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Ruan Q, Chen Y, Kong X, Hua Y. Analysis using fluorescence labeling and mass spectrometry of disulfide-mediated interactions of soy protein when heated. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:3524-3533. [PMID: 25715170 DOI: 10.1021/jf504519z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
It is well-known that disulfide-mediated interactions are important when soy protein is heated, in which soy proteins are dissociated and rearranged to some new forms. In this study, the disulfide bond (SS) linked polymer, which was composed of the acidic (A) polypeptides of glycinin, basic (B) polypeptides of glycinin, and a small amount of α' and α of β-conglycinin, was formed as the major product, accompanied by the formation of SS-linked dimer of B and monomer of A as minor products. The role of sulfhydryl (SH) of different subunits/polypeptides for forming intermolecular SS was investigated. The SH of B in glycinin (Cys298 of G1, Cys289 of G2, Cys440 of G4) was transformed into SS in polymer identified by mass spectrometry analysis. The SH content of polymer was lower than that of glycinin and β-conglycinin subunits when heated. The SH content of B in polymer was lower than that in glycinin subunit, and both of them were decreased by heating. The SH content of A in polymer was increased and higher than that of B in polymer and A in glycinin subunit when heated. These results indicated that the SH of B in glycinin subunit was subjected to not only SH oxidation but also SH-SS exchange (with SS of A) for forming intermolecular SS of polymer. The SH oxidation and SH-SS exchange were proven by the change of SH content for the first time. The SH of B was suggested to be reactive for forming intermolecular SS of polymer.
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Affiliation(s)
- Qijun Ruan
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, People's Republic of China
| | - Yeming Chen
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, People's Republic of China
| | - Xiangzhen Kong
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, People's Republic of China
| | - Yufei Hua
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, People's Republic of China
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Ionic matrices pre-spotted matrix-assisted laser desorption/ionization plates for patient maker following in course of treatment, drug titration, and MALDI mass spectrometry imaging. Anal Biochem 2013; 434:187-98. [DOI: 10.1016/j.ab.2012.10.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 10/24/2012] [Accepted: 10/25/2012] [Indexed: 11/18/2022]
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Totir M, Echols N, Nanao M, Gee CL, Moskaleva A, Gradia S, Iavarone AT, Berger JM, May AP, Zubieta C, Alber T. Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization. PLoS One 2012; 7:e32498. [PMID: 22393408 PMCID: PMC3290569 DOI: 10.1371/journal.pone.0032498] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 01/27/2012] [Indexed: 01/07/2023] Open
Abstract
Structural biology and structural genomics projects routinely rely on recombinantly expressed proteins, but many proteins and complexes are difficult to obtain by this approach. We investigated native source proteins for high-throughput protein crystallography applications. The Escherichia coli proteome was fractionated, purified, crystallized, and structurally characterized. Macro-scale fermentation and fractionation were used to subdivide the soluble proteome into 408 unique fractions of which 295 fractions yielded crystals in microfluidic crystallization chips. Of the 295 crystals, 152 were selected for optimization, diffraction screening, and data collection. Twenty-three structures were determined, four of which were novel. This study demonstrates the utility of native source proteins for high-throughput crystallography.
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Affiliation(s)
- Monica Totir
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Nathaniel Echols
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Max Nanao
- European Molecular Biology Laboratory, Grenoble, France
| | - Christine L. Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Alisa Moskaleva
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Scott Gradia
- QB3 Institute, Berkeley, California, United States of America
| | | | - James M. Berger
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Andrew P. May
- Fluidigm Corporation, South San Francisco, California, United States of America
| | - Chloe Zubieta
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- * E-mail: (CZ); (TA)
| | - Tom Alber
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- * E-mail: (CZ); (TA)
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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Tucholska M, Bowden P, Jacks K, Zhu P, Furesz S, Dumbrovsky M, Marshall J. Human serum proteins fractionated by preparative partition chromatography prior to LC-ESI-MS/MS. J Proteome Res 2009; 8:1143-55. [PMID: 19265436 DOI: 10.1021/pr8005217] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many proteomics studies are limited to the identification of only the most abundant proteins in a sample due to the high sample complexity in most proteomes. We have here addressed this problem by prefractionation of human blood samples using microchromatography. We show that our approach resulted in high-stringency tryptic peptides identified by LC-ESI-MS/MS. Serum proteins were fractionated by batch and stepwise preparative chromatography using various types of chromatography resins (propyl sulfate, quaternary amine, diethylaminoethanol, cibachron blue, phenol Sepharose, carboxy methyl sepharose, hydroxyl apatite, heparin, concanavalin A and protein G) that were compared. The efficacy of sample fractionation was determined by protein assays, electrophoresis, and mass spectrometry. Tryptic peptides were separated by C18 liquid chromatography with electrospray ionization via metal needle at 2 microL/min with ion trap tandem mass spectrometry. The MS/MS spectra were correlated to some 4396 distinct sequences of the human forward RefSeq by X!TANDEM. Of these, 61% have been detected by other algorithms, but 3219 (73%) were never previously reported from blood by X!TANDEM. The use of a simple apparatus for making gravity microchromatography columns that permits the rapid side-by-side fractionation of many serum samples is described. Disposable microcolumns rapidly prepared blood samples for LC ESI-MS/MS that detected both tissue and cell leakage proteins known to exist in the approximately 1 ng/mL range and some circulating receptor sequences. Our results demonstrate that the depletion of albumin or IgG was not necessary prior to LC-MS/MS and that multiple forms of protein chromatography will be useful for complete identification of blood proteins.
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Affiliation(s)
- Monika Tucholska
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Canada M5B 2K3
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Aich P, Babiuk LA, Potter AA, Griebel P. Biomarkers for Prediction of Bovine Respiratory Disease Outcome. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2009; 13:199-209. [DOI: 10.1089/omi.2009.0012] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Palok Aich
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
| | | | - Andrew A. Potter
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
| | - Philip Griebel
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
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Jankowski A, Zhu P, Marshall JG. Capture of an activated receptor complex from the surface of live cells by affinity receptor chromatography. Anal Biochem 2008; 380:235-48. [DOI: 10.1016/j.ab.2008.05.047] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Revised: 05/16/2008] [Accepted: 05/18/2008] [Indexed: 11/30/2022]
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Mirza SP, Olivier M. Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry. Physiol Genomics 2008; 33:3-11. [PMID: 18162499 PMCID: PMC2771641 DOI: 10.1152/physiolgenomics.00292.2007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Proteomics has been proposed as one of the key technologies in the postgenomic era. So far, however, the comprehensive analysis of cellular proteomes has been a challenge because of the dynamic nature and complexity of the multitude of proteins in cells and tissues. Various approaches have been established for the analyses of proteins in a cell at a given state, and mass spectrometry (MS) has proven to be an efficient and versatile tool. MS-based proteomics approaches have significantly improved beyond the initial identification of proteins to comprehensive characterization and quantification of proteomes and their posttranslational modifications (PTMs). Despite these advances, there is still ongoing development of new technologies to profile and analyze cellular proteomes more completely and efficiently. In this review, we focus on MS-based techniques, describe basic approaches for MS-based profiling of cellular proteomes and analysis methods to identify proteins in complex mixtures, and discuss the different approaches for quantitative proteome analysis. Finally, we briefly discuss novel developments for the analysis of PTMs. Altered levels of PTM, sometimes in the absence of protein expression changes, are often linked to cellular responses and disease states, and the comprehensive analysis of cellular proteome would not be complete without the identification and quantification of the extent of PTMs of proteins.
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Affiliation(s)
- Shama P Mirza
- National Center for Proteomics Research, Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA. e-mail:
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Comparative Approaches to the Investigation of Responses to Stress and Viral Infection in Cattle. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2007; 11:413-34. [DOI: 10.1089/omi.2007.0023] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Tran NT, Cabanes-Macheteau M, Taverna M. Chapter 20 Analysis of glycoproteins and their glycopeptide and glycan fragments by electrophoresis and capillary electrophoresis. JOURNAL OF CHROMATOGRAPHY LIBRARY 2002. [DOI: 10.1016/s0301-4770(02)80045-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Lee TD, Moore RE, Young MK. Introducing Samples Directly into Electrospray Ionization Mass Spectrometers Using a Nanospray Interface. ACTA ACUST UNITED AC 2001; Chapter 16:Unit 16.8. [DOI: 10.1002/0471140864.ps1608s22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Terry D. Lee
- Beckman Research Institute of the City of Hope Duarte California
| | - Roger E. Moore
- Beckman Research Institute of the City of Hope Duarte California
| | - Mary K. Young
- Beckman Research Institute of the City of Hope Duarte California
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Gilar M, Bouvier ES, Compton BJ. Advances in sample preparation in electromigration, chromatographic and mass spectrometric separation methods. J Chromatogr A 2001; 909:111-35. [PMID: 11269513 DOI: 10.1016/s0021-9673(00)01108-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The quality of sample preparation is a key factor in determining the success of analysis. While analysis of pharmaceutically important compounds in biological matrixes has driven forward the development of sample clean-up procedures in last 20 years, today's chemists face an additional challenge: sample preparation and analysis of complex biochemical samples for characterization of genotypic or phenotypic information contained in DNA and proteins. This review focuses on various sample pretreatment methods designed to meet the requirements for the analysis of biopolymers and small drugs in complex matrices. We discuss the advances in development of solid-phase extraction (SPE) sorbents, on-line SPE, membrane-based sample preparation, and sample clean-up of biopolymers prior to their analysis by mass spectrometry.
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Affiliation(s)
- M Gilar
- Waters Corp., Milford, MA 01757, USA.
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