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Gurdo N, Taylor Parkins SK, Fricano M, Wulff T, Nielsen LK, Nikel PI. Protocol for absolute quantification of proteins in Gram-negative bacteria based on QconCAT-based labeled peptides. STAR Protoc 2023; 4:102060. [PMID: 36853682 PMCID: PMC9881405 DOI: 10.1016/j.xpro.2023.102060] [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: 09/20/2022] [Revised: 10/02/2022] [Accepted: 01/05/2023] [Indexed: 01/26/2023] Open
Abstract
Mass-spectrometry-based absolute protein quantification uses labeled quantification concatamer (QconCAT) as internal standards (ISs). To calculate the amount of protein(s), the ion intensity ratio between the analyte and its cognate IS is compared in each biological sample. The present protocol describes a systematic workflow to design, produce, and purify QconCATs and to quantify soluble proteins in Pseudomonas putida KT2440. Our methodology enables the quantification of detectable peptide and serves as a versatile platform to produce ISs for different biological systems.
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Affiliation(s)
- Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | - Martina Fricano
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Lars Keld Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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2
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Maaß S, Antelo-Varela M, Bonn F, Becher D. Sample Preparation for Mass Spectrometry-Based Absolute Quantification of Bacterial Proteins in Antibiotic Stress Research. Methods Mol Biol 2023; 2601:335-348. [PMID: 36445593 DOI: 10.1007/978-1-0716-2855-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Absolute protein quantification is an essential tool for system biology approaches and elucidation of stoichiometry of multi-protein complexes. In this updated chapter, a universal protocol for gel-free absolute protein quantification in bacterial systems is described, which provides adapted methods for cytosolic and membrane proteins. This protocol can be used for sample preparation prior to miscellaneous mass spectrometry-based quantification workflows like AQUA, Hi3, and emPAI. In addition, a focus has been set to the specific challenges in antibiotic stress research.
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Affiliation(s)
- Sandra Maaß
- Department of Microbial Proteomics, University of Greifswald, Institute of Microbiology, Greifswald, Germany.
| | - Minia Antelo-Varela
- Department of Microbial Proteomics, University of Greifswald, Institute of Microbiology, Greifswald, Germany
- University of Basel, Biozentrum, Focal Area Infection Biology, Basel, Switzerland
| | - Florian Bonn
- Department of Microbial Proteomics, University of Greifswald, Institute of Microbiology, Greifswald, Germany
- Immundiagnostik AG, Bensheim, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, University of Greifswald, Institute of Microbiology, Greifswald, Germany
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3
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Abstract
Microbes that can recycle one-carbon (C1) greenhouse gases into fuels and chemicals are vital for the biosustainability of future industries. Acetogens are the most efficient known microbes for fixing carbon oxides CO2 and CO. Understanding proteome allocation is important for metabolic engineering as it dictates metabolic fitness. Here, we use absolute proteomics to quantify intracellular concentrations for >1,000 proteins in the model acetogen Clostridium autoethanogenum grown autotrophically on three gas mixtures (CO, CO+H2, or CO+CO2+H2). We detect the prioritization of proteome allocation for C1 fixation and the significant expression of proteins involved in the production of acetate and ethanol as well as proteins with unclear functions. The data also revealed which isoenzymes are likely relevant in vivo for CO oxidation, H2 metabolism, and ethanol production. The integration of proteomic and metabolic flux data demonstrated that enzymes catalyze high fluxes with high concentrations and high in vivo catalytic rates. We show that flux adjustments were dominantly accompanied by changing enzyme catalytic rates rather than concentrations. IMPORTANCE Acetogen bacteria are important for maintaining biosustainability as they can recycle gaseous C1 waste feedstocks (e.g., industrial waste gases and syngas from gasified biomass or municipal solid waste) into fuels and chemicals. Notably, the acetogen Clostridium autoethanogenum is being used as a cell factory in industrial-scale gas fermentation. Here, we perform reliable absolute proteome quantification for the first time in an acetogen. This is important as our work advances both rational metabolic engineering of acetogen cell factories and accurate in silico reconstruction of their phenotypes. Furthermore, this absolute proteomics data set serves as a reference toward a better systems-level understanding of the ancient metabolism of acetogens.
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Küchler J, Püttker S, Lahmann P, Genzel Y, Kupke S, Benndorf D, Reichl U. Absolute quantification of viral proteins during single-round replication of MDCK suspension cells. J Proteomics 2022; 259:104544. [PMID: 35240312 DOI: 10.1016/j.jprot.2022.104544] [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: 11/10/2021] [Revised: 02/15/2022] [Accepted: 02/20/2022] [Indexed: 11/17/2022]
Abstract
Madin-Darby canine kidney (MDCK) cells are widely used in basic research and for the propagation of influenza A viruses (IAV) for vaccine production. To identify targets for antiviral therapies and to optimize vaccine manufacturing, a detailed understanding of the viral life cycle is important. This includes the characterization of virus entry, the synthesis of the various viral RNAs and proteins, the transfer of viral compounds in the cell and virus budding. In case quantitative information is available, the analysis can be complemented by mathematical modelling approaches. While comprehensive studies focusing on IAV entry as well as viral mRNA, vRNA and cRNA accumulation in the nucleus of cells have been performed, quantitative data regarding IAV protein synthesis and accumulation was mostly lacking. In this study, we present a mass spectrometry (MS)-based method to evaluate whether an absolute quantification of viral proteins is possible for single-round replication in suspension MDCK cells. Using influenza A/PR/8/34 (H1N1, RKI) as a model strain at a multiplicity of infection of ten, defined amounts of isotopically labelled peptides of synthetic origin of four IAV proteins (hemagglutinin, neuraminidase, nucleoprotein, matrix protein 1) were added as an internal standard before tryptic digestion of samples for absolute quantification (AQUA). The first intracellular protein detected was NP at 1 h post infection (hpi). A maximum extracellular concentration of 7.7E+12 copies/mL was achieved. This was followed by hemagglutinin (3 hpi, maximum 4.1E+12 copies/mL at 13 hpi), matrix protein 1 (5 hpi, maximum 2.2E+12 copies/mL at 13 hpi) and neuraminidase (5 hpi, 6.0E+11 copies/mL at 13 hpi). In sum, for the first time absolute IAV protein copy numbers were quantified by a MS-based method for infected MDCK cells providing important insights into viral protein dynamics during single-round virus replication. SIGNIFICANCE: Influenza A virus is a significant human pathogen worldwide. To improve therapies against influenza and overcome bottlenecks in vaccine production in cell culture, it is critical to gain a detailed understanding of the viral life cycle. In addition to qPCR-based models, this study will examine the dynamics of influenza virus proteins during infection of producer cells to gain initial insights into changes in absolute copy numbers.
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Affiliation(s)
- Jan Küchler
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
| | - Sebastian Püttker
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Patrick Lahmann
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Sascha Kupke
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
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5
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Ehnert S, Seehase J, Müller-Renno C, Hannig M, Ziegler C. Simultaneous quantification of total carbohydrate and protein amounts from aqueous solutions by the sulfuric acid ultraviolet absorption method (SA-UV method). Anal Chim Acta 2021; 1174:338712. [PMID: 34247739 DOI: 10.1016/j.aca.2021.338712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/03/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Based on the sulfuric acid-ultraviolet assay (SA-UV, developed by Albalasmeh et al., 2013), we have further expanded this method for the simultaneous quantification of saccharides (carbohydrates) and proteins by ultraviolet spectrophotometry. The absorbance of saccharides depends on the formation of furfurals by dehydration in the presence of concentrated sulfuric acid, whereas proteins are unaffected and can be quantified by UV active peptide bonds and aromatic amino acid residues. In saccharide/protein mixtures the SA-UV assay offers a good alternative and substitutes the need for two different methods, like the phenol-sulfuric acid (PSA, developed by DuBois et al., 1951) and bicinchoninic acid (BCA, developed by Smith et al., 1985) assays. For the development of this method, we used glucose and BSA as model substrates and performed a method validation in terms of linearity, LOD, LOQ, accuracy, and precision. Simultaneous quantification in glucose/BSA mixtures is possible down to 20 mg/L from 30 μL sample volumes, and even low content mixtures with concentrations down to 2 mg/L can appropriately be quantified from higher volumes by an evaporation technique.
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Affiliation(s)
- Swen Ehnert
- Department of Physics and Research Center OPTIMAS, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Jürgen Seehase
- Department of Physics and Research Center OPTIMAS, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Christine Müller-Renno
- Department of Physics and Research Center OPTIMAS, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University Hospital, 66421 Homburg, Germany
| | - Christiane Ziegler
- Department of Physics and Research Center OPTIMAS, University of Kaiserslautern, 67663 Kaiserslautern, Germany.
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Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. Int J Mol Sci 2020; 21:E9162. [PMID: 33271881 PMCID: PMC7729594 DOI: 10.3390/ijms21239162] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Daria Gorbach
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Gregory Mavropolo-Stolyarenko
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Ekaterina Romanovskaya
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Ekaterina Podolskaya
- Institute of Analytical Instrumentation, Russian Academy of Science; 190103 St. Petersburg, Russia;
- Institute of Toxicology, Russian Federal Medical Agency; 192019 St. Petersburg, Russia
| | - Vladimir Zhukov
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
- Department of Genetics and Biotechnology, St. Petersburg State University; 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
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7
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Strutz J, Martin J, Greene J, Broadbelt L, Tyo K. Metabolic kinetic modeling provides insight into complex biological questions, but hurdles remain. Curr Opin Biotechnol 2019; 59:24-30. [PMID: 30851632 DOI: 10.1016/j.copbio.2019.02.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/25/2019] [Accepted: 02/04/2019] [Indexed: 01/16/2023]
Abstract
Metabolic models containing kinetic information can answer unique questions about cellular metabolism that are useful to metabolic engineering. Several kinetic modeling frameworks have recently been developed or improved. In addition, techniques for systematic identification of model structure, including regulatory interactions, have been reported. Each framework has advantages and limitations, which can make it difficult to choose the most appropriate framework. Common limitations are data availability and computational time, especially in large-scale modeling efforts. However, recently developed experimental techniques, parameter identification algorithms, as well as model reduction techniques help alleviate these computational bottlenecks. Opportunities for additional improvements may come from the rich literature in catalysis and chemical networks. In all, kinetic models are positioned to make significant impact in cellular engineering.
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Affiliation(s)
- Jonathan Strutz
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Jacob Martin
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Jennifer Greene
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Linda Broadbelt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Keith Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
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8
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Hakobyan A, Liesack W, Glatter T. Crude-MS Strategy for in-Depth Proteome Analysis of the Methane-Oxidizing Methylocystis sp. strain SC2. J Proteome Res 2018; 17:3086-3103. [DOI: 10.1021/acs.jproteome.8b00216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Werner Liesack
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 16, D-35043 Marburg, Germany
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9
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Manes NP, Nita-Lazar A. Application of targeted mass spectrometry in bottom-up proteomics for systems biology research. J Proteomics 2018; 189:75-90. [PMID: 29452276 DOI: 10.1016/j.jprot.2018.02.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/25/2018] [Accepted: 02/07/2018] [Indexed: 02/08/2023]
Abstract
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples. Consequently, targeted LC-MS is rapidly advancing biomedical research, especially systems biology research in diverse areas that include proteogenomics, interactomics, kinomics, and biological pathway modeling. With the recent development of targeted LC-MS assays for nearly the entire human proteome, targeted LC-MS is positioned to enable quantitative proteomic profiling of unprecedented quality and accessibility to support fundamental and clinical research. Here we review recent applications of bottom-up proteomics using targeted LC-MS for systems biology research. SIGNIFICANCE: Advances in targeted proteomics are rapidly advancing systems biology research. Recent applications include systems-level investigations focused on posttranslational modifications (such as phosphoproteomics), protein conformation, protein-protein interaction, kinomics, proteogenomics, and metabolic and signaling pathways. Notably, absolute quantification of metabolic and signaling pathway proteins has enabled accurate pathway modeling and engineering. Integration of targeted proteomics with other technologies, such as RNA-seq, has facilitated diverse research such as the identification of hundreds of "missing" human proteins (genes and transcripts that appear to encode proteins but direct experimental evidence was lacking).
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Affiliation(s)
- Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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10
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Abstract
Absolute protein quantification for the analysis of proteome dynamics is more and more required by the scientific community. Therefore a number of methods have recently been reported that aim at determining concentrations of single proteins in complex samples, all of them having their advantages and limitations. However, for all of these methods an accurate and protein unspecific determination of the total protein amount in a given sample is urgently needed. Here a ninhydrin-based assay established to reach this goal is described. Moreover, an optimized protocol for protein digestion is an inevitable prerequisite for all mass spectrometry-based approaches aiming at absolute protein quantification. In this chapter, various aspects are described which have to be considered during validation of a suitable digestion method and a detailed protocol is presented that can be applied to the digestion of soluble proteins originated from microbes.In order to provide an absolute protein quantification workflow applicable for small scale and large scale approaches, a step-by-step guide is provided for the so-called AQUA-strategy (AQUA = absolute quantification), including selection of suited standard peptides, the development of optimized MS methods and the determination of absolute protein concentration using stable isotope dilution and selected reaction monitoring (SID-SRM). Subsequently, a workflow is introduced that combines targeted mass spectrometry and two-dimensional polyacrylamide gel electrophoresis for the large-scale determination of absolute protein amounts.
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Affiliation(s)
- Sandra Maaß
- Department of Microbial Proteomics, Institute for Microbiology, University Greifswald, Greifswald, Germany.
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11
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Sample Preparation for Mass-Spectrometry Based Absolute Protein Quantification in Antibiotic Stress Research. Methods Mol Biol 2017; 1520:281-289. [PMID: 27873259 DOI: 10.1007/978-1-4939-6634-9_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Absolute protein quantification is an essential tool for system biology approaches and elucidation of stoichiometry of multi-protein complexes. In this chapter, a universal protocol for gel free absolute protein quantification in bacterial systems is described, which can be used for sample preparation prior to miscellaneous mass-spectrometry-based quantification workflows like AQUA, Hi3, and emPAI. In addition, a focus has been set to the specific challenges in antibiotic stress research.
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12
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Osbak KK, Houston S, Lithgow KV, Meehan CJ, Strouhal M, Šmajs D, Cameron CE, Van Ostade X, Kenyon CR, Van Raemdonck GA. Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry. PLoS Negl Trop Dis 2016; 10:e0004988. [PMID: 27606673 PMCID: PMC5015957 DOI: 10.1371/journal.pntd.0004988] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/19/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The spirochete bacterium Treponema pallidum ssp. pallidum is the etiological agent of syphilis, a chronic multistage disease. Little is known about the global T. pallidum proteome, therefore mass spectrometry studies are needed to bring insights into pathogenicity and protein expression profiles during infection. METHODOLOGY/PRINCIPAL FINDINGS To better understand the T. pallidum proteome profile during infection, we studied T. pallidum ssp. pallidum DAL-1 strain bacteria isolated from rabbits using complementary mass spectrometry techniques, including multidimensional peptide separation and protein identification via matrix-assisted laser desorption ionization-time of flight (MALDI-TOF/TOF) and electrospray ionization (ESI-LTQ-Orbitrap) tandem mass spectrometry. A total of 6033 peptides were detected, corresponding to 557 unique T. pallidum proteins at a high level of confidence, representing 54% of the predicted proteome. A previous gel-based T. pallidum MS proteome study detected 58 of these proteins. One hundred fourteen of the detected proteins were previously annotated as hypothetical or uncharacterized proteins; this is the first account of 106 of these proteins at the protein level. Detected proteins were characterized according to their predicted biological function and localization; half were allocated into a wide range of functional categories. Proteins annotated as potential membrane proteins and proteins with unclear functional annotations were subjected to an additional bioinformatics pipeline analysis to facilitate further characterization. A total of 116 potential membrane proteins were identified, of which 16 have evidence supporting outer membrane localization. We found 8/12 proteins related to the paralogous tpr gene family: TprB, TprC/D, TprE, TprG, TprH, TprI and TprJ. Protein abundance was semi-quantified using label-free spectral counting methods. A low correlation (r = 0.26) was found between previous microarray signal data and protein abundance. CONCLUSIONS This is the most comprehensive description of the global T. pallidum proteome to date. These data provide valuable insights into in vivo T. pallidum protein expression, paving the way for improved understanding of the pathogenicity of this enigmatic organism.
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Affiliation(s)
- Kara K Osbak
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Simon Houston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Karen V Lithgow
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Conor J Meehan
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Caroline E Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Xaveer Van Ostade
- Laboratory for Protein Science, Proteomics and Epigenetic Signaling (PPES) and Centre for Proteomics (CFP), University of Antwerp, Wilrijk, Belgium
| | - Chris R Kenyon
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium.,Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, South Africa
| | - Geert A Van Raemdonck
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium.,Laboratory for Protein Science, Proteomics and Epigenetic Signaling (PPES) and Centre for Proteomics (CFP), University of Antwerp, Wilrijk, Belgium
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