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Maxwell CB, Sandhu JK, Cao TH, McCann GP, Ng LL, Jones DJL. The Edge Effect in High-Throughput Proteomics: A Cautionary Tale. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37155737 DOI: 10.1021/jasms.3c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In order for mass spectrometry to continue to grow as a platform for high-throughput clinical and translational research, careful consideration must be given to quality control by ensuring that the assay performs reproducibly and accurately and precisely. In particular, the throughput required for large cohort clinical validation in biomarker discovery and diagnostic screening has driven the growth of multiplexed targeted liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) assays paired with sample preparation and analysis in multiwell plates. However, large scale MS-based proteomics studies are often plagued by batch effects: sources of technical variation in the data, which can arise from a diverse array of sources such as sample preparation batches, different reagent lots, or indeed MS signal drift. These batch effects can confound the detection of true signal differences, resulting in incorrect conclusions being drawn about significant biological effects or lack thereof. Here, we present an intraplate batch effect termed the edge effect arising from temperature gradients in multiwell plates, commonly reported in preclinical cell culture studies but not yet reported in a clinical proteomics setting. We present methods herein to ameliorate the phenomenon including proper assessment of heating techniques for multiwell plates and incorporation of surrogate standards, which can normalize for intraplate variation.
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Affiliation(s)
- Colleen B Maxwell
- The Leicester van Geest MultiOmics Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Jatinderpal K Sandhu
- The Leicester van Geest MultiOmics Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Thong H Cao
- The Leicester van Geest MultiOmics Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Gerry P McCann
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Leong L Ng
- The Leicester van Geest MultiOmics Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Donald J L Jones
- The Leicester van Geest MultiOmics Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
- Leicester Cancer Research Centre, RKCSB, University of Leicester, Leicester LE2 7LX, United Kingdom
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2
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Gygli G. On the reproducibility of enzyme reactions and kinetic modelling. Biol Chem 2022; 403:717-730. [PMID: 35357794 DOI: 10.1515/hsz-2021-0393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/09/2022] [Indexed: 12/20/2022]
Abstract
Enzyme reactions are highly dependent on reaction conditions. To ensure reproducibility of enzyme reaction parameters, experiments need to be carefully designed and kinetic modeling meticulously executed. Furthermore, to enable quality control of enzyme reaction parameters, the experimental conditions, the modeling process as well as the raw data need to be reported comprehensively. By taking these steps, enzyme reaction parameters can be open and FAIR (findable, accessible, interoperable, re-usable) as well as repeatable, replicable and reproducible. This review discusses these requirements and provides a practical guide to designing initial rate experiments for the determination of enzyme reaction parameters and gives an open, FAIR and re-editable example of the kinetic modeling of an enzyme reaction. Both the guide and example are scripted with Python in Jupyter Notebooks and are publicly available (https://fairdomhub.org/investigations/483/snapshots/1). Finally, the prerequisites of automated data analysis and machine learning algorithms are briefly discussed to provide further motivation for the comprehensive, open and FAIR reporting of enzyme reaction parameters.
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Affiliation(s)
- Gudrun Gygli
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
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3
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Ott F, Rabe KS, Niemeyer CM, Gygli G. Toward Reproducible Enzyme Modeling with Isothermal Titration Calorimetry. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Felix Ott
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Kersten S. Rabe
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Gudrun Gygli
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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Mansoury M, Hamed M, Karmustaji R, Al Hannan F, Safrany ST. The edge effect: A global problem. The trouble with culturing cells in 96-well plates. Biochem Biophys Rep 2021; 26:100987. [PMID: 33855228 PMCID: PMC8024881 DOI: 10.1016/j.bbrep.2021.100987] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The use of 96-well plates is ubiquitous in preclinical studies. Corner and edge wells have been observed to be more prone to evaporation compared to interior wells. METHODS Mammalian cells were cultured in 96-well plates over a period of 72 h. VWR and Greiner plates were tested. MTS reagent was added, and metabolic activity was determined after 2 h. RESULTS When using VWR plates, cells showed a highly heterogeneous pattern of cell growth. The outer wells showed 35% lower metabolic activity than the central wells. Cells grown in rows two and three also grew sub-optimally (25% and 10% reduction compared to central wells). Greiner plates showed better homogeneity. Cells grown in the outer wells showed 16% lower metabolic activity while cells in rows two and three showed reductions of 7 and 1%, respectively. This edge effect was partially mitigated by storing the plates in loosely sealed wrapping during incubation. Placing a buffer between the wells of the plate further improved homogeneity for the Greiner plates. CONCLUSION Different brands of 96-well plates show different levels of the edge effect. Some clearly are inappropriate for such studies. GENERAL SIGNIFICANCE Each laboratory needs to determine their own optimum conditions for culturing cells empirically before continuing to use multiwell plates. Otherwise, large artifacts may arise, affecting the quality of data, with the potential of introducing type I or type II errors.
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Affiliation(s)
| | - Maya Hamed
- RCSI-Bahrain, PO Box 15503, Adliya, Bahrain
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5
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Azevedo NF, Allkja J, Goeres DM. Biofilms vs. cities and humans vs. aliens - a tale of reproducibility in biofilms. Trends Microbiol 2021; 29:1062-1071. [PMID: 34088548 DOI: 10.1016/j.tim.2021.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/14/2022]
Abstract
Biofilms are complex and dynamic structures that include many more components than just viable cells. Therefore, the apparently simple goal of growing reproducible biofilms is often elusive. One of the challenges in defining reproducibility for biofilm research is that different research fields use a spectrum of parameters to define reproducibility for their particular application. For instance, is the researcher interested in achieving a similar population density, height of biofilm structures, or function of the biofilm in a certain ecosystem/industrial context? Within this article we categorize reproducibility into four different levels: level 1, no reproducibility; level 2, standard reproducibility; level 3, potential standard reproducibility; and level 4, total reproducibility. To better understand the need for these different levels of reproducibility, we expand on the 'cities of microbes' analogy for biofilms by imagining that a new civilization has reached the Earth's outskirts and starts studying the Earth's cities. This will provide a better sense of scale and illustrate how small details can impact profoundly on the growth and behavior of a biofilm and our understanding of reproducibility.
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Affiliation(s)
- Nuno F Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal.
| | - Jontana Allkja
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal
| | - Darla M Goeres
- Montana State University, Center for Biofilm Engineering, 366 Barnard Hall, Bozeman, MT 59717, USA
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Tang Y, Li Z, Nellikkal MAN, Eramian H, Chan EM, Norquist AJ, Hsu DF, Schrier J. Improving Data and Prediction Quality of High-Throughput Perovskite Synthesis with Model Fusion. J Chem Inf Model 2021; 61:1593-1602. [PMID: 33797887 DOI: 10.1021/acs.jcim.0c01307] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Combinatorial fusion analysis (CFA) is an approach for combining multiple scoring systems using the rank-score characteristic function and cognitive diversity measure. One example is to combine diverse machine learning models to achieve better prediction quality. In this work, we apply CFA to the synthesis of metal halide perovskites containing organic ammonium cations via inverse temperature crystallization. Using a data set generated by high-throughput experimentation, four individual models (support vector machines, random forests, weighted logistic classifier, and gradient boosted trees) were developed. We characterize each of these scoring systems and explore 66 possible combinations of the models. When measured by the precision on predicting crystal formation, the majority of the combination models improves the individual model results. The best combination models outperform the best individual models by 3.9 percentage points in precision. In addition to improving prediction quality, we demonstrate how the fusion models can be used to identify mislabeled input data and address issues of data quality. In particular, we identify example cases where all single models and all fusion models do not give the correct prediction. Experimental replication of these syntheses reveals that these compositions are sensitive to modest temperature variations across the different locations of the heating element that can hinder or enhance the crystallization process. In summary, we demonstrate that model fusion using CFA can not only identify a previously unconsidered influence on reaction outcome but also be used as a form of quality control for high-throughput experimentation.
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Affiliation(s)
- Yuanqing Tang
- Laboratory of Informatics and Data Mining (LIDM), Department of Computer and Information Science, Fordham University, 113 West 60th Street, New York, New York 10023, United States
| | - Zhi Li
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | | | - Hamed Eramian
- Netrias LLC, 3100 Clarendon Boulevard, Suite 200, Arlington, Virginia 22201, United States
| | - Emory M Chan
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Alexander J Norquist
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041, United States
| | - D Frank Hsu
- Laboratory of Informatics and Data Mining (LIDM), Department of Computer and Information Science, Fordham University, 113 West 60th Street, New York, New York 10023, United States
| | - Joshua Schrier
- Department of Chemistry, Fordham University, 441 East Fordham Road, The Bronx, New York 10458, United States
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7
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Soori T, Ward T. De-pinning instability of an evaporating-bounded liquid bridge: Experiments and axisymmetric analysis. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.124664] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kolmar JF, Thum O, Baganz F. Customized microscale approach for optimizing two-phase bio-oxidations of alkanes with high reproducibility. Microb Cell Fact 2017; 16:174. [PMID: 29017530 PMCID: PMC5634833 DOI: 10.1186/s12934-017-0788-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/03/2017] [Indexed: 11/10/2022] Open
Abstract
Background Numerous challenges remain to achieve industrially competitive space–time yields for bio-oxidations. The ability to rapidly screen bioconversion reactions for characterization and optimization is of major importance in bioprocess development and biocatalyst selection; studies at conventional lab scale are time consuming and labor intensive with low experimental throughput. The direct ω-oxyfunctionalization of aliphatic alkanes in a regio- and chemoselective manner is efficiently catalyzed by monooxygenases such as the AlkBGT enzyme complex from Pseudomonas putida under mild conditions. However, the adoption of microscale tools for these highly volatile substrates has been hindered by excessive evaporation and material incompatibility. Results This study developed and validated a robust high-throughput microwell platform for whole-cell two-liquid phase bio-oxidations of highly volatile n-alkanes. Using microwell plates machined from polytetrafluoroethylene and a sealing clamp, highly reproducible results were achieved with no significant variability such as edge effects determined. A design of experiment approach using a response surface methodology was adopted to systematically characterize the system and identify non-limiting conditions for a whole cell bioconversion of dodecane. Using resting E. coli cells to control cell concentration and reducing the fill volume it is possible to operate in non-limiting conditions with respect to oxygen and glucose whilst achieving relevant total product yields (combining 1-dodecanol, dodecanal and dodecanoic acid) of up to 1.5 mmol gDCW−1. Conclusions Overall, the developed microwell plate greatly improves experimental throughput, accelerating the screening procedures specifically for biocatalytic processes in non-conventional media. Its simplicity, robustness and standardization ensure high reliability of results. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0788-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johannes F Kolmar
- Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Bernard Katz Building, Gordon Street, London, WC1H 0AH, UK
| | - Oliver Thum
- Evonik Creavis GmbH, Paul-Baumann-Straße 1, 45772, Marl, Germany
| | - Frank Baganz
- Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Bernard Katz Building, Gordon Street, London, WC1H 0AH, UK.
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9
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Ohs R, Wendlandt J, Spiess AC. How graphical analysis helps interpreting optimal experimental designs for nonlinear enzyme kinetic models. AIChE J 2017. [DOI: 10.1002/aic.15814] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rüdiger Ohs
- Faculty of Mechanical Engineering, RWTH Aachen University, Aachener Verfahrenstechnik - Enzyme Process Technology; Worringerweg 1, 52056 Aachen Germany
- DWI - Leibniz Institute for Interactive Materials Research; Forckenbeckstrasse 50, 52074 Aachen Germany
| | - Jan Wendlandt
- Faculty of Mechanical Engineering, RWTH Aachen University, Aachener Verfahrenstechnik - Enzyme Process Technology; Worringerweg 1, 52056 Aachen Germany
| | - Antje C. Spiess
- Faculty of Mechanical Engineering, RWTH Aachen University, Aachener Verfahrenstechnik - Enzyme Process Technology; Worringerweg 1, 52056 Aachen Germany
- DWI - Leibniz Institute for Interactive Materials Research; Forckenbeckstrasse 50, 52074 Aachen Germany
- Department of Mechanical Engineering, Technical University of Braunschweig, Institute of Biochemical Engineering; Rebenring 56, 38106 Braunschweig Germany
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10
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Grosch JH, Wagner D, Nistelkas V, Spieß AC. Thermodynamic activity-based intrinsic enzyme kinetic sheds light on enzyme-solvent interactions. Biotechnol Prog 2016; 33:96-103. [DOI: 10.1002/btpr.2401] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/28/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Jan-Hendrik Grosch
- RWTH Aachen University, AVT - Enzyme Process Technology; Worringer Weg 1 Aachen 52074 Germany
- Institute of Biochemical Engineering; TU Braunschweig, Rebenring 56; Braunschweig 38106 Germany
| | - David Wagner
- RWTH Aachen University, AVT - Enzyme Process Technology; Worringer Weg 1 Aachen 52074 Germany
- DWI-Leibniz-Institute for Interactive Materials, Forckenbeckstraße 50; Aachen 52074 Germany
| | - Vasilios Nistelkas
- RWTH Aachen University, AVT - Enzyme Process Technology; Worringer Weg 1 Aachen 52074 Germany
| | - Antje C. Spieß
- RWTH Aachen University, AVT - Enzyme Process Technology; Worringer Weg 1 Aachen 52074 Germany
- Institute of Biochemical Engineering; TU Braunschweig, Rebenring 56; Braunschweig 38106 Germany
- DWI-Leibniz-Institute for Interactive Materials, Forckenbeckstraße 50; Aachen 52074 Germany
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11
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Influence of the experimental setup on the determination of enzyme kinetic parameters. Biotechnol Prog 2016; 33:87-95. [DOI: 10.1002/btpr.2390] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/21/2016] [Indexed: 11/07/2022]
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12
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Sieben M, Giese H, Grosch JH, Kauffmann K, Büchs J. Permeability of currently available microtiter plate sealing tapes fail to fulfil the requirements for aerobic microbial cultivation. Biotechnol J 2016; 11:1525-1538. [DOI: 10.1002/biot.201600054] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/25/2016] [Accepted: 08/30/2016] [Indexed: 01/27/2023]
Affiliation(s)
- Michaela Sieben
- RWTH Aachen University; AVT - Biochemical Engineering; Aachen Germany
| | - Heiner Giese
- RWTH Aachen University; AVT - Biochemical Engineering; Aachen Germany
| | - Jan-Hendrik Grosch
- TU Braunschweig; Institute of Biochemical Engineering; Braunschweig Germany
| | - Kira Kauffmann
- RWTH Aachen University; AVT - Biochemical Engineering; Aachen Germany
| | - Jochen Büchs
- RWTH Aachen University; AVT - Biochemical Engineering; Aachen Germany
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