). The peak area intra-day precisions for Ang II and Ang-(1-7) were in the range 3.0-5.1 and 3.5-5.8, respectively, with corresponding accuracy of 95.4-103.5% and 95.6-106.3%. Plasma angiotensin profile was substantially modified in ApoE/LDLR knock-out mice with increase in concentration of Ang II from 37.6±21.3pgmL(-1) in WT to 200.2±47.6pgmL(-1). Concentrations of Ang I, III and IV were also increased 3-10 fold in ApoE/LDLR (--/--) mice while that of Ang-(1-7) was unchanged. We conclude that the method developed could be effectively used for accurate, comprehensive profiling of angiotensin peptides in mouse plasma. We identified substantial changes in renin-angiotensin system in a genetic mouse model of atherosclerosis consistent with the overactivation of angiotensin converting enzyme (ACE) and the impairment of ACE2.
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