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Adnane M, de Almeida AM, Chapwanya A. Unveiling the power of proteomics in advancing tropical animal health and production. Trop Anim Health Prod 2024; 56:182. [PMID: 38825622 DOI: 10.1007/s11250-024-04037-4] [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] [Received: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/04/2024]
Abstract
Proteomics, the large-scale study of proteins in biological systems has emerged as a pivotal tool in the field of animal and veterinary sciences, mainly for investigating local and rustic breeds. Proteomics provides valuable insights into biological processes underlying animal growth, reproduction, health, and disease. In this review, we highlight the key proteomics technologies, methodologies, and their applications in domestic animals, particularly in the tropical context. We also discuss advances in proteomics research, including integration of multi-omics data, single-cell proteomics, and proteogenomics, all of which are promising for improving animal health, adaptation, welfare, and productivity. However, proteomics research in domestic animals faces challenges, such as sample preparation variation, data quality control, privacy and ethical considerations relating to animal welfare. We also provide recommendations for overcoming these challenges, emphasizing the importance of following best practices in sample preparation, data quality control, and ethical compliance. We therefore aim for this review to harness the full potential of proteomics in advancing our understanding of animal biology and ultimately improve animal health and productivity in local breeds of diverse animal species in a tropical context.
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Affiliation(s)
- Mounir Adnane
- Department of Biomedicine, Institute of Veterinary Sciences, University of Tiaret, Tiaret, 14000, Algeria.
| | - André M de Almeida
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, 1349-017, Portugal
| | - Aspinas Chapwanya
- Department of Clinical Sciences, Ross University School of Veterinary Medicine, Basseterre, 00265, Saint Kitts and Nevis
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2
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Rudolf-Scholik J, Lilek D, Maier M, Reischenböck T, Maisl C, Allram J, Herbinger B, Rechthaler J. Increasing protein identifications in bottom-up proteomics of T. castaneum - Exploiting synergies of protein biochemistry and bioinformatics. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1240:124128. [PMID: 38759531 DOI: 10.1016/j.jchromb.2024.124128] [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] [Received: 01/04/2024] [Revised: 03/29/2024] [Accepted: 04/14/2024] [Indexed: 05/19/2024]
Abstract
Depending on the respective research question, LC-MS/MS based bottom-up proteomics poses challenges from the initial biological sample all the way to data evaluation. The focus of this study was to investigate the influence of sample preparation techniques and data analysis parameters on protein identification in Tribolium castaneum by applying free software proteomics platform Max Quant. Multidimensional protein extraction strategies in combination with electrophoretic or chromatographic off-line protein pre-fractionation were applied to enhance the spectrum of isolated proteins from T. castaneum and reduce the effect of co-elution and ion suppression effects during nano-LC-MS/MS measurements of peptides. For comprehensive data analysis, MaxQuant was used for protein identification and R for data evaluation. A wide range of parameters were evaluated to gain reproducible, reliable, and significant protein identifications. A simple phosphate buffer, pH 8, containing protease and phosphatase inhibitor cocktail and application of gentle extraction conditions were used as a first extraction step for T.castaneum proteins. Furthermore, a two-dimensional extraction procedure in combination with electrophoretic pre-fractionation of extracted proteins and subsequent in-gel digest resulted in almost 100% increase of identified proteins when compared to chromatographic fractionation as well as one-pot-analysis. The additionally identified proteins could be assigned to new molecular functions or cell compartments, emphasizing the positive effect of extended sample preparation in bottom-up proteomics. Besides the number of peptides during post-processing, MaxQuant's Match between Runs exhibited a crucial effect on the number of identified proteins. A maximum relative standard deviation of 2% must be considered for the data analysis. Our work with Tribolium castaneum larvae demonstrates that sometimes - depending on matrix and research question - more complex and time-consuming sample preparation can be advantageous for isolation and identification of additional proteins in bottom-up proteomics.
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Affiliation(s)
- J Rudolf-Scholik
- University of Applied Sciences Wiener Neustadt, Biotech Campus Tulln, AUSTRIA.
| | - D Lilek
- University of Applied Sciences Wiener Neustadt, Biotech Campus Tulln, AUSTRIA
| | - M Maier
- University of Applied Sciences Wiener Neustadt, Biotech Campus Tulln, AUSTRIA
| | - T Reischenböck
- University of Applied Sciences Wiener Neustadt, Biotech Campus Tulln, AUSTRIA
| | - C Maisl
- University of Applied Sciences Wiener Neustadt, Biotech Campus Tulln, AUSTRIA
| | - J Allram
- University of Applied Sciences Wiener Neustadt, Biotech Campus Tulln, AUSTRIA
| | - B Herbinger
- University of Applied Sciences Wiener Neustadt, Biotech Campus Tulln, AUSTRIA
| | - J Rechthaler
- University of Applied Sciences Wiener Neustadt, Biotech Campus Tulln, AUSTRIA
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3
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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4
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Hove HTB, Næsheim T, Kögel T. Quick and efficient microplastic isolation from fatty fish tissues by surfactant-enhanced alkaline digestion. MARINE POLLUTION BULLETIN 2023; 197:115726. [PMID: 37925993 DOI: 10.1016/j.marpolbul.2023.115726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
For monitoring microplastic contamination in fish tissues, tissue digestion into filterable components prior to microplastic identification and quantification should be quick and efficient, providing satisfying microplastic recoveries of relevant particle sizes. Filtration with a small pore size, necessary to target small particles, is a challenge. Some proposed protocols take several days. To improve this, a combination of surfactants (Tween®-20 and Triton™ X-100) with potassium hydroxide (KOH) and pH neutralization was used. Fish bones were removed in tissue preparation prior to digestion. Recovery down to ca. 60-80 μm worked well for PA-66, PE, PET, PP, PS and PVC. In conclusion, we developed a comparatively swift digestion protocol, enabling filtration of 100 g samples with a pore size of 10 μm, for fish fillets with high (mackerel), intermediate (salmon, plaice) and low (cod) fat contents, fish liver, head kidney and oil samples, within 16-24 h.
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Affiliation(s)
| | - Thomas Næsheim
- Institute of Marine Research, P.O. Box 1870 Nordnes, 5817 Bergen, Norway; EUROFINS, Sandviksveien 110, 5035 Bergen, Norway.
| | - Tanja Kögel
- Institute of Marine Research, P.O. Box 1870 Nordnes, 5817 Bergen, Norway.
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5
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Riisom M, Jamieson SMF, Hartinger CG. Critical evaluation of cell lysis methods for metallodrug studies in cancer cells. Metallomics 2023; 15:mfad048. [PMID: 37596065 DOI: 10.1093/mtomcs/mfad048] [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] [Received: 06/20/2023] [Accepted: 08/01/2023] [Indexed: 08/20/2023]
Abstract
Intracellular accumulation studies are a key step in metallodrug development but often variable results are obtained. Therefore, we aimed here to investigate different protocols for efficient and reproducible lysis of cancer cells in terms of protein content in lysates and in cell uptake studies of the Ru anticancer complex [chlorido(8-oxyquinolinato)(η6-p-cymene)ruthenium(II)] ([Ru(cym)(HQ)Cl]). The physical lysis methods osmosis and sonication were chosen for comparison with chemical lysis with the radioimmunoprecipitation assay (RIPA) buffer. Based on the protein content and the total Ru accumulated in the lysates, the latter determined using inductively coupled plasma-mass spectrometry, RIPA buffer was the most efficient lysis method. Measurements of plastic adsorption blanks revealed that the higher Ru content determined in the RIPA buffer lysis samples may be due a higher amount of Ru extracted from the plastic incubation plates compared with osmosis and sonication. Overall, we found that the choice of lysis method needs to be matched to the information sought and we suggest the least disruptive osmosis method might be the best choice for labile drug-biomolecule adducts. Minimal differences were found for experiments aimed at measuring the overall cell uptake of the Ru complex.
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Affiliation(s)
- Mie Riisom
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Auckland Cancer Society Research Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Stephen M F Jamieson
- Auckland Cancer Society Research Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Christian G Hartinger
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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6
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Emergence of mass spectrometry detergents for membrane proteomics. Anal Bioanal Chem 2023:10.1007/s00216-023-04584-z. [PMID: 36808272 PMCID: PMC10328889 DOI: 10.1007/s00216-023-04584-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/21/2023]
Abstract
Detergents enable the investigation of membrane proteins by mass spectrometry. Detergent designers aim to improve underlying methodologies and are confronted with the challenge to design detergents with optimal solution and gas-phase properties. Herein, we review literature related to the optimization of detergent chemistry and handling and identify an emerging research direction: the optimization of mass spectrometry detergents for individual applications in mass spectrometry-based membrane proteomics. We provide an overview about qualitative design aspects including their relevance for the optimization of detergents in bottom-up proteomics, top-down proteomics, native mass spectrometry, and Nativeomics. In addition to established design aspects, such as charge, concentration, degradability, detergent removal, and detergent exchange, it becomes apparent that detergent heterogeneity is a promising key driver for innovation. We anticipate that rationalizing the role of detergent structures in membrane proteomics will serve as an enabling step for the analysis of challenging biological systems.
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Henehan GT, Ryan BJ, Kinsella GK. Approaches to Avoid Proteolysis During Protein Expression and Purification. Methods Mol Biol 2023; 2699:77-95. [PMID: 37646995 DOI: 10.1007/978-1-0716-3362-5_6] [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: 09/01/2023]
Abstract
All cells contain proteases, which hydrolyze the peptide bonds between amino acids of a protein backbone. Typically, proteases are prevented from nonspecific proteolysis by regulation and by their physical separation into different subcellular compartments; however, this segregation is not retained during cell lysis, which is the initial step in any protein isolation procedure. Prevention of proteolysis during protein purification often takes the form of a two-pronged approach: first, inhibition of proteolysis in situ, followed by the early separation of the protease from the protein of interest via chromatographic purification. Protease inhibitors are routinely used to limit the effect of the proteases before they are physically separated from the protein of interest via column chromatography. In this chapter, commonly used approaches to reducing or avoiding proteolysis during protein expression and purification are reviewed.
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Affiliation(s)
- Gary T Henehan
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman, Dublin, Ireland
| | - Barry J Ryan
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman, Dublin, Ireland
| | - Gemma K Kinsella
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman, Dublin, Ireland.
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8
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van der Pan K, Kassem S, Khatri I, de Ru AH, Janssen GMC, Tjokrodirijo RTN, al Makindji F, Stavrakaki E, de Jager AL, Naber BAE, de Laat IF, Louis A, van den Bossche WBL, Vogelezang LB, Balvers RK, Lamfers MLM, van Veelen PA, Orfao A, van Dongen JJM, Teodosio C, Díez P. Quantitative proteomics of small numbers of closely-related cells: Selection of the optimal method for a clinical setting. Front Med (Lausanne) 2022; 9:997305. [PMID: 36237552 PMCID: PMC9553008 DOI: 10.3389/fmed.2022.997305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Mass spectrometry (MS)-based proteomics profiling has undoubtedly increased the knowledge about cellular processes and functions. However, its applicability for paucicellular sample analyses is currently limited. Although new approaches have been developed for single-cell studies, most of them have not (yet) been standardized and/or require highly specific (often home-built) devices, thereby limiting their broad implementation, particularly in non-specialized settings. To select an optimal MS-oriented proteomics approach applicable in translational research and clinical settings, we assessed 10 different sample preparation procedures in paucicellular samples of closely-related cell types. Particularly, five cell lysis protocols using different chemistries and mechanical forces were combined with two sample clean-up techniques (C18 filter- and SP3-based), followed by tandem mass tag (TMT)-based protein quantification. The evaluation was structured in three phases: first, cell lines from hematopoietic (THP-1) and non-hematopoietic (HT-29) origins were used to test the approaches showing the combination of a urea-based lysis buffer with the SP3 bead-based clean-up system as the best performer. Parameters such as reproducibility, accessibility, spatial distribution, ease of use, processing time and cost were considered. In the second phase, the performance of the method was tested on maturation-related cell populations: three different monocyte subsets from peripheral blood and, for the first time, macrophages/microglia (MAC) from glioblastoma samples, together with T cells from both tissues. The analysis of 50,000 cells down to only 2,500 cells revealed different protein expression profiles associated with the distinct cell populations. Accordingly, a closer relationship was observed between non-classical monocytes and MAC, with the latter showing the co-expression of M1 and M2 macrophage markers, although pro-tumoral and anti-inflammatory proteins were more represented. In the third phase, the results were validated by high-end spectral flow cytometry on paired monocyte/MAC samples to further determine the sensitivity of the MS approach selected. Finally, the feasibility of the method was proven in 194 additional samples corresponding to 38 different cell types, including cells from different tissue origins, cellular lineages, maturation stages and stimuli. In summary, we selected a reproducible, easy-to-implement sample preparation method for MS-based proteomic characterization of paucicellular samples, also applicable in the setting of functionally closely-related cell populations.
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Affiliation(s)
- Kyra van der Pan
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Sara Kassem
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Indu Khatri
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Leiden Computational Biology Center, LUMC, Leiden, Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, LUMC, Leiden, Netherlands
| | | | | | - Fadi al Makindji
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | | | - Anniek L. de Jager
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Brigitta A. E. Naber
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Inge F. de Laat
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Alesha Louis
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | | | | | | | | | | | - Alberto Orfao
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain
- Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Jacques J. M. van Dongen
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain
- Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- *Correspondence: Jacques J. M. van Dongen
| | - Cristina Teodosio
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain
- Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Paula Díez
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain
- Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
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9
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Zhang Y, Dreyer B, Govorukhina N, Heberle AM, Končarević S, Krisp C, Opitz CA, Pfänder P, Bischoff R, Schlüter H, Kwiatkowski M, Thedieck K, Horvatovich PL. Comparative Assessment of Quantification Methods for Tumor Tissue Phosphoproteomics. Anal Chem 2022; 94:10893-10906. [PMID: 35880733 PMCID: PMC9366746 DOI: 10.1021/acs.analchem.2c01036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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With increasing sensitivity and accuracy in mass spectrometry,
the tumor phosphoproteome is getting into reach. However, the selection
of quantitation techniques best-suited to the biomedical question
and diagnostic requirements remains a trial and error decision as
no study has directly compared their performance for tumor tissue
phosphoproteomics. We compared label-free quantification (LFQ), spike-in-SILAC
(stable isotope labeling by amino acids in cell culture), and tandem
mass tag (TMT) isobaric tandem mass tags technology for quantitative
phosphosite profiling in tumor tissue. Compared to the classic SILAC
method, spike-in-SILAC is not limited to cell culture analysis, making
it suitable for quantitative analysis of tumor tissue samples. TMT
offered the lowest accuracy and the highest precision and robustness
toward different phosphosite abundances and matrices. Spike-in-SILAC
offered the best compromise between these features but suffered from
a low phosphosite coverage. LFQ offered the lowest precision but the
highest number of identifications. Both spike-in-SILAC and LFQ presented
susceptibility to matrix effects. Match between run (MBR)-based analysis
enhanced the phosphosite coverage across technical replicates in LFQ
and spike-in-SILAC but further reduced the precision and robustness
of quantification. The choice of quantitative methodology is critical
for both study design such as sample size in sample groups and quantified
phosphosites and comparison of published cancer phosphoproteomes.
Using ovarian cancer tissue as an example, our study builds a resource
for the design and analysis of quantitative phosphoproteomic studies
in cancer research and diagnostics.
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Affiliation(s)
- Yang Zhang
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands.,Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Benjamin Dreyer
- Section/Core Facility Mass Spectrometry and Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Natalia Govorukhina
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Alexander M Heberle
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Saša Končarević
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt/Main, Germany
| | - Christoph Krisp
- Section/Core Facility Mass Spectrometry and Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Christiane A Opitz
- Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Department of Neurology, National Center for Tumor Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Pauline Pfänder
- Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Faculty of Bioscience, Heidelberg University, 69117 Heidelberg, Germany
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Hartmut Schlüter
- Section/Core Facility Mass Spectrometry and Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marcel Kwiatkowski
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy, University of Groningen, Groningen 9700 AD, The Netherlands.,Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen 9700 AD, The Netherlands
| | - Kathrin Thedieck
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands.,Department of Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26129 Oldenburg, Germany
| | - Peter L Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
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Voß H, Moritz M, Pelczar P, Gagliani N, Huber S, Nippert V, Schlüter H, Hahn J. Tissue Sampling and Homogenization with NIRL Enables Spatially Resolved Cell Layer Specific Proteomic Analysis of the Murine Intestine. Int J Mol Sci 2022; 23:ijms23116132. [PMID: 35682811 PMCID: PMC9181169 DOI: 10.3390/ijms23116132] [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: 04/30/2022] [Revised: 05/18/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023] Open
Abstract
For investigating the molecular physiology and pathophysiology in organs, the most exact data should be obtained; if not, organ-specific cell lines are analyzed, or the whole organ is homogenized, followed by the analysis of its biomolecules. However, if the morphological organization of the organ can be addressed, then, in the best case, the composition of molecules in single cells of the target organ can be analyzed. Laser capture microdissection (LCM) is a technique which enables the selection of specific cells of a tissue for further analysis of their molecules. However, LCM is a time-consuming two-dimensional technique, and optimal results are only obtained if the tissue is fixed, e.g., by formalin. Especially for proteome analysis, formalin fixation reduced the number of identifiable proteins, and this is an additional drawback. Recently, it was demonstrated that sampling of fresh-frozen (non-fixed) tissue with an infrared-laser is giving higher yields with respect to the absolute protein amount and number of identifiable proteins than conventional mechanical homogenization of tissues. In this study, the applicability of the infrared laser tissue sampling for the proteome analysis of different cell layers of murine intestine was investigated, using LC–MS/MS-based differential quantitative bottom-up proteomics. By laser ablation, eight consecutive layers of colon tissue were obtained and analyzed. However, a clear distinguishability of protein profiles between ascending, descending, and transversal colon was made, and we identified the different intestinal-cell-layer proteins, which are cell-specific, as confirmed by data from the Human Protein Atlas. Thus, for the first time, sampling directly from intact fresh-frozen tissue with three-dimensional resolution is giving access to the different proteomes of different cell layers of colon tissue.
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Affiliation(s)
- Hannah Voß
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
| | - Manuela Moritz
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
| | - Penelope Pelczar
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (P.P.); (N.G.); (S.H.)
| | - Nicola Gagliani
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (P.P.); (N.G.); (S.H.)
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany
| | - Samuel Huber
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (P.P.); (N.G.); (S.H.)
| | - Vivien Nippert
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
| | - Hartmut Schlüter
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
- Correspondence: (H.S.); (J.H.); Tel.: +49-1575-6085997 (H.S.); +49-1522-2827168 (J.H.)
| | - Jan Hahn
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
- Correspondence: (H.S.); (J.H.); Tel.: +49-1575-6085997 (H.S.); +49-1522-2827168 (J.H.)
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11
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Zarei M, Wang P, Jonveaux J, Haller FM, Gu B, Koulov AV, Jahn M. A novel protocol for in-depth analysis of recombinant adeno-associated virus capsid proteins using UHPLC-MS/MS. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9247. [PMID: 34951071 DOI: 10.1002/rcm.9247] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/16/2021] [Accepted: 12/19/2021] [Indexed: 06/14/2023]
Abstract
RATIONALE In-depth characterization of the three capsid viral proteins (VPs 1, 2, and 3) of adeno-associated viruses (AAVs) is immediately needed to ensure the consistency in gene therapy products and processes. These proteins are typically present at very low concentrations in matrices containing high concentrations of excipients and salts. Thus, there is a need for convenient methods for sample preparation before proteomic analysis. The aim of this study was to meet this need by developing a fast, reliable approach for isolating VPs in a manner enabling their efficient digestion and in-depth characterization using liquid chromatography-mass spectrometry (LC-MS). METHODS VPs from Anc80 were precipitated with different organic solvents, and the resulting precipitates were dissolved in either sodium deoxycholate (SDC) and N-dodecyl-beta-D-maltoside (DDM) or guanidine hydrochloride (Gu-HCl). The peptides obtained by the following enzymatic digestion by either trypsin or Asp-N were analyzed using LC-MS/MS. RESULTS We found that precipitation with chloroform/methanol/water results in fast, efficient preparation of VP samples, allowing 100% and 99.2% amino acid sequence coverage of VP1 for trypsin and Asp-N digestion, respectively. This also allowed complete sequence confirmation of VP1, VP2, and VP3 of Anc80, as well as characterization of the amino acid sequences of the N- and C-terminal regions of each VP, together with their post-translational modifications (PTMs). CONCLUSIONS The presented method enables fast, reliable, and relatively cheap sample preparation for identifying AAV serotypes and characterizing the heterogeneity of capsid viral proteins, including their PTMs.
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Affiliation(s)
| | - Peng Wang
- Lonza Houston, Inc., Houston, Texas, USA
| | | | | | - Bingnan Gu
- Lonza Houston, Inc., Houston, Texas, USA
| | | | - Michael Jahn
- Lonza AG, Drug Product Services, Basel, Switzerland
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12
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High Throughput Identification of the Potential Antioxidant Peptides in Ophiocordyceps sinensis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27020438. [PMID: 35056752 PMCID: PMC8780859 DOI: 10.3390/molecules27020438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 11/17/2022]
Abstract
Ophiocordyceps sinensis, an ascomycete caterpillar fungus, has been used as a Traditional Chinese Medicine owing to its bioactive properties. However, until now the bio-active peptides have not been identified in this fungus. Here, the raw RNA sequences of three crucial growth stages of the artificially cultivated O. sinensis and the wild-grown mature fruit-body were aligned to the genome of O. sinensis. Both homology-based prediction and de novo-based prediction methods were used to identify 8541 putative antioxidant peptides (pAOPs). The expression profiles of the cultivated mature fruiting body were similar to those found in the wild specimens. The differential expression of 1008 pAOPs matched genes had the highest difference between ST and MF, suggesting that the pAOPs were primarily induced and play important roles in the process of the fruit-body maturation. Gene ontology analysis showed that most of pAOPs matched genes were enriched in terms of ‘cell redox homeostasis’, ‘response to oxidative stresses’, ‘catalase activity’, and ‘ integral component of cell membrane’. A total of 1655 pAOPs was identified in our protein-seqs, and some crucial pAOPs were selected, including catalase, peroxiredoxin, and SOD [Cu–Zn]. Our findings offer the first identification of the active peptide ingredients in O. sinensis, facilitating the discovery of anti-infectious bio-activity and the understanding of the roles of AOPs in fungal pathogenicity and the high-altitude adaptation in this medicinal fungus.
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Abstract
Peptides play a crucial role in many vitally important functions of living organisms. The goal of peptidomics is the identification of the "peptidome," the whole peptide content of a cell, organ, tissue, body fluid, or organism. In peptidomic or proteomic studies, capillary electrophoresis (CE) is an alternative technique for liquid chromatography. It is a highly efficient and fast separation method requiring extremely low amounts of sample. In peptidomic approaches, CE is commonly combined with mass spectrometric (MS) detection. Most often, CE is coupled with electrospray ionization MS and less frequently with matrix-assisted laser desorption/ionization MS. CE-MS has been employed in numerous studies dealing with determination of peptide biomarkers in different body fluids for various diseases, or in food peptidomic research for the analysis and identification of peptides with special biological activities. In addition to the above topics, sample preparation techniques commonly applied in peptidomics before CE separation and possibilities for peptide identification and quantification by CE-MS or CE-MS/MS methods are discussed in this chapter.
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Chen X, Sun Y, Zhang T, Shu L, Roepstorff P, Yang F. Quantitative Proteomics Using Isobaric Labeling: A Practical Guide. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:689-706. [PMID: 35007772 PMCID: PMC9170757 DOI: 10.1016/j.gpb.2021.08.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 05/19/2021] [Accepted: 09/27/2021] [Indexed: 01/09/2023]
Abstract
In the past decade, relative proteomic quantification using isobaric labeling technology has developed into a key tool for comparing the expression of proteins in biological samples. Although its multiplexing capacity and flexibility make this a valuable technology for addressing various biological questions, its quantitative accuracy and precision still pose significant challenges to the reliability of its quantification results. Here, we give a detailed overview of the different kinds of isobaric mass tags and the advantages and disadvantages of the isobaric labeling method. We also discuss which precautions should be taken at each step of the isobaric labeling workflow, to obtain reliable quantification results in large-scale quantitative proteomics experiments. In the last section, we discuss the broad applications of the isobaric labeling technology in biological and clinical studies, with an emphasis on thermal proteome profiling and proteogenomics.
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Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China.
| | - Yaping Sun
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Tingting Zhang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Lian Shu
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China.
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15
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16
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Sartori GP, da Costa A, Macarini FLDS, Mariano DOC, Pimenta DC, Spencer PJ, Nali LHDS, Galisteo AJ. Characterization and evaluation of the enzymatic activity of tetanus toxin submitted to cobalt-60 gamma radiation. J Venom Anim Toxins Incl Trop Dis 2021; 27:e20200140. [PMID: 33995513 PMCID: PMC8092855 DOI: 10.1590/1678-9199-jvatitd-2020-0140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/25/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Tetanus toxin blocks the release of the inhibitory neurotransmitters in the central nervous system and causes tetanus and its main form of prevention is through vaccination. The vaccine is produced by inactivation of tetanus toxin with formaldehyde, which may cause side effects. An alternative way is the use of ionizing radiation for inactivation of the toxin and also to improve the potential immunogenic response and to reduce the post-vaccination side effects. Therefore, the aim of this study was to characterize the tetanus toxin structure after different doses of ionizing radiation of 60Co. METHODS Irradiated and native tetanus toxin was characterized by SDS PAGE in reducing and non-reducing conditions and MALD-TOF. Enzymatic activity was measured by FRET substrate. Also, antigenic properties were assessed by ELISA and Western Blot data. RESULTS Characterization analysis revealed gradual modification on the tetanus toxin structure according to doses increase. Also, fragmentation and possible aggregations of the protein fragments were observed in higher doses. In the analysis of peptide preservation by enzymatic digestion and mass spectrometry, there was a slight modification in the identification up to the dose of 4 kGy. At subsequent doses, peptide identification was minimal. The analysis of the enzymatic activity by fluorescence showed 35 % attenuation in the activity even at higher doses. In the antigenic evaluation, anti-tetanus toxin antibodies were detected against the irradiated toxins at the different doses, with a gradual decrease as the dose increased, but remaining at satisfactory levels. CONCLUSION Ionizing radiation promoted structural changes in the tetanus toxin such as fragmentation and/or aggregation and attenuation of enzymatic activity as the dose increased, but antigenic recognition of the toxin remained at good levels indicating its possible use as an immunogen. However, studies of enzymatic activity of tetanus toxin irradiated with doses above 8 kGy should be further analyzed.
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Affiliation(s)
- Giselle Pacifico Sartori
- Laboratory of Protozoology, Institute of Tropical Medicine,
University of São Paulo (IMT/FMUSP), São Paulo, SP, Brazil
| | - Andréa da Costa
- Laboratory of Protozoology, Institute of Tropical Medicine,
University of São Paulo (IMT/FMUSP), São Paulo, SP, Brazil
| | | | | | | | - Patrick Jack Spencer
- Biotechnology Center, Nuclear and Energy Research Institute
(IPEN/CNEN/SP), São Paulo, SP, Brazil
| | | | - Andrés Jimenez Galisteo
- Laboratory of Protozoology, Institute of Tropical Medicine,
University of São Paulo (IMT/FMUSP), São Paulo, SP, Brazil
- LIM49, Hospital das Clínicas HCFMUSP, School of Medicine, University
of São Paulo, São Paulo, SP, Brazil
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17
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Sedaghat B, Hajjaran H, Sadjjadi FS, Heidari S, Sadjjadi SM. Proteomic characterization of hydatid cyst fluid: two-dimensional electrophoresis (2-DE) setup through optimizing protein extraction. BMC Res Notes 2021; 14:22. [PMID: 33430965 PMCID: PMC7802163 DOI: 10.1186/s13104-020-05433-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/24/2020] [Indexed: 12/04/2022] Open
Abstract
Objective Proper characterization of hydatid cyst fluid (HCF) is useful for diagnostic and follow up purposes of cystic echinococcosis/hydatidosis, which is an important zoonotic disease. In this regard, proteomics methods are very helpful. The present study was conducted to compare three protein extraction methods for HCF collected from sheep liver hydatid cysts including, trichloracetic acid (TCA)/Acetone precipitation, TCA/Acetone along with dialysis, and combination of 2-D Clean-up Kit and dialysis followed by two-dimensional electrophoresis (2-DE), to achieve better resolution in the proteomic characterization of HCF proteins. Results The 2-DE of TCA/Acetone products showed a lot of smears in the background of gels; TCA/Acetone with dialysis showed greatly reduced smears while the 2-D Clean-up Kit together with dialysis showed sharp spots and least smears. Three-dimensional images of separated spots created by Progenesis SameSpots software showed the best result was achieved by 2-D Clean-up Kit and dialysis.
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Affiliation(s)
- Bahareh Sedaghat
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Homa Hajjaran
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Fatemeh Sadat Sadjjadi
- Faculty of Paramedical Sciences, Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudabeh Heidari
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mahmoud Sadjjadi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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18
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Deng L, Handler DCL, Multari DH, Haynes PA. Comparison of protein and peptide fractionation approaches in protein identification and quantification from Saccharomyces cerevisiae. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1162:122453. [PMID: 33279813 DOI: 10.1016/j.jchromb.2020.122453] [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: 05/25/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 11/29/2022]
Abstract
Shotgun proteomics is a high-throughput technology which has been developed with the aim of investigating the maximum number of proteins in cells in a given experiment. However, protein discovery and data generation vary in depth and coverage when different technical strategies are selected. In this study, three different sample preparation approaches, and peptide or protein fractionation methods, were applied to identify and quantify proteins from log-phase yeast lysate: sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), filter-aided sample preparation coupled with gas phase fractionation (FASP-GPF), and FASP - high pH reversed phase fractionation (HpH). Fractions were initially analyzed and compared using nanoflow liquid chromatography - tandem mass spectrometry (nanoLC-MS/MS) employing data dependent acquisition on a linear ion trap instrument. The number of fractions and analytical replicates was adjusted so that each experiment used a similar amount of mass spectrometric instrument time. A second set of experiments was performed, comparing FASP-GPF, SDS-PAGE and FASP-HpH using a Q Exactive Orbitrap mass spectrometer. Compared with results from the linear ion trap mass spectrometer, the use of a Q Exactive Orbitrap mass spectrometer enabled a substantial increase in protein identifications, and an even greater increase in peptide identifications. This shows that the main advantage of using the higher resolution instrument is in increased proteome coverage. A total of 1035, 1357 and 2134 proteins were separately identified by FASP-GPF, SDS-PAGE and FASP-HpH. Combining results from the Orbitrap experiments, there were a total of 2269 proteins found, with 94% of them identified using the FASP-HpH method. Therefore, the FASP-HpH method is the optimal choice among these approaches, when applied to this type of sample.
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Affiliation(s)
- Liting Deng
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - David C L Handler
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Dylan H Multari
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia; Biomolecular Discovery Research Centre, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia.
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19
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Levernæs MCS, Moe AU, Bøe SL, Paus E, Reubsaet L, Halvorsen TG. Liquid chromatography mass spectrometry based characterization of epitope configurations. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:5476-5484. [PMID: 33141131 DOI: 10.1039/d0ay01283a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Here we evaluate a quick and easy tool for determination of epitope configuration using immunocapture and liquid chromatography mass spectrometry (LC-MS) subsequent to pre-treatment of the target protein to disrupt its three-dimensional structure. The approach can be a valuable screening tool to identify antibodies that can be used in peptide capture by anti-protein antibodies. The experimental set-up was established using seven monoclonal antibodies (mAbs) with known linear or conformational epitope recognition. The mAbs were developed to target either of the two biomarkers, progastrin releasing peptide (ProGRP) or human chorionic gonadotropin (hCG). Best coherence with established epitope configuration was seen when using both denaturation, reduction and alkylation as pre-treatment method of the proteins (≥70% reduction in MS signal intensity compared to control) prior to immunocapture and LC-MS determination. The final method was used to determine the epitope configuration of four anti-thyroglobulin mAbs with unknown epitope configuration; all four mAbs showed configurational epitope recognition. These results were also supported by western blots of native, and reduced and alkylated protein using three of the evaluated mAbs, and by analysis native, and reduced and alkylated protein in a routine immunofluorometric assay employing the four evaluated antibodies.
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20
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Efficient Confirmation of Plant Viral Proteins and Identification of Specific Viral Strains by nanoLC-ESI-Q-TOF Using Single-Leaf-Tissue Samples. Pathogens 2020; 9:pathogens9110966. [PMID: 33228257 PMCID: PMC7699591 DOI: 10.3390/pathogens9110966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/11/2020] [Accepted: 11/17/2020] [Indexed: 12/03/2022] Open
Abstract
Plant viruses are important pathogens that cause significant crop losses. A plant protein extraction protocol that combines crushing the tissue by a pestle in liquid nitrogen with subsequent crushing by a roller-ball crusher in urea solution, followed by RuBisCO depletion, reduction, alkylation, protein digestion, and ZipTip purification allowed us to substantially simplify the sample preparation by removing any other precipitation steps and to detect viral proteins from samples, even with less than 0.2 g of leaf tissue, by a medium resolution nanoLC-ESI-Q-TOF. The presence of capsid proteins or polyproteins of fourteen important viruses from seven different families (Geminiviridae, Luteoviridae, Bromoviridae, Caulimoviridae, Virgaviridae, Potyviridae, and Secoviridae) isolated from ten different economically important plant hosts was confirmed through many identified pathogen-specific peptides from a protein database of host proteins and potential pathogen proteins assembled separately for each host and based on existing online plant virus pathogen databases. The presented extraction protocol, combined with a medium resolution LC-MS/MS, represents a cost-efficient virus protein confirmation method that proved to be effective at identifying virus strains (as demonstrated for PPV, WDV) and distinct disease species of BYDV, as well as putative new viral protein sequences from single-plant-leaf tissue samples. Data are available via ProteomeXchange with identifier PXD022456.
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21
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Mielczarek P, Silberring J, Smoluch M. MINIATURIZATION IN MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2020; 39:453-470. [PMID: 31793697 DOI: 10.1002/mas.21614] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
Expectations for continuous miniaturization in mass spectrometry are not declining for years. Portable instruments are highly welcome by the industry, science, space agencies, forensic laboratories, and many other units. All are striving for the small, cheap, and as good as possible instruments. This review describes the recent developments of miniature mass spectrometers and also provides selected applications where these devices are used. Upcoming perspectives of further development are also discussed. @ 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Przemyslaw Mielczarek
- Department of Biochemistry and Neurobiology, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Mickiewicza 30, 30-059, Krakow, Poland
- Laboratory of Proteomics and Mass Spectrometry, Maj Institute of Pharmacology, Polish Academy of Sciences, Smetna 12, 31-343, Krakow, Poland
| | - Jerzy Silberring
- Department of Biochemistry and Neurobiology, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Mickiewicza 30, 30-059, Krakow, Poland
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, Curie-Sklodowskiej St. 34, 41-819, Zabrze, Poland
| | - Marek Smoluch
- Department of Biochemistry and Neurobiology, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Mickiewicza 30, 30-059, Krakow, Poland
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22
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Matas-Nadal C, Bech-Serra JJ, Guasch-Vallés M, Fernández-Armenteros JM, Barceló C, Casanova JM, de la Torre Gómez C, Aguayo Ortiz R, Garí E. Evaluation of Tumor Interstitial Fluid-Extraction Methods for Proteome Analysis: Comparison of Biopsy Elution versus Centrifugation. J Proteome Res 2020; 19:2598-2605. [PMID: 31877049 DOI: 10.1021/acs.jproteome.9b00770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The analysis of tumor interstitial fluid (TIF) composition is a valuable procedure to identify antimetastatic targets, and different laboratories have set up techniques for TIF isolation and proteomic analyses. However, those methods had never been compared in samples from the same tumor and patient. In this work, we compared the two most used methods, elution and centrifugation, in pieces of the same biopsy samples of cutaneous squamous cell carcinoma (cSCC). First, we established that high G-force (10 000g) was required to obtain TIF from cSCC by centrifugation. Second, we compared the centrifugation method with the elution method in pieces of three different cSCC tumors. We found that the mean protein intensities based in the number of peptide spectrum matches was significantly higher in the centrifuged samples than in the eluted samples. Regarding the robustness of the methods, we observed higher overlapping between both methods (77-80%) than among samples (50%). These results suggest that there exists an elevated consistence of TIF composition independently of the method used. However, we observed a 3-fold increase of extracellular proteins in nonoverlapped proteome obtained by centrifugation. We therefore conclude that centrifugation is the method of choice to study the proteome of TIF from cutaneous biopsies.
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Affiliation(s)
- Clara Matas-Nadal
- Cell Cycle Laboratory, Institut de Recerca Biomèdica de Lleida (IRB Lleida), Lleida, 25198, Spain
| | - Joan Josep Bech-Serra
- Proteomics Unit, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, 08916, Spain
| | - Marta Guasch-Vallés
- Cell Cycle Laboratory, Institut de Recerca Biomèdica de Lleida (IRB Lleida), Lleida, 25198, Spain.,Department de Ciències Mèdiques Bàsiques. Facultat de Medicina, Universitat de Lleida, Lleida, 25003, Spain
| | - Josep Manel Fernández-Armenteros
- Cell Cycle Laboratory, Institut de Recerca Biomèdica de Lleida (IRB Lleida), Lleida, 25198, Spain.,Servei de Dermatologia, Hospital Universitari Arnau de Vilanova, Lleida, 25198, Spain
| | - Carla Barceló
- Cell Cycle Laboratory, Institut de Recerca Biomèdica de Lleida (IRB Lleida), Lleida, 25198, Spain
| | - Josep Manel Casanova
- Cell Cycle Laboratory, Institut de Recerca Biomèdica de Lleida (IRB Lleida), Lleida, 25198, Spain.,Department de Ciències Mèdiques Bàsiques. Facultat de Medicina, Universitat de Lleida, Lleida, 25003, Spain.,Servei de Dermatologia, Hospital Universitari Arnau de Vilanova, Lleida, 25198, Spain
| | | | - Rafael Aguayo Ortiz
- Cell Cycle Laboratory, Institut de Recerca Biomèdica de Lleida (IRB Lleida), Lleida, 25198, Spain.,Servei de Dermatologia, Hospital Universitari Arnau de Vilanova, Lleida, 25198, Spain
| | - Eloi Garí
- Cell Cycle Laboratory, Institut de Recerca Biomèdica de Lleida (IRB Lleida), Lleida, 25198, Spain.,Department de Ciències Mèdiques Bàsiques. Facultat de Medicina, Universitat de Lleida, Lleida, 25003, Spain
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23
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Itze-Mayrhofer C, Brem G. Quantitative proteomic strategies to study reproduction in farm animals: Female reproductive fluids. J Proteomics 2020; 225:103884. [PMID: 32593762 DOI: 10.1016/j.jprot.2020.103884] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/10/2020] [Accepted: 06/21/2020] [Indexed: 02/06/2023]
Abstract
Reproductive fluids from the female reproductive tract are gaining attention for their potential to support and optimize reproductive processes, including gamete maturation and embryo culture in vitro. Quantitative proteomics is a powerful way to decipher the proteome of reproductive tract fluids and to identify biologically relevant proteins. The present review describes proteomic strategies for analysing female reproductive fluid proteins. In addition, it considers the strategies for the preparation of oviductal, uterine and follicular fluid samples. Finally, it highlights the main results of quantitative proteomic studies, providing insights into the biological processes related to reproductive biology in farm animals. SIGNIFICANCE: Assisted reproductive technologies (ARTs) have become vitally important for farm animal breeding and much effort is going into the optimization and refinement of the techniques. There are also attempts to imitate physiological conditions by adding reproductive fluids or individual fluid proteins to improve in vitro procedures. A detailed knowledge of the reproductive fluid proteomes is indispensable. The present review summarizes the most widely used quantitative proteomic approaches for the analysis of fluids from the female reproductive tract and highlights the potential of quantitative proteomics to delineate reproductive processes and identify candidate proteins for ARTs in farm animals.
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Affiliation(s)
- Corina Itze-Mayrhofer
- Institute of Animal Breeding and Genetics, Group Molecular Reproduction IFA-Tulln, University of Veterinary Medicine, Vienna, Austria.
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
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24
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Zhou M, Uwugiaren N, Williams SM, Moore RJ, Zhao R, Goodlett D, Dapic I, Paša-Tolić L, Zhu Y. Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform. Anal Chem 2020; 92:7087-7095. [PMID: 32374172 DOI: 10.1021/acs.analchem.0c00467] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Top-down proteomics is a powerful tool for characterizing genetic variations and post-translational modifications at intact protein level. However, one significant technical gap of top-down proteomics is the inability to analyze a low amount of biological samples, which limits its access to isolated rare cells, fine needle aspiration biopsies, and tissue substructures. Herein, we developed an ultrasensitive top-down platform by incorporating a microfluidic sample preparation system, termed nanoPOTS (nanodroplet processing in one pot for trace samples), into a top-down proteomic workflow. A unique combination of a nonionic detergent dodecyl-β-d-maltopyranoside (DDM) with urea as protein extraction buffer significantly improved both protein extraction efficiency and sample recovery. We hypothesize that the DDM detergent improves protein recovery by efficiently reducing nonspecific adsorption of intact proteins on container surfaces, while urea serves as a strong denaturant to disrupt noncovalent complexes and release intact proteins for downstream analysis. The nanoPOTS-based top-down platform reproducibly and quantitatively identified ∼170 to ∼620 proteoforms from ∼70 to ∼770 HeLa cells containing ∼10 to ∼115 ng of total protein. A variety of post-translational modifications including acetylation, myristoylation, and iron binding were identified using only less than 800 cells. We anticipate the nanoPOTS top-down proteomics platform will be broadly applicable in biomedical research, particularly where clinical specimens are not available in amounts amenable to standard workflows.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - David Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland.,Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
| | - Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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Schira-Heinen J, Grube L, Waldera-Lupa DM, Baberg F, Langini M, Etemad-Parishanzadeh O, Poschmann G, Stühler K. Pitfalls and opportunities in the characterization of unconventionally secreted proteins by secretome analysis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140237. [DOI: 10.1016/j.bbapap.2019.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/04/2019] [Accepted: 06/06/2019] [Indexed: 02/07/2023]
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Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
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Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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27
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Ner-Kluza J, Wawrzykowski J, Franczyk M, Siberring J, Kankofer M. Identification of protein patterns in bovine placenta at early-mid pregnancy - Pilot studies. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1084-1090. [PMID: 30912867 DOI: 10.1002/rcm.8444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/26/2019] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Placenta is a crucial tissue for an appropriate development of the fetus and the course of pregnancy. Its composition and structure change dynamically along pregnancy but the full pattern of these changes is not fully described in cows yet. The aim of the present study was to detect qualitative and quantitative protein profiles of bovine placenta during early-mid pregnancy at the time of placental formation. METHODS Placental tissues from healthy cows (n = 3) in early pregnancy (3-5 months) were collected at the slaughterhouse. Maternal and fetal parts were manually divided prior to homogenization. Further analysis was done in triplicates on the maternal and fetal parts separately and subjected to one-dimensional (1D) electrophoretic separation, followed by identification of peptide maps by nanospray liquid chromatography/tandem mass spectrometry (nanoLC/MS/MS). Proteins were identified by use of the MASCOT software with the SwissProt database. RESULTS Proteomic analysis showed more than 4000 differentially expressed proteins in maternal and fetal parts of placenta. Each part expressed around 900 proteins, of which ca. 90 were common. The identified proteins were analyzed in accordance to molecular function and their participation in biological processes. CONCLUSIONS The obtained results provide new insight into the knowledge about biochemical characteristics of placenta (new proteins) and serve for further studies on the possible markers of physiological/pathological pregnancy or function of placenta. Moreover, our data can be a good starting point for further studies on the processes underlying the attachment of placenta.
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Affiliation(s)
- Joanna Ner-Kluza
- Department of Biochemistry and Neurobiology, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, 30-059, Krakow, Mickiewicza 30 ave., Poland
| | - Jacek Wawrzykowski
- Department of Biochemistry, Faculty of Veterinary Medicine, University of Life Science in Lublin, 20-033, Lublin, Akademicka 12, Poland
| | - Monika Franczyk
- Department of Biochemistry, Faculty of Veterinary Medicine, University of Life Science in Lublin, 20-033, Lublin, Akademicka 12, Poland
| | - Jerzy Siberring
- Department of Biochemistry and Neurobiology, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, 30-059, Krakow, Mickiewicza 30 ave., Poland
| | - Marta Kankofer
- Department of Biochemistry, Faculty of Veterinary Medicine, University of Life Science in Lublin, 20-033, Lublin, Akademicka 12, Poland
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Plaxton WC. Avoiding Proteolysis during the Extraction and Purification of Active Plant Enzymes. PLANT & CELL PHYSIOLOGY 2019; 60:715-724. [PMID: 30753712 DOI: 10.1093/pcp/pcz028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/03/2019] [Indexed: 06/09/2023]
Abstract
The aim of this article is to discuss approaches to diagnose and prevent unwanted proteolysis during extraction and isolation of active enzymes from plant tissues. Enzymes are protein catalysts that require great care during sample processing in order to ensure that they remain intact and fully active. Preventing artifactual enzyme modifications ex planta is of utmost importance in order to obtain biologically relevant data. This is particularly problematic following enzyme extraction from plant tissues, which relative to microbes or animals contain relatively low protein amounts coupled with high concentrations of vacuolar proteases. Although cytoplasmic enzymes are not directly accessible to vacuolar proteases owing their physical segregation into different subcellular compartments, this compartmentation is destroyed during cell lysis. Unwanted proteolysis by endogenous proteases is an insidious problem because in many cases the enzyme of interest is only partially degraded and retains catalytic activity. This can not only lead to erroneous conclusions about an enzyme's size, subunit structure and post-translational modifications, but can also result in striking changes to its kinetic and regulatory (i.e. allosteric) properties. Furthermore, the routine addition of class-specific protease inhibitors and/or commercially available (and expensive) protease inhibitor cocktails to extraction and purification buffers does not necessarily preclude partial proteolysis of plant enzymes by endogenous proteases. When antibodies are available, plant scientists are advised to employ immunoblotting to diagnose potential in vitro proteolytic truncation of the enzymes that they wish to characterize, as well as to test the effectiveness of specific protease inhibitors in overcoming this recurrent issue.
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Affiliation(s)
- William C Plaxton
- Department of Biology, Queen's University, Kingston, Ontario, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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29
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Applications and challenges of forensic proteomics. Forensic Sci Int 2019; 297:350-363. [DOI: 10.1016/j.forsciint.2019.01.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/23/2022]
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30
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Grochowski C, Blicharska E, Krukow P, Jonak K, Maciejewski M, Szczepanek D, Jonak K, Flieger J, Maciejewski R. Analysis of Trace Elements in Human Brain: Its Aim, Methods, and Concentration Levels. Front Chem 2019; 7:115. [PMID: 30891444 PMCID: PMC6411644 DOI: 10.3389/fchem.2019.00115] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/14/2019] [Indexed: 12/20/2022] Open
Abstract
Trace elements play a crucial role in many biochemical processes, mainly as components of vitamins and enzymes. Although small amounts of metal ions have protective properties, excess metal levels result in oxidative injury, which is why metal ion homeostasis is crucial for the proper functioning of the brain. The changes of their level in the brain have been proven to be a risk factor for Alzheimer's, Parkinson's, and Huntington's diseases, as well as amyotrophic lateral sclerosis. Therefore, it is currently an important application of various analytical methods. This review covers the most important of them: inductively coupled ground mass spectrometry (ICP-MS), flame-induced atomic absorption spectrometry (FAAS), electrothermal atomic absorption spectrometry (GFAAS), optical emission spectrometry with excitation in inductively coupled plasma (ICP-OES), X-ray fluorescence spectrometry (XRF), and neutron activation analysis (NAA). Additionally, we present a summary of concentration values found by different research groups.
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Affiliation(s)
- Cezary Grochowski
- Department of Anatomy, Medical University of Lublin, Lublin, Poland
- Department of Neurosurgery and Pediatric Neurosurgery, Medical University of Lublin, Lublin, Poland
| | - Eliza Blicharska
- Department of Analytical Chemistry, Medical University of Lublin, Lublin, Poland
| | - Paweł Krukow
- Department of Clinical Neuropsychiatry, Medical University of Lublin, Lublin, Poland
| | - Kamil Jonak
- Department of Psychiatry, Psychotherapy and Early Intervention, Medical University of Lublin, Lublin, Poland
- Department of Biomedical Engineering, Lublin University of Technology, Lublin, Poland
| | - Marcin Maciejewski
- Institute of Electronics and Information Technology, Lublin University of Technology, Lublin, Poland
| | - Dariusz Szczepanek
- Department of Neurosurgery and Pediatric Neurosurgery, Medical University of Lublin, Lublin, Poland
| | - Katarzyna Jonak
- Department of Foreign Languages, Medical University of Lublin, Lublin, Poland
| | - Jolanta Flieger
- Department of Analytical Chemistry, Medical University of Lublin, Lublin, Poland
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31
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Štěpánová S, Kašička V. Recent developments and applications of capillary and microchip electrophoresis in proteomics and peptidomics (2015-mid 2018). J Sep Sci 2018; 42:398-414. [DOI: 10.1002/jssc.201801090] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/15/2018] [Accepted: 11/16/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Sille Štěpánová
- Institute of Organic Chemistry and Biochemistry; The Czech Academy of Sciences; Prague 6 Czechia
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry; The Czech Academy of Sciences; Prague 6 Czechia
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Khudyakov JI, Deyarmin JS, Hekman RM, Pujade Busqueta L, Maan R, Mody MJ, Banerjee R, Crocker DE, Champagne CD. A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics. Biol Open 2018; 7:bio.036731. [PMID: 30361411 PMCID: PMC6262853 DOI: 10.1242/bio.036731] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Animals with large adipose stores, such as marine mammals, may provide insights into the evolution and function of this multifunctional tissue in health and disease. In the absence of sequenced genomes, molecular information can be rapidly obtained by proteomics and transcriptomics, but their application to adipose tissue is hindered by low nucleic acid and protein yields. We sequenced and compared proteomes isolated from the blubber of four elephant seals using phenol and guanidine thiocyanate (Qiazol) or detergent (sodium deoxycholate) buffer. Qiazol recovered more subcellular proteins such as metabolic enzymes, in addition to extracting RNA, facilitating proteogenomic analyses of small lipid-rich tissue biopsies. We also compared proteomics data analysis platforms and found that de novo peptide sequencing improved protein identification sensitivity compared to database search alone. We report sample preparation and data analysis workflows for proteogenomics and a proteome of elephant seal blubber containing 2678 proteins, including many of interest for further functional studies. This article has an associated First Person interview with the first author of the paper. Summary: Proteins that are compatible with shotgun proteomics can be isolated from small amounts of adipose tissue at the same time as RNA, facilitating proteogenomics studies in non-model animals.
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Affiliation(s)
- Jane I Khudyakov
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA .,Conservation and Biological Research Program, National Marine Mammal Foundation, San Diego, CA, USA
| | - Jared S Deyarmin
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Ryan M Hekman
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | | | - Rasool Maan
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Melony J Mody
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Reeti Banerjee
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Daniel E Crocker
- Department of Biology, Sonoma State University, Rohnert Park, CA, USA
| | - Cory D Champagne
- Conservation and Biological Research Program, National Marine Mammal Foundation, San Diego, CA, USA
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33
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Dams M, Dores-Sousa JL, Lamers RJ, Treumann A, Eeltink S. High-Resolution Nano-Liquid Chromatography with Tandem Mass Spectrometric Detection for the Bottom-Up Analysis of Complex Proteomic Samples. Chromatographia 2018. [DOI: 10.1007/s10337-018-3647-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Bittremieux W, Tabb DL, Impens F, Staes A, Timmerman E, Martens L, Laukens K. Quality control in mass spectrometry-based proteomics. MASS SPECTROMETRY REVIEWS 2018; 37:697-711. [PMID: 28802010 DOI: 10.1002/mas.21544] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 05/21/2023]
Abstract
Mass spectrometry is a highly complex analytical technique and mass spectrometry-based proteomics experiments can be subject to a large variability, which forms an obstacle to obtaining accurate and reproducible results. Therefore, a comprehensive and systematic approach to quality control is an essential requirement to inspire confidence in the generated results. A typical mass spectrometry experiment consists of multiple different phases including the sample preparation, liquid chromatography, mass spectrometry, and bioinformatics stages. We review potential sources of variability that can impact the results of a mass spectrometry experiment occurring in all of these steps, and we discuss how to monitor and remedy the negative influences on the experimental results. Furthermore, we describe how specialized quality control samples of varying sample complexity can be incorporated into the experimental workflow and how they can be used to rigorously assess detailed aspects of the instrument performance.
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Affiliation(s)
- Wout Bittremieux
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (Biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - David L Tabb
- Division of Molecular Biology and Human Genetics, Stellenbosch University Faculty of Medicine and Health Sciences, Tygerberg Hospital, Cape Town, South Africa
| | - Francis Impens
- VIB Proteomics Core, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - An Staes
- VIB Proteomics Core, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Evy Timmerman
- VIB Proteomics Core, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Zwijnaarde, Belgium
| | - Kris Laukens
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (Biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
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35
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Evaluation of the Use of TRIzol-Based Protein Extraction Approach for Gel-Based Proteomic Analysis of Dried Seafood Products and Chinese Tonic Foods. Int J Mol Sci 2018; 19:ijms19071998. [PMID: 29987231 PMCID: PMC6073523 DOI: 10.3390/ijms19071998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/30/2018] [Accepted: 07/06/2018] [Indexed: 12/15/2022] Open
Abstract
Although the emergence of gel-free approaches has greatly enhanced proteomic studies, two-dimensional gel electrophoresis (2-DE) remains one of the most widely used proteomic techniques for its high resolving power, relatively low cost, robustness, and high resolution. Preparation of high-quality protein samples remains the key in high-quality 2-DE for proteomic analysis. Samples with high endogenous levels of interfering molecules, such as salts, nucleic acids, lipids, and polysaccharides, would yield a low-quality 2-DE gel and hinder the analysis. Recently, a TRIzol-based protein extraction method has gained prominence and has attracted attention due to its promising performance in high-quality 2-DE. The authors evaluate the use of this approach for four valuable dried food products, namely two dried seafood products (abalone slices and whelk slices) and two traditional Chinese tonic foods (ganoderma and caterpillar fungus). The results indicate that 2-DE gels obtained through the TRIzol-based method are of high-quality and are comparable to those obtained through the trichloroacetic acid⁻acetone method in terms of spot number, spot intensity, and resolution. The TRIzol-based method is generally applicable to dried food samples and is simple and fast, which greatly streamlines the protein extraction procedure. Additionally, it enables the concurrent extraction and analysis of RNA, DNA, and protein from the same sample.
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36
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Andjelković U, Josić D. Mass spectrometry based proteomics as foodomics tool in research and assurance of food quality and safety. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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37
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Green Fluorescent Protein-Based Viability Assay in a Multiparametric Configuration. Molecules 2018; 23:molecules23071575. [PMID: 29958475 PMCID: PMC6100089 DOI: 10.3390/molecules23071575] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 06/24/2018] [Accepted: 06/26/2018] [Indexed: 11/29/2022] Open
Abstract
Green fluorescent protein (GFP) is considered to be suitable for cell viability testing. In our study, GFP transfected A549 lung carcinoma cell line was treated with sodium fluoride (NaF), cycloheximide (CHX) and ochratoxin A (OTA). GFP fluorescence, intracellular ATP, nucleic acid and protein contents were quantified by a luminescence microplate assay developed in our laboratory. Flow cytometry was used to confirm the findings and to assess the intensity of GFP during different types of cell death. A 24 h NaF and CHX exposure caused a dramatic decrease in ATP contents (p < 0.05) compared with those of the controls. GFP fluorescence of the cells was in close correlation with total protein; however, GFP/ATP increased at NaF and decreased at CHX treatments (p < 0.05). ATP/protein and ATP/propidium iodide (PI) were largely decreased at NaF exposure in a dose-dependent manner (p < 0.05), while CHX and OTA showed markedly fewer effects. Both treatments caused apoptosis/necrosis at different rates. NaF induced mainly late apoptosis while OTA, mainly apoptosis. CHX effects varied by the incubation time with 100-fold elevation in late apoptotic cells at 24 h treatment. GFP intensity did not show a significant difference between live and apoptotic populations. Our results suggest when using GFP, a multiparametric assay is necessary for more precise interpretation of cell viability.
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38
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Kahle J, Wätzig H. Determination of protein charge variants with (imaged) capillary isoelectric focusing and capillary zone electrophoresis. Electrophoresis 2018; 39:2492-2511. [DOI: 10.1002/elps.201800079] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/03/2018] [Accepted: 04/17/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Julia Kahle
- Technische Universität Braunschweig; Institute of Medicinal and Pharmaceutical Chemistry; Braunschweig Germany
| | - Hermann Wätzig
- Technische Universität Braunschweig; Institute of Medicinal and Pharmaceutical Chemistry; Braunschweig Germany
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39
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Kayili HM, Barlas N, Atakay M, Salih B. Fast purification of glycans and glycopeptides using silk-packed micropipette tip for matrix-assisted laser desorption/ionization-mass spectrometry and high-performance liquid chromatography-fluorescence detection analysis. Microchem J 2018. [DOI: 10.1016/j.microc.2018.03.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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Innovative methods for biomarker discovery in the evaluation and development of cancer precision therapies. Cancer Metastasis Rev 2018; 37:125-145. [PMID: 29392535 DOI: 10.1007/s10555-017-9710-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The discovery of biomarkers able to detect cancer at an early stage, to evaluate its aggressiveness, and to predict the response to therapy remains a major challenge in clinical oncology and precision medicine. In this review, we summarize recent achievements in the discovery and development of cancer biomarkers. We also highlight emerging innovative methods in biomarker discovery and provide insights into the challenges faced in their evaluation and validation.
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41
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Abstract
All cells contain proteases which hydrolyze the peptide bonds between amino acids in a protein backbone. Typically, proteases are prevented from nonspecific proteolysis by regulation and by their physical separation into different subcellular compartments; however, this segregation is not retained during cell lysis, which is the initial step in any protein isolation procedure. Prevention of proteolysis during protein purification often takes the form of a two-pronged approach; firstly inhibition of proteolysis in situ, followed by the early separation of the protease from the protein of interest via chromatographical purification. Protease inhibitors are routinely used to limit the effect of the proteases before they are physically separated from the protein of interest via column chromatography. Here, commonly used approaches to reducing or avoiding proteolysis during protein purification and subsequent chromatography are reviewed.
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42
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Li SY, Ng IS, Chen PT, Chiang CJ, Chao YP. Biorefining of protein waste for production of sustainable fuels and chemicals. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:256. [PMID: 30250508 PMCID: PMC6146663 DOI: 10.1186/s13068-018-1234-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/22/2018] [Indexed: 05/21/2023]
Abstract
To mitigate the climate change caused by CO2 emission, the global incentive to the low-carbon alternatives as replacement of fossil fuel-derived products continuously expands the need for renewable feedstock. There will be accompanied by the generation of enormous protein waste as a result. The economical viability of the biorefinery platform can be realized once the surplus protein waste is recycled in a circular economy scenario. In this context, the present review focuses on the current development of biotechnology with the emphasis on biotransformation and metabolic engineering to refine protein-derived amino acids for production of fuels and chemicals. Its scope starts with the explosion of potential feedstock sources rich in protein waste. The availability of techniques is applied for purification and hydrolysis of various feedstock proteins to amino acids. Useful lessons are leaned from the microbial catabolism of amino acids and lay a foundation for the development of the protein-based biotechnology. At last, the future perspective of the biorefinery scheme based on protein waste is discussed associated with remarks on possible solutions to overcome the technical bottlenecks.
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Affiliation(s)
- Si-Yu Li
- Department of Chemical Engineering, National Chung Hsing University, Taichung, 402 Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101 Taiwan
| | - Po Ting Chen
- Department of Biotechnology, Southern Taiwan University of Science and Technology, Tainan, 710 Taiwan
| | - Chung-Jen Chiang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung, 40402 Taiwan
| | - Yun-Peng Chao
- Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan
- Department of Health and Nutrition Biotechnology, Asia University, Taichung, 41354 Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, 40447 Taiwan
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43
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Andjelković U, Šrajer Gajdošik M, Gašo-Sokač D, Martinović T, Josić D. Foodomics and Food Safety: Where We Are. Food Technol Biotechnol 2017; 55:290-307. [PMID: 29089845 PMCID: PMC5654429 DOI: 10.17113/ftb.55.03.17.5044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 05/31/2017] [Indexed: 12/21/2022] Open
Abstract
The power of foodomics as a discipline that is now broadly used for quality assurance of food products and adulteration identification, as well as for determining the safety of food, is presented. Concerning sample preparation and application, maintenance of highly sophisticated instruments for both high-performance and high-throughput techniques, and analysis and data interpretation, special attention has to be paid to the development of skilled analysts. The obtained data shall be integrated under a strong bioinformatics environment. Modern mass spectrometry is an extremely powerful analytical tool since it can provide direct qualitative and quantitative information about a molecule of interest from only a minute amount of sample. Quality of this information is influenced by the sample preparation procedure, the type of mass spectrometer used and the analyst's skills. Technical advances are bringing new instruments of increased sensitivity, resolution and speed to the market. Other methods presented here give additional information and can be used as complementary tools to mass spectrometry or for validation of obtained results. Genomics and transcriptomics, as well as affinity-based methods, still have a broad use in food analysis. Serious drawbacks of some of them, especially the affinity-based methods, are the cross-reactivity between similar molecules and the influence of complex food matrices. However, these techniques can be used for pre-screening in order to reduce the large number of samples. Great progress has been made in the application of bioinformatics in foodomics. These developments enabled processing of large amounts of generated data for both identification and quantification, and for corresponding modeling.
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Affiliation(s)
- Uroš Andjelković
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, RS-11000 Belgrade, Serbia
| | - Martina Šrajer Gajdošik
- Department of Chemistry, J. J. Strossmayer University of Osijek, Cara Hadrijana 8/A, HR-31000 Osijek, Croatia
| | - Dajana Gašo-Sokač
- Faculty of Food Technology, J. J. Strossmayer University of Osijek, Franje Kuhača 20, HR-31000 Osijek, Croatia
| | - Tamara Martinović
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
| | - Djuro Josić
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
- Warren Alpert Medical School, Brown University, 222 Richmond St, Providence, RI 02903, USA
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44
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Govaert E, Van Steendam K, Willems S, Vossaert L, Dhaenens M, Deforce D. Comparison of fractionation proteomics for local SWATH library building. Proteomics 2017; 17:1700052. [PMID: 28664598 PMCID: PMC5601298 DOI: 10.1002/pmic.201700052] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/23/2017] [Accepted: 06/28/2017] [Indexed: 01/08/2023]
Abstract
For data-independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data-dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. The quality and coverage of such a reference library is therefore essential when processing SWATH data. In general, library sizes can be increased by reducing the impact of DDA precursor selection with replicate runs or fractionation. However, these strategies can affect the match between the library and SWATH measurement, and thus larger library sizes do not necessarily correspond to improved SWATH quantification. Here, three fractionation strategies to increase local library size were compared to standard library building using replicate DDA injection: protein SDS-PAGE fractionation, peptide high-pH RP-HPLC fractionation and MS-acquisition gas phase fractionation. The impact of these libraries on SWATH performance was evaluated in terms of the number of extracted peptides and proteins, the match quality of the peptides and the extraction reproducibility of the transitions. These analyses were conducted using the hydrophilic proteome of differentiating human embryonic stem cells. Our results show that SWATH quantitative results and interpretations are affected by choice of fractionation technique. Data are available via ProteomeXchange with identifier PXD006190.
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Affiliation(s)
- Elisabeth Govaert
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
| | | | - Sander Willems
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
| | - Liesbeth Vossaert
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
| | - Maarten Dhaenens
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical BiotechnologyGhent UniversityGhentBelgium
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45
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Abramowicz A, Widlak P, Pietrowska M. Proteomic analysis of exosomal cargo: the challenge of high purity vesicle isolation. MOLECULAR BIOSYSTEMS 2017; 12:1407-19. [PMID: 27030573 DOI: 10.1039/c6mb00082g] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The re-discovery of exosomes as intercellular messengers with high potential for diagnostic and therapeutic utility has led to them becoming a popular topic of research in recent years. One of the essential research areas in this field is the characterization of exosomal cargo, which includes numerous non-randomly packed proteins and nucleic acids. Unexpectedly, a very challenging aspect of exploration of extracellular vesicles has turned out to be their effective and selective isolation. The plurality of developed protocols leads to qualitative and quantitative variability in terms of the obtained exosomes, which significantly affects the results of downstream analyses and makes them difficult to compare, reproduce and interpret between research groups. Currently, there is a general consensus among the exosome-oriented community concerning the urgent need for the optimization and standardization of methods employed for the purification of these vesicles. Hence, we review here several strategies for exosome preparation including ultracentrifugation, chemical precipitation, affinity capturing and filtration techniques. The advantages and disadvantages of different approaches are discussed with special emphasis being placed on their adequacy for proteomics applications, which are particularly sensitive to sample quality. We conclude that certain methods, exemplified by ultracentrifugation combined with iodixanol density gradient centrifugation or gel filtration, although labor-intensive, provide superior quality exosome preparations suitable for reliable analysis by mass spectrometry.
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Affiliation(s)
- Agata Abramowicz
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland.
| | - Piotr Widlak
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland.
| | - Monika Pietrowska
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland.
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46
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Ortiz-Martinez M, Gonzalez de Mejia E, García-Lara S, Aguilar O, Lopez-Castillo LM, Otero-Pappatheodorou JT. Antiproliferative effect of peptide fractions isolated from a quality protein maize, a white hybrid maize, and their derived peptides on hepatocarcinoma human HepG2 cells. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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47
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Šalplachta J, Horká M, Šlais K. Preparative isoelectric focusing in a cellulose-based separation medium. J Sep Sci 2017; 40:2498-2505. [PMID: 28432777 DOI: 10.1002/jssc.201700036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/04/2017] [Accepted: 04/10/2017] [Indexed: 01/04/2023]
Abstract
An improved preparative method based on isoelectric focusing of analytes in a cellulose-based separation medium is described in this study. Cellulose is suspended in an aqueous solution of simple buffers, ethylene glycol, glycerol, nonionic surfactant, and colored pI markers. Water partially evaporates during focusing run and the separation takes place in an in situ generated layer of cellulose, which has a gel-like appearance at the end of analysis. Final positions of analytes are indicated by the positions of zones of focused pI markers. Fractions, segments of the separation medium with analytes, can be simply collected by spatula and analyzed by downstream analytical methods. Good focusing ability of the new method and almost quantitative recovery of model proteins, cytochrome c and bovine serum albumin, was verified by gel electrophoresis and capillary isoelectric focusing of the collected fractions.
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Affiliation(s)
- Jiří Šalplachta
- Institute of Analytical Chemistry of the CAS, Brno, Czech Republic
| | - Marie Horká
- Institute of Analytical Chemistry of the CAS, Brno, Czech Republic
| | - Karel Šlais
- Institute of Analytical Chemistry of the CAS, Brno, Czech Republic
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48
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Ashwin NMR, Barnabas L, Ramesh Sundar A, Malathi P, Viswanathan R, Masi A, Agrawal GK, Rakwal R. Advances in proteomic technologies and their scope of application in understanding plant–pathogen interactions. JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY 2017. [DOI: 10.1007/s13562-017-0402-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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49
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Zou J, Wu C, Robertson WD, Zhigilei LV, Miller RJD. Molecular dynamics investigation of desorption and ion separation following picosecond infrared laser (PIRL) ablation of an ionic aqueous protein solution. J Chem Phys 2017; 145:204202. [PMID: 27908131 DOI: 10.1063/1.4967164] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular dynamics simulations were performed to characterize the ablation process induced by a picosecond infrared laser (PIRL) operating in the regime of desorption by impulsive vibrational excitation (DIVE) of a model peptide (lysozyme)/counter-ion system in aqueous solution. The simulations were performed for ablation under typical experimental conditions found within a time-of-flight mass spectrometer (TOF-MS), that is in vacuum with an applied electric field (E = ± 107 V/m), for up to 2 ns post-ablation and compared to the standard PIRL-DIVE ablation condition (E = 0 V/m). Further, a simulation of ablation under an extreme field condition (E = 1010 V/m) was performed for comparison to extend the effective dynamic range of the effect of the field on charge separation. The results show that the plume dynamics were retained under a typical TOF-MS condition within the first 1 ns of ablation. Efficient desorption was observed with more than 90% of water molecules interacting with lysozyme stripped off within 1 ns post-ablation. The processes of ablation and desolvation of analytes were shown to be independent of the applied electric field and thus decoupled from the ion separation process. Unlike under the extreme field conditions, the electric field inside a typical TOF-MS was shown to modify the ions' motion over a longer time and in a soft manner with no enhancement to fragmentation observed as compared to the standard PIRL-DIVE. The study indicates that the PIRL-DIVE ablation mechanism could be used as a new, intrinsically versatile, and highly sensitive ion source for quantitative mass spectrometry.
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Affiliation(s)
- J Zou
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - C Wu
- Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22904-4745, USA
| | - W D Robertson
- Max Plank Institute for the Structure and Dynamics of Matter, 149 Luruper Chaussee, 27761 Hamburg, Germany
| | - L V Zhigilei
- Department of Materials Science and Engineering, University of Virginia, Charlottesville, Virginia 22904-4745, USA
| | - R J D Miller
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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50
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Abstract
Food allergy is a public health concern especially after recognizing its constantly increased prevalence and severity. Despite careful reading of food ingredient statements, food allergic individuals may experience reactions caused by "hidden", "masked", or "contaminated" proteins that are known major allergens. Many techniques have been developed to detect even small traces of food allergens, for clinical or laboratory purposes. Enzyme-linked immunosorbent assay (ELISA) is one of the best validated and most routinely used immunoassay in allergy research, in allergy diagnosis in allergy-related quality control in various industries. Although as a technique it has been implemented for the last 45 years, the evolution in biochemistry allowed the development of ultrasensitive ELISA variations that are capable of measuring quantities in the scale of picograms, rendering ELISA attractive, robust, and very famous.
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Affiliation(s)
- George N Konstantinou
- Department of Allergy and Clinical Immunology, 424 General Military Training Hospital, 11 Eleftheriou Venizelou Street, Kalamaria, 55 133, Thessaloniki, Greece.
- Division of Allergy and Immunology, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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