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Du Y, Li H, Shao J, Wu T, Xu W, Hu X, Chen J. Adhesion and Colonization of the Probiotic Lactobacillus plantarum HC-2 in the Intestine of Litopenaeus Vannamei Are Associated With Bacterial Surface Proteins. Front Microbiol 2022; 13:878874. [PMID: 35535252 PMCID: PMC9076606 DOI: 10.3389/fmicb.2022.878874] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Surface proteins are a type of proteins expressed on the surface of bacteria that play an important role in cell wall synthesis, maintenance of cell morphology, and signaling with the host. Our previous study showed that the probiotic Lactobacillus plantarum HC-2 improved the growth performance and immune response of Litopenaeus vannamei. To further investigate the probiotic mechanism, we determined the automatic aggregation ability of the bacteria and surface hydrophobicity of HC-2 after being treated with 5 M of lithium chloride (LiCl) and observed the morphology and adhesion of the bacteria to HCT116 cells. The results showed that with the removal of the HC-2 surface protein, the auto-aggregation ability and surface hydrophobicity of HC-2 decreased, and the crude mucus layer coated on the bacterial surface gradually dissociated. The adhesion rate of HC-2 to HCT116 cells decreased from 98.1 to 20.9%. Moreover, a total of 201 unique proteins were identified from the mixture of the surface proteins by mass spectrometry (MS). Several proteins are involved in transcription and translation, biosynthetic or metabolic process, cell cycle or division, cell wall synthesis, and emergency response. Meanwhile, a quantitative real-time PCR qPCR_ showed that HC-2 was mainly colonized in the midgut of shrimp, and the colonization numbers were 15 times higher than that in the foregut, while the colonization rate in the hindgut was lower. The adhesion activity measurement showed that the adhesion level of HC-2 to crude intestinal mucus of L. vannamei was higher than that of bovine serum albumin (BSA) and collagen, and the adhesion capacity of the bacterial cells decreased with the extension of LiCl-treatment time. Finally, we identified the elongation factor Tu, Type I glyceraldehyde-3-phosphate dehydrogenase, small heat shock protein, and 30S ribosomal protein from the surface proteins, which may be the adhesion proteins of HC-2 colonization in the shrimp intestine. The above results indicate that surface proteins play an important role in maintaining the cell structure stability and cell adhesion. Surface proteomics analysis contributes to describing potential protein-mediated probiotic-host interactions. The identification of some interacting proteins in this work may be beneficial to further understand the adhesion/colonization mechanism and probiotic properties of L. plantarum HC-2 in the shrimp intestine.
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Affiliation(s)
- Yang Du
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China.,Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo, China.,Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hao Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China.,Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
| | - Jianchun Shao
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ting Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China.,Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
| | - WenLong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China.,Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
| | - Xiaoman Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China.,Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China.,Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
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2
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Chen Z, Zhong X, Tie C, Chen B, Zhang X, Li L. Development of a hydrophilic interaction liquid chromatography coupled with matrix-assisted laser desorption/ionization-mass spectrometric imaging platform for N-glycan relative quantitation using stable-isotope labeled hydrazide reagents. Anal Bioanal Chem 2017; 409:4437-4447. [PMID: 28540462 DOI: 10.1007/s00216-017-0387-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/20/2017] [Accepted: 04/28/2017] [Indexed: 12/21/2022]
Abstract
In this work, the capability of newly developed hydrophilic interaction liquid chromatography (HILIC) coupled with matrix-assisted laser desorption/ionization-mass spectrometric imaging (MALDI-MSI) platform for quantitative analysis of N-glycans has been demonstrated. As a proof-of-principle experiment, heavy and light stable-isotope labeled hydrazide reagents labeled maltodextrin ladder were used to demonstrate the feasibility of the HILIC-MALDI-MSI platform for reliable quantitative analysis of N-glycans. MALDI-MSI analysis by an Orbitrap mass spectrometer enabled high-resolution and high-sensitivity detection of N-glycans eluted from HILIC column, allowing the re-construction of LC chromatograms as well as accurate mass measurements for structural inference. MALDI-MSI analysis of the collected LC traces showed that the chromatographic resolution was preserved. The N-glycans released from human serum was used to demonstrate the utility of this novel platform in quantitative analysis of N-glycans from a complex sample. Benefiting from the minimized ion suppression provided by HILIC separation, comparison between MALDI-MS and the newly developed platform HILIC-MALDI-MSI revealed that HILIC-MALDI-MSI provided higher N-glycan coverage as well as better quantitation accuracy in the quantitative analysis of N-glycans released from human serum. Graphical abstract Reconstructed chromatograms based on HILIC-MALDI-MSI results of heavy and light labeled maltodextrin enabling quantitative glycan analysis.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
| | - Xuefei Zhong
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Cai Tie
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Bingming Chen
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Xinxiang Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA.
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI, 53705, USA.
- School of Life Sciences, Tianjin University, No.92 Weijin Road, Nankai District, Tianjin, 300072, China.
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3
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Zhou L, Qian Y, Zhang X, Ruan Y, Ren S, Gu J. Elucidation of differences in N-glycosylation between different molecular weight forms of recombinant CLEC-2 by LC MALDI tandem MS. Carbohydr Res 2015; 402:180-8. [DOI: 10.1016/j.carres.2014.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/17/2014] [Accepted: 07/07/2014] [Indexed: 10/25/2022]
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4
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Bhargava M, Higgins L, Wendt CH, Ingbar DH. Application of clinical proteomics in acute respiratory distress syndrome. Clin Transl Med 2014; 3:34. [PMID: 26932378 PMCID: PMC4883989 DOI: 10.1186/s40169-014-0034-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/18/2014] [Indexed: 12/25/2022] Open
Abstract
Acute Respiratory Distress Syndrome (ARDS) is a devastating cause of hypoxic respiratory failure, which continues to have high mortality. It is expected that a comprehensive systems- level approach will identify global and complex changes that contribute to the development of ARDS and subsequent repair of the damaged lung. In the last decade, powerful genome-wide analytical and informatics tools have been developed, that have provided valuable insights into the mechanisms of complex diseases such as ARDS. These tools include the rapid and precise measure of gene expression at the proteomic level. This article reviews the contemporary proteomics platforms that are available for comprehensive studies in ARDS. The challenges of various biofluids that could be investigated and some of the studies performed are also discussed.
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Affiliation(s)
- Maneesh Bhargava
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Minnesota, Minneapolis, USA.
| | - LeeAnn Higgins
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, USA.
| | - Christine H Wendt
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Minnesota, Minneapolis, USA. .,Minneapolis Veterans Affairs Medical Center, Minneapolis, MN, USA.
| | - David H Ingbar
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Minnesota, Minneapolis, USA.
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5
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Hioki Y, Tanimura R, Iwamoto S, Tanaka K. Nano-LC/MALDI-MS Using a Column-Integrated Spotting Probe for Analysis of Complex Biomolecule Samples. Anal Chem 2014; 86:2549-58. [DOI: 10.1021/ac4037069] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yusaku Hioki
- Koichi Tanaka Laboratory
of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabara-cho,
Nakagyo-ku, Kyoto 604-8511, Japan
| | - Ritsuko Tanimura
- Koichi Tanaka Laboratory
of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabara-cho,
Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shinichi Iwamoto
- Koichi Tanaka Laboratory
of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabara-cho,
Nakagyo-ku, Kyoto 604-8511, Japan
| | - Koichi Tanaka
- Koichi Tanaka Laboratory
of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabara-cho,
Nakagyo-ku, Kyoto 604-8511, Japan
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6
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Chen G, Pramanik BN. LC-MS for protein characterization: current capabilities and future trends. Expert Rev Proteomics 2014; 5:435-44. [DOI: 10.1586/14789450.5.3.435] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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7
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Fernández-Puente P, Mateos J, Blanco FJ, Ruiz-Romero C. LC-MALDI-TOF/TOF for shotgun proteomics. Methods Mol Biol 2014; 1156:27-38. [PMID: 24791979 DOI: 10.1007/978-1-4939-0685-7_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Automated liquid chromatography tandem mass spectrometry (LC-MS/MS) is a well-established technique for identification of components from complex mixtures in shotgun proteomics experiments. Approaches involving the use of matrix-assisted laser desorption/ionization mass spectrometry (LC-MALDI-MS/MS) comprise the preparation of protein extracts, their enzymatic digestion, the separation of the resulting peptides by nanoscale liquid chromatography coupled to a collector that deposits the microfractions onto a MALDI plate, and finally the mass spectrometry analysis of the fractions. Using an LC-MALDI strategy, the rate of the collection of MS/MS data is decoupled from the chromatographic separation, thus allowing high-quality data which are often complementary to electrospray ionization (LC-ESI-MS/MS) techniques.
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Affiliation(s)
- Patricia Fernández-Puente
- Rheumatology Division, ProteoRed/ISCIII Proteomics Group INIBIC - Hospital Universitario de A Coruña, A Coruña, Spain
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8
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Wöhlbrand L, Trautwein K, Rabus R. Proteomic tools for environmental microbiology-A roadmap from sample preparation to protein identification and quantification. Proteomics 2013; 13:2700-30. [DOI: 10.1002/pmic.201300175] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/07/2013] [Accepted: 06/28/2013] [Indexed: 02/03/2023]
Affiliation(s)
- Lars Wöhlbrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
| | - Kathleen Trautwein
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
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9
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Hessling B, Büttner K, Hecker M, Becher D. Global relative quantification with liquid chromatography-matrix-assisted laser desorption ionization time-of-flight (LC-MALDI-TOF)--cross-validation with LTQ-Orbitrap proves reliability and reveals complementary ionization preferences. Mol Cell Proteomics 2013; 12:2911-20. [PMID: 23788530 DOI: 10.1074/mcp.m112.023457] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Quantitative LC-MALDI is an underrepresented method, especially in large-scale experiments. The additional fractionation step that is needed for most MALDI-TOF-TOF instruments, the comparatively long analysis time, and the very limited number of established software tools for the data analysis render LC-MALDI a niche application for large quantitative analyses beside the widespread LC-electrospray ionization workflows. Here, we used LC-MALDI in a relative quantification analysis of Staphylococcus aureus for the first time on a proteome-wide scale. Samples were analyzed in parallel with an LTQ-Orbitrap, which allowed cross-validation with a well-established workflow. With nearly 850 proteins identified in the cytosolic fraction and quantitative data for more than 550 proteins obtained with the MASCOT Distiller software, we were able to prove that LC-MALDI is able to process highly complex samples. The good correlation of quantities determined via this method and the LTQ-Orbitrap workflow confirmed the high reliability of our LC-MALDI approach for global quantification analysis. Because the existing literature reports differences for MALDI and electrospray ionization preferences and the respective experimental work was limited by technical or methodological constraints, we systematically compared biochemical attributes of peptides identified with either instrument. This genome-wide, comprehensive study revealed biases toward certain peptide properties for both MALDI-TOF-TOF- and LTQ-Orbitrap-based approaches. These biases are based on almost 13,000 peptides and result in a general complementarity of the two approaches that should be exploited in future experiments.
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Affiliation(s)
- Bernd Hessling
- Ernst Moritz Arndt University Greifswald, Institute for Microbiology, Friedrich-Ludwig-Jahn-Straβe 15, 17487 Greifswald, Germany
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10
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Fornai L, Angelini A, Klinkert I, Giskes F, Kiss A, Eijkel G, Hove EAAV, Klerk LA, Fedrigo M, Pieraccini G, Moneti G, Valente M, Thiene G, Heeren RMA. Three-dimensional molecular reconstruction of rat heart with mass spectrometry imaging. Anal Bioanal Chem 2012; 404:2927-38. [DOI: 10.1007/s00216-012-6451-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 09/17/2012] [Accepted: 09/21/2012] [Indexed: 01/03/2023]
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11
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Benk AS, Roesli C. Label-free quantification using MALDI mass spectrometry: considerations and perspectives. Anal Bioanal Chem 2012; 404:1039-56. [DOI: 10.1007/s00216-012-5832-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 01/27/2012] [Accepted: 02/01/2012] [Indexed: 01/17/2023]
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12
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Gerszten RE, Asnani A, Carr SA. Status and prospects for discovery and verification of new biomarkers of cardiovascular disease by proteomics. Circ Res 2011; 109:463-74. [PMID: 21817166 PMCID: PMC3973157 DOI: 10.1161/circresaha.110.225003] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 05/10/2011] [Indexed: 12/21/2022]
Abstract
Despite unmet needs for cardiovascular biomarkers, few new protein markers have been approved by the US Food and Drug Administration for the diagnosis or screening of cardiovascular diseases. Mass spectrometry-based proteomics technologies are capable of identifying hundreds to thousands of proteins in cells, tissues, and biofluids. Proteomics may therefore provide the opportunity to elucidate new biomarkers and pathways without a prior known association with cardiovascular disease; however, important obstacles remain. In this review, we focus on emerging techniques that may form a coherently integrated pipeline to overcome present limitations to both the discovery and validation processes.
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Affiliation(s)
- Robert E. Gerszten
- Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Aarti Asnani
- Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston, MA
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13
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Ishihara T, Fukuda I, Morita A, Takinami Y, Okamoto H, Nishimura SI, Numata Y. Development of quantitative plasma N-glycoproteomics using label-free 2-D LC-MALDI MS and its applicability for biomarker discovery in hepatocellular carcinoma. J Proteomics 2011; 74:2159-68. [PMID: 21704746 DOI: 10.1016/j.jprot.2011.06.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 06/07/2011] [Accepted: 06/12/2011] [Indexed: 01/04/2023]
Abstract
There has been rapid progress in the development of clinical proteomic methodologies with improvements in mass spectrometric technologies and bioinformatics, leading to many new methodologies for biomarker discovery from human plasma. However, it is not easy to find new biomarkers because of the wide dynamic range of plasma proteins and the need for their quantification. Here, we report a new methodology for relative quantitative proteomic analysis combining large-scale glycoproteomics with label-free 2-D LC-MALDI MS. In this method, enrichment of glycopeptides using hydrazide resin enables focusing on plasma proteins with lower abundance corresponding to the tissue leakage region. On quantitative analysis, signal intensities by 2-D LC-MALDI MS were normalized using a peptide internal control, and the values linked to LC data were treated with DeView™ software. Our proteomic method revealed that the quantitative dynamic ranged from 10² to 10⁶ pg/mL of plasma proteins with good reproducibility, and the limit of detection was of the order of a few ng/mL of proteins in biological samples. To evaluate the applicability of our method for biomarker discovery, we performed a feasibility study using plasma samples from patients with hepatocellular carcinoma, and identified biomarker candidates, including ceruloplasmin, alpha-1 antichymotrypsin, and multimerin-1.
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Affiliation(s)
- Takeshi Ishihara
- Discovery Research Laboratories, Shionogi & Co. Ltd., Fukushima-ku, Osaka 553-0002, Japan
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14
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Baeumlisberger D, Rohmer M, Arrey TN, Mueller BF, Beckhaus T, Bahr U, Barka G, Karas M. Simple Dual-Spotting Procedure Enhances nLC–MALDI MS/MS Analysis of Digests with Less Specific Enzymes. J Proteome Res 2011; 10:2889-94. [DOI: 10.1021/pr2001644] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Dominic Baeumlisberger
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Marion Rohmer
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Tabiwang N. Arrey
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Benjamin F. Mueller
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Tobias Beckhaus
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Ute Bahr
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Guenes Barka
- SunChrom Wissenschaftliche Geräte GmbH, Max-Planck-Strasse 22, 61381 Friedrichsdorf, Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
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15
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Kool J, de Kloe G, Denker AD, van Altena K, Smoluch M, van Iperen D, Nahar TT, Limburg RJ, Niessen WMA, Lingeman H, Leurs R, de Esch IJP, Smit AB, Irth H. Nanofractionation Spotter Technology for Rapid Contactless and High-Resolution Deposition of LC Eluent for Further Off-Line Analysis. Anal Chem 2010; 83:125-32. [DOI: 10.1021/ac102001g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeroen Kool
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Gerdien de Kloe
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Arnoud D. Denker
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Klaas van Altena
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Marek Smoluch
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Dick van Iperen
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Tariq T. Nahar
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Rob J. Limburg
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Wilfried M. A. Niessen
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Henk Lingeman
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Rob Leurs
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Iwan J. P. de Esch
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - August B. Smit
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Hubertus Irth
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
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16
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Advances in mass spectrometry-based post-column bioaffinity profiling of mixtures. Anal Bioanal Chem 2010; 399:2655-68. [PMID: 21107824 PMCID: PMC3043236 DOI: 10.1007/s00216-010-4406-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 10/29/2010] [Accepted: 10/31/2010] [Indexed: 10/29/2022]
Abstract
In the screening of complex mixtures, for example combinatorial libraries, natural extracts, and metabolic incubations, different approaches are used for integrated bioaffinity screening. Four major strategies can be used for screening of bioactive mixtures for protein targets-pre-column and post-column off-line, at-line, and on-line strategies. The focus of this review is on recent developments in post-column on-line screening, and the role of mass spectrometry (MS) in these systems. On-line screening systems integrate separation sciences, mass spectrometry, and biochemical methodology, enabling screening for active compounds in complex mixtures. There are three main variants of on-line MS based bioassays: the mass spectrometer is used for ligand identification only; the mass spectrometer is used for both ligand identification and bioassay readout; or MS detection is conducted in parallel with at-line microfractionation with off-line bioaffinity analysis. On the basis of the different fields of application of on-line screening, the principles are explained and their usefulness in the different fields of drug research is critically evaluated. Furthermore, off-line screening is discussed briefly with the on-line and at-line approaches.
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17
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Abstract
Automated multidimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS) is routinely applied in large scale proteome profiling. However global proteome analysis remains a technical challenge due to the issues associated with sample complexity by tryptic digestion. The application of tag containing peptide enrichment approach for sample pre-separation could reduce the complexity of protein digest. Here, we demonstrated a simple and highly efficient cysteine-containing peptide enrichment method using a thiol specific covalent resin. The cysteine-containing peptides from the tryptic digests of the complex protein mixtures were selected by covalent chromatography based on thiol-disulfide exchange, identified by mass spectrometry. The strategy was firstly optimized and evaluated by using the tryptic peptides of bovine serum albumin (BSA). Then the method was applied with a relatively complicated sample from a five standard protein mixture. The results of these studies show that the enrichment method of cysteine-containing peptides is highly specific, efficient and reproducible. The effectiveness of this method in reducing the sample complexity and improving the identification of peptides by mass spectrometry has enabled high-throughput, automatic and large-scale qualitative and quantitative proteome analyses.
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Tan Y, Bideshi DK, Johnson JJ, Bigot Y, Federici BA. Proteomic analysis of the Spodoptera frugiperda ascovirus 1a virion reveals 21 proteins. J Gen Virol 2009; 90:359-365. [PMID: 19141444 DOI: 10.1099/vir.0.005934-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Spodoptera frugiperda ascovirus 1a (SfAV-1a) is a double-stranded DNA virus that attacks lepidopteran larvae, in which it produces enveloped virions with complex symmetry which have an average diameter of 130 nm and length of 400 nm. Here, we report identification of 21 SfAV-1a-encoded proteins that occur in the virion, as determined by nano-liquid chromatography/tandem mass spectrometry. These included a helicase (ORF009), nuclease (ORF075), ATPase (ORF047), serine/threonine-like protein kinase (ORF064), inhibitor of apoptosis-like protein (ORF015), thiol oxidoreductase-like protein (ORF061), CTD phosphatase (ORF109), major capsid protein (ORF041) and a highly basic protein, P64 (ORF048). The latter two were the most abundant. Apart from ascoviruses, the closest orthologues were found in iridoviruses, providing further evidence that ascoviruses evolved from invertebrate iridoviruses. These results establish a foundation for investigating how ascovirus virion proteins interact to form their complex asymmetrical structure, as well as for elucidating the mechanisms involved in SfAV-1a virion morphogenesis.
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Affiliation(s)
- Yeping Tan
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
| | - Dennis K Bideshi
- California Baptist University, Department of Natural and Mathematical Sciences, 8432 Magnolia Avenue Riverside, CA 92504, USA.,Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
| | - Jeffrey J Johnson
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
| | - Yves Bigot
- CHRU de Tours, Université Francois Rabelais, UFR des Sciences & Techniques, Parc de Grandmont, 37200 Tours, France.,CNRS, UMR 6239, Génétique, Immunothérapie, Chimie et Cancer, Université Francois Rabelais, UFR des Sciences & Techniques, Parc de Grandmont, 37200 Tours, France
| | - Brian A Federici
- Interdepartmental Graduate Programs in Genetics and Cell, Molecular & Developmental Biology, University of California Riverside, Riverside, CA 92521, USA.,Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
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Sánchez B, Bressollier P, Chaignepain S, Schmitter JM, Urdaci MC. Identification of surface-associated proteins in the probiotic bacterium Lactobacillus rhamnosus GG. Int Dairy J 2009. [DOI: 10.1016/j.idairyj.2008.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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20
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Abstract
This review focuses on the chromatography research that has been carried out within industry or in close cooperation with industry and that has been reported in the scientific literature between 2006 and mid-2008. Companies in the health care sector, such as pharmaceutical and biotechnology companies, are the largest contributors. Industrial research seems to take place in an open environment in cooperation with academia, peer companies, and institutions. Industry appears ready to embrace new technologies as they emerge, but they focus strongly on making chromatography work robustly, reliably, rapidly, and automatically. "Hyphenated" systems that incorporate on-line sample-preparation techniques and mass-spectrometric detection are the rule rather than the exception. Various multidimensional separation methods are finding numerous applications. Strategies aimed at speeding up the development of new chromatographic methods remain the focus of attention. Also, there is a clear trend toward exploring chromatographic methods for parallel processing along with other strategies for high-throughput analysis.
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Affiliation(s)
- Peter Schoenmakers
- Polymer Analysis Group, Faculty of Science, University of Amsterdam, 1018 WV Amsterdam, The Netherlands.
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21
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Monroe EB, Annangudi SP, Hatcher NG, Gutstein HB, Rubakhin SS, Sweedler JV. SIMS and MALDI MS imaging of the spinal cord. Proteomics 2008; 8:3746-54. [PMID: 18712768 DOI: 10.1002/pmic.200800127] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The application of MS to imaging, or MS imaging (MSI), allows for the direct investigation of tissue sections to identify biological compounds and determine their spatial distribution. We present an approach to MSI that combines secondary ion MS (SIMS) and MALDI MS for the imaging and analysis of rat spinal cord sections, thereby enhancing the chemical coverage obtained from an MSI experiment. The spinal cord is organized into discrete, anatomically defined areas that include motor and sensory networks composed of chemically diverse cells. The MSI data presented here reveal the spatial distribution of multiple phospholipids, proteins, and neuropeptides obtained within single, 20 mum sections of rat spinal cord. Analyte identities are initially determined by primary mass match and confirmed in follow-up experiments using LC MS/MS from extracts of adjacent spinal cord sections. Additionally, a regional analysis of differentially localized signals serves to rapidly screen compounds of varying intensities across multiple spinal regions. These MSI analyses reveal new insights into the chemical architecture of the spinal cord and set the stage for future imaging studies of the chemical changes induced by pain, anesthesia, and drug tolerance.
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Affiliation(s)
- Eric B Monroe
- Department of Chemistry, Beckman Institute, University of Illinois, Urbana, IL, USA
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Automated normal phase nano high performance liquid chromatography/matrix assisted laser desorption/ionization mass spectrometry for analysis of neutral and acidic glycosphingolipids. Anal Bioanal Chem 2008; 391:289-97. [DOI: 10.1007/s00216-008-1932-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Revised: 01/28/2008] [Accepted: 02/01/2008] [Indexed: 10/22/2022]
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