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Dapic I, Uwugiaren N, Jansen PJ, Corthals GL. Fast and Simple Protocols for Mass Spectrometry-Based Proteomics of Small Fresh Frozen Uterine Tissue Sections. Anal Chem 2017; 89:10769-10775. [PMID: 28910098 PMCID: PMC5647562 DOI: 10.1021/acs.analchem.7b01937] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Human
tissues are an important link between organ-specific spatial
molecular information, patient pathology, and patient treatment options.
However, patient tissues are uniquely obtained by time and location,
and limited in their availability and size. Currently, little knowledge
exists about appropriate and simplified protocols for routine MS-based
analysis of the various types and sizes of tissues. Following standard
procedures used in pathology, we selected small fresh frozen uterine
tissue samples to investigate how the tissue preparation protocol
affected the subsequent proteomics analysis. First, we observed that
protein extraction with 0.1% SDS followed by extraction with a 30%
ACN/urea resulted in a decrease in the number of identified proteins,
when compared to extraction with 30% ACN/urea only. The decrease in
the number of proteins was approximately 55% and 20%, for 10 and 16
μm thick tissue, respectively. Interestingly, the relative abundance
of the proteins shared between the two methods was higher when SDS/ACN/urea
was used, compared to the 30% ACN/urea extraction, indicating the
role of SDS to be beneficial for protein solubility. Second, the influence
of tissue thickness was investigated by comparing the results obtained
for 10, 16, and 20 μm thick (1 mm2) tissue using
urea/30% ACN. We observed an increase in the number of identified
proteins and corresponding quantity with an increase in the tissue
thickness. Finally, by analyzing very small amounts of tissues (∼0.2
mm2) of 10, 16, and 20 μm thickness, we observed
that the increase in tissue thickness resulted in a higher number
of protein identifications and corresponding quantitative values.
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Affiliation(s)
- Irena Dapic
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Naomi Uwugiaren
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Petra J Jansen
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Garry L Corthals
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
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2
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Procopio N, Chamberlain AT, Buckley M. Intra- and Interskeletal Proteome Variations in Fresh and Buried Bones. J Proteome Res 2017; 16:2016-2029. [PMID: 28436665 DOI: 10.1021/acs.jproteome.6b01070] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteomic methods are acquiring greater importance in archaeology and palaeontology due to the longevity of proteins in skeletal remains. There are also developing interests in forensic applications, offering the potential to shed light on post-mortem intervals and age at death estimation. However, our understanding of intra- and interskeletal proteome variations is currently severely limited. Here, we evaluated the proteomes obtained from five distinct subsamples of different skeletal elements from buried pig carcasses to ascertain the extent of variation within and between individuals. We found that reproducibility of data depends on the skeletal element used for sampling and that intrabone differences exceed those observed between the same skeletal element sampled from different individuals. Interestingly, the abundance of several serum proteins appeared to correlate with biological age with relative concentrations of alpha-1 antitrypsin and chromogranin-A increasing and those of fetuin-A decreasing. We also observed a surprising level of divergence in data from different LC-MS/MS runs on aliquots of similar samples analyzed months apart, adding constraints to the comparison of results of such methods across different studies.
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Affiliation(s)
- Noemi Procopio
- School of Earth and Environmental Sciences, The University of Manchester, Manchester Institute of Biotechnology , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Andrew T Chamberlain
- School of Earth and Environmental Sciences, The University of Manchester , Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Michael Buckley
- School of Earth and Environmental Sciences, The University of Manchester, Manchester Institute of Biotechnology , 131 Princess Street, Manchester, M1 7DN, United Kingdom
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3
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Naryzhny SN, Zgoda VG, Maynskova MA, Ronzhina NL, Belyakova NV, Legina OK, Archakov AI. [Experimental estimation of proteome size for cells and human plasma]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 61:279-85. [PMID: 25978394 DOI: 10.18097/pbmc20156102279] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Huge range of concentrations of different protein and insufficient sensitivity of methods for detection of proteins at a single molecule level does not yet allow obtaining the whole image of human proteome. In our investigations, we tried to evaluate the size of different proteomes (cells and plasma). The approach used is based on detection of protein spots in 2-DE after staining by protein dyes with different sensitivities. The function representing the dependence of the number of protein spots on sensitivity of protein dyes was generated. Next, by extrapolation of this function curve to theoretical point of the maximum sensitivity (detection of a single smallest polypeptide) it was calculated that a single human cell (HepG2) may contain minimum 70,000 proteoforms, and plasma--1.5 mln. Utilization of this approach to other, smaller proteomes showed the competency of this extrapolation. For instance, the size of mycoplas ma (Acholeplasma laidlawii) was estimated in 1100 proteoforms, yeast (Saccharomyces cerevisiae)--40,000, E. coli--6200, P. furiosus--3400. In hepatocytes, the amount of proteoforms was the same as in HepG2--70,000. Significance of obtained data is in possibilities to estimating the proteome organization and planning next steps in its study.
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Affiliation(s)
- S N Naryzhny
- Institute of Biomedical Chemistry, Moscow, Russia; Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Leningrad District, Russia
| | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - N L Ronzhina
- Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Leningrad District, Russia
| | - N V Belyakova
- Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Leningrad District, Russia
| | - O K Legina
- Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Leningrad District, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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4
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Chen J, Han G, Shang C, Li J, Zhang H, Liu F, Wang J, Liu H, Zhang Y. Proteomic analyses reveal differences in cold acclimation mechanisms in freezing-tolerant and freezing-sensitive cultivars of alfalfa. FRONTIERS IN PLANT SCIENCE 2015; 6:105. [PMID: 25774161 PMCID: PMC4343008 DOI: 10.3389/fpls.2015.00105] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/09/2015] [Indexed: 05/11/2023]
Abstract
Cold acclimation in alfalfa (Medicago sativa L.) plays a crucial role in cold tolerance to harsh winters. To examine the cold acclimation mechanisms in freezing-tolerant alfalfa (ZD) and freezing-sensitive alfalfa (W5), holoproteins, and low-abundance proteins (after the removal of RuBisCO) from leaves were extracted to analyze differences at the protein level. A total of 84 spots were selected, and 67 spots were identified. Of these, the abundance of 49 spots and 24 spots in ZD and W5, respectively, were altered during adaptation to chilling stress. Proteomic results revealed that proteins involved in photosynthesis, protein metabolism, energy metabolism, stress and redox and other proteins were mobilized in adaptation to chilling stress. In ZD, a greater number of changes were observed in proteins, and autologous metabolism and biosynthesis were slowed in response to chilling stress, thereby reducing consumption, allowing for homeostasis. The capability for protein folding and protein biosynthesis in W5 was enhanced, which allows protection against chilling stress. The ability to perceive low temperatures was more sensitive in freezing-tolerant alfalfa compared to freezing-sensitive alfalfa. This proteomics study provides new insights into the cold acclimation mechanism in alfalfa.
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Affiliation(s)
- Jing Chen
- College of Life Sciences and Technology, Harbin Normal UniversityHarbin, China
| | - Guiqing Han
- College of Life Sciences and Technology, Harbin Normal UniversityHarbin, China
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Chen Shang
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Jikai Li
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Hailing Zhang
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Fengqi Liu
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Jianli Wang
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Huiying Liu
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Yuexue Zhang
- Institute of Grass Research, Heilongjiang Academy of Agricultural SciencesHarbin, China
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5
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Proteomic Analysis of the Defense Response of Wheat to the Powdery Mildew Fungus, Blumeria graminis f. sp. tritici. Protein J 2014; 33:513-24. [DOI: 10.1007/s10930-014-9583-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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6
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Jianzhen H, Haitian M, Liming Y, Sixiang Z. Developmental changes of protein profiles in the embryonic Sanhuang chicken liver. ACTA ACUST UNITED AC 2007; 54:464-9. [PMID: 17931218 DOI: 10.1111/j.1439-0442.2007.00990.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Understanding embryonic liver development bears the potential to provide important insights into treatments and preventative strategies for paediatric liver disease. Using Sanhuang (SH) chicken as a model system, we sought to identify the proteomic changes associated with embryonic liver development using differential display of proteins with two-dimensional (2-D) polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry analysis. Embryonic livers from 200 SH chicken embryos were isolated on days 9, 14 and 19 during incubation and also immediately after hatching. Six hundred and two protein spots were displayed on 2-D gels stained with colloidal Coomassie brilliant blue, of which, 25 protein spots were found to have changes up to threefold in abundance during development. We identified these spots using MALDI-TOF mass spectrometry and found 23 of 25 proteins to be associated with carbohydrate metabolism, cell division, lipid metabolism and signal transduction. Our results provide insight into the biochemical events taking place during the development of SH chicken embryonic liver and highlight the value of proteomics in characterizing complex biochemical processes. Furthermore, the proteome maps may facilitate future studies addressing the effects of genetic and environmental factors and related studies on the development and quality of chicken embryonic liver.
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Affiliation(s)
- H Jianzhen
- Key Laboratory of Animal Physiology and Biochemistry, Nanjing Agricultural University, Nanjing 210095, China
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7
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Rohrbough JG, Galgiani JN, Wysocki VH. The Application of Proteomic Techniques to Fungal Protein Identification and Quantification. Ann N Y Acad Sci 2007; 1111:133-46. [PMID: 17344531 DOI: 10.1196/annals.1406.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The number of sequenced genomes has increased rapidly in the last few years, supporting a revolution in bioinformatics that has been leveraged by scientists seeking to analyze the proteomes of numerous biological systems. The primary technique employed for the identification of peptides and proteins from biological sources is mass spectrometry (MS). This analytical process is usually in the form of whole-protein analysis (termed "top-down" proteomics) or analysis of enzymatically produced peptides (known as the "bottom-up" approach). This article will focus primarily on the more common bottom-up proteomics to include topics such as sample preparation, separation strategies, MS instrumentation, data analysis, and techniques for protein quantification. Strategies for preparation of samples for proteomic analysis, as well as tools for protein and peptide separation will be discussed. A general description of common MS instruments along with tandem mass spectrometry (MS/MS) will be given. Different methodologies of sample ionization including matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) will be discussed. Data analysis methods including database search algorithms and tools for protein sequence analysis will be introduced. We will also discuss experimental strategies for MS protein quantification using stable isotope labeling techniques and fluorescent labeling. We will introduce several fungal proteomic studies to illustrate the use of these methods. This article will allow investigators to gain a working knowledge of proteomics along with some strengths and weaknesses associated with the techniques presented.
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8
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Phillips CI, Bogyo M. Proteomics meets microbiology: technical advances in the global mapping of protein expression and function. Cell Microbiol 2005; 7:1061-76. [PMID: 16008574 DOI: 10.1111/j.1462-5822.2005.00554.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The availability of complete genome sequences for a large number of pathogenic organisms has opened the door for large-scale proteomic studies to dissect both protein expression/regulation and function. This review highlights key proteomic methods including two-dimensional gel electrophoresis, reference mapping, protein expression profiling and recent advances in gel-free separation techniques that have made a significant impact on the resolution of complex proteomes. In addition, we highlight recent developments in the field of chemical proteomics, a branch of proteomics aimed at functionally profiling a proteome. These techniques include the development of activity-based probes and activity-based protein profiling methods as well as the use of synthetic small molecule libraries to screen for pharmacological tools to perturb basic biological processes. This review will focus on the applications of these technologies to the field of microbiology.
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Affiliation(s)
- Carolyn I Phillips
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5324, USA
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9
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Ramachandran N, Larson DN, Stark PRH, Hainsworth E, LaBaer J. Emerging tools for real-time label-free detection of interactions on functional protein microarrays. FEBS J 2005; 272:5412-25. [PMID: 16262683 DOI: 10.1111/j.1742-4658.2005.04971.x] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The availability of extensive genomic information and content has spawned an era of high-throughput screening that is generating large sets of functional genomic data. In particular, the need to understand the biochemical wiring within a cell has introduced novel approaches to map the intricate networks of biological interactions arising from the interactions of proteins. The current technologies for assaying protein interactions--yeast two-hybrid and immunoprecipitation with mass spectrometric detection--have met with considerable success. However, the parallel use of these approaches has identified only a small fraction of physiologically relevant interactions among proteins, neglecting all nonprotein interactions, such as with metabolites, lipids, DNA and small molecules. This highlights the need for further development of proteome scale technologies that enable the study of protein function. Here we discuss recent advances in high-throughput technologies for displaying proteins on functional protein microarrays and the real-time label-free detection of interactions using probes of the local index of refraction, carbon nanotubes and nanowires, or microelectromechanical systems cantilevers. The combination of these technologies will facilitate the large-scale study of protein interactions with proteins as well as with other biomolecules.
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Affiliation(s)
- Niroshan Ramachandran
- Harvard Institute of Proteomics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Cambridge, MA 02141, USA
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10
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Lescuyer P, Chevallet M, Rabilloud T. L’analyse protéomique : concepts, réalités et perspectives en thérapeutique. Med Sci (Paris) 2004; 20:587-92. [PMID: 15190480 DOI: 10.1051/medsci/2004205587] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The present paper aims at clarifying some important aspects of proteomics, i.e. the large scale analysis of proteins. To this purpose, the main types of proteomic analyses are presented, i.e. those aiming at determining expression levels and those aiming at unravelling protein-protein interactions networks. Their performances and limitations are outlined, as well as their potential applications in biomedicine, to give an reasoned view of the current state of the art.
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Affiliation(s)
- Pierre Lescuyer
- Laboratoire de bioénergétique cellulaire et pathologique, DRDC/BECP, CEA-Grenoble, 17, rue des Martyrs, 38054 Grenoble 9, France
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11
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Nomanbhoy TK, Rosenblum J, Aban A, Burbaum JJ. Inhibitor Focusing: Direct Selection of Drug Targets from Proteomes Using Activity-Based Probes. Assay Drug Dev Technol 2003; 1:137-46. [PMID: 15090140 DOI: 10.1089/154065803321537854] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In the latter stages of drug discovery and development, assays that establish drug selectivity and toxicity are important when side effects, which are often due to lack of specificity, determine drug candidate viability. There has been no comprehensive or systematic methodology to measure these factors outside of whole-animal assays, and such phenomenological assays generally fail to establish the additional targets of a given small molecule, or the molecular origin of toxicity. Consequently, small-molecule development programs destined for failure often reach advanced stages of testing, and the money and time invested in such programs could be saved if information on selectivity were available early in the process. Here, we present a methodology that utilizes chemical ABPs in combination with small-molecule inhibitors to selectively label small-molecule binding sites in whole proteomic samples. In principle, the ABP and small molecule will compete for similar binding sites, such that the small molecule will protect against modification by the ABP. Thus, after removal of the small molecule, the binding site for the ABP will be revealed, and a second probe can then be used to label the small-molecule binding sites selectively. To demonstrate this experimentally, we mapped the binding sites of the DPP4 inhibitor, IT, in a number of different tissue types.
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Affiliation(s)
- Tyzoon K Nomanbhoy
- ActivX Biosciences Inc., 11025 N. Torrey Pines Road #120, La Jolla, CA 92037, USA.
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12
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Abstract
Proteomics is a rapidly emerging set of key technologies that are being used to identify proteins and map their interactions in a cellular context. With the sequencing of the human genome, the scope of proteomics has shifted from protein identification and characterization to include protein structure, function and protein-protein interactions. Technologies used in proteomic research include two-dimensional gel electrophoresis, mass spectrometry, yeast two-hybrids screens, and computational prediction programs. While some of these technologies have been in use for a long time, they are currently being applied to study physiology and cellular processes in high-throughput formats. It is the high-throughput approach that defines and characterizes modern proteomics. In this review, we discuss the current status of these experimental and computational technologies relevant to the three major aspects of proteomics-characterization of proteomes, identification of proteins, and determination of protein function. We also briefly discuss the development of new proteomic technologies that are based on recent advances in analytical and biochemical techniques, engineering, microfabrication, and computational prowess. The integration of these advances with established technologies is invaluable for the drive toward a comprehensive understanding of protein structure and function in the cellular milieu.
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MESH Headings
- Electrophoresis, Gel, Two-Dimensional/instrumentation
- Electrophoresis, Gel, Two-Dimensional/methods
- Electrophoresis, Gel, Two-Dimensional/trends
- Gene Expression Profiling/instrumentation
- Gene Expression Profiling/methods
- Gene Expression Profiling/trends
- Protein Interaction Mapping/instrumentation
- Protein Interaction Mapping/methods
- Proteome/chemistry
- Proteome/genetics
- Proteome/physiology
- Sensitivity and Specificity
- Sequence Analysis, Protein/instrumentation
- Sequence Analysis, Protein/methods
- Sequence Analysis, Protein/trends
- Spectrometry, Mass, Electrospray Ionization/instrumentation
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Electrospray Ionization/trends
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/trends
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Affiliation(s)
- Martin L Yarmush
- Center for Engineering in Medicine/Surgical Services, Massachusetts General Hospital, Harvard Medical School, Boston 02114, USA.
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13
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Abstract
With the human genome sequence now determined, the field of molecular medicine is moving beyond genomics to proteomics. In the field of cancer research, the key question is: how can oncologists best use techniques of proteomics in basic research and clinical application? In the postgenomic era, proteomics promises the discovery of biomarkers and tumor markers for early detection and diagnosis, novel protein-based drug targets for anticancer therapy, and new endpoints for the assessment of therapeutic efficacy and toxicity. This review paper will explore key themes in proteomics and their application in clinical cancer research.
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Affiliation(s)
- W Wu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030-4009, USA.
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