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Muroski JM, Fu JY, Nguyen HH, Wofford NQ, Mouttaki H, James KL, McInerney MJ, Gunsalus RP, Loo JA, Ogorzalek Loo RR. The acyl-proteome of Syntrophus aciditrophicus reveals metabolic relationships in benzoate degradation. Mol Cell Proteomics 2022; 21:100215. [PMID: 35189333 PMCID: PMC8942843 DOI: 10.1016/j.mcpro.2022.100215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 01/13/2022] [Accepted: 02/17/2022] [Indexed: 11/08/2022] Open
Abstract
Syntrophus aciditrophicus is a model syntrophic bacterium that degrades fatty and aromatic acids into acetate, CO2, formate, and H2 that are utilized by methanogens and other hydrogen-consuming microbes. S. aciditrophicus benzoate degradation proceeds by a multistep pathway with many intermediate reactive acyl-coenzyme A species (RACS) that can potentially Nε-acylate lysine residues. Herein, we describe the identification and characterization of acyl-lysine modifications that correspond to RACS in the benzoate degradation pathway. The amounts of modified peptides are sufficient to analyze the post-translational modifications without antibody enrichment, enabling a range of acylations located, presumably, on the most extensively acylated proteins throughout the proteome to be studied. Seven types of acyl modifications were identified, six of which correspond directly to RACS that are intermediates in the benzoate degradation pathway including 3-hydroxypimeloylation, a modification first identified in this system. Indeed, benzoate-degrading enzymes are heavily represented among the acylated proteins. A total of 125 sites were identified in 60 proteins. Functional deacylase enzymes are present in the proteome, indicating a potential regulatory system/mechanism by which S. aciditrophicus modulates acylation. Uniquely, Nε-acyl-lysine RACS are highly abundant in these syntrophic bacteria, raising the compelling possibility that post-translational modifications modulate benzoate degradation in this and potentially other, syntrophic bacteria. Our results outline candidates for further study of how acylations impact syntrophic consortia. Abundant lysine modifications in microbes enable unbiased global acylation profiling. Seven types of acyl modifications are found; six from benzoate degradation intermediates. Benzoate-degrading enzymes are prominent among the 60 acylated proteins. Abundant acylation/active deacylases suggest PTMs modulate syntrophic metabolism.
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2
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Naryzhny S, Zgoda V, Kopylov A, Petrenko E, Archakov А. A semi-virtual two dimensional gel electrophoresis: IF-ESI LC-MS/MS. MethodsX 2017; 4:260-264. [PMID: 28913169 PMCID: PMC5587868 DOI: 10.1016/j.mex.2017.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 08/25/2017] [Indexed: 01/30/2023] Open
Abstract
A method for increasing the productivity of ESI LC-MS/MS (electrospray ionization-liquid chromatography-tandem mass spectrometry) was proposed and applied. After IF (isoelectric focusing) of the sample using IPG (immobilized pH gradient) strip, the strip was cut to sections, and every section was treated according to trypsinolysis protocol for MS/MS analysis. The peptides produced were further analyzed by ESI LC-MS/MS. The procedure allows to: identify many more proteins and proteoforms compared to shotgun analysis of extracts. build a semi-virtual 2DE map of identified proteins.
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Affiliation(s)
- Stanislav Naryzhny
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya 10, Moscow, 119121, Russia.,B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova roscha, Gatchina, Leningrad region, 188300, Russia
| | - Victor Zgoda
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya 10, Moscow, 119121, Russia
| | - Artur Kopylov
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya 10, Moscow, 119121, Russia
| | - Elena Petrenko
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya 10, Moscow, 119121, Russia
| | - Аlexander Archakov
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya 10, Moscow, 119121, Russia
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3
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Naryzhny S. Towards the Full Realization of 2DE Power. Proteomes 2016; 4:proteomes4040033. [PMID: 28248243 PMCID: PMC5260966 DOI: 10.3390/proteomes4040033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 01/29/2023] Open
Abstract
Here, approaches that allow disclosure of the information hidden inside and outside of two-dimensional gel electrophoresis (2DE) are described. Experimental identification methods, such as mass spectrometry of high resolution and sensitivity (MALDI-TOF MS and ESI LC-MS/MS) and immunodetection (Western and Far-Western) in combination with bioinformatics (collection of all information about proteoforms), move 2DE to the next level of power. The integration of these technologies will promote 2DE as a powerful methodology of proteomics technology.
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Affiliation(s)
- Stanislav Naryzhny
- Institute of Biomedical Chemistry, Pogodinskaya 10, Moscow 119121, Russia.
- B. P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Leningrad region, Gatchina 188300, Russia.
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4
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Lohnes K, Quebbemann NR, Liu K, Kobzeff F, Loo JA, Ogorzalek Loo RR. Combining high-throughput MALDI-TOF mass spectrometry and isoelectric focusing gel electrophoresis for virtual 2D gel-based proteomics. Methods 2016; 104:163-9. [PMID: 26826592 PMCID: PMC4930893 DOI: 10.1016/j.ymeth.2016.01.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/13/2016] [Accepted: 01/25/2016] [Indexed: 01/07/2023] Open
Abstract
The virtual two-dimensional gel electrophoresis/mass spectrometry (virtual 2D gel/MS) technology combines the premier, high-resolution capabilities of 2D gel electrophoresis with the sensitivity and high mass accuracy of mass spectrometry (MS). Intact proteins separated by isoelectric focusing (IEF) gel electrophoresis are imaged from immobilized pH gradient (IPG) polyacrylamide gels (the first dimension of classic 2D-PAGE) by matrix-assisted laser desorption/ionization (MALDI) MS. Obtaining accurate intact masses from sub-picomole-level proteins embedded in 2D-PAGE gels or in IPG strips is desirable to elucidate how the protein of one spot identified as protein 'A' on a 2D gel differs from the protein of another spot identified as the same protein, whenever tryptic peptide maps fail to resolve the issue. This task, however, has been extremely challenging. Virtual 2D gel/MS provides access to these intact masses. Modifications to our matrix deposition procedure improve the reliability with which IPG gels can be prepared; the new procedure is described. Development of this MALDI MS imaging (MSI) method for high-throughput MS with integrated 'top-down' MS to elucidate protein isoforms from complex biological samples is described and it is demonstrated that a 4-cm IPG gel segment can now be imaged in approximately 5min. Gel-wide chemical and enzymatic methods with further interrogation by MALDI MS/MS provide identifications, sequence-related information, and post-translational/transcriptional modification information. The MSI-based virtual 2D gel/MS platform may potentially link the benefits of 'top-down' and 'bottom-up' proteomics.
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Affiliation(s)
- Karen Lohnes
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Neil R Quebbemann
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kate Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fred Kobzeff
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joseph A Loo
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; DOE/UCLA Institute of Genomics and Proteomics and UCLA Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Rachel R Ogorzalek Loo
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; DOE/UCLA Institute of Genomics and Proteomics and UCLA Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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5
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Calligaris D, Villard C, Lafitte D. Advances in top-down proteomics for disease biomarker discovery. J Proteomics 2011; 74:920-34. [DOI: 10.1016/j.jprot.2011.03.030] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 03/01/2011] [Accepted: 03/29/2011] [Indexed: 11/16/2022]
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6
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Urban PL, Amantonico A, Zenobi R. Lab-on-a-plate: extending the functionality of MALDI-MS and LDI-MS targets. MASS SPECTROMETRY REVIEWS 2011; 30:435-478. [PMID: 21254192 DOI: 10.1002/mas.20288] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We review the literature that describes how (matrix-assisted) laser desorption/ionization (MA)LDI target plates can be used not only as sample supports, but beyond that: as functional parts of analytical protocols that incorporate detection by MALDI-MS or matrix-free LDI-MS. Numerous steps of analytical procedures can be performed directly on the (MA)LDI target plates prior to the ionization of analytes in the ion source of a mass spectrometer. These include homogenization, preconcentration, amplification, purification, extraction, digestion, derivatization, synthesis, separation, detection with complementary techniques, data storage, or other steps. Therefore, we consider it helpful to define the "lab-on-a-plate" as a format for carrying out extensive sample treatment as well as bioassays directly on (MA)LDI target plates. This review introduces the lab-on-plate approach and illustrates it with the aid of relevant examples from the scientific and patent literature.
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Affiliation(s)
- Pawel L Urban
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
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7
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Kaderbhai NN, Broadhurst DI, Ellis DI, Goodacre R, Kell DB. Functional genomics via metabolic footprinting: monitoring metabolite secretion by Escherichia coli tryptophan metabolism mutants using FT-IR and direct injection electrospray mass spectrometry. Comp Funct Genomics 2010; 4:376-91. [PMID: 18629082 PMCID: PMC2447367 DOI: 10.1002/cfg.302] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2003] [Revised: 04/23/2003] [Accepted: 05/22/2003] [Indexed: 12/14/2022] Open
Abstract
We sought to test the hypothesis that mutant bacterial strains could be discriminated from each other on the basis of the metabolites they secrete into the medium (their
‘metabolic footprint’), using two methods of ‘global’ metabolite analysis (FT–IR and
direct injection electrospray mass spectrometry). The biological system used was
based on a published study of Escherichia coli tryptophan mutants that had been
analysed and discriminated by Yanofsky and colleagues using transcriptome analysis.
Wild-type strains supplemented with tryptophan or analogues could be discriminated
from controls using FT–IR of 24 h broths, as could each of the mutant strains in both
minimal and supplemented media. Direct injection electrospray mass spectrometry
with unit mass resolution could also be used to discriminate the strains from each
other, and had the advantage that the discrimination required the use of just two
or three masses in each case. These were determined via a genetic algorithm. Both
methods are rapid, reagentless, reproducible and cheap, and might beneficially be
extended to the analysis of gene knockout libraries.
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Affiliation(s)
- Naheed N Kaderbhai
- Institute of Biological Sciences, University of Wales, Aberystwyth, Wales Ceredigion SY23 3DD, UK
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8
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Microfluidic Device for Coupling Capillary Electrophoresis and Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.jala.2009.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have designed and fabricated a polydimethylsiloxane (PDMS) microfluidic device for coupling capillary electrophoresis (CE) and matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS). The coupling is advantageous in biological research because CE has the power of separating analytes in a sample based on mobility difference and MALDI-MS provides accurate and sensitive mass analysis of the analytes. The goal is realized by fractionating the separated analytes inside the microfluidic device and pushing the analyte fractions into open reservoirs. Each analyte fraction is then mixed with a matrix solution and deposited on a MALDI target for MALDI-MS. Therefore, a two-step analysis of analytes in the form of CE-MALDI-MS is achieved by using the microfluidic device.
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9
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Koomen J, Hawke D, Kobayashi R. Developing an Understanding of Proteomics: An Introduction to Biological Mass Spectrometry. Cancer Invest 2009. [DOI: 10.1081/cnv-46344] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Han X, Aslanian A, Yates JR. Mass spectrometry for proteomics. Curr Opin Chem Biol 2009; 12:483-90. [PMID: 18718552 DOI: 10.1016/j.cbpa.2008.07.024] [Citation(s) in RCA: 455] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Revised: 06/25/2008] [Accepted: 07/17/2008] [Indexed: 01/20/2023]
Abstract
Mass spectrometry has been widely used to analyze biological samples and has evolved into an indispensable tool for proteomics research. Our desire to understand the proteome has led to new technologies that push the boundary of mass spectrometry capabilities, which in return has allowed mass spectrometry to address an ever-increasing array of biological questions. The recent development of a novel mass spectrometer (Orbitrap) and new dissociation methods such as electron-transfer dissociation has made possible the exciting new areas of proteomic application. Although bottom-up proteomics (analysis of proteolytic peptide mixtures) remains the workhorse for proteomic analysis, middle-down and top-down strategies (analysis of longer peptides and intact proteins, respectively) should allow more complete characterization of protein isoforms and post-translational modifications. Finally, stable isotope labeling strategies have transformed mass spectrometry from merely descriptive to a tool for measuring dynamic changes in protein expression, interaction, and modification.
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Affiliation(s)
- Xuemei Han
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrev Pines Road, La Jolla, CA 92037, USA
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11
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Moving reaction boundary and isoelectric focusing: IV. Systemic study on Hjertén's pH gradient mobilization. J Sep Sci 2009; 32:585-96. [DOI: 10.1002/jssc.200800500] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Vaezzadeh AR, Simicevic J, Chauvet A, François P, Zimmermann-Ivol CG, Lescuyer P, Deshusses JPM, Hochstrasser DF. Imaging mass spectrometry using peptide isoelectric focusing. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:2667-2676. [PMID: 18677718 DOI: 10.1002/rcm.3658] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Imaging Mass Spectrometry (IMS) has emerged as a powerful technique in the field of proteomics. The use of Immobilized pH Gradient-IsoElectric Focusing (IPG-IEF) is also a new trend, as the first dimension of separation, in shotgun proteomics. We report a combination of these two outstanding technologies. This approach is based on the separation of shotgun-produced peptides by IPG-IEF. The peptides are then transferred by capillarity to a capture membrane, which is then scanned by the mass spectrometer to generate MS images. This high-throughput methodology allows a preview of the sample to be obtained in a single day. We report the application of this new pipeline for differential comparison of the membrane proteome of two different strains of Staphylococcus aureus bacteria in a proof-of-principle experiment.
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Affiliation(s)
- Ali R Vaezzadeh
- Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, Geneva University, 1 rue Michel Servet, 1211 Geneva, Switzerland.
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13
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Abstract
Top-down mass spectrometry is an emerging technology which strives to preserve the post-translationally modified forms of proteins present in vivo by measuring them intact, rather than measuring peptides produced from them by proteolysis. The top-down technology is beginning to capture the interest of biologists and mass spectrometrists alike, with a main goal of deciphering interaction networks operative in cellular pathways. Here we outline recent approaches and applications of top-down mass spectrometry as well as an outlook for its future.
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Affiliation(s)
- Nertila Siuti
- Department of Chemistry, University of Illinois at Urbana-Champaign, 53 Roger Adams Laboratory, 600 South Matthews Avenue, Urbana, Illinois 61801, USA
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14
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Hardouin J. Protein sequence information by matrix-assisted laser desorption/ionization in-source decay mass spectrometry. MASS SPECTROMETRY REVIEWS 2007; 26:672-82. [PMID: 17492750 DOI: 10.1002/mas.20142] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Proteins from biological samples are often identified by mass spectrometry (MS) with the two following "bottom-up" approaches: peptide mass fingerprinting or peptide sequence tag. Nevertheless, these strategies are time-consuming (digestion, liquid chromatography step, desalting step), the N- (or C-) terminal information often lacks and post-translational modifications (PTMs) are hardly observed. The in-source decay (ISD) occurring in a matrix assisted laser desorption/ionization (MALDI) source appears an interesting analytical tool to obtain N-terminal sequence, to identify proteins and to characterize PTMs by a "top-down" strategy. The goal of this review deals with the usefulness of the ISD technique in MALDI source in proteomics fields. In the first part, the ISD principle is explained and in the second part, the use of ISD in proteomic studies is discussed for protein identification and sequence characterization.
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Affiliation(s)
- Julie Hardouin
- Laboratoire de Biochimie des Protéines et Protéomique, Université Paris XIII, UMR CNRS 7033, 74 rue Marcel Cachin, 93 017, Bobigny Cedex, France.
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15
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Fung ET, Weinberger SR, Gavin E, Zhang F. Bioinformatics approaches in clinical proteomics. Expert Rev Proteomics 2007; 2:847-62. [PMID: 16307515 DOI: 10.1586/14789450.2.6.847] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein expression profiling is increasingly being used to discover, validate and characterize biomarkers that can potentially be used for diagnostic purposes and to aid in pharmaceutical development. Correct analysis of data obtained from these experiments requires an understanding of the underlying analytic procedures used to obtain the data, statistical principles underlying high-dimensional data and clinical statistical tools used to determine the utility of the interpreted data. This review summarizes each of these steps, with the goal of providing the nonstatistician proteomics researcher with a working understanding of the various approaches that may be used by statisticians. Emphasis is placed on the process of mining high-dimensional data to identify a specific set of biomarkers that may be used in a diagnostic or other assay setting.
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Affiliation(s)
- Eric T Fung
- Ciphergen Biosystems, Inc., 6611 Dumbarton Circle, Fremont, CA 94555, USA.
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16
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Patton WF, Panchagnula V, Rockney E, Krull IS. Taking a Walk on the Wild Side with Planar Electrochromatography and Thin‐Layer Electrophoresis: Of Peptides, Proteins, and Proteomics. J LIQ CHROMATOGR R T 2007. [DOI: 10.1080/10826070600574978] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Wayne F. Patton
- a PerkinElmer Life and Analytical Sciences, Life Sciences Division , Boston, Massachusetts, USA
| | | | - Erin Rockney
- a PerkinElmer Life and Analytical Sciences, Life Sciences Division , Boston, Massachusetts, USA
| | - Ira S. Krull
- b Department of Chemistry and Chemical Biology , Northeastern University , Boston, Massachusetts, USA
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17
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Han MJ, Lee SY. The Escherichia coli proteome: past, present, and future prospects. Microbiol Mol Biol Rev 2006; 70:362-439. [PMID: 16760308 PMCID: PMC1489533 DOI: 10.1128/mmbr.00036-05] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proteomics has emerged as an indispensable methodology for large-scale protein analysis in functional genomics. The Escherichia coli proteome has been extensively studied and is well defined in terms of biochemical, biological, and biotechnological data. Even before the entire E. coli proteome was fully elucidated, the largest available data set had been integrated to decipher regulatory circuits and metabolic pathways, providing valuable insights into global cellular physiology and the development of metabolic and cellular engineering strategies. With the recent advent of advanced proteomic technologies, the E. coli proteome has been used for the validation of new technologies and methodologies such as sample prefractionation, protein enrichment, two-dimensional gel electrophoresis, protein detection, mass spectrometry (MS), combinatorial assays with n-dimensional chromatographies and MS, and image analysis software. These important technologies will not only provide a great amount of additional information on the E. coli proteome but also synergistically contribute to other proteomic studies. Here, we review the past development and current status of E. coli proteome research in terms of its biological, biotechnological, and methodological significance and suggest future prospects.
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Affiliation(s)
- Mee-Jung Han
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 305-701, Republic of Korea
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18
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VerBerkmoes NC, Connelly HM, Pan C, Hettich RL. Mass spectrometric approaches for characterizing bacterial proteomes. Expert Rev Proteomics 2006; 1:433-47. [PMID: 15966840 DOI: 10.1586/14789450.1.4.433] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The emergence of advanced liquid chromatography mass spectrometry technologies for characterizing very complex mixtures of proteins has greatly propelled the field of proteomics, the goal of which is the simultaneous examination of all the proteins expressed by an organism. This research area represents a paradigm shift in molecular biology by attempting to provide a top-down qualitative and quantitative view of all the proteins (including their modifications and interactions) that are essential for an organism's life cycle, rather than targeting a particular protein family. This level of global protein information about an organism such as a bacterium can be combined with genomic and metabolomic data to enable a systems biology approach for understanding how these organisms live and function.
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Affiliation(s)
- Nathan C VerBerkmoes
- Genome Science & Technology Graduate School, University of Tennessee, Knoxville, TN 37996, USA
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19
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Berg M, Parbel A, Pettersen H, Fenyö D, Björkesten L. Detection of artifacts and peptide modifications in liquid chromatography/mass spectrometry data using two-dimensional signal intensity map data visualization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2006; 20:1558-62. [PMID: 16628601 DOI: 10.1002/rcm.2476] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We demonstrate how visualization of liquid chromatography/mass spectrometry data as a two-dimensional signal intensity map can be used to assess the overall quality of the data, for the identification of polymer contaminants and artifacts, as well as for the confirmation of post-translational modifications.
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Affiliation(s)
- Matthias Berg
- GE Healthcare, Oskar Schlemmer Str. 11, D-80807 München, Germany.
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20
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Jin Y, Manabe T. Direct targeting of human plasma for matrix-assisted laser desorption/ionization and analysis of plasma proteins by time of flight-mass spectrometry. Electrophoresis 2005; 26:2823-34. [PMID: 15934056 DOI: 10.1002/elps.200410421] [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: 11/09/2022]
Abstract
A method to analyze human plasma proteins without fractionation, directly applying a plasma-matrix mixture on the target plate of a matrix-assisted laser desorption/ionization-time of flight-mass spectrometer (MALDI-TOF-MS), has been described. Peaks of ionized plasma proteins could not be detected applying a mixture of an undiluted plasma sample and a matrix solution, but they appeared when the plasma was diluted before mixing with the matrix. Tenfold diluted plasma provided well-resolved protein peaks in the m/z range from 4000 to 30,000. The addition of a simple post-crystallization washing procedure performed on the target plate further improved the quality of mass spectra. We numbered 58 peaks in the range of 4-160 kDa and 32 out of which were assigned to the plasma protein species which have been reported. Especially high sensitivity and resolution were obtained in the region < 30 kDa, where multiple isoforms of apolipoprotein A-I, apolipoprotein A-II, apolipoprotein C-I, apolipoprotein C-II, apolipoprotein C-III, and transthyretin could be assigned. Various post-translational modifications are involved in the isoforms, e.g., proteolytic cleavage, glycosylation and chemical modifications. This method will become complementary with the present electrophoretic techniques, especially for the analysis of low-molecular-mass proteins.
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Affiliation(s)
- Ya Jin
- Department of Chemistry, Faculty of Science, Ehime University, Matsuyama, Japan
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21
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Wang Y, Balgley BM, Rudnick PA, Lee CS. Effects of chromatography conditions on intact protein separations for top-down proteomics. J Chromatogr A 2005; 1073:35-41. [PMID: 15909503 DOI: 10.1016/j.chroma.2004.08.140] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
For top-down proteomics, nano-reversed phase liquid chromatography (RPLC) plays a major role in both single and multidimensional protein separations in an effort to increase the overall peak capacity for the resolution of complex protein mixtures prior to mass spectrometry analysis. Effects of various chromatography conditions, including alkyl chain length in the stationary phase, capillary column temperature, and ion-pairing agent, on the resolution of intact proteins are studied using nano-RPLC-electrospray ionization-mass spectrometry. Optimal chromatography conditions include the use of C18 column heated at 60 degrees C and the addition of trifluoroacetic acid instead of heptafluorobutyric acid as the ion-paring agent in the mobile phase. Under optimized chromatography conditions, there are no significant differences in the separation performance of yeast cell lysates present in the native versus denatured states. Denatured yeast proteins resolved and eluted from nano-RPLC can be subjected to proteolytic digestion in an on- or off-line approach to provide improved protein sequence coverage toward protein identification in a combined top-down/bottom-up proteome platform.
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Affiliation(s)
- Yueju Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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22
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Wang Y, Balgley BM, Rudnick PA, Evans EL, DeVoe DL, Lee CS. Integrated Capillary Isoelectric Focusing/Nano-reversed Phase Liquid Chromatography Coupled with ESI−MS for Characterization of Intact Yeast Proteins. J Proteome Res 2005; 4:36-42. [PMID: 15707355 DOI: 10.1021/pr049876l] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An integrated protein concentration/separation platform, combining capillary isoelectric focusing (CIEF) with nano-reversed phase liquid chromatography (nano-RPLC), is developed to provide significant protein concentration and high resolving power for the analysis of complex protein mixtures. Upon completion of protein focusing, the proteins are sequentially and hydrodynamically loaded into individual trap columns using a group of microinjection and microselection valves. Repeated pro-tein loadings and injections into trap columns are carried out automatically until the entire CIEF cap-illary content is sampled and fractionated. Each CIEF fraction "parked" in separate trap columns is further resolved using nano-RPLC, and the eluants are analyzed using electrospray ionization-mass spectrometry.
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Affiliation(s)
- Yueju Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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23
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Ackloo S, Loboda A. Applications of a matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometer. l. Metastable decay and collision-induced dissociation for sequencing peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:213-220. [PMID: 15593255 DOI: 10.1002/rcm.1775] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The use of a high-performance orthogonal time-of-flight (o-TOF) mass spectrometer for sequence analysis is described. The mass spectrometer is equipped with a matrix-assisted laser desorption/ionization (MALDI) source that operates at elevated pressure, 0.01-1 Torr. Ion fragmentation is controlled by varying the pressure of the buffer gas, the laser energy, the voltage difference between the MALDI target and the adjacent sampling cone, and between the cone and the quadrupole ion guide. The peptides were analyzed under optimal ionization conditions to obtain their molecular mass, and under conditions that promote ion dissociation via metastable decomposition or collision-induced dissociation (CID). The fragmentation spectra were used to obtain sequence information. Ion dissociation was promoted via three configurations of the ionization parameters. All methods yielded sequencing-grade b- and y-type ions. Two binary mixtures of peptides were used to demonstrate that: (1) external calibration provides a standard deviation (sigma) of 4 ppm with a mode of 9 ppm; and (2) that peptides with molecular masses that differ by a factor of two may be independently fragmented by appropriately choosing the CID energy and the low-mass cut-off. Analyses of tryptic digests employed liquid chromatography (LC), deposition of the eluant on a target, and finally MALDI-TOF mass spectrometry. The mass fingerprint and the (partial) sequence of the tryptic peptides were matched to their precursor protein via database searches.
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Affiliation(s)
- Suzanne Ackloo
- MDS Sciex, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada.
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24
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Kurogochi M, Nishimura SI, Lee YC. Mechanism-based Fluorescent Labeling of β-Galactosidases. J Biol Chem 2004; 279:44704-12. [PMID: 15308675 DOI: 10.1074/jbc.m401718200] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
(4-N-5-Dimethylaminonaphthalene-1-sulfonyl-2-difluoromethylphenyl)-beta-d-galactopyranoside was synthesized and successfully tested on beta-galactosidases from Xanthomonas manihotis (Wong-Madden, S. T., and Landry, D. Glycobiology (1995) 5, 19-28 and Taron, C. H., Benner, J. S., Hornstra, L. J., and Guthrie, E. P. (1995) Glycobiology 5, 603-610), Escherichia coli (Jacobson, R. H., Zhang, X. J., DuBose, R. F., and Matthews, B. W. (1994) Nature 369, 761-766), and Bacillus circulans (Fujimoto, H., Miyasato, M., Ito, Y., Sasaki, T., and Ajisaka, K. (1988) Glycoconj. J. 15, 155-160) for the rapid identification of the catalytic site. Reaction of the irreversible inhibitor with enzymes proceeded to afford a fluorescence-labeled protein suitable for further high throughput characterization by using antidansyl antibody and matrix-assisted laser desorption ionization time-of-flight/time-of-flight (MALDI-TOF/TOF). Specific probing by a fluorescent aglycon greatly facilitated identification of the labeled peptide fragments from beta-galactosidases. It was demonstrated by using X. manihotis beta-galactosidase that the Arg-58 residue, which is located within a sequence of 56IPRAYWKD63, was labeled by nucleophilic attack of the guanidinyl group. This sequence including Arg-58 (Leu-46 to Tyr-194) was similar to that (Met-1 to Tyr-151) of Thermus thermophilus A4, which is the first known structure of glycoside hydrolases family 42 (Hidaka, M., Fushinobu, S., Ohtsu, N., Motoshima, H., Matsuzawa, H., Shoun, H., and Wakagi, T. (2002) J. Mol. Biol. 322, 79-91). A catalytic glutamic acid (Glu-537) of E. coli beta-galactosidase was proved to be labeled by the same procedure, suggesting that the modification site with this irreversible substrate might depend both on the nucleophilicity of the amino acids and their spatial arrangement in the individual catalytic cavity. Similarly, a Glu-259 in 257TLEE260 was selectively labeled using B. circulans beta-galactosidase, indicating that Glu-259 is one of the nucleophiles in the active site. The present method can be readily extended to other glycosidases and should greatly aid the high throughput proteomics of many glycoside hydrolases showing both retaining- and inverting-type mechanisms.
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Affiliation(s)
- Masaki Kurogochi
- Division of Biological Sciences, Graduate School of Science, Frontier Research Center for Post-Genomic Science and Technology, Hokkaido University, N21, W11, Sapporo 001-0021, Japan
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25
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Sowell RA, Koeniger SL, Valentine SJ, Moon MH, Clemmer DE. Nanoflow LC/IMS-MS and LC/IMS-CID/MS of protein mixtures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:1341-1353. [PMID: 15337515 DOI: 10.1016/j.jasms.2004.06.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Revised: 06/23/2004] [Accepted: 06/23/2004] [Indexed: 05/24/2023]
Abstract
A simple ion trap/ion mobility/time-of-flight (TOF) mass spectrometer has been coupled with nanoflow liquid chromatography to examine the feasibility of analyzing mixtures of intact proteins. In this approach proteins are separated using reversed-phase chromatography. As components elute from the column, they are electrosprayed into the gas phase and separated again in a drift tube prior to being dispersed and analyzed in a TOF mass spectrometer. The mobilities of ions through a buffer gas depend upon their collision cross sections and charge states; separation based on these gas-phase parameters provides a new means of simplifying mass spectra and characterizing mixtures. Additionally it is possible to induce dissociation at the exit of the drift tube and examine the fragmentation patterns of specific protein ion charge states and conformations. The approach is demonstrated by examining a simple three-component mixture containing ubiquitin, cytochrome c, and myoglobin and several larger prepared protein mixtures. The potential of this approach for use in proteomic applications is considered.
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Affiliation(s)
- Renã A Sowell
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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26
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Williams TL, Callahan JH, Monday SR, Feng PCH, Musser SM. Relative Quantitation of Intact Proteins of Bacterial Cell Extracts Using Coextracted Proteins as Internal Standards. Anal Chem 2004; 76:1002-7. [PMID: 14961731 DOI: 10.1021/ac034820g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A method for quantitating protein expression using LC/MS of whole proteins is described. This method is based on the fact that some proteins present in cells are abundant universal proteins whose expression levels exhibit little variation. This method demonstrates that these coextracted proteins can be used as internal standards to which the other proteins in the sample can be compared. By comparing the intensities of a selected protein to marker proteins, or internal standards, a relative ratio is obtained. This ratio can then be used to determine the relative amount of protein expression between cellular extracts. The validity of this approach is described for a standard protein mixture, as well as, E. coli cells that were known to differentially express green fluorescent protein.
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Affiliation(s)
- Tracie L Williams
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740-3835, USA.
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27
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Lee PS, Lee KH. Escherichia coli?a model system that benefits from and contributes to the evolution of proteomics. Biotechnol Bioeng 2003; 84:801-14. [PMID: 14708121 DOI: 10.1002/bit.10848] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The large body of knowledge about Escherichia coli makes it a useful model organism for the expression of heterologous proteins. Proteomic studies have helped to elucidate the complex cellular responses of E. coli and facilitated its use in a variety of biotechnology applications. Knowledge of basic cellular processes provides the means for better control of heterologous protein expression. Beyond such important applications, E. coli is an ideal organism for testing new analytical technologies because of the extensive knowledge base available about the organism. For example, improved technology for characterization of unknown proteins using mass spectrometry has made two-dimensional electrophoresis (2DE) studies more useful and more rewarding, and much of the initial testing of novel protocols is based on well-studied samples derived from E. coli. These techniques have facilitated the construction of more accurate 2DE maps. In this review, we present work that led to the 2DE databases, including a new map based on tandem time-of-flight (TOF) mass spectrometry (MS); describe cellular responses relevant to biotechnology applications; and discuss some emerging proteomic techniques.
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Affiliation(s)
- Pat S Lee
- School of Chemical and Biomolecular Engineering, Cornell University, 102 Olin Hall, Ithaca, New York 14853, USA
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28
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Cristoni S, Bernardi LR. Development of new methodologies for the mass spectrometry study of bioorganic macromolecules. MASS SPECTROMETRY REVIEWS 2003; 22:369-406. [PMID: 14528493 DOI: 10.1002/mas.10062] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In recent years, mass spectrometry has been increasingly used for the analysis of various macromolecules of biological, biomedical, and biochemical interest. This increase has been made possible by two key developments: the advent of electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) sources. The two new techniques produce a significant increase in mass range and in sensitivity that led to the development of new applications and of new analyzer designs, software, and robotics. This review, apart from the description of the status of mass spectrometry in the analysis of bioorganic macromolecules, is mainly devoted to the illustration of the more recent promising techniques and on their possible future evolution.
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Affiliation(s)
- Simone Cristoni
- Università degli Studi di Milano, Centro Interdisciplinare Studi Bio-molecolari e Applicazioni Industriali CISI, Via Fratelli Cervi 93, 20090 Segrate Milano, Italy.
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29
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Nemeth-Cawley JF, Tangarone BS, Rouse JC. “Top Down” Characterization Is a Complementary Technique to Peptide Sequencing for Identifying Protein Species in Complex Mixtures. J Proteome Res 2003; 2:495-505. [PMID: 14582646 DOI: 10.1021/pr034008u] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
At present, mass spectrometry provides a rapid and sensitive means for making conclusive protein identifications from complex mixtures. Sequencing tryptic peptides derived from proteolyzed protein samples, also known as the "Bottom Up" approach, is the mass spectrometric gold standard for identifying unknowns. An alternative technology, "Top Down" characterization, is emerging as a viable option for protein identifications, which involves analyzing the intact unknowns for accurate mass and amino acid sequence tags. In this paper, both characterization methods were employed to more comprehensively differentiate two early-eluting peaks in a process-scale size-exclusion chromatography (SEC) step for a recombinant, immunoglobulin gamma-1 (IgG-1) fusion protein. The contents of each SEC peak were enzymatically digested, and the resulting peptides were mapped using reversed-phase (RP) HPLC-ion trap MS. Many low-level UV signals were observed among the fusion protein-related peptide peaks. These unknowns were collected, concentrated, and analyzed using nanoelectrospray (nanoES) collision-induced dissociation (CID) tandem (MS/MS) mass spectrometry for identification. The peptide sequencing experiments resulted in the identification of twenty host cell-related proteins. Following peptide mapping, the contents of the two SEC peaks were protein mass profiled using on-line RP HPLC coupled to a high-resolution, quadrupole time-of-flight (Qq/TOF) MS. Unknown proteins were also collected, concentrated, and dissociated using nanoES CID MS/MS. Intact protein CID experiments and accurate molecular weight information allowed for the identification of three full length host cell-derived proteins and numerous clips from these and additional proteins. The accurate molecular weight values allowed for the assignment of N- and C-terminal processing, which is difficult to conclusively access from peptide mapping data. The peptide-mapping experiments proved to be far more effective for making protein identifications from complex mixtures, whereas the protein mass profiling was useful for assessing modifications and distinguishing protein clips from full length species.
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30
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Corbin RW, Paliy O, Yang F, Shabanowitz J, Platt M, Lyons CE, Root K, McAuliffe J, Jordan MI, Kustu S, Soupene E, Hunt DF. Toward a protein profile of Escherichia coli: comparison to its transcription profile. Proc Natl Acad Sci U S A 2003; 100:9232-7. [PMID: 12878731 PMCID: PMC170901 DOI: 10.1073/pnas.1533294100] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
High-pressure liquid chromatography-tandem mass spectrometry was used to obtain a protein profile of Escherichia coli strain MG1655 grown in minimal medium with glycerol as the carbon source. By using cell lysate from only 3 x 108 cells, at least four different tryptic peptides were detected for each of 404 proteins in a short 4-h experiment. At least one peptide with a high reliability score was detected for 986 proteins. Because membrane proteins were underrepresented, a second experiment was performed with a preparation enriched in membranes. An additional 161 proteins were detected, of which from half to two-thirds were membrane proteins. Overall, 1,147 different E. coli proteins were identified, almost 4 times as many as had been identified previously by using other tools. The protein list was compared with the transcription profile obtained on Affymetrix GeneChips. Expression of 1,113 (97%) of the genes whose protein products were found was detected at the mRNA level. The arithmetic mean mRNA signal intensity for these genes was 3-fold higher than that for all 4,300 protein-coding genes of E. coli. Thus, GeneChip data confirmed the high reliability of the protein list, which contains about one-fourth of the proteins of E. coli. Detection of even those membrane proteins and proteins of undefined function that are encoded by the same operons (transcriptional units) encoding proteins on the list remained low.
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Affiliation(s)
- Rebecca W Corbin
- Department of Chemistry, University of Virginia, Charlottesville, VA 22901, USA
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31
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Hall MP, Ashrafi S, Obegi I, Petesch R, Peterson JN, Schneider LV. "Mass defect" tags for biomolecular mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2003; 38:809-816. [PMID: 12938101 DOI: 10.1002/jms.493] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We present a new class of "mass defect" tags with utility in biomolecular mass spectrometry. These tags, incorporating element(s) with atomic numbers between 17 (Cl) and 77 (Ir), have a substantially different nuclear binding energy (mass defect) from the elements common to biomolecules. This mass defect yields a readily resolvable mass difference between tagged and untagged species in high-resolution mass spectrometers. We present the use of a subset of these tags in a new protein sequencing application. This sequencing technique has advantages over existing mass spectral protein identification methodologies: intact proteins are quickly sequenced and unambiguously identified using only an inexpensive, robust mass spectrometer. We discuss the potential broader utility of these tags for the sequencing of other biomolecules, differential display applications and combinatorial methods.
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Affiliation(s)
- Michael P Hall
- Target Discovery, Inc., 4015 Fabian Way, Palo Alto, CA 94303, USA.
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32
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Coon JJ, Steele HA, Laipis PJ, Harrison WW. Direct Atmospheric Pressure Coupling of Polyacrylamide Gel Electrophoresis to Mass Spectrometry for Rapid Protein Sequence Analysis. J Proteome Res 2003; 2:610-7. [PMID: 14692454 DOI: 10.1021/pr034031f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using laser desorption-atmospheric pressure chemical ionization we describe a novel approach for coupling mass spectrometry to polyacrylamide gel electrophoresis. In contrast to other approaches, the method allows for the direct sampling of a polyacrylamide gel-embedded protein without the addition of any exogenous matrixes and is performed at atmospheric pressure. After electrophoresis and enzymatic digestion, the gel is analyzed at AP by photons that desorb neutral peptide molecules, followed by corona discharge ionization in the gas-phase, and subsequent mass analysis. Our experimental results demonstrate the method to (1) rapidly identify electrophoresed proteins via "peptide fingerprinting" using protein databases, (2) detect single-amino acid polymorphisms, and (3) has potential for sub-picomole sensitivity while still maintaining in situ gel desorption-ionization at ambient conditions.
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Affiliation(s)
- Joshua J Coon
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
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33
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Iyer S, Olivares J. Trypsin digestion of proteins on intact immobilized pH gradient strips for surface matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:2323-2326. [PMID: 14558133 DOI: 10.1002/rcm.1199] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Isolelectric focusing (IEF) of proteins on immobilized pH gradient (IPG) strips is an integral part of two-dimensional (2D) electrophoresis-based proteomics. Proteins can be effectively analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) on the intact strip itself, leading to the creation of a virtual 2D map giving pI and MW information, bypassing the second dimension SDS-PAGE. Further, trypsin digestion of proteins on the strip can significantly aid the identification of IPG-separated proteins. However, the small size of the peptides leads to diffusion along and outside the gel matrix. In this study, we describe a simple spray-based procedure to perform 'on-strip' trypsin digestion of proteins embedded in IPG strips. Examination of intact myoglobin and its tryptic peptides shows that post-digestion diffusion of tryptic peptides is significantly minimized using this approach.
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Affiliation(s)
- Srinivas Iyer
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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34
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Cristoni S, Bernardi LR, Biunno I, Tubaro M, Guidugli F. Surface-activated no-discharge atmospheric pressure chemical ionization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:1973-1981. [PMID: 12913861 DOI: 10.1002/rcm.1141] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A new ionization method named surface-activated chemical ionization (SACI) has been realized. In this invention a commercially available atmospheric pressure chemical ionization (APCI) chamber, employed without any corona discharge (no-discharge APCI), has been modified with the insertion of a gold surface, leading to a significant improvement in the ionization efficiency. The ionization of the sample takes place by both gas-phase and surface-activated processes. This new ionization source is able to generate ions with high molecular mass and low charge states, leading to improved sensitivity and reduced noise. The new device has been tested in the analysis of some peptides. A comparison between the performance with and without the presence of the surface, and the optimization of the operating conditions (nebulizing gas flow, sample solution flow, pH of solution, and surface area), are reported and discussed.
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Affiliation(s)
- Simone Cristoni
- Università degli Studi di Milano, Centro Interdisciplinare Studi Bio-molecolari e Applicazioni Industriali CISI, Via Fratelli Cervi 93, 20090 Segrate, Milano, Italy.
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35
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Van Berkel GJ. An overview of some recent developments in ionization methods for mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2003; 9:539-562. [PMID: 15100466 DOI: 10.1255/ejms.586] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
An overview of some recent advances in ionization sources for mass spectrometry is presented. Limitations were set so that the overview covers ionization techniques relevant to organic and biological analysis that have appeared in the literature since the year 2000. No effort is made to be comprehensive. Rather, a broad sweep overview of author-subjective highlights among a wide variety of sources is presented. These ionization sources include electron ionization, chemical ionization, various atmospheric plasma ionization sources, laser desorption sources, sonic spray and electrospray ionization sources.
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Affiliation(s)
- Gary J Van Berkel
- Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6131, USA.
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36
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Coon JJ, Steele HA, Laipis PJ, Harrison WW. Laser desorption-atmospheric pressure chemical ionization: a novel ion source for the direct coupling of polyacrylamide gel electrophoresis to mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2002; 37:1163-1167. [PMID: 12447894 DOI: 10.1002/jms.385] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Laser desorption-atmospheric pressure chemical ionization-mass spectrometry (LD-APCI-MS) is presented for the atmospheric pressure (AP) sampling of tryptic peptides directly from a polyacrylamide gel. In contrast to other gel sampling mass spectrometric approaches, this technique does not require the addition of any exogenous matrices to the gel to assist with ionization. In this arrangement, a CO(2) laser at 10.6 micro m is used to desorb intact neutral peptide molecules from the gel, followed by ionization in the gas-phase with APCI. The ions are then sampled via a heated capillary inlet and transferred to a quadrupole ion trap mass spectrometer for mass analysis. Preliminary results suggest the polyacrylamide gel electrophoresis-LD-APCI-MS technique provides several advantages that could translate into a more convenient, robust methodology for the rapid identification and characterization of proteins. Finally, strategies regarding the further development of the method are presented.
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Affiliation(s)
- Joshua J Coon
- Department of Chemistry, University of Florida, Gainesville, FL 32606, USA
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37
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Ogorzalek Loo RR, Loo JA, Du P, Holler T. In vivo labeling: a glimpse of the dynamic proteome and additional constraints for protein identification. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:804-812. [PMID: 12148805 DOI: 10.1016/s1044-0305(02)00408-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Identities ascribed to the intact protein ions detected in MALDI-MS of whole bacterial cells or from other complex mixtures are often ambiguous. Isolation of candidate proteins can establish that they are of correct molecular mass and sufficiently abundant, but by itself is not definitive. An in vivo labeling strategy replacing methionine with selenomethionine has been employed to deliver an additional constraint for protein identification, i.e., number of methionine residues, derived from the shift in mass of labeled versus unlabeled proteins. By stressing a culture and simultaneously labeling, it was possible to specifically image the cells' response to the perturbation. Because labeled protein is only synthesized after application of the stress, it provides a means to view dynamic changes in the cellular proteome. These methods have been applied to identify a 15,879 Da protein ion from E. coli that was induced by an antibacterial agent with an unknown mechanism of action as SpY, a stress protein produced abundantly in spheroplasts. It has also allowed us to propose protein identities (and eliminate others from consideration) for many of the ions observed in MALDI (and ESI-MS) whole cell profiling at a specified growth condition.
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Affiliation(s)
- Rachel R Ogorzalek Loo
- Department of Biological Chemistry, University of California-Los Angeles, 90095-1570, USA.
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38
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Abstract
Common strategies employed for general protein detection include organic dye, silver stain, radiolabeling, reverse stain, fluorescent stain, chemiluminescent stain and mass spectrometry-based approaches. Fluorescence-based protein detection methods have recently surpassed conventional technologies such as colloidal Coomassie blue and silver staining in terms of quantitative accuracy, detection sensitivity, and compatibility with modern downstream protein identification and characterization procedures, such as mass spectrometry. Additionally, specific detection methods suitable for revealing protein post-translational modifications have been devised over the years. These include methods for the detection of glycoproteins, phosphoproteins, proteolytic modifications, S-nitrosylation, arginine methylation and ADP-ribosylation. Methods for the detection of a range of reporter enzymes and epitope tags are now available as well, including those for visualizing beta-glucuronidase, beta-galactosidase, oligohistidine tags and green fluorescent protein. Fluorescence-based and mass spectrometry-based methodologies are just beginning to offer unparalleled new capabilities in the field of proteomics through the performance of multiplexed quantitative analysis. The primary objective of differential display proteomics is to increase the information content and throughput of proteomics studies through multiplexed analysis. Currently, three principal approaches to differential display proteomics are being actively pursued, difference gel electrophoresis (DIGE), multiplexed proteomics (MP) and isotope-coded affinity tagging (ICAT). New multiplexing capabilities should greatly enhance the applicability of the two-dimensional gel electrophoresis technique with respect to addressing fundamental questions related to proteome-wide changes in protein expression and post-translational modification.
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Affiliation(s)
- Wayne F Patton
- Proteomics Section, Biosciences Department, Molecular Probes, Inc., 4849 Pitchford Avenue, Eugene, OR 97402-9165, USA.
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39
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2002. [PMCID: PMC2447231 DOI: 10.1002/cfg.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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40
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Cristoni S, Bernardi LR, Biunno I, Guidugli F. Analysis of protein ions in the range 3000-12000 Th under partial (no discharge) atmospheric pressure chemical ionization conditions using ion trap mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2002; 16:1153-1159. [PMID: 12112265 DOI: 10.1002/rcm.693] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A new approach, based on the use of atmospheric pressure chemical ionization ion trap mass spectrometry (APCI-ITMS), but without a corona discharge, was investigated for application to creating and monitoring protein ions. It must be emphasized that APCI is not usually used in protein analysis. In order to verify the applicability of the proposed method to the analysis of proteins, two standard proteins (horse cytochrome c and horse myoglobin) were analyzed. A mixture of the two proteins was also analyzed showing that this novel approach, based on the use of APCI, can be used in the analysis of protein mixtures.
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Affiliation(s)
- Simone Cristoni
- Università degli Studi di Milano, Centro Interdisciplinare Studi Bio-Molecolari Applicazioni Industriali CISI, Via Fratelli Cervi 93, 20090 Segrate, Milano, Italy.
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2002; 37:119-132. [PMID: 11813320 DOI: 10.1002/jms.248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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