1
|
Kang C, Huh S, Nam D, Kim H, Hong J, Hwang D, Lee SW. Novel Online Three-Dimensional Separation Expands the Detectable Functional Landscape of Cellular Phosphoproteome. Anal Chem 2022; 94:12185-12195. [PMID: 35994246 DOI: 10.1021/acs.analchem.2c02641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein phosphorylation is a prevalent post-translational modification that regulates essentially every aspect of cellular processes. Currently, liquid chromatography-tandem mass spectrometry (LC-MS/MS) with an extensive offline sample fractionation and a phosphopeptide enrichment method is a best practice for deep phosphoproteome profiling, but balancing throughput and profiling depth remains a practical challenge. We present an online three-dimensional separation method for ultradeep phosphoproteome profiling that combines an online two-dimensional liquid chromatography separation and an additional gas-phase separation. This method identified over 100,000 phosphopeptides (>60,000 phosphosites) in HeLa cells during 1.5 days of data acquisition, and the largest HeLa cell phosphoproteome significantly expanded the detectable functional landscape of cellular phosphoproteome.
Collapse
Affiliation(s)
- Chaewon Kang
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
| | - Sunghyun Huh
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.,Bertis R&D Division, Bertis Inc., Seongnam-si, Gyeonggi-do 13605, Republic of Korea
| | - Dowoon Nam
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
| | - Hokeun Kim
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
| | - Jiwon Hong
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.,Bioinformatics Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Won Lee
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
| |
Collapse
|
2
|
Jakobsen SS, Christensen JH, Verdier S, Mallet CR, Nielsen NJ. Increasing Flexibility in Two-Dimensional Liquid Chromatography by Pulsed Elution of the First Dimension: A Proof of Concept. Anal Chem 2017; 89:8723-8730. [DOI: 10.1021/acs.analchem.7b00758] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simon S. Jakobsen
- Department
of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
- Haldor Topsoe A/S, Haldor Topsøes
Allé 1, DK-2800 Kongens Lyngby, Denmark
| | - Jan H. Christensen
- Department
of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Sylvain Verdier
- Haldor Topsoe A/S, Haldor Topsøes
Allé 1, DK-2800 Kongens Lyngby, Denmark
| | - Claude R. Mallet
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757, United States
| | - Nikoline J. Nielsen
- Department
of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| |
Collapse
|
3
|
Ouyang X, Leonards PEG, Tousova Z, Slobodnik J, de Boer J, Lamoree MH. Rapid Screening of Acetylcholinesterase Inhibitors by Effect-Directed Analysis Using LC × LC Fractionation, a High Throughput in Vitro Assay, and Parallel Identification by Time of Flight Mass Spectrometry. Anal Chem 2016; 88:2353-60. [DOI: 10.1021/acs.analchem.5b04311] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Xiyu Ouyang
- Institute
for Environmental Studies (IVM), VU University Amsterdam, De Boelelaan
1087, 1081 HV Amsterdam, The Netherlands
| | - Pim E. G. Leonards
- Institute
for Environmental Studies (IVM), VU University Amsterdam, De Boelelaan
1087, 1081 HV Amsterdam, The Netherlands
| | - Zuzana Tousova
- Environmental Institute (EI), Okruzna
784/42, 972 41 Kos, Slovak Republic
- Faculty
of Science, Masaryk University, RECETOX, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jaroslav Slobodnik
- Environmental Institute (EI), Okruzna
784/42, 972 41 Kos, Slovak Republic
| | - Jacob de Boer
- Institute
for Environmental Studies (IVM), VU University Amsterdam, De Boelelaan
1087, 1081 HV Amsterdam, The Netherlands
| | - Marja H. Lamoree
- Institute
for Environmental Studies (IVM), VU University Amsterdam, De Boelelaan
1087, 1081 HV Amsterdam, The Netherlands
| |
Collapse
|
4
|
van de Ven H, Gargano A, van der Wal S, Schoenmakers P. Switching solvent and enhancing analyte concentrations in small effluent fractions using in-column focusing. J Chromatogr A 2016; 1427:90-5. [DOI: 10.1016/j.chroma.2015.11.082] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 11/23/2015] [Accepted: 11/24/2015] [Indexed: 02/07/2023]
|
5
|
Abstract
This article summarizes the most important developments in the use of 2D-LC for bioanalysis in the last 5 years. While several interesting and powerful applications have been developed recently, this work has been supported by continued, significant development of theoretical concepts, instrument development and practical aspects of method development. Some of the most exciting applications have been focused on the use of 2D-LC and characterize proteins both as biotherapeutic drug substances, and in formulations. These materials are inherently complex, difficult to resolve chromatographically and present problems that are essentially unknown (e.g., aggregation) in the small molecule world, thus 2D-LC can be leveraged very effectively to address these challenges.
Collapse
|
6
|
Vonk RJ, Gargano AFG, Davydova E, Dekker HL, Eeltink S, de Koning LJ, Schoenmakers PJ. Comprehensive Two-Dimensional Liquid Chromatography with Stationary-Phase-Assisted Modulation Coupled to High-Resolution Mass Spectrometry Applied to Proteome Analysis of Saccharomyces cerevisiae. Anal Chem 2015; 87:5387-94. [DOI: 10.1021/acs.analchem.5b00708] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
| | | | | | | | - Sebastiaan Eeltink
- Vrije Universiteit Brussel, Department of Chemical
Engineering, Pleinlaan
2, B-1050 Brussels, Belgium
| | | | | |
Collapse
|
7
|
Garg N, Kapono C, Lim YW, Koyama N, Vermeij MJ, Conrad D, Rohwer F, Dorrestein PC. Mass spectral similarity for untargeted metabolomics data analysis of complex mixtures. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 377:719-717. [PMID: 25844058 PMCID: PMC4379709 DOI: 10.1016/j.ijms.2014.06.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
While in nucleotide sequencing, the analysis of DNA from complex mixtures of organisms is common, this is not yet true for mass spectrometric data analysis of complex mixtures. The comparative analyses of mass spectrometry data of microbial communities at the molecular level is difficult to perform, especially in the context of a host. The challenge does not lie in generating the mass spectrometry data, rather much of the difficulty falls in the realm of how to derive relevant information from this data. The informatics based techniques to visualize and organize datasets are well established for metagenome sequencing; however, due to the scarcity of informatics strategies in mass spectrometry, it is currently difficult to cross correlate two very different mass spectrometry data sets from microbial communities and their hosts. We highlight that molecular networking can be used as an organizational tool of tandem mass spectrometry data, automated database search for rapid identification of metabolites, and as a workflow to manage and compare mass spectrometry data from complex mixtures of organisms. To demonstrate this platform, we show data analysis from hard corals and a human lung associated with cystic fibrosis.
Collapse
Affiliation(s)
- Neha Garg
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
| | - Clifford Kapono
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, USA
| | - Yan Wei Lim
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Nobuhiro Koyama
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
- School of Pharmacy, Kitasato University, Tokyo, Japan
| | - Mark J.A Vermeij
- CARMABI, Willemstad, Curaçao, & Department of Aquatic Microbiology, University of Amsterdam, Amsterdam, The Netherlands
| | - Douglas Conrad
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, USA
- Department of Pharmacology, University of California at San Diego, La Jolla, California
- Corresponding author: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC0751, La Jolla, CA 92093-0751. Phone: +1 (858) 534-6607. Fax: +1 (858) 822-0041.
| |
Collapse
|
8
|
LIM LW. Development of Micro-Flow-Controlled Techniques and Novel Stationary Phases in Capillary Liquid Chromatography. CHROMATOGRAPHY 2015. [DOI: 10.15583/jpchrom.2015.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Lee Wah LIM
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University
| |
Collapse
|
9
|
Comprehensive two-dimensional liquid chromatography coupled to high resolution time of flight mass spectrometry for chemical characterization of sewage treatment plant effluents. J Chromatogr A 2014; 1380:139-45. [PMID: 25578044 DOI: 10.1016/j.chroma.2014.12.075] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/22/2014] [Accepted: 12/23/2014] [Indexed: 11/21/2022]
Abstract
For the first time a comprehensive two-dimensional liquid chromatography (LC×LC) system coupled with a high resolution time-of-flight mass spectrometer (HR-ToF MS) was developed and applied for analysis of emerging toxicants in wastewater effluent. The system was optimized and validated using environmental standard compound mixtures of e.g. carbamate pesticides and polycyclic aromatic hydrocarbons (PAHs), to characterize the chromatographic system, to test the stability of the retention times and orthogonality. Various stationary phases in the second dimension were compared for the LC×LC analysis of silicon rubber passive sampler extracts of a wastewater effluent. A combination of C18 and Pentafluorophenyl (PFP) was found to be most effective. Finally, the hyphenation of LC×LC with HR-ToF MS was optimized, including splitter settings, transfer of data files between the different software packages and background subtraction using instrument software tools, after which tentative identification of 20 environmental contaminants was achieved, including pesticides, pharmaceuticals and food additives. As examples, three pesticides (isoproturon, terbutryn and diazinon) were confirmed by two-dimensional retention alignment.
Collapse
|
10
|
Jiang L, Tao Y, Wang D, Tang C, Shao Y, Wang Q, Zhao X, Zhang Y, Mei L. A novel two-dimensional preparative chromatography method designed for the separation of traditional animal Tibetan medicine Osteon Myospalacem Baileyi. J Sep Sci 2014; 37:3060-6. [DOI: 10.1002/jssc.201400564] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 08/05/2014] [Accepted: 08/06/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Lei Jiang
- Key Laboratory of Tibetan Medicine Research; Northwest Plateau Institute of Biology; Chinese Academy of Sciences; Xining P.R. China
- University of Chinese Academy of Sciences; Beijing P.R. China
| | - Yanduo Tao
- Key Laboratory of Tibetan Medicine Research; Northwest Plateau Institute of Biology; Chinese Academy of Sciences; Xining P.R. China
| | - Dan Wang
- School of Pharmaceutical Science and Technology; Tianjin University; Tianjin P. R. China
| | - Chuchen Tang
- College of Life Science; Zhejiang Sci-Tech University; Hangzhou P.R. China
| | - Yun Shao
- Key Laboratory of Tibetan Medicine Research; Northwest Plateau Institute of Biology; Chinese Academy of Sciences; Xining P.R. China
| | - Qilan Wang
- Key Laboratory of Tibetan Medicine Research; Northwest Plateau Institute of Biology; Chinese Academy of Sciences; Xining P.R. China
| | - Xiaohui Zhao
- Key Laboratory of Tibetan Medicine Research; Northwest Plateau Institute of Biology; Chinese Academy of Sciences; Xining P.R. China
| | - Yaozhou Zhang
- University of Chinese Academy of Sciences; Beijing P.R. China
- Tianjin International Joint Academy of Biomedicine; Tianjin P.R. China
| | - Lijuan Mei
- Key Laboratory of Tibetan Medicine Research; Northwest Plateau Institute of Biology; Chinese Academy of Sciences; Xining P.R. China
| |
Collapse
|
11
|
Comparative analysis of secretomes in basidiomycete fungi. J Proteomics 2014; 102:28-43. [DOI: 10.1016/j.jprot.2014.03.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/19/2014] [Accepted: 03/03/2014] [Indexed: 12/29/2022]
|
12
|
Abstract
During the last decade, a major breakthrough in the field of proteomics has been achieved. This review describes available techniques for proteomic analyses, both gel and non-gel based, particularly concentrating on relative quantification techniques. The principle of the different techniques is discussed, highlighting the advantages and drawbacks of recently available visualization methods in gel-based assays. In addition, recent developments for quantitative analysis in non-gel-based approaches are summarized. This review focuses on applications in Type 1 diabetes. These mainly include proteomic studies on pancreatic islets in animal models and in the human situation. Also discussed are mass spectrometry-based studies on T-cells, and studies on the development of diagnostic markers for diabetic nephropathology by capillary electrophoresis coupled to mass spectrometry.
Collapse
Affiliation(s)
- Wannes D'Hertog
- Laboratory for Experimental Medicine & Endocrinology (LEGENDO), University Hospital Gasthuisberg, Herestraat 49, Catholic University of Leuven, Leuven, Belgium.
| | | | | |
Collapse
|
13
|
Ecelbarger CA. Targeted proteomics using immunoblotting technique for studying dysregulation of ion transporters in renal disorders. Expert Rev Proteomics 2014; 1:219-27. [PMID: 15966816 DOI: 10.1586/14789450.1.2.219] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Renal salt and water transport physiology has benefited tremendously from the rapid advance of proteomics. Proteomics developed as a fast-throughput means of screening for global changes in proteins in a selected tissue, organ or cell type, as a logical offshoot of similar comprehensive, messenger RNA array-type technology. Targeted proteomics utilizes similar techniques but examines a predetermined set of proteins. One approach that has been rigorously employed over the last 10 years to evaluate differences in renal protein abundances due to a treatment or genotype has been parallel semiquantitative immunoblotting using antibody arrays. This approach, and newer ones on the horizon, provide a rapid global overview of regulation of the individual proteins whose integrated action determines overall renal sodium or water reabsorption.
Collapse
Affiliation(s)
- Carolyn A Ecelbarger
- Department of Medicine, Georgetown University, Box 571412, Washington, DC 20057-1412, USA.
| |
Collapse
|
14
|
Gao M, Qi D, Zhang P, Deng C, Zhang X. Development of multidimensional liquid chromatography and application in proteomic analysis. Expert Rev Proteomics 2014; 7:665-78. [DOI: 10.1586/epr.10.49] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
15
|
Combination of two different stationary phases for on-line pre-concentration and separation of basic drugs by using nano-liquid chromatography. J Chromatogr A 2013; 1285:118-23. [DOI: 10.1016/j.chroma.2013.02.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 02/06/2013] [Accepted: 02/09/2013] [Indexed: 11/20/2022]
|
16
|
Lee JH, Hyung SW, Mun DG, Jung HJ, Kim H, Lee H, Kim SJ, Park KS, Moore RJ, Smith RD, Lee SW. Fully automated multifunctional ultrahigh pressure liquid chromatography system for advanced proteome analyses. J Proteome Res 2012; 11:4373-81. [PMID: 22709424 DOI: 10.1021/pr3004166] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A multifunctional liquid chromatography system that performs 1-dimensional, 2-dimensional (strong cation exchange/reverse phase liquid chromatography or SCX/RPLC) separations and online phosphopeptide enrichment using a single binary nanoflow pump has been developed. With a simple operation of a function selection valve equipped with a SCX column and a TiO2 (titanium dioxide) column, a fully automated selection of three different experiment modes was achieved. Because the current system uses essentially the same solvent flow paths, the same trap column, and the same separation column for reverse-phase separation of 1D, 2D, and online phosphopeptides enrichment experiments, the elution time information obtained from these experiments is in excellent agreement, which facilitates correlating peptide information from different experiments. The final reverse-phase separation of the three experiments is completely decoupled from all of the function selection processes; thereby salts or acids from SCX or TiO2 column do not affect the efficiency of the reverse-phase separation.
Collapse
Affiliation(s)
- Jung Hwa Lee
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, South Korea
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Displacement chromatography as first separating step in online two-dimensional liquid chromatography coupled to mass spectrometry analysis of a complex protein sample—The proteome of neutrophils. J Chromatogr A 2012; 1232:288-94. [DOI: 10.1016/j.chroma.2012.02.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 02/07/2012] [Accepted: 02/12/2012] [Indexed: 01/01/2023]
|
18
|
Griffiths JR, Perkins S, Connolly Y, Zhang L, Holland M, Barattini V, Pereira L, Edge A, Ritchie H, Smith DL. The utility of porous graphitic carbon as a stationary phase in proteomics workflows: Two-dimensional chromatography of complex peptide samples. J Chromatogr A 2012; 1232:276-80. [DOI: 10.1016/j.chroma.2012.01.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 01/04/2012] [Accepted: 01/05/2012] [Indexed: 01/23/2023]
|
19
|
Shang F, Guihen E, Glennon JD. Recent advances in miniaturisation - The role of microchip electrophoresis in clinical analysis. Electrophoresis 2011; 33:105-16. [DOI: 10.1002/elps.201100454] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/12/2011] [Accepted: 10/13/2011] [Indexed: 01/27/2023]
|
20
|
Kong RP, Siu S, Lee SS, Lo C, Chu IK. Development of online high-/low-pH reversed-phase–reversed-phase two-dimensional liquid chromatography for shotgun proteomics: A reversed-phase-strong cation exchange-reversed-phase approach. J Chromatogr A 2011; 1218:3681-8. [DOI: 10.1016/j.chroma.2011.04.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 03/30/2011] [Accepted: 04/07/2011] [Indexed: 01/06/2023]
|
21
|
Quantitative proteomic profiling of the Escherichia coli response to metallic copper surfaces. Biometals 2011; 24:429-44. [PMID: 21384090 DOI: 10.1007/s10534-011-9434-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Accepted: 02/24/2011] [Indexed: 12/18/2022]
Abstract
Metallic copper surfaces have strong antimicrobial properties and kill bacteria, such as Escherichia coli, within minutes in a process called contact killing. These bacteria are exposed to acute copper stress under dry conditions which is different from chronic copper stress in growing liquid cultures. Currently, the physiological changes of E. coli during the acute contact killing process are largely unknown. Here, a label-free, quantitative proteomic approach was employed to identify the differential proteome profiles of E. coli cells after sub-lethal and lethal exposure to dry metallic copper. Of the 509 proteins identified, 110 proteins were differentially expressed after sub-lethal exposure, whereas 136 proteins had significant differences in their abundance levels after lethal exposure to copper compared to unexposed cells. A total of 210 proteins were identified only in copper-responsive proteomes. Copper surface stress coincided with increased abundance of proteins involved in secondary metabolite biosynthesis, transport and catabolism, including efflux proteins and multidrug resistance proteins. Proteins involved in translation, ribosomal structure and biogenesis functions were down-regulated after contact to metallic copper. The set of changes invoked by copper surface-exposure was diverse without a clear connection to copper ion stress but was different from that caused by exposure to stainless steel. Oxidative posttranslational modifications of proteins were observed in cells exposed to copper but also from stainless steel surfaces. However, proteins from copper stressed cells exhibited a higher degree of oxidative proline and threonine modifications.
Collapse
|
22
|
Ly L, Wasinger VC. Protein and peptide fractionation, enrichment and depletion: Tools for the complex proteome. Proteomics 2011; 11:513-34. [DOI: 10.1002/pmic.201000394] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 10/03/2010] [Accepted: 10/18/2010] [Indexed: 12/28/2022]
|
23
|
Jabbour RE, Wade MM, Deshpande SV, Stanford MF, Wick CH, Zulich AW, Snyder AP. Identification of Yersinia pestis and Escherichia coli Strains by Whole Cell and Outer Membrane Protein Extracts with Mass Spectrometry-Based Proteomics. J Proteome Res 2010; 9:3647-55. [DOI: 10.1021/pr100402y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Rabih E. Jabbour
- SAIC, Aberdeen Proving Ground, Maryland 21010, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and Science and Technology Corporation, Edgewood, Maryland 21040
| | - Mary Margaret Wade
- SAIC, Aberdeen Proving Ground, Maryland 21010, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and Science and Technology Corporation, Edgewood, Maryland 21040
| | - Samir V. Deshpande
- SAIC, Aberdeen Proving Ground, Maryland 21010, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and Science and Technology Corporation, Edgewood, Maryland 21040
| | - Michael F. Stanford
- SAIC, Aberdeen Proving Ground, Maryland 21010, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and Science and Technology Corporation, Edgewood, Maryland 21040
| | - Charles H. Wick
- SAIC, Aberdeen Proving Ground, Maryland 21010, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and Science and Technology Corporation, Edgewood, Maryland 21040
| | - Alan W. Zulich
- SAIC, Aberdeen Proving Ground, Maryland 21010, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and Science and Technology Corporation, Edgewood, Maryland 21040
| | - A. Peter Snyder
- SAIC, Aberdeen Proving Ground, Maryland 21010, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and Science and Technology Corporation, Edgewood, Maryland 21040
| |
Collapse
|
24
|
Lee J, Soper SA, Murray KK. Development of an efficient on-chip digestion system for protein analysis using MALDI-TOF MS. Analyst 2009; 134:2426-33. [PMID: 19918612 DOI: 10.1039/b916556h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A solid-phase trypsin microreactor was constructed and operated with electrokinetically-driven flow for the digestion of proteins and coupled off-line with MALDI-TOF MS. The bioreactor was fabricated from poly(methyl methacrylate), PMMA, by hot embossing using a mold master prepared by micro-milling. The solid-phase bioreactor consisted of a 4 cm long, 200 microm wide, and 50 microm deep microfluidic channel that was populated with an array of 50 microm diameter micropost structures with a 50 microm inter-post spacing. The bioreactor was prepared by covalently attaching the proteolytic enzyme, trypsin, to the UV-modified surface of the PMMA microstructures using the appropriate coupling reagents. The performance of the system was evaluated using a set of proteins. The bioreactor provided efficient digestion of cytochrome c at a field strength of 375 V/cm, producing a reaction time of approximately 20 s to produce 97% sequence coverage for protein identification. Bovine serum albumin (BSA), phosphorylase b, and beta-casein were also assessed and the sequence coverages were 46, 63, and 79%, respectively, using the same reactor residence time. Furthermore, Escherichia coli was used as a model to demonstrate the feasibility of fingerprint analysis for intact cells using this solid-phase bioreactor.
Collapse
Affiliation(s)
- Jeonghoon Lee
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | | |
Collapse
|
25
|
Wei Y, Lan T, Tang T, Zhang L, Wang F, Li T, Du Y, Zhang W. A comprehensive two-dimensional normal-phase x reversed-phase liquid chromatography based on the modification of mobile phases. J Chromatogr A 2009; 1216:7466-71. [PMID: 19712935 DOI: 10.1016/j.chroma.2009.08.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 07/08/2009] [Accepted: 08/10/2009] [Indexed: 11/28/2022]
Abstract
A comprehensive orthogonal two-dimensional liquid chromatography (2D-LC) based on the modification of mobile phases was developed with a sample loop-valve interface. To improve the compatibility of mobile phases and analysis speed, some special solvents were chosen as the mobile phases, and the column temperature was elevated to decrease the viscosity of mobile phases of reversed-phase liquid chromatography (RPLC). Based on this principle, the first dimension was normal-phase liquid chromatography (NPLC) with a SiO2 column, and the second dimension was reversed-phase liquid chromatography containing two tandem C18 columns. 1,4-Dioxane was used in the NPLC mobile phase, and isopropyl alcohol was employed in the RPLC mobile phase. Moreover, the elevated column temperature enabled the reduction of the backpressure and using tandem C18 columns to improve the resolving power in RPLC. The new comprehensive 2D-LC system and applied strategy offered a novel idea for construction of 2D-LC system. A traditional Chinese medicine, Zhengtian pill, was used as the test sample to evaluate the constructed 2D-LC system. 876 peaks were detected, and the peak capacity reached 1740.
Collapse
Affiliation(s)
- Yuanlong Wei
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Lee J, Soper SA, Murray KK. Microfluidics with MALDI analysis for proteomics--a review. Anal Chim Acta 2009; 649:180-90. [PMID: 19699392 DOI: 10.1016/j.aca.2009.07.037] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 07/13/2009] [Accepted: 07/15/2009] [Indexed: 01/01/2023]
Abstract
Various microfluidic devices have been developed for proteomic analyses and many of these have been designed specifically for mass spectrometry detection. In this review, we present an overview of chip fabrication, microfluidic components, and the interfacing of these devices to matrix-assisted laser desorption ionization (MALDI) mass spectrometry. These devices can be directly coupled to the mass spectrometer for on-line analysis in real-time, or samples can be analyzed on-chip or deposited onto targets for off-line readout. Several approaches for combining microfluidic devices with analytical functions such as sample cleanup, digestion, and separations with MALDI mass spectrometry are discussed.
Collapse
Affiliation(s)
- Jeonghoon Lee
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | | |
Collapse
|
27
|
Lee J, Soper SA, Murray KK. Microfluidic chips for mass spectrometry-based proteomics. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:579-93. [PMID: 19373851 DOI: 10.1002/jms.1585] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Microfluidic devices coupled to mass spectrometers have emerged as excellent tools for solving the complex analytical challenges associated with the field of proteomics. Current proteome identification procedures are accomplished through a series of steps that require many hours of labor-intensive work. Microfluidics can play an important role in proteomic sample preparation steps prior to mass spectral identification such as sample cleanup, digestion, and separations due to its ability to handle small sample quantities with the potential for high-throughput parallel analysis. To utilize microfluidic devices for proteomic analysis, an efficient interface between the microchip and the mass spectrometer is required. This tutorial provides an overview of the technologies and applications of microfluidic chips coupled to mass spectrometry for proteome analysis. Various approaches for combining microfluidic devices with electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) are summarized and applications of chip-based separations and digestion technologies to proteomic analysis are presented.
Collapse
Affiliation(s)
- Jeonghoon Lee
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | | | | |
Collapse
|
28
|
Matharoo-Ball B, Miles AK, Creaser CS, Ball G, Rees R. Serum biomarker profiling in cancer studies: a question of standardisation? Vet Comp Oncol 2009; 6:224-47. [PMID: 19178682 DOI: 10.1111/j.1476-5829.2008.00171.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Companion animals are exposed to similar environmental conditions and carcinogens as humans. In some animal cancers, there also appears to be the same genetic changes associated as in humans. However, little work has been carried out in cancer biomarker identification in animals. The recent dramatic advances in molecular medicine, genomics, proteomics and translational research will allow biomarker identification, which may provide the best strategies for veterinarians and clinicians to combat disease by early diagnosis and administration of effective treatments. Proteomics may have important applications in cancer diagnosis, prognosis and predictive clinical outcome that could directly change clinical practice by affecting critical elemen-ts of care and management. This review summarizes the advances in proteomics that has propelled us to this exciting age of clinical proteomics, and highlights the future work that is required for this to become a reality. In this review, we will discuss the available proteomic technologies and their limitations, and highlight the key areas of research and how they have been used to discover cancer biomarkers. The principles described here are equally applicable to human and animal disease, but implementation of 'omic' technologies requires stringent guidelines for collection of clinical material, the application of analytical techniques and interpretation of the data.
Collapse
Affiliation(s)
- B Matharoo-Ball
- The John Van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | | | | | | | | |
Collapse
|
29
|
François I, Cabooter D, Sandra K, Lynen F, Desmet G, Sandra P. Tryptic digest analysis by comprehensive reversed phase×two reversed phase liquid chromatography (RP-LC×2RP-LC) at different pH's. J Sep Sci 2009; 32:1137-44. [DOI: 10.1002/jssc.200800578] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
30
|
Immunodepletion of high abundance proteins coupled on-line with reversed-phase liquid chromatography: A two-dimensional LC sample enrichment and fractionation technique for mammalian proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:79-85. [DOI: 10.1016/j.jchromb.2008.11.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 11/10/2008] [Accepted: 11/12/2008] [Indexed: 01/06/2023]
|
31
|
Jiang X, Dong J, Wang F, Feng S, Ye M, Zou H. Automation of nanoflow liquid chromatography-tandem mass spectrometry for proteome and peptide profiling analysis by using a monolithic analytical capillary column. Electrophoresis 2008; 29:1612-8. [DOI: 10.1002/elps.200700513] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
32
|
Development of a comprehensive multidimensional liquid chromatography system with tandem mass spectrometry detection for detailed characterization of recombinant proteins. J Chromatogr A 2008; 1189:183-95. [DOI: 10.1016/j.chroma.2007.11.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 10/12/2007] [Accepted: 11/09/2007] [Indexed: 11/21/2022]
|
33
|
Development and optimization of a system for comprehensive two-dimensional liquid chromatography with UV and mass spectrometric detection for the separation of complex samples by multi-step gradient elution. J Chromatogr A 2008; 1188:216-26. [DOI: 10.1016/j.chroma.2008.02.072] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 02/08/2008] [Accepted: 02/12/2008] [Indexed: 11/19/2022]
|
34
|
Fournier ML, Gilmore JM, Martin-Brown SA, Washburn MP. Multidimensional Separations-Based Shotgun Proteomics. Chem Rev 2007; 107:3654-86. [PMID: 17649983 DOI: 10.1021/cr068279a] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
35
|
Gedela S, Medicherla NR. Chromatographic Techniques for the Separation of Peptides: Application to Proteomics. Chromatographia 2007. [DOI: 10.1365/s10337-007-0215-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
36
|
Want EJ, Nordström A, Morita H, Siuzdak G. From exogenous to endogenous: the inevitable imprint of mass spectrometry in metabolomics. J Proteome Res 2007; 6:459-68. [PMID: 17269703 DOI: 10.1021/pr060505+] [Citation(s) in RCA: 197] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mass spectrometry (MS) is an established technology in drug metabolite analysis and is now expanding into endogenous metabolite research. Its utility derives from its wide dynamic range, reproducible quantitative analysis, and the ability to analyze biofluids with extreme molecular complexity. The aims of developing mass spectrometry for metabolomics range from understanding basic biochemistry to biomarker discovery and the structural characterization of physiologically important metabolites. In this review, we will discuss the techniques involved in this exciting area and the current and future applications of this field.
Collapse
Affiliation(s)
- Elizabeth J Want
- Department of Molecular Biology, The Scripps Center for Mass Spectrometry, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | | | | |
Collapse
|
37
|
Jiang X, Feng S, Tian R, Han G, Jiang X, Ye M, Zou H. Automation of nanoflow liquid chromatography-tandem mass spectrometry for proteome analysis by using a strong cation exchange trap column. Proteomics 2007; 7:528-539. [PMID: 17309098 DOI: 10.1002/pmic.200600661] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
An approach was developed to automate sample introduction for nanoflow LC-MS/MS (microLC-MS/MS) analysis using a strong cation exchange (SCX) trap column. The system consisted of a 100 microm id x 2 cm SCX trap column and a 75 microm id x 12 cm C18 RP analytical column. During the sample loading step, the flow passing through the SCX trap column was directed to waste for loading a large volume of sample at high flow rate. Then the peptides bound on the SCX trap column were eluted onto the RP analytical column by a high salt buffer followed by RP chromatographic separation of the peptides at nanoliter flow rate. It was observed that higher performance of separation could be achieved with the system using SCX trap column than with the system using C18 trap column. The high proteomic coverage using this approach was demonstrated in the analysis of tryptic digest of BSA and yeast cell lysate. In addition, this system was also applied to two-dimensional separation of tryptic digest of human hepatocellular carcinoma cell line SMMC-7721 for large scale proteome analysis. This system was fully automated and required minimum changes on current microLC-MS/MS system. This system represented a promising platform for routine proteome analysis.
Collapse
Affiliation(s)
- Xiaogang Jiang
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- School of Medicine, Suzhou University, Suzhou, Jiangsu, China
| | - Shun Feng
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Ruijun Tian
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Guanghui Han
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xinning Jiang
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Mingliang Ye
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Hanfa Zou
- National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| |
Collapse
|
38
|
Song L, Choi K, Park Y, Kazim AL, Marlar K, Kong E, Park E, Kim YH, Koo K, Chae HZ. Capillary‐LC‐µESI‐MS/MS and Nano‐LC‐Nano ESI‐MS/MS Analysis Using a Single Binary Pump Capillary LC System: Applications in Proteomics. J LIQ CHROMATOGR R T 2007. [DOI: 10.1081/jlc-200054754] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Liguo Song
- a Department of Cellular Stress Biology, and Proteomics Resource , Roswell Park Cancer Institute , Buffalo, New York, USA
| | - Kyoung‐Soo Choi
- a Department of Cellular Stress Biology, and Proteomics Resource , Roswell Park Cancer Institute , Buffalo, New York, USA
| | - Young‐Mee Park
- a Department of Cellular Stress Biology, and Proteomics Resource , Roswell Park Cancer Institute , Buffalo, New York, USA
| | - A. Latif Kazim
- b Department of Cellular Stress Biology , Roswell Park Cancer Institute , Buffalo, New York
| | - Khin Marlar
- b Department of Cellular Stress Biology , Roswell Park Cancer Institute , Buffalo, New York
| | - Eung‐Sik Kong
- b Department of Cellular Stress Biology , Roswell Park Cancer Institute , Buffalo, New York
| | - Eun‐Mi Park
- b Department of Cellular Stress Biology , Roswell Park Cancer Institute , Buffalo, New York
| | - Yeul Hong Kim
- c Genomic Research Center for Lung and Breast/Ovarian Cancer , Korean University Medical School , Korera
| | - Kyung‐Hee Koo
- d School of Biological Sciences and Technology , Chonnam National University , Korera
| | - Ho Zoon Chae
- d School of Biological Sciences and Technology , Chonnam National University , Korera
| |
Collapse
|
39
|
Ye M, Jiang X, Feng S, Tian R, Zou H. Advances in chromatographic techniques and methods in shotgun proteome analysis. Trends Analyt Chem 2007. [DOI: 10.1016/j.trac.2006.10.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
40
|
Liu H, Finch JW, Luongo JA, Li GZ, Gebler JC. Development of an online two-dimensional nano-scale liquid chromatography/mass spectrometry method for improved chromatographic performance and hydrophobic peptide recovery. J Chromatogr A 2006; 1135:43-51. [PMID: 17027011 DOI: 10.1016/j.chroma.2006.09.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2006] [Revised: 09/07/2006] [Accepted: 09/12/2006] [Indexed: 11/30/2022]
Abstract
An online two-dimensional (2D) strong cation-exchange (SCX)/reversed-phase (RP) nano-scale liquid chromatography/mass spectrometry (nanoLC/MS) method was developed for improved separation and hydrophobic peptide recovery. Sharper and more symmetric RP peaks were observed with the use of a "band re-focusing method", in which an analytical RP column with more hydrophobicity than the RP trap column was used in the system. To recover hydrophobic peptides still unreleased from the SCX column after a conventional salt step gradient due to hydrophobic interaction, a RP step gradient from 10% to 30% acetonitrile (ACN) was applied to the SCX column in the presence of a high salt concentration following the salt gradient. There were 301 unique hydrophobic E. coli peptides identified from the RP fractions. These peptides, which were 19% of all E. coli peptides identified from a 2D run, would not have been identified without the application of the RP gradient to the SCX column.
Collapse
Affiliation(s)
- Hongji Liu
- Waters Corporation, Milford, MA 01757, USA.
| | | | | | | | | |
Collapse
|
41
|
Rieux L, Lubda D, Niederländer HAG, Verpoorte E, Bischoff R. Fast, high-efficiency peptide separations on a 50-μm reversed-phase silica monolith in a nanoLC–MS set-up. J Chromatogr A 2006; 1120:165-72. [PMID: 16472536 DOI: 10.1016/j.chroma.2006.01.038] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Revised: 10/24/2005] [Accepted: 01/12/2006] [Indexed: 11/24/2022]
Abstract
Proteomic studies have stimulated the development of novel stationary phases in miniaturised chromatographic columns that permit high linear flow velocities and exhibit high resolving power. In this work, a 50-microm reversed-phase silica-based monolith was chromatographically characterised for its use in proteomics applications using a nanoLC-MS set-up. It showed high efficiency for the separation of tryptic peptides under isocratic elution conditions (HETP(min)=5-10 microm at 2.4 mm/s). Flow rates up to 1.95 microL/min (18.4 mm/s) and gradient slopes up to an unusually fast 9% could be used. This resulted in rapid separations of peptide mixtures, with peak widths at half height of between 5 and 10 s. The 50-microm monolithic column was used to analyse depleted serum from a cervical cancer patient at a throughput of one sample per 30 min.
Collapse
Affiliation(s)
- Laurent Rieux
- Pharmaceutical Analysis, University Centre for Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | | | | | | |
Collapse
|
42
|
Rozenbrand J, van Bennekom WP, Unger KK, de Jong GJ. Fast LC separation of a myoglobin digest: a case study using monolithic and particulate RP 18 silica capillary columns. Anal Bioanal Chem 2006; 385:1055-61. [PMID: 16736167 DOI: 10.1007/s00216-006-0520-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Revised: 04/26/2006] [Accepted: 05/02/2006] [Indexed: 10/24/2022]
Abstract
A method was developed for the fast separation of a myoglobin digest using a monolithic RP 18 silica capillary column of 100 microm I.D. The results were compared with those obtained with a particulate RP 18 silica capillary column of 100 microm I.D. at a flow-rate between 0.6 and 1.2 microl/min. The digest was analyzed at the monolithic column at a flow-rate up to 2.8 microl/min. This high flow-rate could not be applied to the particulate column due to the high back-pressure. When the starting composition of the gradient was changed from 0 to 20% and a gradient steepness of 16%/min was used, the analysis time was less than 4 min. A positive Mascot identification score of 115 was achieved for the MS-MS data. When a lower gradient steepness was employed, the chromatographic resolution and the peak capacity did not increase for most compounds. The intraday repeatability for the retention time of the monolithic column was better than 1.5% at 2.8 microl/min and even less than 0.5% using a flow-rate of 0.6 or 1.0 microl/min. For the particulate column, it was between 0.5 and 1.4% for a flow-rate of 0.6 microl/min, probably due to the high column back-pressure. The interday reproducibility for the retention time of the monolithic column was less than 0.9% using a flow-rate of 1.0 microl/min.
Collapse
Affiliation(s)
- Johan Rozenbrand
- Department of Biomedical Analysis, Faculty of Sciences, Utrecht University, P.O. Box 80082, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.
| | | | | | | |
Collapse
|
43
|
Lim LW, Tomatsu M, Takeuchi T. Development of an on-line immobilized-enzyme reversed-phase HPLC method for protein digestion and peptide separation. Anal Bioanal Chem 2006; 386:614-20. [PMID: 16724223 DOI: 10.1007/s00216-006-0458-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Revised: 03/28/2006] [Accepted: 03/30/2006] [Indexed: 10/24/2022]
Abstract
This paper describes use of a novel glass bead-based immobilized-enzyme micro column for simple and swift on-line protein digestion then peptide separation by reversed-phase HPLC. The inexpensive and easily made immobilized-enzyme micro column was prepared from aminopropyl controlled-pore glass that was reacted first with glutaraldehyde then with trypsin in the presence of phosphate buffer. Tryptic digestion of bovine serum albumin (BSA) was achieved simply by passing pretreated protein solution through the laboratory made immobilized-trypsin column; the tryptic fragments were then separated by reversed-phase HPLC. The peptide separation was found to be identical to separation of a sample which had undergone conventional enzymatic protein digestion in solution. Digestion of BSA by the immobilized-trypsin column decreased with increasing flow rate of the solution through the column, and 1.0 muL min(-1) was found to be the optimum flow rate for on-line protein digestion with our system. It was also found that the sample required pretreatment with urea before injection, because of a change in the properties of the protein in the presence of urea, and the immobilized-trypsin column lost its function in the presence of acetonitrile. This on-line proteomics system enables simple and rapid protein digestion and was successfully applied to partially micro two-dimensional (2D) chromatographic separation of proteins.
Collapse
Affiliation(s)
- Lee Wah Lim
- Department of Chemistry, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
| | | | | |
Collapse
|
44
|
Nägele E, Vollmer M, Hörth P, Vad C. 2D-LC/MS techniques for the identification of proteins in highly complex mixtures. Expert Rev Proteomics 2006; 1:37-46. [PMID: 15966797 DOI: 10.1586/14789450.1.1.37] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Today, 2D online or offline liquid chromatography/mass spectrometry is state of the art for the identification of proteins from complex proteome samples in many laboratories. Both 2D liquid chromatography methods use two orthogonal liquid chromatography separation techniques. The most commonly used techniques are strong cation exchange chromatography for the first dimension and reversed phase separation for the second dimension. In order to improve sensitivity the reversed phase separation is usually performed in the nanoflow scale and mass spectrometry is used as the final detection method. The high-performance liquid chromatography techniques complement the 2D-gel techniques supporting their weaknesses. This is especially true for the gel separation of hydrophobic membrane proteins, which play an important role in living cells as well as being important targets for future pharmaceutical drugs.
Collapse
Affiliation(s)
- Edgar Nägele
- Agilent Technologies, R&D and Marketing GmbH & Co. KG, Hewlett-Packard-Str. 8, Waldbronn, Germany.
| | | | | | | |
Collapse
|
45
|
Want EJ, Cravatt BF, Siuzdak G. The expanding role of mass spectrometry in metabolite profiling and characterization. Chembiochem 2006; 6:1941-51. [PMID: 16206229 DOI: 10.1002/cbic.200500151] [Citation(s) in RCA: 175] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mass spectrometry has a strong history in drug-metabolite analysis and has recently emerged as the foremost technology in endogenous metabolite research. The advantages of mass spectrometry include a wide dynamic range, the ability to observe a diverse number of molecular species, and reproducible quantitative analysis. These attributes are important in addressing the issue of metabolite profiling, as the dynamic range easily exceeds nine orders of magnitude in biofluids, and the diversity of species ranges from simple amino acids to lipids to complex carbohydrates. The goals of the application of mass spectrometry range from basic biochemistry to clinical biomarker discovery with challenges in generating a comprehensive profile, data analysis, and structurally characterizing physiologically important metabolites. The precedent for this work has already been set in neonatal screening, as blood samples from millions of neonates are tested routinely by mass spectrometry as a diagnostic tool for inborn errors of metabolism. In this review, we will discuss the background from which contemporary metabolite research emerged, the techniques involved in this exciting area, and the current and future applications of this field.
Collapse
Affiliation(s)
- Elizabeth J Want
- Department of Molecular Biology and The Center for Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | | | | |
Collapse
|
46
|
Choi KS, Song L, Park YM, Marshall J, Lund AL, Shion H, Park EM, Chae HZ, Park JH. Analysis of Human Plasma Proteome by 2DE‐ and 2D nanoLC‐Based Mass Spectrometry. Prep Biochem Biotechnol 2006; 36:3-17. [PMID: 16428136 DOI: 10.1080/10826060500388447] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We compared the 2DE coupled to MALDI-TOF-MS and ESI-MS/MS analysis (2DE-MS) and the on-line 2D nanoLC, followed by nanoESI-MS/MS analysis (2DLC-MS), for the separation and identification of proteins in high abundance protein-depleted human plasma. Identification of proteins in the plasma by the two methods demonstrated that the majority of the identified protein set was unique to each method. Therefore, if a comprehensive coverage of the proteome identification is desired, it is ideal to apply both methods. The 2DE-MS method is amenable to protein spot-based quantitation, whereas the 2DLC-MS method may provide an advantage of the high throughput application.
Collapse
Affiliation(s)
- Kyoung-Soo Choi
- Department of Cellular Stress Biology, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Vanrobaeys F, Van Coster R, Dhondt G, Devreese B, Van Beeumen J. Profiling of Myelin Proteins by 2D-Gel Electrophoresis and Multidimensional Liquid Chromatography Coupled to MALDI TOF−TOF Mass Spectrometry. J Proteome Res 2005; 4:2283-93. [PMID: 16335977 DOI: 10.1021/pr050205c] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The myelin sheath is an electrically insulating layer that consists of lipids and proteins. It plays a key role in the functioning of the nervous system by allowing fast saltatory conduction of nerve pulses. Profiling of the proteins present in myelin is an indispensable prerequisite to better understand the molecular aspects of this dynamic, functionally active membrane. Two types of protein, the myelin basic protein and the proteolipid protein, account for nearly 85% of the protein content in myelin. Identification and characterization of the other "minor" proteins is, in this respect, a real challenge. In the present work, two proteomic strategies were applied in order to study the protein composition of myelin from the murine central nervous system. First, the protein mixture was separated by 2D-gel electrophoresis and, after spot excision and in-gel digestion, samples were analyzed by mass spectrometry. Via this approach, we identified 57 protein spots, corresponding to 38 unique proteins. Alternatively, the myelin sample was digested by trypsin and the resulting peptide mixture was further analyzed by off-line 2D-liquid chromatography. After the second-dimension separation (nanoLC), the peptides were spotted "on-line" onto a MALDI target and analyzed by MALDI TOF-TOF mass spectrometry. We identified 812 peptides by MALDI MS/MS, representing 93 proteins. Membrane proteins, low abundant proteins, and highly basic proteins were all represented in this shotgun proteomic approach. By combining the results of both approaches, we can present a comprehensive proteomic map of myelin, comprising a total of 103 protein identifications, which is of utmost importance for the molecular understanding of white matter and its disorders.
Collapse
Affiliation(s)
- Frank Vanrobaeys
- Laboratory of Protein Biochemistry and Protein Engineering, Ghent University, Belgium
| | | | | | | | | |
Collapse
|
48
|
Ihling C, Sinz A. Proteome analysis of Escherichia coli using high-performance liquid chromatography and Fourier transform ion cyclotron resonance mass spectrometry. Proteomics 2005; 5:2029-42. [PMID: 15852340 DOI: 10.1002/pmic.200401122] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The basic problem of complexity poses a significant challenge for proteomic studies. To date two-dimensional gel electrophoresis (2-DE) followed by enzymatic in-gel digestion of the peptides, and subsequent identification by mass spectrometry (MS) is the most commonly used method to analyze complex protein mixtures. However, 2-DE is a slow and labor-intensive technique, which is not able to resolve all proteins of a proteome. To overcome these limitations gel-free approaches are developed based on high performance liquid chromatography (HPLC) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The high resolution and excellent mass accuracy of FT-ICR MS provides a basis for simultaneous analysis of numerous compounds. In the present study, a small protein subfraction of an Escherichia coli cell lysate was prepared by size-exclusion chromatography and proteins were analyzed using C4 reversed phase (RP)-HPLC for pre-separation followed by C18 RP nanoHPLC/nanoESI FT-ICR MS for analysis of the peptide mixtures after tryptic digestion of the protein fractions. We identified 231 proteins and thus demonstrated that a combination of two RP separation steps - one on the protein and one on the peptide level - in combination with high-resolution FT-ICR MS has the potential to become a powerful method for global proteomics studies.
Collapse
Affiliation(s)
- Christian Ihling
- Biotechnological-Biomedical Center, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany
| | | |
Collapse
|
49
|
Abstract
Shotgun proteomics has emerged as a powerful approach for the analysis of complex protein mixtures, including biofluids, tissues, cells, organelles or protein complexes. Having evolved from the integration of chromatography and mass spectrometry, innovations in sample preparation, multidimensional chromatography, mass spectrometry and proteomic informatics continually facilitate, enable and challenge shotgun proteomics. As a result, shotgun proteomics continues to evolve and enable new areas of biological research, and is beginning to impact human disease diagnosis and therapeutic intervention.
Collapse
Affiliation(s)
- Selene K Swanson
- Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA
| | | |
Collapse
|
50
|
Winnik WM. Continuous pH/Salt Gradient and Peptide Score for Strong Cation Exchange Chromatography in 2D-Nano-LC/MS/MS Peptide Identification for Proteomics. Anal Chem 2005; 77:4991-8. [PMID: 16053314 DOI: 10.1021/ac0503714] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Tryptic digests of human serum albumin and human lung epithelial cell lysates were used as test samples in a novel proteomics study. Peptides were separated and analyzed using 2D-nano-LC/MS/MS with strong cation exchange (SCX) and reversed-phase chromatography and continuous gradient elution. The peptide elution conditions combined simultaneous pH gradient with ammonium acetate salt gradient elution modes. A novel empirical SCX peptide elution score was developed, which accounts for both the number of basic and acidic residues and, in part, their location within a sequence of a peptide. Average scores calculated for the fractionated peptide sequences correlated well with the pH of SCX elution fractions. Multiple peptides with identical amino acid sequences, but differing in cysteine tags possessing different positive charge and different SCX elution properties, were obtained by subjecting the samples to reduction and alkylation with different cysteine alkylating reagents: iodoacetamide, 4-vinylpyridine, and (3-acrylamidopropyl) trimethylammonium chloride. The structurally similar peptides were used as elution standards.
Collapse
Affiliation(s)
- Witold M Winnik
- National Health and Environmental Effects Research Laboratory, Environmental Carcinogenesis Division, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
| |
Collapse
|