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Bailey BL, Nguyen W, Cowman AF, Sleebs BE. Chemo-proteomics in antimalarial target identification and engagement. Med Res Rev 2023; 43:2303-2351. [PMID: 37232495 PMCID: PMC10947479 DOI: 10.1002/med.21975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 04/24/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
Humans have lived in tenuous battle with malaria over millennia. Today, while much of the world is free of the disease, areas of South America, Asia, and Africa still wage this war with substantial impacts on their social and economic development. The threat of widespread resistance to all currently available antimalarial therapies continues to raise concern. Therefore, it is imperative that novel antimalarial chemotypes be developed to populate the pipeline going forward. Phenotypic screening has been responsible for the majority of the new chemotypes emerging in the past few decades. However, this can result in limited information on the molecular target of these compounds which may serve as an unknown variable complicating their progression into clinical development. Target identification and validation is a process that incorporates techniques from a range of different disciplines. Chemical biology and more specifically chemo-proteomics have been heavily utilized for this purpose. This review provides an in-depth summary of the application of chemo-proteomics in antimalarial development. Here we focus particularly on the methodology, practicalities, merits, and limitations of designing these experiments. Together this provides learnings on the future use of chemo-proteomics in antimalarial development.
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Affiliation(s)
- Brodie L. Bailey
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - William Nguyen
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Alan F. Cowman
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
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2
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Tian X, Permentier HP, Bischoff R. Chemical isotope labeling for quantitative proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:546-576. [PMID: 34091937 PMCID: PMC10078755 DOI: 10.1002/mas.21709] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 05/05/2023]
Abstract
Advancements in liquid chromatography and mass spectrometry over the last decades have led to a significant development in mass spectrometry-based proteome quantification approaches. An increasingly attractive strategy is multiplex isotope labeling, which significantly improves the accuracy, precision and throughput of quantitative proteomics in the data-dependent acquisition mode. Isotope labeling-based approaches can be classified into MS1-based and MS2-based quantification. In this review, we give an overview of approaches based on chemical isotope labeling and discuss their principles, benefits, and limitations with the goal to give insights into fundamental questions and provide a useful reference for choosing a method for quantitative proteomics. As a perspective, we discuss the current possibilities and limitations of multiplex, isotope labeling approaches for the data-independent acquisition mode, which is increasing in popularity.
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Affiliation(s)
- Xiaobo Tian
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
| | - Hjalmar P. Permentier
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
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3
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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4
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Affiliation(s)
- Albert B. Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã A. S. Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
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5
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Lehmann WD. A timeline of stable isotopes and mass spectrometry in the life sciences. MASS SPECTROMETRY REVIEWS 2017; 36:58-85. [PMID: 26919394 DOI: 10.1002/mas.21497] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 01/21/2016] [Indexed: 06/05/2023]
Abstract
This review retraces the role of stable isotopes and mass spectrometry in the life sciences. The timeline is divided into four segments covering the years 1920-1950, 1950-1980, 1980-2000, and 2000 until today. For each period methodic progress and typical applications are discussed. Application of stable isotopes is driven by improvements of mass spectrometry, chromatography, and related fields in sensitivity, mass accuracy, structural specificity, complex sample handling ability, data output, and data evaluation. We currently experience the vision of omics-type analyses, that is, the comprehensive identification and quantification of a complete compound class within one or a few analytical runs. This development is driven by stable isotopes without competition by radioisotopes. In metabolic studies as classic field of isotopic tracer experiments, stable isotopes and radioisotopes were competing solutions, with stable isotopes as the long-term junior partner. Since the 1990s the number of metabolic studies with radioisotopes decreases, whereas stable isotope studies retain their slow but stable upward tendency. Unique fields of stable isotopes are metabolic tests in newborns, metabolic experiments in healthy controls, newborn screening for inborn errors, quantification of drugs and drug metabolites in doping control, natural isotope fractionation in geology, ecology, food authentication, or doping control, and more recently the field of quantitative omics-type analyses. There, cells or whole organisms are systematically labeled with stable isotopes to study proteomic differences or specific responses to stimuli or genetic manipulation. The duo of stable isotopes and mass spectrometry will probably continue to grow in the life sciences, since it delivers reference-quality quantitative data with molecular specificity, often combined with informative isotope effects. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:58-85, 2017.
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Affiliation(s)
- Wolf D Lehmann
- German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
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6
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Duncan MW, Hunsucker SW. Proteomics as a Tool for Clinically Relevant Biomarker Discovery and Validation. Exp Biol Med (Maywood) 2016; 230:808-17. [PMID: 16339745 DOI: 10.1177/153537020523001105] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The excitement associated with clinical applications of proteomics was initially focused on its potential to serve as a vehicle for both biomarker discovery and drug discovery and routine clinical sample analysis. Some approaches were thought to be able to “identify” mass spectral characteristics that distinguished between control and disease samples, and thereafter it was believed that the same tool could be employed to screen samples in a high-throughput clinical setting. However, this has been difficult to achieve, and the early promise is yet to be fully realized. While we see an important place for mass spectrometry in drug and biomarker discovery, we believe that alternative strategies will prove more fruitful for routine analysis. Here we discuss the power and versatility of 2D gels and mass spectrometry in the discovery phase of biomarker work but argue that it is better to rely on immunochemical methods for high-throughput validation and routine assay applications.
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Affiliation(s)
- Mark W Duncan
- Department of Pediatrics, Section of Pulmonary Medicine, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA.
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7
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Sinzinger MD, Chung YD, Adjobo-Hermans MJW, Brock R. A microarray-based approach to evaluate the functional significance of protein-binding motifs. Anal Bioanal Chem 2016; 408:3177-84. [PMID: 26892640 PMCID: PMC4830892 DOI: 10.1007/s00216-016-9382-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 01/14/2016] [Accepted: 02/01/2016] [Indexed: 11/25/2022]
Abstract
Intracellular proteins comprise numerous peptide motifs that interact with protein-binding domains. However, using sequence information alone, the identification of functionally relevant interaction motifs remains a challenge. Here, we present a microarray-based approach for the evaluation of peptides as protein-binding motifs. To this end, peptides corresponding to protein interaction motifs were spotted as a microarray. First, peptides were titrated with a pan-specific binder and the apparent Kd value of this binder for each peptide was determined. For phosphotyrosine-containing peptides, an anti-phosphotyrosine antibody was employed. Then, in the presence of the pan-specific binder, arrays were competitively titrated with cell lysate and competition constants were determined. Using the Cheng-Prusoff equation, binding constants for the pan-specific binder and inhibition constants for the lysates were converted into affinity constants for the lysate. We experimentally validate this method using a phosphotyrosine-binding SH2 domain as a further reference. Furthermore, strong binders correlated with binding motifs engaging in numerous interactions as predicted by Scansite. This method provides a highly parallel and robust approach to identify peptides corresponding to interaction motifs with strong binding capacity for proteins in the cell lysate. Using an antibody as a pan-specific binder the capacity of interaction motifs to bind to proteins from cell lysates can be probed. Competition of the antibody is observed for only those peptides to which a lysate protein binds ![]()
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Affiliation(s)
- Michael D Sinzinger
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Yi-Da Chung
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Merel J W Adjobo-Hermans
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands.
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8
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Affiliation(s)
- Divya Seth
- From the Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University (D.S., J.S.S.) and Harrington Discovery Institute (J.S.S.), University Hospitals Case Medical Center, Cleveland, OH
| | - Jonathan S Stamler
- From the Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University (D.S., J.S.S.) and Harrington Discovery Institute (J.S.S.), University Hospitals Case Medical Center, Cleveland, OH.
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9
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Abstract
Compared to genomics or transcriptomics, proteomics is often regarded as an "emerging technology," i.e., as not having reached the same level of maturity. While the successful implementation of proteomics workflows and technology still requires significant levels of expertise and specialization, great strides have been made to make the technology more powerful, streamlined and accessible. In 2014, two landmark studies published the first draft versions of the human proteome.We aim to provide an introduction specifically into the background of mass spectrometry (MS)-based proteomics. Within the field, mass spectrometry has emerged as a core technology. Coupled to increasingly powerful separations and data processing and bioinformatics solution, it allows the quantitative analysis of whole proteomes within a matter of days, a timescale that has made global comparative proteome studies feasible at last. We present and discuss the basic concepts behind proteomics mass spectrometry and the accompanying topic of protein and peptide separations, with a focus on the properties of datasets emerging from such studies.
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10
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Chan JCY, Zhou L, Chan ECY. The Isotope-Coded Affinity Tag Method for Quantitative Protein Profile Comparison and Relative Quantitation of Cysteine Redox Modifications. ACTA ACUST UNITED AC 2015; 82:23.2.1-23.2.19. [PMID: 26521713 DOI: 10.1002/0471140864.ps2302s82] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The isotope-coded affinity tag (ICAT) technique has been applied to measure pairwise changes in protein expression through differential stable isotopic labeling of proteins or peptides followed by identification and quantification using a mass spectrometer. Changes in protein expression are observed when the identical peptide from each of two biological conditions is identified and a difference is detected in the measurements comparing the peptide labeled with the heavy isotope to the one with a normal isotopic distribution. This approach allows the simultaneous comparison of the expression of many proteins between two different biological states (e.g., yeast grown on galactose versus glucose, or normal versus cancer cells). Due to the cysteine-specificity of the ICAT reagents, the ICAT technique has also been applied to perform relative quantitation of cysteine redox modifications such as oxidation and nitrosylation. This unit describes both protein quantitation and profiling of cysteine redox modifications using the ICAT technique.
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Affiliation(s)
| | - Lei Zhou
- Singapore Eye Research Institute, Singapore
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11
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Frost DC, Greer T, Xiang F, Liang Z, Li L. Development and characterization of novel 8-plex DiLeu isobaric labels for quantitative proteomics and peptidomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1115-24. [PMID: 25981542 PMCID: PMC4837894 DOI: 10.1002/rcm.7201] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 03/05/2015] [Accepted: 03/22/2015] [Indexed: 05/08/2023]
Abstract
RATIONALE Relative quantification of proteins via their enzymatically digested peptide products determines disease biomarker candidate lists in discovery studies. Isobaric label-based strategies using TMT and iTRAQ allow for up to 10 samples to be multiplexed in one experiment, but their expense limits their use. The demand for cost-effective tagging reagents capable of multiplexing many samples led us to develop an 8-plex version of our isobaric labeling reagent, DiLeu. METHODS The original 4-plex DiLeu reagent was extended to an 8-plex set by coupling isotopic variants of dimethylated leucine to an alanine balance group designed to offset the increasing mass of the label's reporter group. Tryptic peptides from a single protein digest, a protein mixture digest, and Saccharomyces cerevisiae lysate digest were labeled with 8-plex DiLeu and analyzed via nanospray liquid chromatography/tandem mass spectrometry (nanoLC/MS(2) ) on a Q-Exactive Orbitrap mass spectrometer. Characteristics of 8-plex DiLeu-labeled peptides, including quantitative accuracy and fragmentation, were examined. RESULTS An 8-plex set of DiLeu reagents with 1 Da spaced reporters was synthesized at a yield of 36%. The average cost to label eight 100 µg peptide samples was calculated to be approximately $15. Normalized collision energy tests on the Q-Exactive revealed that a higher-energy collisional dissociation value of 27 generated the optimum number of high-quality spectral matches. Relative quantification of DiLeu-labeled peptides yielded normalized median ratios accurate to within 12% of their expected values. CONCLUSIONS Cost-effective 8-plex DiLeu reagents can be synthesized and applied to relative peptide and protein quantification. These labels increase the multiplexing capacity of our previous 4-plex implementation without requiring high-resolution instrumentation to resolve reporter ion signals.
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Affiliation(s)
| | - Tyler Greer
- Department of Chemistry, University of Wisconsin–Madison
| | - Feng Xiang
- School of Pharmacy, University of Wisconsin–Madison
| | - Zhidan Liang
- School of Pharmacy, University of Wisconsin–Madison
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin–Madison
- Department of Chemistry, University of Wisconsin–Madison
- Address reprint requests to: Dr. Lingjun Li, School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI 53705, USA. . Phone: (608) 265-8491, Fax: (608) 262-5345
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12
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A proteomic analysis of placental trophoblastic cells in preeclampsia-eclampsia. Cell Biochem Biophys 2014; 69:247-58. [PMID: 24343450 DOI: 10.1007/s12013-013-9792-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
To explore the proteomic changes of placental trophoblastic cells in preeclampsia-eclampsia (PE), placental trophoblastic cells from normally pregnant women and women with hypertension during gestational period were prepared by laser capture microdissection (LCM), and proteins isolated from these cells were subjected to labeling and proteolysis with isotope-coded affinity tag reagent. A qualitative and quantitative analysis of the proteome expression of placental trophoblastic cells was made using two-dimensional liquid chromatography tandem mass spectrometry (2D LC-MS/MS). A total of 831 proteins in placental trophoblastic cells were identified by combined use of LCM technique and 2D LC-MS/MS. The result was superior to that of conventional two-dimensional electrophoresis method. There were marked differences in 169 proteins of placental trophoblastic cells between normally pregnant women and women with PE. Of 70 (41.4 %) proteins with more than twofold differences, 31 proteins were down-regulated, and 39 were up-regulated in placental trophoblastic cells of the woman with PE. Laminin expression in placenta trophoblastic cells of women with PE was significantly down-regulated as confirmed by Western blot analysis. These findings provide insights into the proteomic changes in placental trophoblastic cells in response to PE and may identify novel protein targets associated with the pathogenesis of PE.
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13
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de Roos B. Proteomic analysis of human plasma and blood cells in nutritional studies: development of biomarkers to aid disease prevention. Expert Rev Proteomics 2014; 5:819-26. [DOI: 10.1586/14789450.5.6.819] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Semba RD, Enghild JJ, Venkatraman V, Dyrlund TF, Van Eyk JE. The Human Eye Proteome Project: perspectives on an emerging proteome. Proteomics 2013; 13:2500-11. [PMID: 23749747 PMCID: PMC3978387 DOI: 10.1002/pmic.201300075] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/26/2013] [Accepted: 05/15/2013] [Indexed: 12/22/2022]
Abstract
There are an estimated 285 million people with visual impairment worldwide, of whom 39 million are blind. The pathogenesis of many eye diseases remains poorly understood. The human eye is currently an emerging proteome that may provide key insight into the biological pathways of disease. We review proteomic investigations of the human eye and present a catalogue of 4842 nonredundant proteins identified in human eye tissues and biofluids to date. We highlight the need to identify new biomarkers for eye diseases using proteomics. Recent advances in proteomics do now allow the identification of hundreds to thousands of proteins in tissues and fluids, characterization of various PTMs and simultaneous quantification of multiple proteins. To facilitate proteomic studies of the eye, the Human Eye Proteome Project (HEPP) was organized in September 2012. The HEPP is one of the most recent components of the Biology/Disease-driven Human Proteome Project (B/D-HPP) whose overarching goal is to support the broad application of state-of-the-art measurements of proteins and proteomes by life scientists studying the molecular mechanisms of biological processes and human disease. The large repertoire of investigative proteomic tools has great potential to transform vision science and enhance understanding of physiology and disease processes that affect sight.
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Affiliation(s)
- Richard D Semba
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Abreu IA, Farinha AP, Negrão S, Gonçalves N, Fonseca C, Rodrigues M, Batista R, Saibo NJM, Oliveira MM. Coping with abiotic stress: proteome changes for crop improvement. J Proteomics 2013; 93:145-68. [PMID: 23886779 DOI: 10.1016/j.jprot.2013.07.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 07/02/2013] [Accepted: 07/08/2013] [Indexed: 12/20/2022]
Abstract
Plant breeders need new and more precise tools to accelerate breeding programs that address the increasing needs for food, feed, energy and raw materials, while facing a changing environment in which high salinity and drought have major impacts on crop losses worldwide. This review covers the achievements and bottlenecks in the identification and validation of proteins with relevance in abiotic stress tolerance, also mentioning the unexpected consequences of the stress in allergen expression. While addressing the key pathways regulating abiotic stress plant adaptation, comprehensive data is presented on the proteins confirmed as relevant to confer tolerance. Promising candidates still to be confirmed are also highlighted, as well as the specific protein families and protein modifications for which detection and characterization is still a challenge. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Affiliation(s)
- Isabel A Abreu
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Genomics of Plant Stress Laboratory (GPlantS Lab), Av. da República, 2780-157 Oeiras, Portugal; iBET, Apartado 12, 2781-901 Oeiras, Portugal
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Barrero CA, Datta PK, Sen S, Deshmane S, Amini S, Khalili K, Merali S. HIV-1 Vpr modulates macrophage metabolic pathways: a SILAC-based quantitative analysis. PLoS One 2013; 8:e68376. [PMID: 23874603 PMCID: PMC3709966 DOI: 10.1371/journal.pone.0068376] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 05/29/2013] [Indexed: 01/09/2023] Open
Abstract
Human immunodeficiency virus type 1 encoded viral protein Vpr is essential for infection of macrophages by HIV-1. Furthermore, these macrophages are resistant to cell death and are viral reservoir. However, the impact of Vpr on the macrophage proteome is yet to be comprehended. The goal of the present study was to use a stable-isotope labeling by amino acids in cell culture (SILAC) coupled with mass spectrometry-based proteomics approach to characterize the Vpr response in macrophages. Cultured human monocytic cells, U937, were differentiated into macrophages and transduced with adenovirus construct harboring the Vpr gene. More than 600 proteins were quantified in SILAC coupled with LC-MS/MS approach, among which 136 were significantly altered upon Vpr overexpression in macrophages. Quantified proteins were selected and clustered by biological functions, pathway and network analysis using Ingenuity computational pathway analysis. The proteomic data illustrating increase in abundance of enzymes in the glycolytic pathway (pentose phosphate and pyruvate metabolism) was further validated by western blot analysis. In addition, the proteomic data demonstrate down regulation of some key mitochondrial enzymes such as glutamate dehydrogenase 2 (GLUD2), adenylate kinase 2 (AK2) and transketolase (TKT). Based on these observations we postulate that HIV-1 hijacks the macrophage glucose metabolism pathway via the Vpr-hypoxia inducible factor 1 alpha (HIF-1 alpha) axis to induce expression of hexokinase (HK), glucose-6-phosphate dehyrogenase (G6PD) and pyruvate kinase muscle type 2 (PKM2) that facilitates viral replication and biogenesis, and long-term survival of macrophages. Furthermore, dysregulation of mitochondrial glutamate metabolism in macrophages can contribute to neurodegeneration via neuroexcitotoxic mechanisms in the context of NeuroAIDS.
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Affiliation(s)
- Carlos A. Barrero
- Department of Biochemistry, Temple University School of Medicine, Fels Institute, Philadelphia, Pennsylvania, United States of America
- Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Prasun K. Datta
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| | - Satarupa Sen
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Satish Deshmane
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Shohreh Amini
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Kamel Khalili
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Salim Merali
- Department of Biochemistry, Temple University School of Medicine, Fels Institute, Philadelphia, Pennsylvania, United States of America
- Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania, United States of America
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Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 986] [Impact Index Per Article: 89.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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18
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Konzer A, Ruhs A, Braun H, Jungblut B, Braun T, Krüger M. Stable isotope labeling in zebrafish allows in vivo monitoring of cardiac morphogenesis. Mol Cell Proteomics 2013; 12:1502-12. [PMID: 23412571 DOI: 10.1074/mcp.m111.015594] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Quantitative proteomics is an important tool to study biological processes, but so far it has been challenging to apply to zebrafish. Here, we describe a large scale quantitative analysis of the zebrafish proteome using a combination of stable isotope labeling and liquid chromatography-mass spectrometry (LC-MS). Proteins derived from the fully labeled fish were used as a standard to quantify changes during embryonic heart development. LC-MS-assisted analysis of the proteome of activated leukocyte cell adhesion molecule zebrafish morphants revealed a down-regulation of components of the network required for cell adhesion and maintenance of cell shape as well as secondary changes due to arrest of cellular differentiation. Quantitative proteomics in zebrafish using the stable isotope-labeling technique provides an unprecedented resource to study developmental processes in zebrafish.
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Affiliation(s)
- Anne Konzer
- §Max-Planck-Institute for Heart and Lung Research, Ludwigstrasse 43, 61231 Bad Nauheim, Germany
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Smirle J, Au CE, Jain M, Dejgaard K, Nilsson T, Bergeron J. Cell biology of the endoplasmic reticulum and the Golgi apparatus through proteomics. Cold Spring Harb Perspect Biol 2013; 5:a015073. [PMID: 23284051 DOI: 10.1101/cshperspect.a015073] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Enriched endoplasmic reticulum (ER) and Golgi membranes subjected to mass spectrometry have uncovered over a thousand different proteins assigned to the ER and Golgi apparatus of rat liver. This, in turn, led to the uncovering of several hundred proteins of poorly understood function and, through hierarchical clustering, showed that proteins distributed in patterns suggestive of microdomains in cognate organelles. This has led to new insights with respect to their intracellular localization and function. Another outcome has been the critical testing of the cisternal maturation hypothesis showing overwhelming support for a predominant role of COPI vesicles in the transport of resident proteins of the ER and Golgi apparatus (as opposed to biosynthetic cargo). Here we will discuss new insights gained and also highlight new avenues undertaken to further explore the cell biology of the ER and the Golgi apparatus through tandem mass spectrometry.
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Affiliation(s)
- Jeffrey Smirle
- The Research Institute of the McGill University Health Centre and the Department of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
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20
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Rombouts I, Lagrain B, Brunnbauer M, Delcour JA, Koehler P. Improved identification of wheat gluten proteins through alkylation of cysteine residues and peptide-based mass spectrometry. Sci Rep 2013; 3:2279. [PMID: 23880742 PMCID: PMC3721084 DOI: 10.1038/srep02279] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/09/2013] [Indexed: 11/22/2022] Open
Abstract
The concentration and composition of wheat gluten proteins and the presence, concentration and location of cysteine residues therein are important for wheat flour quality. However, it is difficult to identify gluten proteins, as they are an extremely polymorphic mixture of prolamins. We here present methods for cysteine labeling of wheat prolamins with 4-vinylpyridine (4-VP) and iodoacetamide (IDAM) which, as compared to label-free analysis, substantially improve identification of cysteine-containing peptides in enzymic prolamin digests by electrospray ionization--tandem mass spectrometry. Both chymotrypsin and thermolysin yielded cysteine-containing peptides from different gluten proteins, but more proteins could be identified after chymotryptic digestion. In addition, to the best of our knowledge, we were the first to label prolamins with isotope coded affinity tags (ICAT), which are commonly used for quantitative proteomics. However, more peptides were detected after labeling gluten proteins with 4-VP and IDAM than with ICAT.
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Affiliation(s)
- Ine Rombouts
- German Research Center for Food Chemistry, Leibniz Institute, Lise-Meitner-Strasse 34, D-85354 Freising, Germany.
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21
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Proteomic technologies for the study of osteosarcoma. Sarcoma 2012; 2012:169416. [PMID: 22550414 PMCID: PMC3329661 DOI: 10.1155/2012/169416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 12/04/2011] [Indexed: 02/07/2023] Open
Abstract
Osteosarcoma is the most common primary bone cancer of children and is established during stages of rapid bone growth. The disease is a consequence of immature osteoblast differentiation, which gives way to a rapidly synthesized incompletely mineralized and disorganized bone matrix. The mechanism of osteosarcoma tumorogenesis is poorly understood, and few proteomic studies have been used to interrogate the disease thus far. Accordingly, these studies have identified proteins that have been known to be associated with other malignancies, rather than being osteosarcoma specific. In this paper, we focus on the growing list of available state-of-the-art proteomic technologies and their specific application to the discovery of novel osteosarcoma diagnostic and therapeutic targets. The current signaling markers/pathways associated with primary and metastatic osteosarcoma that have been identified by early-stage proteomic technologies thus far are also described.
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22
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Shimada T, Kuyama H, Sato TA, Tanaka K. Development of iodoacetic acid-based cysteine mass tags: Detection enhancement for cysteine-containing peptide by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Biochem 2012; 421:785-7. [DOI: 10.1016/j.ab.2011.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/12/2011] [Accepted: 12/02/2011] [Indexed: 01/23/2023]
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Di Domenico F, Coccia R, Butterfield DA, Perluigi M. Circulating biomarkers of protein oxidation for Alzheimer disease: expectations within limits. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1785-95. [PMID: 22019699 DOI: 10.1016/j.bbapap.2011.10.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 09/30/2011] [Accepted: 10/05/2011] [Indexed: 12/11/2022]
Abstract
Alzheimer disease (AD), the most common dementing disorder, is a multifactorial disease with complex etiology. Among different hypotheses proposed for AD one of the most corroborated is the "oxidative stress hypothesis". Although recent studies extensively demonstrated the specific oxidative modification of selected proteins in the brain of AD patients and how their dysfunction possibly correlates with the pathology, there is still an urgent need to extend these findings to peripheral tissue. So far very few studies showed oxidative damage of proteins in peripheral tissues and current findings need to be replicated. Another limit in AD research is represented by the lack of highly specific diagnostic tools for early diagnosis. For a full screening and early diagnosis, biomarkers easily detectable in biological samples, such as blood, are needed. The search of reliable biomarkers for AD in peripheral blood is a great challenge. A few studies described a set of plasma markers that differentiated AD from controls and were shown to be useful in predicting conversion from mild cognitive impairment, which is considered a prodromal stage, to AD. We review the current state of knowledge on peripheral oxidative biomarkers for AD, including proteomics, which might be useful for early diagnosis and prognosis.
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Affiliation(s)
- Fabio Di Domenico
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
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Sultana R, Butterfield DA. Identification of the oxidative stress proteome in the brain. Free Radic Biol Med 2011; 50:487-94. [PMID: 21111808 PMCID: PMC3052741 DOI: 10.1016/j.freeradbiomed.2010.11.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 11/14/2010] [Accepted: 11/16/2010] [Indexed: 12/15/2022]
Abstract
The redox proteomics technique normally combines two-dimensional gel electrophoresis, mass spectrometry, and protein databases to analyze the cell proteome from various samples, thereby leading to the identification of specific targets of oxidative modification. Oxidative stress that occurs because of increased levels of reactive oxygen species and reactive nitrogen species can target most biomolecules, consequently leading to altered physiological function of the cells. Redox proteomics has identified oxidatively modified protein targets in various pathological conditions, consequently providing insight into the pathways involved in the pathogenesis of these conditions. This approach also can be used to identify possible protective mechanisms to prevent or delay these disorders.
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Affiliation(s)
- Rukhsana Sultana
- Department of Chemistry, University of Kentucky, Lexington, KY 40506
- Center of Membrane Sciences, University of Kentucky, Lexington, KY 40506, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
| | - D. Allan Butterfield
- Department of Chemistry, University of Kentucky, Lexington, KY 40506
- Center of Membrane Sciences, University of Kentucky, Lexington, KY 40506, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506, USA
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Lyons CE, Victor KG, Moshnikov SA, Bachmann LM, Baras AS, Dettmann KM, Cross JV, Templeton DJ. PICquant: a quantitative platform to measure differential peptide abundance using dual-isotopic labeling with 12C6- and 13C6-phenyl isocyanate. Anal Chem 2011; 83:856-65. [PMID: 21192683 PMCID: PMC3079250 DOI: 10.1021/ac102461e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We have developed a complete system for the isotopic labeling, fractionation, and automated quantification of differentially expressed peptides that significantly facilitates candidate biomarker discovery. We describe a new stable mass tagging reagent pair, (12)C(6)- and (13)C(6)-phenyl isocyanate (PIC), that offers significant advantages over currently available tags. Peptides are labeled predominantly at their amino termini and exhibit elution profiles that are independent of label isotope. Importantly, PIC-labeled peptides have unique neutral-mass losses upon CID fragmentation that enable charge state and label isotope identification and, thereby, decouple the sequence identification from the quantification of candidate biomarkers. To exploit these properties, we have coupled peptide fractionation protocols with a Thermo LTQ-XL LC-MS(2) data acquisition strategy and a suite of automated spectrum analysis software that identifies quantitative differences between labeled samples. This approach, dubbed the PICquant platform, is independent of protein sequence identification and excludes unlabeled peptides that otherwise confound biomarker discovery. Application of the PICquant platform to a set of complex clinical samples showed that the system allows rapid identification of peptides that are differentially expressed between control and patient groups.
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Affiliation(s)
| | - Ken G. Victor
- Corresponding authors: Department of Pathology, PO Box 800904, MR5 Room 3334, University of Virginia, Charlottesville, VA 22908-0214, USA. KGV: ; DJT, , Phone: +1 434-924-1946; Fax: +1 434-924-9312
| | - Sergey A. Moshnikov
- Collaborative Mass Spectrometry Facility, Department of Pathology, University of Virginia, Charlottesville, Virginia, USA
| | | | - Alexander S. Baras
- Collaborative Mass Spectrometry Facility, Department of Pathology, University of Virginia, Charlottesville, Virginia, USA
| | - Kathleen M. Dettmann
- Collaborative Mass Spectrometry Facility, Department of Pathology, University of Virginia, Charlottesville, Virginia, USA
| | - Janet V. Cross
- Collaborative Mass Spectrometry Facility, Department of Pathology, University of Virginia, Charlottesville, Virginia, USA
| | - Dennis J. Templeton
- Collaborative Mass Spectrometry Facility, Department of Pathology, University of Virginia, Charlottesville, Virginia, USA
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Abstract
Genetic, chemical, and environmental perturbations can all induce large changes in cellular proteomes, and research aimed at quantifying these changes are an important part of modern biology. Although improvements in the hardware and software of mass spectrometers have produced increased throughput and accuracy of such measurements, new uses of heavy isotope internal standards that assist in this process have emerged. Surprisingly, even complex life forms such as mammals can be grown to near-complete replacement with heavy isotopes of common biological elements such as (15)N, and these isotopically labeled organisms provide excellent controls for isolating and identifying experimental variables such as extraction or fractionation efficiencies. We discuss here the theory and practice of these technologies, as well as provide a review of significant recent biological applications.
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Affiliation(s)
- Kelli G Kline
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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27
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Zhan X, Desiderio DM. The use of variations in proteomes to predict, prevent, and personalize treatment for clinically nonfunctional pituitary adenomas. EPMA J 2010. [PMID: 23199087 PMCID: PMC3405333 DOI: 10.1007/s13167-010-0028-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Pituitary adenomas account for ∼10% of intracranial tumors, and they cause the compression of nearby structures and the inappropriate expression of pituitary hormones. Unlike functional pituitary adenomas, nonfunctional (NF) pituitary adenomas account for ∼30% of pituitary tumors, and are large enough to cause blindness; because they do not cause any clinical hormone hypersecretion, they are difficult to detect at an early stage; and hypopituitarism results. No effective molecular biomarkers or chemical therapy have been approved for the clinical setting. Because an NF pituitary adenoma is highly heterogeneous, differences in the proteins (the proteome) can distinguish among those heterogeneity structures. The components of a proteome dynamically change as an NF adenoma progresses. Changes in protein expression and protein modifications, individually or in combination, might be biomarkers to predict the disease, monitor the tumor progression, and develop an accurate molecular classification for personalized patient treatment. The modalities of proteomic variation might also be useful in the interventional prevention and personalized treatment of patients to halt the occurrence and progression of NF pituitary adenomas.
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Affiliation(s)
- Xianquan Zhan
- Charles B. Stout Neuroscience Mass Spectrometry Laboratory, The University of Tennessee Health Science Center, 847 Monroe Avenue, Room 117, Memphis, TN 38163 USA
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28
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Abstract
Honglian (HL) cytoplasmic male sterility (CMS) is one of the rice CMS types and has been widely used in hybrid rice production in China. The CMS line (Yuetai A, YTA) has a Yuetai B (maintainer line, YTB) nuclear genome, but has a rearranged mitochondrial (mt) genome consisting of Yuetai B. The fertility of hybrid (HL-6) was restored by restorer gene in nuclear genome of restorer line (9311). We used isotope-code affinity tag (ICAT) technology to perform the protein profiling of uninucleate stage rice anther and identify the CMS-HL related proteins. Two separate ICAT analyses were performed in this study: (1) anthers from YTA versus anthers from YTB, and (2) anthers from YTA versus anthers from HL-6. Based on the two analyses, a total of 97 unique proteins were identified and quantified in uninucleate stage rice anther under the error rate of less than 10%, of which eight proteins showed abundance changes of at least twofold between YTA and YTB. Triosephosphate isomerase, fructokinase II, DNA-binding protein GBP16 and ribosomal protein L3B were over-expressed in YTB, while oligopeptide transporter, floral organ regulator 1, kinase and S-adenosyl-L: -methionine synthetase were over-expressed in YTA. Reduction of the proteins associated with energy production and lesser ATP equivalents detected in CMS anther indicated that the low level of energy production played an important role in inducing CMS-HL.
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29
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Analysis of protein expression in pure cell nuclei populations isolated from human breast cancer tissue by DNA flow cytometric sorting. J Proteomics 2010; 73:1111-6. [PMID: 19995621 DOI: 10.1016/j.jprot.2009.11.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 11/26/2009] [Accepted: 11/30/2009] [Indexed: 11/21/2022]
Abstract
In this study, cell nuclei from aneuploid breast cancer samples were sorted with respect to DNA content into pure diploid and aneuploid fractions using flow cytometry. The nuclear proteins were then separated by one-dimensional gel electrophoresis (1D-PAGE) and differences in protein expression patterns, between diploid and aneuploid nuclei from the same tumours, were compared. Using a combination of peptide finger printing and peptide identification by MALDI-TOF mass spectrometry, we identified proteins and confirmed that the proteins were of nuclear origins. The results in this study add further information to the knowledge about the breast cancer disease complexity and heterogeneity at molecular level. For some of the tumours studied different nuclei protein patterns were obtained, in the diploid respective aneuploid nuclei populations, whilst other tumours did not show these differences.
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30
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Todorović V, Desai BV, Eigenheer RA, Yin T, Amargo EV, Mrksich M, Green KJ, Patterson MJS. Detection of differentially expressed basal cell proteins by mass spectrometry. Mol Cell Proteomics 2009; 9:351-61. [PMID: 19955077 DOI: 10.1074/mcp.m900358-mcp200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The ability of cells to modulate interactions with each other and the substrate is essential for epithelial tissue remodeling during processes such as wound healing and tumor progression. However, despite strides made in the field of proteomics, proteins involved in adhesion have been difficult to study. Here, we report a method for the enrichment and analysis of proteins associated with the basal surface of the cell and its underlying matrix. The enrichment involves deroofing the cells with 20 mM ammonium hydroxide and the removal of cytosolic and organellar proteins by stringent water wash. Proteomic profiling was achieved by LC-FTMS, which allowed comparison of differentially expressed or shared proteins under different cell states. First, we analyzed and compared the basal cell components of mouse keratinocytes lacking the cell-cell junction molecule plakoglobin with their control counterparts. Changes in the molecules involved in motility and invasion were detected in plakoglobin-deficient cells, including decreased detection of fibronectin, integrin beta(4), and FAT tumor suppressor. Second, we assessed the differences in basal cell components between two human oral squamous cell carcinoma lines originating from different sites in the oral cavity (CAL33 and UM-SCC-1). The data show differences between the two lines in the type and abundance of proteins specific to cell adhesion, migration, and angiogenesis. Therefore, the method described here has the potential to serve as a platform to assess proteomic changes in basal cell components including extracellular and adhesion-specific proteins involved in wound healing, cancer, and chronic and acquired adhesion-related disorders.
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Affiliation(s)
- Viktor Todorović
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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31
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Prahalad AK, Hock JM. Proteomic characteristics of ex vivo-enriched adult human bone marrow mononuclear cells in continuous perfusion cultures. J Proteome Res 2009; 8:2079-89. [PMID: 19714820 DOI: 10.1021/pr801064u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A major challenge in developing cell therapies is reliable characterization of the cell product at the molecular level. Fresh autologous and passaged human bone marrow enriched for stem and mesenchymal stromal stem cells have been used to regenerate bone. We report the proteome of an innovative autologous human bone marrow-derived mixed cell product (BMMCP), cultured ex vivo for 12 days, in automated continuous media perfusion system to avoid passaging, and discuss reproducibility of protein composition. Each BMMCP is compared to its originating human adult bone marrow mononuclear cells (BMMNC). With the use of 2-D LC-MS/MS approach, 638 (BMMNC) and 867 (BMMCP) distinct proteins were identified including cell adhesion molecules, extracellular matrix and growth factors. Overlap of protein identifications revealed that 67% of the BMMNC proteome was retained in the BMMCP, and protein expression of selected cell lineages was enhanced. Isotope-coded affinity tags (ICAT) and MS/MS were used to identify and quantify relative changes in the proteome of BMMNC and their related BMMCP, obtained from 3 separate donors. In 3 separate ICAT experiments, 57% of proteome identified was shared between donors. Measurable and definable proteomic characterization of BMMCP will facilitate their use in clinical trials and provide insight into cell functionality needed to support multiple therapeutic indications.
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Affiliation(s)
- Agasanur K Prahalad
- Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.
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32
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Kline KG, Finney GL, Wu CC. Quantitative strategies to fuel the merger of discovery and hypothesis-driven shotgun proteomics. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:114-25. [PMID: 19398505 DOI: 10.1093/bfgp/elp008] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The ultimate goal of most shotgun proteomic pipelines is the discovery of novel biomarkers to direct the development of quantitative diagnostics for the detection and treatment of disease. Differential comparisons of biological samples identify candidate peptides that can serve as proxys of candidate proteins. While these discovery approaches are robust and fairly comprehensive, they have relatively low throughput. When merged with targeted mass spectrometry, this pipeline can fuel hypothesis-driven studies and the development of novel diagnostics and therapeutics.
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Abstract
A major scientific challenge at the present time for cancer research is the determination of the underlying biological basis for cancer development. It is further complicated by the heterogeneity of cancer's origin. Understanding the molecular basis of cancer requires studying the dynamic and spatial interactions among proteins in cells, signaling events among cancer cells, and interactions between the cancer cells and the tumor microenvironment. Recently, it has been proposed that large-scale protein expression analysis of cancer cell proteomes promises to be valuable for investigating mechanisms of cancer transformation. Advances in mass spectrometry technologies and bioinformatics tools provide a tremendous opportunity to qualitatively and quantitatively interrogate dynamic protein-protein interactions and differential regulation of cellular signaling pathways associated with tumor development. In this review, progress in shotgun proteomics technologies for examining the molecular basis of cancer development will be presented and discussed.
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Affiliation(s)
- Emily I Chen
- Department of Cell Biology, 10550 North Torrey Pines Road, SR11, The Scripps Research Institute, La Jolla, CA 92037, USA
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34
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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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35
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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.
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Affiliation(s)
- B Matharoo-Ball
- The John Van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK
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36
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Rivera-Monroy Z, Bonn GK, Guttman A. Fluorescent isotope-coded affinity tag 2: Peptide labeling and affinity capture. Electrophoresis 2009; 30:1111-8. [DOI: 10.1002/elps.200800830] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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37
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The analysis of phosphoproteomes by selective labelling and advanced mass spectrometric techniques. Methods Mol Biol 2009; 527:173-90, ix. [PMID: 19241013 DOI: 10.1007/978-1-60327-834-8_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This chapter focuses on the development of new proteomic approaches based on classical biochemical procedures coupled with new mass spectrometry methods to study the phosphorylation, the most important and abundant PTMs in modulating protein activity and propagating signals within cellular pathways and networks. These phosphoproteome studies aim at comprehensive analysis of protein phosphorylation by identification of the phosphoproteins, exact localization of phosphorylated residues, and preferably quantification of the phosphorylation. Because of low stoichiometry, heterogeneity, and low abundance, enrichment of phosphopeptides is an important step of this analysis. The first section is focused on the development of new enrichment methods coupled to mass spectrometry. Thus, improved approach, based on simple chemical manipulations and mass spectrometric procedures, for the selective analysis of phosphoserine and phosphothreonine in protein mixtures, following conversion of the peptide phosphate moiety into DTT derivatives, is described. However the major aim of this work is devoted to the use of isotopically labelled DTT, thus allowing a simple and direct quantitative MS analysis. The final part of the work is focused on the development of a strategy to study phosphorylation without preliminary enrichment but using the high performance of a novel hybrid mass spectrometer linear ion trap.
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38
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Sowell RA, Owen JB, Butterfield DA. Proteomics in animal models of Alzheimer's and Parkinson's diseases. Ageing Res Rev 2009; 8:1-17. [PMID: 18703168 DOI: 10.1016/j.arr.2008.07.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 07/04/2008] [Accepted: 07/08/2008] [Indexed: 01/06/2023]
Abstract
The risk of developing neurodegenerative disorders such as Alzheimer's disease (AD) and Parkinson's disease (PD) increases with age. AD and PD are the two most common neurodegenerative diseases that currently affect millions of persons within the United States population. While many clues about the mechanisms of these disorders have been uncovered, to date, the molecular mechanisms associated with the cause of these diseases are not completely understood. Furthermore, there are no available cures or preventive treatments for either disorder. Animal models of AD and PD, though not perfect, offer a means to gain knowledge of the basic biochemistry associated with these disorders and with drug efficacy. The field of proteomics which focuses on identifying the dynamic nature of the protein content expressed within a particular cell, tissue, or organism, has provided many insights into these disturbing disorders. Proteomic studies have revealed many pathways that are associated with disease pathogenesis and that may lead to the development of potential therapeutic targets. This review provides a discussion of key findings from AD and PD proteomics-based studies in various animal models of disease.
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Affiliation(s)
- Renã A Sowell
- Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, USA
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39
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Ward DG, Roberts K, Stonelake P, Goon P, Zampronio CG, Martin A, Johnson PJ, Iqbal T, Tselepis C. SELDI-TOF-MS determination of hepcidin in clinical samples using stable isotope labelled hepcidin as an internal standard. Proteome Sci 2008; 6:28. [PMID: 18854031 PMCID: PMC2571088 DOI: 10.1186/1477-5956-6-28] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2008] [Accepted: 10/14/2008] [Indexed: 11/18/2022] Open
Abstract
Background Hepcidin is a 25-residue peptide hormone crucial to iron homeostasis. It is essential to measure the concentration of hepcidin in cells, tissues and body fluids to understand its mechanisms and roles in physiology and pathophysiology. With a mass of 2791 Da hepcidin is readily detectable by mass spectrometry and LC-ESI, MALDI and SELDI have been used to estimate systemic hepcidin concentrations by analysing serum or urine. However, peak heights in mass spectra may not always reflect concentrations in samples due to competition during binding steps and variations in ionisation efficiency. Thus the purpose of this study was to develop a robust assay for measuring hepcidin using a stable isotope labelled hepcidin spiking approach in conjunction with SELDI-TOF-MS. Results We synthesised and re-folded hepcidin labelled with 13C/15N phenylalanine at position 9 to generate an internal standard for mass spectrometry experiments. This labelled hepcidin is 10 Daltons heavier than the endogenous peptides and does not overlap with the isotopic envelope of the endogenous hepcidin or other common peaks in human serum or urine mass spectra and can be distinguished in low resolution mass spectrometers. We report the validation of adding labelled hepcidin into serum followed by SELDI analysis to generate an improved assay for hepcidin. Conclusion We demonstrate that without utilising a spiking approach the hepcidin peak height in SELDI spectra gives a good indication of hepcidin concentration. However, a stable isotope labelled hepcidin spiking approach provides a more robust assay, measures the absolute concentration of hepcidin and should facilitate inter-laboratory hepcidin comparisons.
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Seo J, Suh MS, Thangadurai TD, Kim J, Rhee YH, Yoon HJ, Shin SK. Mass-Balanced 1H/2H Isotope Dipeptide Tag for Simultaneous Protein Quantitation and Identification. Anal Chem 2008; 80:6145-53. [DOI: 10.1021/ac801007y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jongcheol Seo
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Min-Soo Suh
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - T. Daniel Thangadurai
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Jinhee Kim
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Young Ho Rhee
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Hye-Joo Yoon
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
| | - Seung Koo Shin
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, San31 Hyojadong Namgu, Pohang, Korea 790-784
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Becker GW. Stable isotopic labeling of proteins for quantitative proteomic applications. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 7:371-82. [DOI: 10.1093/bfgp/eln047] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Proteomics as a tool for the modelling of biological processes and biomarker development in nutrition research. Br J Nutr 2008; 99 Suppl 3:S66-71. [DOI: 10.1017/s0007114508006909] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Nutrition research has slowly started to adopt the proteomics techniques to measure changes in the protein complement of a biological system. This enables modelling of biological processes in response to dietary interventions, as well as the elucidation of novel biomarkers for health or disease that are sensitive to such interventions. There are limited studies on the effect of micronutrients on the proteome, so this review concentrates rather more on dietary intervention studies that have used proteomics (mainly classical 2D gel electrophoresis combined with mass spectrometry) to elucidate changes in pathways that relate to glucose and fatty acid metabolism, oxidative stress, anti-oxidant defence mechanisms and redox status. The ability to measure regulation of more low abundant proteins, such as those involved in inflammatory pathways, as well as the evaluation and validation of newly discovered candidate biomarkers in human biofluids, may depend on the introduction of more quantitative and sensitive methods like multiple reaction monitoring (MRM) and multiplexed immunoassays in nutrition research.
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Bonfim V, Ponce-Soto L, Martins de Souza D, Souza G, Baldasso P, Eberlin M, Marangoni S. Structural and functional characterization of myotoxin, Cr-IV 1, a phospholipase A2 D49 from the venom of the snake Calloselasma rhodostoma. Biologicals 2008; 36:168-76. [DOI: 10.1016/j.biologicals.2007.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 10/24/2007] [Accepted: 10/25/2007] [Indexed: 11/16/2022] Open
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Sun MC, Chen CD, Huang YS, Wu ZS, Ho YP. Matrix-assisted laser desorption/ionization-MS-based relative quantification of peptides and proteins using iodoacetamide and N-methyliodoacetamide as labeling reagents. J Sep Sci 2008; 31:538-47. [PMID: 18210377 DOI: 10.1002/jssc.200700440] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The use of iodoacetamide (IAA) and N-methyliodoacetamide (MIAA) as labeling agents for the relative measurements of proteins using MALDI-MS is described herein. These reagents, which alkylate the thiol groups of cysteine residues in proteins, were introduced during the alkylation step of a common protein denaturation and digestion process. This approach is simpler and cheaper than those involving isotope labeling agents. The labeling agents described herein displayed good dynamic ranges and correlation coefficients for protein quantification analyses when the proteins were treated through either in-solution or in-gel digestion. The best dynamic ranges (in the molar ratio) for proteins lysozyme, transferrin, and BSA (in-solution digestion) are 0.1-10, 0.1-8, and 0.1-8, respectively. The corresponding correlation coefficients are greater than 0.99. The IAA/MIAA labeling is a useful method for the relative quantification of peptides and digested proteins when the chromatographic isotope effect is not a major concern.
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Affiliation(s)
- Mei-Chuan Sun
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan, ROC
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Yi EC, Goodlett DR. Quantitative protein profile comparisons using the isotope-coded affinity tag method. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2008; Chapter 23:23.2.1-23.2.11. [PMID: 18429263 DOI: 10.1002/0471140864.ps2302s34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Current methods for measuring pairwise changes in protein expression involve differential stable isotopic labeling of proteins or peptides either in vivo or in vitro followed by identification and quantification using a mass spectrometer. In these methods, the mass spectrometer detects two different masses, which correspond to a single protein from two different samples that have been labeled with either a heavy or normal isotope. Changes in protein expression are observed when the identical peptide from each of two biological conditions is identified and a difference is detected in the measurements comparing the peptide labeled with the heavy isotope to the one with a normal isotopic distribution. This approach allows the simultaneous comparison of the expression of many proteins between two different biological states (e.g., yeast grown on galactose versus glucose, or normal versus cancer cells). This unit describes one of these popular methods for quantitative protein profiling using the isotope-coded affinity tag (ICAT) technique.
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Affiliation(s)
- Eugene C Yi
- Institute for Systems Biology, Seattle, Washington, USA
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Shen Y, Senzer NN, Nemunaitis JJ. Use of Proteomics Analysis for Molecular Precision Approaches in Cancer Therapy. Drug Target Insights 2008. [DOI: 10.4137/dti.s649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
| | - Neil N. Senzer
- LEAD Therapeutics, Inc., San Bruno, CA
- Mary Crowley Cancer Research Centers, Dallas, TX
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Qiu H, Wang Y. Quantitative analysis of surface plasma membrane proteins of primary and metastatic melanoma cells. J Proteome Res 2008; 7:1904-15. [PMID: 18410138 DOI: 10.1021/pr700651b] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Plasma membrane proteins play critical roles in cell-to-cell recognition, signal transduction and material transport. Because of their accessibility, membrane proteins constitute the major targets for protein-based drugs. Here, we described an approach, which included stable isotope labeling by amino acids in cell culture (SILAC), cell surface biotinylation, affinity peptide purification and LC-MS/MS for the identification and quantification of cell surface membrane proteins. We applied the strategy for the quantitative analysis of membrane proteins expressed by a pair of human melanoma cell lines, WM-115 and WM-266-4, which were derived initially from the primary and metastatic tumor sites of the same individual. We were able to identify more than 100 membrane and membrane-associated proteins from these two cell lines, including cell surface histones. We further confirmed the surface localization of histone H2B and three other proteins by immunocytochemical analysis with confocal microscopy. The contamination from cytoplasmic and other nonmembrane-related sources is greatly reduced by using cell surface biotinylation and affinity purification of biotinylated peptides. We also quantified the relative expression of 62 identified proteins in the two types of melanoma cells. The application to quantitative analysis of membrane proteins of primary and metastatic melanoma cells revealed great potential of the method in the comprehensive identification of tumor progression markers as well as in the discovery of new protein-based therapeutic targets.
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Affiliation(s)
- Haibo Qiu
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
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Parker L, Engel-Hall A, Drew K, Steinhardt G, Helseth DL, Jabon D, McMurry T, Angulo DS, Kron SJ. Investigating quantitation of phosphorylation using MALDI-TOF mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:518-527. [PMID: 18064576 PMCID: PMC2874747 DOI: 10.1002/jms.1342] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Despite advances in methods and instrumentation for analysis of phosphopeptides using mass spectrometry, it is still difficult to quantify the extent of phosphorylation of a substrate because of physiochemical differences between unphosphorylated and phosphorylated peptides. Here we report experiments to investigate those differences using MALDI-TOF mass spectrometry for a set of synthetic peptides by creating calibration curves of known input ratios of peptides/phosphopeptides and analyzing their resulting signal intensity ratios. These calibration curves reveal subtleties in sequence-dependent differences for relative desorption/ionization efficiencies that cannot be seen from single-point calibrations. We found that the behaviors were reproducible with a variability of 5-10% for observed phosphopeptide signal. Although these data allow us to begin addressing the issues related to modeling these properties and predicting relative signal strengths for other peptide sequences, it is clear that this behavior is highly complex and needs to be further explored.
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Affiliation(s)
- Laurie Parker
- Ludwig Center for Metastasis Research, University of Chicago, Knapp R322, 924 E. 57th Street, Chicago, IL 60637, USA.
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Mirza SP, Olivier M. Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry. Physiol Genomics 2008; 33:3-11. [PMID: 18162499 PMCID: PMC2771641 DOI: 10.1152/physiolgenomics.00292.2007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Proteomics has been proposed as one of the key technologies in the postgenomic era. So far, however, the comprehensive analysis of cellular proteomes has been a challenge because of the dynamic nature and complexity of the multitude of proteins in cells and tissues. Various approaches have been established for the analyses of proteins in a cell at a given state, and mass spectrometry (MS) has proven to be an efficient and versatile tool. MS-based proteomics approaches have significantly improved beyond the initial identification of proteins to comprehensive characterization and quantification of proteomes and their posttranslational modifications (PTMs). Despite these advances, there is still ongoing development of new technologies to profile and analyze cellular proteomes more completely and efficiently. In this review, we focus on MS-based techniques, describe basic approaches for MS-based profiling of cellular proteomes and analysis methods to identify proteins in complex mixtures, and discuss the different approaches for quantitative proteome analysis. Finally, we briefly discuss novel developments for the analysis of PTMs. Altered levels of PTM, sometimes in the absence of protein expression changes, are often linked to cellular responses and disease states, and the comprehensive analysis of cellular proteome would not be complete without the identification and quantification of the extent of PTMs of proteins.
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Affiliation(s)
- Shama P Mirza
- National Center for Proteomics Research, Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA. e-mail:
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Audhya A, Desai A. Proteomics in Caenorhabditis elegans. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 7:205-10. [DOI: 10.1093/bfgp/eln014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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