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Gabant G, Stekovic M, Nemcic M, Pinêtre J, Cadene M. A sDOE (Simple Design-of-Experiment) Approach for Parameter Optimization in Mass Spectrometry. Part 1. Parameter Selection and Interference Effects in Top-Down ETD Fragmentation of Proteins in a UHR-QTOF Instrument. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:27-35. [PMID: 36479974 DOI: 10.1021/jasms.2c00215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Design-of-experiment (DOE) approaches, originally conceived by Fischer, are widely applied in industry, particularly in the context of production for which they have been greatly expended. In a research and development context, DOE can be of great use for method development. Specifically, DOE can greatly speed up instrument parameter optimization by first identifying parameters that are critical to a given outcome, showing parameter interdependency where it occurs and accelerating optimization of said parameters using matrices of experimental conditions. While DOE approaches have been applied in mass spectrometry experiments, they have so far failed to gain widespread adoption. This could be attributed to the fact that DOE can get quite complex and daunting to the everyday user. Here we make the case that a subset of DOE tools, hereafter called SimpleDOE (sDOE), can make DOE accessible and useful to the Mass Spectrometry community at large. We illustrate the progressive gains from a purely manual approach to sDOE through a stepwise optimization of parameters affecting the efficiency of top-down ETD fragmentation of proteins on a high-resolution Q-TOF mass spectrometer, where the aim is to maximize sequence coverage of fragmentation events.
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Affiliation(s)
- Guillaume Gabant
- Centre de Biophysique Moléculaire, UPR4301, CNRS, affiliated to Université d'Orléans, Rue Charles Sadron, Orléans45071 Cedex 2, France
| | - Martin Stekovic
- Centre de Biophysique Moléculaire, UPR4301, CNRS, affiliated to Université d'Orléans, Rue Charles Sadron, Orléans45071 Cedex 2, France
| | - Matej Nemcic
- Centre de Biophysique Moléculaire, UPR4301, CNRS, affiliated to Université d'Orléans, Rue Charles Sadron, Orléans45071 Cedex 2, France
| | - Justine Pinêtre
- Centre de Biophysique Moléculaire, UPR4301, CNRS, affiliated to Université d'Orléans, Rue Charles Sadron, Orléans45071 Cedex 2, France
| | - Martine Cadene
- Centre de Biophysique Moléculaire, UPR4301, CNRS, affiliated to Université d'Orléans, Rue Charles Sadron, Orléans45071 Cedex 2, France
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Ng TYS, Viriya V, Chew TL, Yeong YF, Ahmad AL, Ho CD, Jawad ZA. Optimization of CO 2/H 2 Separation over Ba-SAPO-34 Zeolite Membrane Synthesized by Microwave Heating. MEMBRANES 2022; 12:membranes12090850. [PMID: 36135868 PMCID: PMC9501348 DOI: 10.3390/membranes12090850] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/03/2022] [Accepted: 08/12/2022] [Indexed: 05/31/2023]
Abstract
CO2/H2 separation using membrane technology is an important research area in order to obtain high purity hydrogen as one source of clean energy. Finding a suitable inorganic membrane is one of the critical issues, which needs to be explored for CO2/H2 separation. In the present study, Ba-SAPO-34 zeolite membrane was synthesized and followed by a modification process. CO2/H2 separation of the membrane was investigated by varying the independent process variables (CO2 % in the feed, pressure difference across the membrane and temperature). Modeling and optimization for the responses (CO2/H2 separation selectivity and CO2 permeance) was performed by applying response surface methodology and central composite design, which is available in Design Expert software. The accuracy of the models in predicting the response was tested by comparing with the experimental value of response and the two values were in good agreement. The optimization of the models gave CO2 permeance of 19.23 × 10-7 mol/m2 s Pa and CO2/H2 separation selectivity of 11.6 at 5% CO2 in the feed, a pressure difference of 100 kPa, and temperature of 30 °C for Ba-SAPO-34 zeolite membrane.
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Affiliation(s)
- Tiffany Yit Siew Ng
- CO2 Research Centre (CO2RES), Institute of Contaminant Management, Universiti Teknologi PETRONAS, Seri Iskandar 32610, Perak, Malaysia
- Department of Chemical Engineering, Universiti Teknologi PETRONAS, Seri Iskandar 32610, Perak, Malaysia
| | - Vinosha Viriya
- CO2 Research Centre (CO2RES), Institute of Contaminant Management, Universiti Teknologi PETRONAS, Seri Iskandar 32610, Perak, Malaysia
- Department of Chemical Engineering, Universiti Teknologi PETRONAS, Seri Iskandar 32610, Perak, Malaysia
| | - Thiam Leng Chew
- CO2 Research Centre (CO2RES), Institute of Contaminant Management, Universiti Teknologi PETRONAS, Seri Iskandar 32610, Perak, Malaysia
- Department of Chemical Engineering, Universiti Teknologi PETRONAS, Seri Iskandar 32610, Perak, Malaysia
| | - Yin Fong Yeong
- CO2 Research Centre (CO2RES), Institute of Contaminant Management, Universiti Teknologi PETRONAS, Seri Iskandar 32610, Perak, Malaysia
- Department of Chemical Engineering, Universiti Teknologi PETRONAS, Seri Iskandar 32610, Perak, Malaysia
| | - Abdul Latif Ahmad
- School of Chemical Engineering, Universiti Sains Malaysia, Nibong Tebal 14300, Penang, Malaysia
| | - Chii-Dong Ho
- Department of Chemical and Materials Engineering, Tamkang University, New Taipei City 25137, Taiwan
| | - Zeinab Abbas Jawad
- Department of Chemical Engineering, College of Engineering, Qatar University, Doha P.O. Box 2713, Qatar
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3
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Gong S, Hu X, Chen S, Sun B, Wu JL, Li N. Dual roles of drug or its metabolite-protein conjugate: Cutting-edge strategy of drug discovery using shotgun proteomics. Med Res Rev 2022; 42:1704-1734. [PMID: 35638460 DOI: 10.1002/med.21889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/24/2022] [Accepted: 05/04/2022] [Indexed: 11/11/2022]
Abstract
Many drugs can bind directly to proteins or be bioactivated by metabolizing enzymes to form reactive metabolites (RMs) that rapidly bind to proteins to form drug-protein conjugates or metabolite-protein conjugates (DMPCs). The close relationship between DMPCs and idiosyncratic adverse drug reactions (IADRs) has been recognized; drug discovery teams tend to avoid covalent interactions in drug discovery projects. Covalent interactions in DMPCs can provide high potency and long action duration and conquer the intractable targets, inspiring drug design, and development. This forms the dual role feature of DMPCs. Understanding the functional implications of DMPCs in IADR control and therapeutic applications requires precise identification of these conjugates from complex biological samples. While classical biochemical methods have contributed significantly to DMPC detection in the past decades, the low abundance and low coverage of DMPCs have become a bottleneck in this field. An emerging transformation toward shotgun proteomics is on the rise. The evolving shotgun proteomics techniques offer improved reproducibility, throughput, specificity, operability, and standardization. Here, we review recent progress in the systematic discovery of DMPCs using shotgun proteomics. Furthermore, the applications of shotgun proteomics supporting drug development, toxicity mechanism investigation, and drug repurposing processes are also reviewed and prospected.
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Affiliation(s)
- Shilin Gong
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Xiaolan Hu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Shengshuang Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Respiratory Medical Center, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian-Lin Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Na Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
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Ito K, Matsuda Y, Mine A, Shikida N, Takahashi K, Miyairi K, Shimbo K, Kikuchi Y, Konishi A. Single-chain tandem macrocyclic peptides as a scaffold for growth factor and cytokine mimetics. Commun Biol 2022; 5:56. [PMID: 35031676 PMCID: PMC8760323 DOI: 10.1038/s42003-022-03015-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/28/2021] [Indexed: 11/28/2022] Open
Abstract
Mimetics of growth factors and cytokines are promising tools for culturing large numbers of cells and manufacturing regenerative medicine products. In this study, we report single-chain tandem macrocyclic peptides (STaMPtides) as mimetics in a new multivalent peptide format. STaMPtides, which contain two or more macrocyclic peptides with a disulfide-closed backbone and peptide linkers, are successfully secreted into the supernatant by Corynebacterium glutamicum-based secretion technology. Without post-secretion modification steps, such as macrocyclization or enzymatic treatment, bacterially secreted STaMPtides form disulfide bonds, as designed; are biologically active; and show agonistic activities against respective target receptors. We also demonstrate, by cell-based assays, the potential of STaMPtides, which mimic growth factors and cytokines, in cell culture. The STaMPtide technology can be applied to the design, screening, and production of growth factor and cytokine mimetics.
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Affiliation(s)
- Kenichiro Ito
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan.
| | - Yoshihiko Matsuda
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Ayako Mine
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Natsuki Shikida
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Kazutoshi Takahashi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Kyohei Miyairi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Kazutaka Shimbo
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Yoshimi Kikuchi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Atsushi Konishi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
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5
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Ultrafast enzymatic digestion of proteins by microdroplet mass spectrometry. Nat Commun 2020; 11:1049. [PMID: 32103000 PMCID: PMC7044307 DOI: 10.1038/s41467-020-14877-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/21/2020] [Indexed: 11/15/2022] Open
Abstract
Enzymatic digestion for protein sequencing usually requires much time, and does not always result in high sequence coverage. Here we report the use of aqueous microdroplets to accelerate enzymatic reactions and, in particular, to improve protein sequencing. When a room temperature aqueous solution containing 10 µM myoglobin and 5 µg mL−1 trypsin is electrosonically sprayed (−3 kV) from a homemade setup to produce tiny (∼9 µm) microdroplets, we obtain 100% sequence coverage in less than 1 ms of digestion time, in sharp contrast to 60% coverage achieved by incubating the same solution at 37 °C for 14 h followed by analysis with a commercial electrospray ionization source that produces larger (∼60 µm) droplets. We also confirm the sequence of the therapeutic antibody trastuzumab (∼148 kDa), with a sequence coverage of 100% for light chains and 85% for heavy chains, demonstrating the practical utility of microdroplets in drug development. Mass spectrometry (MS)-based protein sequencing usually relies on in-solution proteolytic digestion, which is time-consuming and inefficient for certain proteins. Here, the authors achieve full protein sequence coverage in less than 1 ms by subjecting protein-protease mixtures to electrosonic spray ionization-MS.
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Porras MA, Ramos FD, Diaz MS, Cubitto MA, Villar MA. Modeling the bioconversion of starch to P(HB-co-HV) optimized by experimental design using Bacillus megaterium BBST4 strain. ENVIRONMENTAL TECHNOLOGY 2019; 40:1185-1202. [PMID: 29243993 DOI: 10.1080/09593330.2017.1418436] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/13/2017] [Indexed: 06/07/2023]
Abstract
Poly(hydroxybutyrate-co-hydroxyvalerate) (P(HB-co-HV)) is a prominent biopolymer as a potential candidate for use in the biomedical area. Several Bacillus spp. strains show promising characteristics in the use of several carbon sources and are an interesting alternative for the production of P(HB-co-HV). Sewage from the agricultural and food processing industries can be used to obtain abundantly starch as a carbon source for PHA production. The aim of the present study was to optimize by response surface methodology and desirability, the production of PHA by a Bacillus megaterium strain using starch as the sole carbon source. Two optimal conditions were determined without sporulation and were used to perform new experiments to calibrate and validate a mechanistic model, developed to simulate the dynamics of PHA and biomass production. The developed model successfully represents the kinetics of the microorganism. Employing different characterization techniques, it was determined that the PHA produced by the strain is a copolymer composed of different HB:HV proportions. Using starch as the sole carbon source in a minimal salt medium, this work shows the first reports in the literature of: 1) a mathematical model for predicting growth kinetic and PHA production for B. megaterium strain and 2) a Bacillus spp. producing P(HB-co-HV) copolymer.
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Affiliation(s)
- Mauricio A Porras
- a Departamento de Biología, Bioquímica y Farmacia , Universidad Nacional del Sur , Bahía Blanca , Argentina
- b Planta Piloto de Ingeniería Química, PLAPIQUI (UNS-CONICET) , Bahía Blanca , Argentina
| | - Fernando D Ramos
- b Planta Piloto de Ingeniería Química, PLAPIQUI (UNS-CONICET) , Bahía Blanca , Argentina
- c Departamento de Ingeniería Química , Universidad Nacional del Sur , Bahía Blanca , Argentina
| | - María S Diaz
- b Planta Piloto de Ingeniería Química, PLAPIQUI (UNS-CONICET) , Bahía Blanca , Argentina
- c Departamento de Ingeniería Química , Universidad Nacional del Sur , Bahía Blanca , Argentina
| | - María A Cubitto
- a Departamento de Biología, Bioquímica y Farmacia , Universidad Nacional del Sur , Bahía Blanca , Argentina
- d Centro de Recursos Naturales Renovables de la Zona Semiárida, CERZOS (UNS-CONICET) , Bahía Blanca , Argentina
| | - Marcelo A Villar
- b Planta Piloto de Ingeniería Química, PLAPIQUI (UNS-CONICET) , Bahía Blanca , Argentina
- c Departamento de Ingeniería Química , Universidad Nacional del Sur , Bahía Blanca , Argentina
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7
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Shahamirifard SAR, Ghaedi M, Montazerozohori M, Masoudiasl A. Carbon dots as absorbance promoter probes for detection of Cu(ii) ions in aqueous solution: central composite design approach. Photochem Photobiol Sci 2018; 17:245-255. [DOI: 10.1039/c7pp00454k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, the use of carbon dots (CDs) as a complexing agent and sensitizer in a polymeric matrix for determination of copper(ii) by UV-vis spectroscopy is reported for the first time.
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Affiliation(s)
| | - M. Ghaedi
- Chemistry Department
- Yasouj University
- Yasouj 75918-74831
- Iran
| | | | - A. Masoudiasl
- Chemistry Department
- Yasouj University
- Yasouj 75918-74831
- Iran
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8
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Shahamirifard SA, Ghaedi M. Design of novel and modified dual optode membrane based on carbon dots for both ultratrace copper(ii) and cobalt(ii): derivative spectrophotometric and central composite design study. NEW J CHEM 2018. [DOI: 10.1039/c7nj04695b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A selective, accurate and highly sensitive optical chemical sensor (optode) for the simultaneous determination of copper(ii) and cobalt(ii) without any prior separation or purification ion sensing was developed.
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Liu S, Ferreira JFDS, Liu L, Tang Y, Tian D, Liu Z, Tian N. Isolation of Dihydroartemisinic Acid from Artemisia annua L. By-Product by Combining Ultrasound-Assisted Extraction with Response Surface Methodology. Chem Pharm Bull (Tokyo) 2017; 65:746-753. [PMID: 28566563 DOI: 10.1248/cpb.c17-00192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Malaria is the most devastating parasitic disease worldwide. Artemisinin is the only drug that can cure malaria that is resistant to quinine-derived drugs. After the commercial extraction of artemisinin from Artemisia annua, the recovery of dihydroartemisinic acid (DHAA) from artemisinin extraction by-product has the potential to increase artemisinin commercial yield. Here we describe the development and optimization of an ultrasound-assisted alkaline procedure for the extraction of DHAA from artemisinin production waste using response surface methodology. Our results using this methodology established that NaOH at 0.36%, extraction time of 67.96 min, liquid-solid ratio of 5.89, and ultrasonic power of 83.9 W were the optimal conditions to extract DHAA from artemisinin production waste. Under these optimal conditions, we achieved a DHAA yield of 2.7%. Finally, we conducted a validation experiment, and the results confirmed the prediction generated by the regression model developed in this study. This work provides a novel way to increase the production of artemisinin per cultivated area and to reduce artemisinin production costs by recycling its commercial waste to obtain DHAA, an immediate precursor of artemisinin. The use of this technology may reduce the costs of artemisinin-based antimalarial medicines.
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Affiliation(s)
- Shuoqian Liu
- Department of Tea Science, College of Horticulture and Hardening, Hunan Agricultural University.,National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals
| | | | - Liping Liu
- Department of Tea Science, College of Horticulture and Hardening, Hunan Agricultural University
| | - Yuwei Tang
- Department of Tea Science, College of Horticulture and Hardening, Hunan Agricultural University
| | - Dongming Tian
- National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals
| | - Zhonghua Liu
- Department of Tea Science, College of Horticulture and Hardening, Hunan Agricultural University.,National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals
| | - Na Tian
- Department of Tea Science, College of Horticulture and Hardening, Hunan Agricultural University
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Abstract
Because proteomics experiments are so complex they can readily fail, and do so without clear cause. Using standard experimental design techniques and incorporating quality control can greatly increase the chances of success. This chapter introduces the relevant concepts and provides examples specific to proteomic workflows. Applying these notions to design successful proteomics experiments is straightforward. It can help identify failure causes and greatly increase the likelihood of inter-laboratory reproducibility.
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Affiliation(s)
- Daniel Ruderman
- Lawrence J. Ellison Institute for Transformative Medicine of USC, Keck School of Medicine of USC, 2250 Alcazar St. CSC-240, Los Angeles, CA, 90033, USA.
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11
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Luo L, Zheng S, Huang Y, Qin T, Xing J, Niu Y, Bo R, Liu Z, Huang Y, Hu Y, Liu J, Wu Y, Wang D. Preparation and characterization of Chinese yam polysaccharide PLGA nanoparticles and their immunological activity. Int J Pharm 2016; 511:140-150. [DOI: 10.1016/j.ijpharm.2016.06.130] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/16/2016] [Accepted: 06/29/2016] [Indexed: 12/22/2022]
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12
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Hecht ES, Oberg AL, Muddiman DC. Optimizing Mass Spectrometry Analyses: A Tailored Review on the Utility of Design of Experiments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:767-85. [PMID: 26951559 PMCID: PMC4841694 DOI: 10.1007/s13361-016-1344-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/14/2016] [Accepted: 01/16/2016] [Indexed: 05/07/2023]
Abstract
Mass spectrometry (MS) has emerged as a tool that can analyze nearly all classes of molecules, with its scope rapidly expanding in the areas of post-translational modifications, MS instrumentation, and many others. Yet integration of novel analyte preparatory and purification methods with existing or novel mass spectrometers can introduce new challenges for MS sensitivity. The mechanisms that govern detection by MS are particularly complex and interdependent, including ionization efficiency, ion suppression, and transmission. Performance of both off-line and MS methods can be optimized separately or, when appropriate, simultaneously through statistical designs, broadly referred to as "design of experiments" (DOE). The following review provides a tutorial-like guide into the selection of DOE for MS experiments, the practices for modeling and optimization of response variables, and the available software tools that support DOE implementation in any laboratory. This review comes 3 years after the latest DOE review (Hibbert DB, 2012), which provided a comprehensive overview on the types of designs available and their statistical construction. Since that time, new classes of DOE, such as the definitive screening design, have emerged and new calls have been made for mass spectrometrists to adopt the practice. Rather than exhaustively cover all possible designs, we have highlighted the three most practical DOE classes available to mass spectrometrists. This review further differentiates itself by providing expert recommendations for experimental setup and defining DOE entirely in the context of three case-studies that highlight the utility of different designs to achieve different goals. A step-by-step tutorial is also provided.
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Affiliation(s)
- Elizabeth S Hecht
- W. M. Keck FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ann L Oberg
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - David C Muddiman
- W. M. Keck FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA.
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Liato V, Labrie S, Benali M, Aider M. Application of response surface methodology for the optimization of the production of electro-activated solutions in a three-cell reactor. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.eaef.2015.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Lambrinidis G, Vallianatou T, Tsantili-Kakoulidou A. In vitro, in silico and integrated strategies for the estimation of plasma protein binding. A review. Adv Drug Deliv Rev 2015; 86:27-45. [PMID: 25819487 DOI: 10.1016/j.addr.2015.03.011] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 02/11/2015] [Accepted: 03/20/2015] [Indexed: 12/28/2022]
Abstract
Plasma protein binding (PPB) strongly affects drug distribution and pharmacokinetic behavior with consequences in overall pharmacological action. Extended plasma protein binding may be associated with drug safety issues and several adverse effects, like low clearance, low brain penetration, drug-drug interactions, loss of efficacy, while influencing the fate of enantiomers and diastereoisomers by stereoselective binding within the body. Therefore in holistic drug design approaches, where ADME(T) properties are considered in parallel with target affinity, considerable efforts are focused in early estimation of PPB mainly in regard to human serum albumin (HSA), which is the most abundant and most important plasma protein. The second critical serum protein α1-acid glycoprotein (AGP), although often underscored, plays also an important and complicated role in clinical therapy and thus the last years it has been studied thoroughly too. In the present review, after an overview of the principles of HSA and AGP binding as well as the structure topology of the proteins, the current trends and perspectives in the field of PPB predictions are presented and discussed considering both HSA and AGP binding. Since however for the latter protein systematic studies have started only the last years, the review focuses mainly to HSA. One part of the review highlights the challenge to develop rapid techniques for HSA and AGP binding simulation and their performance in assessment of PPB. The second part focuses on in silico approaches to predict HSA and AGP binding, analyzing and evaluating structure-based and ligand-based methods, as well as combination of both methods in the aim to exploit the different information and overcome the limitations of each individual approach. Ligand-based methods use the Quantitative Structure-Activity Relationships (QSAR) methodology to establish quantitate models for the prediction of binding constants from molecular descriptors, while they provide only indirect information on binding mechanism. Efforts for the establishment of global models, automated workflows and web-based platforms for PPB predictions are presented and discussed. Structure-based methods relying on the crystal structures of drug-protein complexes provide detailed information on the underlying mechanism but are usually restricted to specific compounds. They are useful to identify the specific binding site while they may be important in investigating drug-drug interactions, related to PPB. Moreover, chemometrics or structure-based modeling may be supported by experimental data a promising integrated alternative strategy for ADME(T) properties optimization. In the case of PPB the use of molecular modeling combined with bioanalytical techniques is frequently used for the investigation of AGP binding.
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15
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Ghaedi M, Shahamiri A, Mirtamizdoust B, Hajati S, Taghizadeh F. A novel polyvinyl chloride-membrane optical sensor for the determination of Cu(2+) ion based on synthesized (N'(1)E,N'(2)E)-N'(1),N'(2)-bis(pyridine-2-ylmethylene)oxalohydrazide: experimental design and optimization. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 138:878-884. [PMID: 25484254 DOI: 10.1016/j.saa.2014.10.077] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 10/12/2014] [Accepted: 10/19/2014] [Indexed: 06/04/2023]
Abstract
A copper (Cu(2+)) ion-selective bulk optode was constructed by using (N'(1)E,N'(2)E)-N'(1),N'(2)-bis(pyridine-2-ylmethylene)oxalohydrazide as ionophore and NaTPB in DBP matrices. Central composite design under response surface methodology was applied for the optimization of variables including pH, amount of ligand, amount of additive and response time which significantly affect the response of proposed sensor. At optimum specified conditions, the high stability, reproducibility and relatively long lifetime of the optical sensor suggest its ability for accurate and precise monitoring of Cu(2+) ion content in various real samples over a concentration range of 1.6×10(-6) to 3.17×10(-5)molL(-1) with a limit of detection of 8.1×10(-7)molL(-1) during response time 6.9min. The proposed optical sensor was successfully applied for the determination of Cu(2+) ion in tap water and different samples.
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Affiliation(s)
- M Ghaedi
- Chemistry Department, Yasouj University, Yasouj 75914-35, Iran.
| | - A Shahamiri
- Chemistry Department, Yasouj University, Yasouj 75914-35, Iran
| | - B Mirtamizdoust
- Chemistry Department, Yasouj University, Yasouj 75914-35, Iran; Department of Chemistry, Faculty of Science, University of Qom, Qom 37185-359, Iran
| | - S Hajati
- Department of Physics, Yasouj University, Yasouj 75914-35, Iran
| | - F Taghizadeh
- Department of Physics, Yasouj University, Yasouj 75914-35, Iran
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Fu S, Zhang J, Li T, Wang S, Ding W, Zhao M, Du Y, Wang Q, Jia J. Multi-responses extraction optimization based on response surface methodology combined with polarity switching HPLC–MS/MS for the simultaneous quantitation of 11 compounds in Cortex Fraxini: Application to four species of Cortex Fraxini and its 3 confusable species. J Pharm Biomed Anal 2014; 91:210-21. [DOI: 10.1016/j.jpba.2013.12.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 12/22/2013] [Accepted: 12/26/2013] [Indexed: 11/29/2022]
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17
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Comparison of (bio-)transformation methods for the generation of metabolite-like compound libraries of p38α MAP kinase inhibitors using high-resolution screening. J Pharm Biomed Anal 2014; 88:235-44. [DOI: 10.1016/j.jpba.2013.08.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/26/2013] [Accepted: 08/27/2013] [Indexed: 11/17/2022]
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Switzar L, van Angeren J, Pinkse M, Kool J, Niessen WMA. A high-throughput sample preparation method for cellular proteomics using 96-well filter plates. Proteomics 2013; 13:2980-3. [PMID: 23943524 DOI: 10.1002/pmic.201300080] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 05/15/2013] [Accepted: 07/23/2013] [Indexed: 11/09/2022]
Abstract
A high-throughput sample preparation protocol based on the use of 96-well molecular weight cutoff (MWCO) filter plates was developed for shotgun proteomics of cell lysates. All sample preparation steps, including cell lysis, buffer exchange, protein denaturation, reduction, alkylation and proteolytic digestion are performed in a 96-well plate format, making the platform extremely well suited for processing large numbers of samples and directly compatible with functional assays for cellular proteomics. In addition, the usage of a single plate for all sample preparation steps following cell lysis reduces potential samples losses and allows for automation. The MWCO filter also enables sample concentration, thereby increasing the overall sensitivity, and implementation of washing steps involving organic solvents, for example, to remove cell membranes constituents. The optimized protocol allowed for higher throughput with improved sensitivity in terms of the number of identified cellular proteins when compared to an established protocol employing gel-filtration columns.
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Affiliation(s)
- Linda Switzar
- AIMMS Division of BioMolecular Analysis, VU University, Amsterdam, The Netherlands
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19
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Abstract
There is increasing interest within the pharmaceutical industry in the development of proteins and peptides as drugs in addition to their use as biomarkers. Immunochemistry-based techniques have been traditionally used for the quantitation of proteins and peptides; however, LC-MS-based methodologies are being increasingly adopted as they offer several advantages. UHPLC is well established within the small-molecule community as a means to increase resolution and/or the speed of separations prior to MS detection; however, it is rarely applied to proteins or peptides separations. In this paper, current applications of UHPLC to such separations are reviewed, as well as considerations with regard to the effect of altering various chromatographic parameters.
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Switzar L, Giera M, Niessen WMA. Protein Digestion: An Overview of the Available Techniques and Recent Developments. J Proteome Res 2013; 12:1067-77. [DOI: 10.1021/pr301201x] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Switzar
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Martin Giera
- Division of Molecular Cell Physiology,
Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Wilfried M. A. Niessen
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
- hyphen MassSpec, de Wetstraat 8, 2332 XT Leiden, The Netherlands
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Identification and quantification of drug-albumin adducts in serum samples from a drug exposure study in mice. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 917-918:53-61. [PMID: 23353939 DOI: 10.1016/j.jchromb.2012.12.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 12/07/2012] [Accepted: 12/10/2012] [Indexed: 01/11/2023]
Abstract
The formation of drug-protein adducts following the bioactivation of drugs to reactive metabolites has been linked to adverse drug reactions (ADRs) and is a major complication in drug discovery and development. Identification and quantification of drug-protein adducts in vivo may lead to a better understanding of drug toxicity, but is challenging due to their low abundance in the complex biological samples. Human serum albumin (HSA) is a well-known target of reactive drug metabolites due to the free cysteine on position 34 and is often the first target to be investigated in covalent drug binding studies. Presented here is an optimized strategy for targeted analysis of low-level drug-albumin adducts in serum. This strategy is based on selective extraction of albumin from serum through affinity chromatography, efficient sample treatment and clean-up using gel filtration chromatography followed by tryptic digestion and LC-MS analysis. Quantification of the level of albumin modification was performed through a comparison of non-modified and drug-modified protein based on the relative peak area of the tryptic peptide containing the free cysteine residue. The analysis strategy was applied to serum samples resulting from a drug exposure experiment in mice, which was designed to study the effects of different acetaminophen (APAP) treatments on drug toxicity. APAP is bioactivated to N-acetyl-p-benzoquinoneimine (NAPQI) in both humans and mice and is known to bind to cysteine 34 (cys34) of HSA. Analysis of the mouse serum samples revealed the presence of extremely low-level NAPQI-albumin adducts of approximately 0.2% of the total mouse serum albumin (MSA), regardless of the length of drug exposure. Due to the targeted nature of the strategy, the NAPQI-adduct formation on cys34 could be confirmed while adducts to the second free cysteine on position 579 of MSA were not detected.
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22
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Experimental design in chromatography: A tutorial review. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 910:2-13. [DOI: 10.1016/j.jchromb.2012.01.020] [Citation(s) in RCA: 292] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 01/03/2012] [Accepted: 01/19/2012] [Indexed: 12/15/2022]
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