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Li S, An M, Zhao Y, Zhao W, Li P, Du B. Immunomodulatory peptides from sturgeon cartilage: Isolation, identification, molecular docking and effects on RAW264.7 cells. Food Chem X 2024; 24:101863. [PMID: 39431208 PMCID: PMC11488438 DOI: 10.1016/j.fochx.2024.101863] [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: 08/08/2024] [Revised: 09/25/2024] [Accepted: 09/26/2024] [Indexed: 10/22/2024] Open
Abstract
Sturgeons (Acipenseridae), ancient fish known for their caviar, produce underutilized by-products like protein-rich cartilage, which is a source of high-quality bioactive peptides. This study investigates immunomodulatory peptides from sturgeon cartilage hydrolysates mechanisms. The study found that sturgeon cartilage hydrolysate F2-7 and its key peptides(DHVPLPLP and HVPLPLP)significantly promoted RAW267.4 cell proliferation, NO release, and phagocytosis (P < 0.001).Additionally, western blotting confirmed that F2-7 enhances immune response by increasing the expression of P-IKKα/β, IΚΚ, p65, and P-p65 proteins in the NF-κB signalling pathway (P < 0.01). Molecular docking further demonstrated that DHVPLPLP and HVPLPLP bind to NF-κB pathway proteins via hydrogen bonding, with low estimated binding energies (-2.75 and -1.64; -6.04 and -4.75 kcal/mol), thus establishing their role as key immune peptides in F2-7. Therefore, DHVPLPLP and HVPLPLP have the potential to be developed as dietary supplements for immune enhancement. Their ability to enhance immune function provides a theoretical basis for novel immune supplements.
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Affiliation(s)
- Shuchan Li
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Miaoqing An
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Yuxuan Zhao
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Wenjun Zhao
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Pan Li
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Bing Du
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
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2
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Wang W, Liu Z, Liu Y, Su Z, Liu Y. Plant polypeptides: A review on extraction, isolation, bioactivities and prospects. Int J Biol Macromol 2022; 207:169-178. [PMID: 35257730 DOI: 10.1016/j.ijbiomac.2022.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 01/09/2023]
Abstract
The application of traditional Chinese medicine has a long history in China with unique advantages and functions. With the rapid development of separation and purification technologies, more and more polypeptide compounds with specific biological activity and medicinal value were isolated from natural plants. The plant polypeptides have a lot of biological activities, such as antitumor effect, antioxidize effect, antibacterial effect, hypoglycemic effect, blood pressure lowering effect, lipid-lowering effect, anti-fatigue effect, and so on. This review summarized the extraction method, purification method, biological activities, and prospects of plant polypeptides, providing a basis for further study of plant polypeptides.
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Affiliation(s)
- Wenqi Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Zhicheng Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yongjian Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Zhijun Su
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yonggang Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China.
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3
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Wang L, Ma Y, Li H, Yang F, Cheng J. Identification and characterization of yak α-lactalbumin and β-lactoglobulin. J Dairy Sci 2020; 104:2520-2528. [PMID: 33358811 DOI: 10.3168/jds.2020-18546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/24/2020] [Indexed: 11/19/2022]
Abstract
α-Lactalbumin (α-LA) and β-lactoglobulin (β-LG) were isolated from yak milk and identified by mass spectrometry. The variant of α-LA (L8IIC8) in yak milk had 123 amino acids, and the sequence differed from α-LA from bovine milk. The amino acid at site 71 was Asn (N) in domestic yak milk, but Asp (D) in bovine and wild yak milk sequences. Yak β-LG had 2 variants, β-LG A (P02754) and β-LG E (L8J1Z0). Both domestic yak and wild yak milk contained β-LG E, but it was absent in bovine milk. The amino acid at site 158 of β-Lg E was Gly (G) in yak but Glu (E) in bovine. The yak α-LA and β-LG secondary structures were slightly different from those in bovine milk. The denaturation temperatures of yak α-LA and β-LG were 52.1°C and 80.9°C, respectively. This study provides insights relevant to food functionality, food safety control, and the biological properties of yak milk products.
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Affiliation(s)
- Lifeng Wang
- Food Science College, Northeast Agriculture University, Harbin 150036, China
| | - Ying Ma
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - He Li
- School of Health Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Fuming Yang
- Food Science College, Northeast Agriculture University, Harbin 150036, China
| | - Jinju Cheng
- Food Science College, Northeast Agriculture University, Harbin 150036, China
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4
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Ye X, Tang J, Mao Y, Lu X, Yang Y, Chen W, Zhang X, Xu R, Tian R. Integrated proteomics sample preparation and fractionation: Method development and applications. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115667] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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5
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Abstract
PURPOSE The biosimilar development process, comparability for biological agents, and analytic characterization of biosimilars are described. SUMMARY Healthcare providers must understand the requirements for biosimilar approval, including the science behind biosimilar development and testing that contributes to the totality of evidence. The foundation of development is to demonstrate that a biosimilar is highly similar to the reference product through analytic characterization. Advances in analytic techniques enable scientists to extensively characterize biological products to identify potential product differences compared with the reference product that may affect the purity, safety, and efficacy of the biosimilar candidate. When developing a biosimilar, the clinical efficacy of the biological product has been proven with trials from the reference biological product; therefore, analytic testing on the molecular structure and biological function becomes the focus. In addition, nonclinical studies in animals are performed, including toxicology and immunogenicity testing. In humans, clinical pharmacology studies are performed to evaluate the safety and the pharmacokinetic and pharmacodynamic properties of the proposed biosimilar. If there is any residual uncertainty about the proposed biological product after this testing, the developer should use guidance from the Food and Drug Administration to determine what additional clinical studies may be needed to adequately address that uncertainty. CONCLUSION Requirements for the approval of a biosimilar product include analytic characterization, which tests for similarity in primary amino acid structure, analysis of higher-order structure using circular dichroism and nuclear magnetic resonance spectroscopies, detection of posttranslational modifications, assessment of optimal target binding, and testing for impurities and optimal potency.
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6
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Maus A, Mignon R, Basile F. Enhanced protein identification using graphite-modified MALDI plates for offline LC-MALDI-MS/MS bottom-up proteomics. Anal Biochem 2018; 545:31-37. [PMID: 29326070 DOI: 10.1016/j.ab.2018.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/22/2017] [Accepted: 01/02/2018] [Indexed: 10/18/2022]
Abstract
The use of offline liquid chromatography-matrix assisted laser desorption/ionization (LC-MALDI) tandem mass spectrometry (MS/MS) for bottom-up proteomics offers advantages in terms of cost, ease of use, and the time-decoupled nature of the separation step and the mass analysis. A method was developed to improve the capabilities of LC-MALDI-MS/MS in terms of protein identification in a bottom-up proteomic workflow. Enhanced protein identification is achieved by an increase in the MALDI signal intensity of the precursor peptides brought about by coating the MALDI plate with a thin film of graphite powder. Using the Escherichia coli proteome, it is demonstrated that the graphite-modified MALDI plates used in an offline LC-MALDI-MS/MS bottom-up protocol led to a 50-135% increase in the number of peptide identifications, and a concomitant 21%-105% increase in the number of proteins inferred. We identify factors that lead to improvements in peptide sequence identifications and in the number of unique proteins identified when compared to using an unmodified MALDI plate. These improvements are achieved using a low cost approach that it is easy to implement, requires no hardware/protocol modification, it is compatible with LC and adds no additional analysis time.
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Affiliation(s)
- Anthony Maus
- Department of Chemistry, University of Wyoming, 1000 E. University Ave., Laramie, WY 82072, United States
| | - Rudolph Mignon
- Department of Chemistry, University of Wyoming, 1000 E. University Ave., Laramie, WY 82072, United States
| | - Franco Basile
- Department of Chemistry, University of Wyoming, 1000 E. University Ave., Laramie, WY 82072, United States.
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7
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Some Applications of Liquid Chromatography-Mass Spectrometry in the Biomedical Field. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/bs.coac.2017.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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8
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Mulvana H, Browning RJ, Luan Y, de Jong N, Tang MX, Eckersley RJ, Stride E. Characterization of Contrast Agent Microbubbles for Ultrasound Imaging and Therapy Research. IEEE TRANSACTIONS ON ULTRASONICS, FERROELECTRICS, AND FREQUENCY CONTROL 2017; 64:232-251. [PMID: 27810805 DOI: 10.1109/tuffc.2016.2613991] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The high efficiency with which gas microbubbles can scatter ultrasound compared with the surrounding blood pool or tissues has led to their widespread employment as contrast agents in ultrasound imaging. In recent years, their applications have been extended to include super-resolution imaging and the stimulation of localized bio-effects for therapy. The growing exploitation of contrast agents in ultrasound and in particular these recent developments have amplified the need to characterize and fully understand microbubble behavior. The aim in doing so is to more fully exploit their utility for both diagnostic imaging and potential future therapeutic applications. This paper presents the key characteristics of microbubbles that determine their efficacy in diagnostic and therapeutic applications and the corresponding techniques for their measurement. In each case, we have presented information regarding the methods available and their respective strengths and limitations, with the aim of presenting information relevant to the selection of appropriate characterization methods. First, we examine methods for determining the physical properties of microbubble suspensions and then techniques for acoustic characterization of both suspensions and single microbubbles. The next section covers characterization of microbubbles as therapeutic agents, including as drug carriers for which detailed understanding of their surface characteristics and drug loading capacity is required. Finally, we discuss the attempts that have been made to allow comparison across the methods employed by various groups to characterize and describe their microbubble suspensions and promote wider discussion and comparison of microbubble behavior.
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9
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Astefanei A, Dapic I, Camenzuli M. Different Stationary Phase Selectivities and Morphologies for Intact Protein Separations. Chromatographia 2016; 80:665-687. [PMID: 28529348 PMCID: PMC5413533 DOI: 10.1007/s10337-016-3168-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/17/2016] [Accepted: 09/06/2016] [Indexed: 12/18/2022]
Abstract
The central dogma of biology proposed that one gene encodes for one protein. We now know that this does not reflect reality. The human body has approximately 20,000 protein-encoding genes; each of these genes can encode more than one protein. Proteins expressed from a single gene can vary in terms of their post-translational modifications, which often regulate their function within the body. Understanding the proteins within our bodies is a key step in understanding the cause, and perhaps the solution, to disease. This is one of the application areas of proteomics, which is defined as the study of all proteins expressed within an organism at a given point in time. The human proteome is incredibly complex. The complexity of biological samples requires a combination of technologies to achieve high resolution and high sensitivity analysis. Despite the significant advances in mass spectrometry, separation techniques are still essential in this field. Liquid chromatography is an indispensable tool by which low-abundant proteins in complex samples can be enriched and separated. However, advances in chromatography are not as readily adapted in proteomics compared to advances in mass spectrometry. Biologists in this field still favour reversed-phase chromatography with fully porous particles. The purpose of this review is to highlight alternative selectivities and stationary phase morphologies that show potential for application in top-down proteomics; the study of intact proteins.
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Affiliation(s)
- A. Astefanei
- Centre for Analytical Science in Amsterdam (CASA), Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - I. Dapic
- Centre for Analytical Science in Amsterdam (CASA), Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - M. Camenzuli
- Centre for Analytical Science in Amsterdam (CASA), Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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10
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Presence of an isoform of H+-pyrophosphatase located in the alveolar sacs of a scuticociliate parasite of turbot: physiological consequences. Parasitology 2016; 143:576-87. [DOI: 10.1017/s0031182015001997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
SUMMARYH+-pyrophosphatases (H+-PPases) are integral membrane proteins that couple pyrophosphate energy to an electrochemical gradient across biological membranes and promote the acidification of cellular compartments. Eukaryotic organisms, essentially plants and protozoan parasites, contain various types of H+-PPases associated with vacuoles, plasma membrane and acidic Ca+2storage organelles called acidocalcisomes. We used Lysotracker Red DND-99 staining to identify two acidic cellular compartments in trophozoites of the marine scuticociliate parasitePhilasterides dicentrarchi: the phagocytic vacuoles and the alveolar sacs. The membranes of these compartments also contain H+-PPase, which may promote acidification of these cell structures. We also demonstrated for the first time that theP. dicentrarchiH+-PPase has two isoforms: H+-PPase 1 and 2. Isoform 2, which is probably generated by splicing, is located in the membranes of the alveolar sacs and has an amino acid motif recognized by the H+-PPase-specific antibody PABHK. The amino acid sequences of different isolates of this ciliate are highly conserved. Gene and protein expression in this isoform are significantly regulated by variations in salinity, indicating a possible physiological role of this enzyme and the alveolar sacs in osmoregulation and salt tolerance inP. dicentrarchi.
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11
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Simone P, Pierri G, Foglia P, Gasparrini F, Mazzoccanti G, Capriotti AL, Ursini O, Ciogli A, Laganà A. Separation of intact proteins on γ-ray-induced polymethacrylate monolithic columns: A highly permeable stationary phase with high peak capacity for capillary high-performance liquid chromatography with high-resolution mass spectrometry. J Sep Sci 2015; 39:264-71. [PMID: 26530449 DOI: 10.1002/jssc.201500844] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/19/2015] [Accepted: 10/19/2015] [Indexed: 11/09/2022]
Abstract
Polymethacrylate-based monolithic capillary columns, prepared by γ-radiation-induced polymerization, were used to optimize the experimental conditions (nature of the organic modifiers, the content of trifluoroacetic acid and the column temperature) in the separation of nine standard proteins with different hydrophobicities and a wide range of molecular weights. Because of the excellent permeability of the monolithic columns, an ion-pair reversed-phase capillary liquid chromatography with high-resolution mass spectrometry method has been developed by coupling the column directly to the mass spectrometer without a flow-split and using a standard electrospray interface. Additionally, the high working flow and concomitant high efficiency of these columns allowed us to employ a longer column (up to 50 cm) and achieve a peak capacity value superior to 1000. This work is motivated by the need to develop new materials for high-resolution chromatographic separation that combine chemical stability at elevated temperatures (up to 75°C) and a broad pH range, with a high peak capacity value. The advantage of the γ-ray-induced monolithic column lies in the batch-to-batch reproducibility and long-term high-temperature stability. Their proven high loading capacity, recovery, good selectivity and high permeability, moreover, compared well with that of a commercially available poly(styrene-divinylbenzene) monolithic column, which confirms that such monolithic supports might facilitate analysis in proteomics.
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Affiliation(s)
- Patrizia Simone
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, Italy
| | - Giuseppe Pierri
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, Italy
| | - Patrizia Foglia
- Dipartimento di Chimica, Sapienza Università di Roma, Roma, Italy
| | | | - Giulia Mazzoccanti
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, Italy
| | | | - Ornella Ursini
- Istituto di Metodologie Chimiche, Area della Ricerca di Roma del CNR, Monterotondo Stazione, Roma, Italy
| | - Alessia Ciogli
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, Italy
| | - Aldo Laganà
- Dipartimento di Chimica, Sapienza Università di Roma, Roma, Italy
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12
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Akkerman M, Rauh VM, Christensen M, Johansen LB, Hammershøj M, Larsen LB. Effect of heating strategies on whey protein denaturation--Revisited by liquid chromatography quadrupole time-of-flight mass spectrometry. J Dairy Sci 2015; 99:152-66. [PMID: 26506552 DOI: 10.3168/jds.2015-9924] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/01/2015] [Indexed: 11/19/2022]
Abstract
Previous standards in the area of effect of heat treatment processes on milk protein denaturation were based primarily on laboratory-scale analysis and determination of denaturation degrees by, for example, electrophoresis. In this study, whey protein denaturation was revisited by pilot-scale heating strategies and liquid chromatography quadrupole time-of-flight mass spectrometer (LC/MC Q-TOF) analysis. Skim milk was heat treated by the use of 3 heating strategies, namely plate heat exchanger (PHE), tubular heat exchanger (THE), and direct steam injection (DSI), under various heating temperatures (T) and holding times. The effect of heating strategy on the degree of denaturation of β-lactoglobulin and α-lactalbumin was determined using LC/MC Q-TOF of pH 4.5-soluble whey proteins. Furthermore, effect of heating strategy on the rennet-induced coagulation properties was studied by oscillatory rheometry. In addition, rennet-induced coagulation of heat-treated micellar casein concentrate subjected to PHE was studied. For skim milk, the whey protein denaturation increased significantly as T and holding time increased, regardless of heating method. High denaturation degrees were obtained for T >100°C using PHE and THE, whereas DSI resulted in significantly lower denaturation degrees, compared with PHE and THE. Rennet coagulation properties were impaired by increased T and holding time regardless of heating method, although DSI resulted in less impairment compared with PHE and THE. No significant difference was found between THE and PHE for effect on rennet coagulation time, whereas the curd firming rate was significantly larger for THE compared with PHE. Micellar casein concentrate possessed improved rennet coagulation properties compared with skim milk receiving equal heat treatment.
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Affiliation(s)
- M Akkerman
- Department of Food Science, Science and Technology, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark
| | - V M Rauh
- Arla Foods Strategic Innovation Centre, Rørdrumvej 2, DK-8220 Brabrand, Denmark
| | - M Christensen
- Arla Foods Strategic Innovation Centre, Rørdrumvej 2, DK-8220 Brabrand, Denmark
| | - L B Johansen
- Arla Foods Strategic Innovation Centre, Rørdrumvej 2, DK-8220 Brabrand, Denmark
| | - M Hammershøj
- Department of Food Science, Science and Technology, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark
| | - L B Larsen
- Department of Food Science, Science and Technology, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark.
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13
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Capra E, Colombi C, De Poli P, Nocito FF, Cocucci M, Vecchietti A, Marocco A, Stile MR, Rossini L. Protein profiling and tps23 induction in different maize lines in response to methyl jasmonate treatment and Diabrotica virgifera infestation. JOURNAL OF PLANT PHYSIOLOGY 2015; 175:68-77. [PMID: 25506768 DOI: 10.1016/j.jplph.2014.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/03/2014] [Accepted: 10/10/2014] [Indexed: 05/27/2023]
Abstract
Plant responses to herbivore insects involve direct and indirect defense with the production of signal molecules including jasmonic acid (JA) and its derivatives (e.g. methyl jasmonate, MeJA). In maize (Zea mays), root feeding by Diabrotica virgifera larvae activates an indirect defense mechanism, through enthomopathogenic nematodes that are recruited after Terpene Synthase 23 (tps23) upregulation and (E)-β-caryophyllene root emission. In order to gain insight into the correlation between JA signaling and response to Diabrotica attack, we analyzed tps23 expression and protein profiles in maize roots in response to MeJA treatment and insect infestation. Similar to herbivore feeding, MeJA treatment was found to increase tps23 transcript accumulation, with consistent variations for both treatments in maize lines differing in (E)-β-caryophyllene production. Analysis of root protein profiles showed specific alterations leading to the identification of three proteins that were induced by MeJA treatment. We focused on a peroxidase-like protein (Px-like) showing that the corresponding transcripts accumulated in all tested lines. Results show that exogenous application of MeJA upregulates tps23 expression and specifically alters protein patterns in maize roots. Parallel effects on tps23 transcript accumulation were observed upon hormone exposure and insect infestation in different maize lines. In contrast, Px-like transcript profiling showed differences between treatments. These results support the possible involvement of MeJA in mediating the upregulation of tps23 in response to Diabrotica attack.
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Affiliation(s)
- Emanuele Capra
- Istituto di Biologia e Biotecnologia Agraria Consiglio Nazionale delle Ricerche IBBA-CNR, via Einstein, 26900 Lodi, Italy; Biotrack S.r.l., Parco Tecnologico Padano, via Einstein, 26900 Lodi, Italy.
| | - Cinzia Colombi
- Parco Tecnologico Padano, via Einstein, 26900 Lodi, Italy
| | - Pamela De Poli
- Biotrack S.r.l., Parco Tecnologico Padano, via Einstein, 26900 Lodi, Italy
| | | | - Maurizio Cocucci
- Università degli Studi di Milano, DiSAA, via Celoria 2, 20133 Milan, Italy
| | | | - Adriano Marocco
- Istituto di Agronomia, Genetica e Coltivazioni erbacee, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Maria Rosaria Stile
- Parco Tecnologico Padano, via Einstein, 26900 Lodi, Italy; Agroalimentare Sud SpA, Loc. S. Nicola, 85025 Melfi, PZ, Italy
| | - Laura Rossini
- Parco Tecnologico Padano, via Einstein, 26900 Lodi, Italy; Università degli Studi di Milano, DiSAA, via Celoria 2, 20133 Milan, Italy
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14
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Shi Y, Jian L, Han D, Ren Y. Isolation of an Antifungal Pathogenesis-Related Protein from Naked Oat ( Avena nuda) Seeds. Cereal Chem 2015. [DOI: 10.1094/cchem-12-13-0251-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yawei Shi
- Corresponding author. Phone: +86-0351-7018268
| | - Liu Jian
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
| | - Deping Han
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
| | - Yemei Ren
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
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15
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Prediction of individual response to anticancer therapy: historical and future perspectives. Cell Mol Life Sci 2014; 72:729-57. [PMID: 25387856 PMCID: PMC4309902 DOI: 10.1007/s00018-014-1772-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 10/23/2014] [Accepted: 10/27/2014] [Indexed: 02/06/2023]
Abstract
Since the introduction of chemotherapy for cancer treatment in the early 20th century considerable efforts have been made to maximize drug efficiency and at the same time minimize side effects. As there is a great interpatient variability in response to chemotherapy, the development of predictive biomarkers is an ambitious aim for the rapidly growing research area of personalized molecular medicine. The individual prediction of response will improve treatment and thus increase survival and life quality of patients. In the past, cell cultures were used as in vitro models to predict in vivo response to chemotherapy. Several in vitro chemosensitivity assays served as tools to measure miscellaneous endpoints such as DNA damage, apoptosis and cytotoxicity or growth inhibition. Twenty years ago, the development of high-throughput technologies, e.g. cDNA microarrays enabled a more detailed analysis of drug responses. Thousands of genes were screened and expression levels were correlated to drug responses. In addition, mutation analysis became more and more important for the prediction of therapeutic success. Today, as research enters the area of -omics technologies, identification of signaling pathways is a tool to understand molecular mechanism underlying drug resistance. Combining new tissue models, e.g. 3D organoid cultures with modern technologies for biomarker discovery will offer new opportunities to identify new drug targets and in parallel predict individual responses to anticancer therapy. In this review, we present different currently used chemosensitivity assays including 2D and 3D cell culture models and several -omics approaches for the discovery of predictive biomarkers. Furthermore, we discuss the potential of these assays and biomarkers to predict the clinical outcome of individual patients and future perspectives.
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16
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Characterising microbial protein test substances and establishing their equivalence with plant-produced proteins for use in risk assessments of transgenic crops. Transgenic Res 2012; 22:445-60. [PMID: 23065372 PMCID: PMC3591531 DOI: 10.1007/s11248-012-9658-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 09/14/2012] [Indexed: 10/30/2022]
Abstract
Most commercial transgenic crops are genetically engineered to produce new proteins. Studies to assess the risks to human and animal health, and to the environment, from the use of these crops require grams of the transgenic proteins. It is often extremely difficult to produce sufficient purified transgenic protein from the crop. Nevertheless, ample protein of acceptable purity may be produced by over-expressing the protein in microbes such as Escherichia coli. When using microbial proteins in a study for risk assessment, it is essential that their suitability as surrogates for the plant-produced transgenic proteins is established; that is, the proteins are equivalent for the purposes of the study. Equivalence does not imply that the plant and microbial proteins are identical, but that the microbial protein is sufficiently similar biochemically and functionally to the plant protein such that studies using the microbial protein provide reliable information for risk assessment of the transgenic crop. Equivalence is a judgement based on a weight of evidence from comparisons of relevant properties of the microbial and plant proteins, including activity, molecular weight, amino acid sequence, glycosylation and immuno-reactivity. We describe a typical set of methods used to compare proteins in regulatory risk assessments for transgenic crops, and discuss how risk assessors may use comparisons of proteins to judge equivalence.
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Barbey C, Crépin A, Cirou A, Budin-Verneuil A, Orange N, Feuilloley M, Faure D, Dessaux Y, Burini JF, Latour X. Catabolic pathway of gamma-caprolactone in the biocontrol agent Rhodococcus erythropolis. J Proteome Res 2011; 11:206-16. [PMID: 22085026 DOI: 10.1021/pr200936q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gamma-caprolactone (GCL) is well-known as a food flavor and has been recently described as a biostimulant molecule promoting the growth of bacteria with biocontrol activity against soft-rot pathogens. Among these biocontrol agents, Rhodococcus erythropolis, characterized by a remarkable metabolic versatility, assimilates various γ-butyrolactone molecules with a branched-aliphatic chain, such as GCL. The assimilative pathway of GCL in R. erythropolis was investigated by two-dimensional gel electrophoresis coupled to matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) analysis. This analysis suggests the involvement of the lactonase QsdA in ring-opening, a feature confirmed by heterologous expression in Escherichia coli. According to proteome analysis, the open-chain form of GCL was degraded by β- and ω-oxidation coupled to the Krebs cycle and β-ketoadipate pathway. Ubiquity of qsdA gene among environmental R. erythropolis isolates was verified by PCR. In addition to a previous N-acyl homoserine lactone catabolic function, QsdA may therefore be involved in an intermediate degradative step of cyclic recalcitrant molecules or in synthesis of flavoring lactones.
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Affiliation(s)
- Corinne Barbey
- Laboratoire de Microbiologie Signaux et Microenvironnement, Normandie Université, EA 4312 Université de Rouen, IUT Evreux 55 rue Saint-Germain, 27000 Evreux, France
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18
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Becker M, Budich C, Deckert V, Janasek D. Isotachophoretic free-flow electrophoretic focusing and SERS detection of myoglobin inside a miniaturized device. Analyst 2009; 134:38-40. [DOI: 10.1039/b816717f] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Suberbielle E, Gonzalez-Dunia D, Pont F. High reproducibility of two-dimensional liquid chromatography using pH-driven fractionation with a pressure-resistant electrode. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 871:125-9. [PMID: 18635406 DOI: 10.1016/j.jchromb.2008.06.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 06/16/2008] [Accepted: 06/23/2008] [Indexed: 10/21/2022]
Abstract
Automated two-dimensional liquid chromatography using the PF2D system from Beckman Coulter provides a fractionation platform well suited for differential proteomic studies. To date, the reliability and reproducibility of PF2D has not been accurately tested. Here, we used an optimized software and a pressure-resistant pH electrode, allowing a precise and reproducible control of the pH limits for each fraction during PF2D. We tested the reliability of this improved system by performing several rounds of fractionation using the same protein extract. Three UV maps were generated, leading to 54 chromatograms and more than 3000 protein peaks. Using semi-automated software for peak-to-peak comparison between 2D-LC chromatograms, we demonstrate that the peak concordance is very high. The rates of concordance were higher in the second dimension repeatability tests, indicating that the limiting factors for 2D-LC reproducibility rely on the pI fractionation and sample preparation steps. The reproducibility between maps was closely related to pH curves similarities, further stressing the need of careful pH adjustment and precise electrode calibration.
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Abstract
Plasma membrane proteins serve essential functions for cells, interacting with both cellular and extracellular components, structures and signaling molecules. Additionally, plasma membrane proteins comprise more than two-thirds of the known protein targets for existing drugs. Consequently, defining membrane proteomes is crucial to understanding the role of plasma membranes in fundamental biological processes and for finding new targets for action in drug development. MS-based identification methods combined with chromatographic and traditional cell-biology techniques are powerful tools for proteomic mapping of proteins from organelles. However, the separation and identification of plasma membrane proteins remains a challenge for proteomic technology because of their hydrophobicity and microheterogeneity. Creative approaches to solve these problems and potential pitfalls will be discussed. Finally, a representative overview of the impressive achievements in this field will also be given.
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Affiliation(s)
- Djuro Josic
- Department of Medicine, Brown Medical School, Providence, RI, USA.
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21
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Singh AK, Gupta S. Analysis of recombinant human erythropoietin and darbepoietin in spiked plasma. Proteomics Clin Appl 2007; 1:626-39. [DOI: 10.1002/prca.200600972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Indexed: 11/10/2022]
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22
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Wu WW, Wang G, Yu MJ, Knepper MA, Shen RF. Identification and quantification of basic and acidic proteins using solution-based two-dimensional protein fractionation and label-free or 18O-labeling mass spectrometry. J Proteome Res 2007; 6:2447-59. [PMID: 17506541 DOI: 10.1021/pr060621c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reduction in sample complexity enables more thorough proteomic analysis using mass spectrometry (MS). A solution-based two-dimensional (2D) protein fractionation system, ProteomeLab PF 2D, has recently become available for sample fractionation and complexity reduction. PF 2D resolves proteins by isoelectric point (pI) and hydrophobicity in the first and second dimensions, respectively. It offers distinctive advantages over 2D gel electrophoresis with respects to automation of the fractionation processes and characterization of proteins having extreme pIs. Besides fractionation, PF 2D is equipped with built-in UV detectors intended for relative quantification of proteins in contrasting samples using its software tools. In this study, we utilized PF 2D for the identification of basic and acidic proteins in mammalian cells, which are generally under-characterized. In addition, mass spectrometric methods (label-free and 18O-labeling) were employed to complement protein quantification based on UV absorbance. Our studies indicate that the selection of chromatographic fractions could impact protein identification and that the UV-based quantification for contrasting complex proteomes is constrained by coelution or partial coelution of proteins. In contrast, the quantification post PF 2D chromatography based on label-free or 18O-labeling mass spectrometry provides an alternative platform for basic/acidic protein identification and quantification. With the use of HCT116 colon carcinoma cells, a total of 305 basic and 183 acidic proteins was identified. Quantitative proteomics revealed that 17 of these proteins were differentially expressed in HCT116 p53-/- cells.
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Affiliation(s)
- Wells W Wu
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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23
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Lopes AS, Garcia JS, Catharino RR, Santos LS, Eberlin MN, Arruda MAZ. Cloud point extraction applied to casein proteins of cow milk and their identification by mass spectrometry. Anal Chim Acta 2007; 590:166-72. [PMID: 17448341 DOI: 10.1016/j.aca.2007.03.043] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 03/16/2007] [Accepted: 03/22/2007] [Indexed: 10/23/2022]
Abstract
This work describes the optimization of a cloud point extraction (CPE) method for casein proteins from cow milk samples. To promote phase separation, polyoxyethylene(8) isooctylphenyl ether (Triton X-114) and sodium chloride (NaCl) were used as nonionic surfactant and electrolyte, respectively. Using multivariate studies, four major CPE variables were evaluated: Triton X-114 concentration, sample volume, NaCl concentration, and pH. The results show that surfactant concentration and sample volume were the main variable affecting the CPE process, with the following optimized parameters: 1% (w/v) Triton X-114 concentration, 50 microL of sample volume, 6% (w/v) NaCl concentration and extractions carried out at pH 7.0. At these conditions, 923+/-66 and 67+/-2 microg mL(-1) of total protein were found in the surfactant-rich and surfactant-poor phases, respectively. Finally, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was then used to evaluate those target proteins (alpha(s1)-casein, alpha(s2)-casein and beta-casein) separation as well as to check the efficiency of the extraction procedure, making a fingerprint of those target proteins possible.
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Affiliation(s)
- Aline Soriano Lopes
- Universidade Estadual de Campinas, Institute of Chemistry, Spectrometry, Sample Preparation and Mechanization Group, P.O. Box 6154, 13084-862 Campinas, São Paulo, Brazil
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24
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:407-418. [PMID: 17326037 DOI: 10.1002/jms.1072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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25
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Perlman DH, Huang H, Dauly C, Costello CE, McComb ME. Coupling of protein HPLC to MALDI-TOF MS using an on-target device for fraction collection, concentration, digestion, desalting, and matrix/analyte cocrystallization. Anal Chem 2007; 79:2058-66. [PMID: 17256876 DOI: 10.1021/ac061919p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Multidimensional protein chromatography offers an alternative to gel-based separations for large-scale proteomic analyses of highly complex mixtures. However, these liquid separations divide the original mixtures into multitudes of discrete samples, each of which may require numerous steps of sample manipulation, such as fraction collection, buffer exchange, protease digestion, peptide desalting, and, in the case of MALDI-MS, matrix and analyte cocrystallization on target. When traditional high-flow liquid chromatography is used, large volumes of solvent must also be removed from fractions to maximize MS sensitivity. Although robotic liquid-handling devices can facilitate these steps and reduce analyst/sample contact, they remain prototypic and expensive. Here, we explore the use of a novel, one-piece elastomeric device, the BD MALDI sample concentrator, which affixes to a MALDI target to create a prestructured 96-well sample array on the target surface. We have developed methodologies to process high-flow HPLC fractions by collecting them directly into the elastomeric device and then subjecting them to sequential on-target sample concentration, buffer exchange, digestion, desalting, and matrix/analyte cocrystallization for MALDI-MS analyses. We demonstrate that this methodology enables the rapid digestion and analysis of low amounts of proteins and that it is effective in the characterization of an HPLC-fractionated protein mixture by MALDI-TOF MS followed by peptide mass fingerprinting.
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Affiliation(s)
- David H Perlman
- Cardiovascular Proteomics Center, Mass Spectrometry Resource, Departments of Medicine and Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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McComb ME, Perlman DH, Huang H, Costello CE. Evaluation of an on-target sample preparation system for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in conjunction with normal-flow peptide high-performance liquid chromatography for peptide mass fingerprint analyses. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:44-58. [PMID: 17133622 DOI: 10.1002/rcm.2805] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Large-scale mass spectrometry (MS)-based proteomic analyses require high-throughput sample preparation techniques due to the increasing numbers of samples that make up a typical proteomics experiment. Moreover, extensive sample pre-treatment steps are necessary prior to MS acquisition for even the most rapid and robust MS-based proteomics methodology, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS followed by peptide mass fingerprinting (PMF) analysis. These include sample purification and fractionation, removal of digestion buffers or solvents, and spotting of sample with matrix onto the MALDI target. These multiple steps of time-consuming sample handling can result in high overall analysis costs and the likelihood of sample contamination and loss. In order to overcome some of these limitations in sample processing, we have investigated the use of a novel, simple, inexpensive 96-well elastomeric array that affixes to a MALDI target to create an on-target 96-well plate that accommodates a high solution volume (ca. 200 microL), thereby enabling the on-target processing of samples for MALDI-TOFMS. We explored several factors that influence MALDI sample preparation: type of matrix, solution volume, solution organic composition, solution drying rates and matrix/analyte co-crystallization methods. We also investigated the use of the 96-well elastomeric device for coupling MALDI-TOFMS analysis directly to high flow rate (1 mL/min) reversed-phase (rp)-HPLC. By developing an optimized, robust sample preparation protocol, we were able to obtain mass spectra with a high signal-to-noise ratio from peptide standards present at the 50-fmol level in large starting volumes of solution. PMF analyses were possible from 1-pmol and 500-fmol protein-digest standards. Coupling the device to high-flow HPLC (750 microL/min) yielded a robust and semi-automated means to obtain enhanced MALDI-TOFMS data at 500 ng of protein digest. These methodologies developed for this simple, on-target, elastomeric device show promise for streamlining the sample preparation process from HPLC to MALDI-MS.
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Affiliation(s)
- Mark E McComb
- Cardiovascular Proteomics Center, Boston University School of Medicine, Boston, MA 02118-2646, USA.
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Lupulescu C, Abd El Rahim M, Antoine R, Barbaire M, Broyer M, Dagany X, Maurelli J, Rayane D, Dugourd P. Multisample matrix-assisted laser desorption source for molecular beams of neutral peptides. REVIEW OF SCIENTIFIC INSTRUMENTS 2006; 77. [DOI: 10.1063/1.2401150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
We developed and tested a multisample laser desorption source for producing stable molecular beams of neutral peptides. Our apparatus is based on matrix-assisted laser desorption technique. The source consists of 96 different targets which may be scanned by a software control procedure. Examples of molecular beams of neutral peptides are presented, as well as the influence of the different source parameters on the jet.
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Affiliation(s)
- C. Lupulescu
- UMR 5579 Université Lyon 1 and CNRS Laboratoire de Spectrométrie Ionique et Moléculaire, , 43, bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - M. Abd El Rahim
- UMR 5579 Université Lyon 1 and CNRS Laboratoire de Spectrométrie Ionique et Moléculaire, , 43, bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - R. Antoine
- UMR 5579 Université Lyon 1 and CNRS Laboratoire de Spectrométrie Ionique et Moléculaire, , 43, bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - M. Barbaire
- UMR 5579 Université Lyon 1 and CNRS Laboratoire de Spectrométrie Ionique et Moléculaire, , 43, bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - M. Broyer
- UMR 5579 Université Lyon 1 and CNRS Laboratoire de Spectrométrie Ionique et Moléculaire, , 43, bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - X. Dagany
- UMR 5579 Université Lyon 1 and CNRS Laboratoire de Spectrométrie Ionique et Moléculaire, , 43, bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - J. Maurelli
- UMR 5579 Université Lyon 1 and CNRS Laboratoire de Spectrométrie Ionique et Moléculaire, , 43, bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - D. Rayane
- UMR 5579 Université Lyon 1 and CNRS Laboratoire de Spectrométrie Ionique et Moléculaire, , 43, bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - Ph. Dugourd
- UMR 5579 Université Lyon 1 and CNRS Laboratoire de Spectrométrie Ionique et Moléculaire, , 43, bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
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