1
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OFFGEL and GELFrEE fractionation: Novel liquid-phase protein recovery strategies in proteomics studies. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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2
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Dor M, Eperon S, Lalive PH, Guex-Crosier Y, Hamedani M, Salvisberg C, Turck N. Investigation of the global protein content from healthy human tears. Exp Eye Res 2019; 179:64-74. [DOI: 10.1016/j.exer.2018.10.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/01/2018] [Accepted: 10/11/2018] [Indexed: 01/03/2023]
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3
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Conti A, Alessio M. Comparative Proteomics for the Evaluation of Protein Expression and Modifications in Neurodegenerative Diseases. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2015; 121:117-52. [PMID: 26315764 DOI: 10.1016/bs.irn.2015.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Together with hypothesis-driven approaches, high-throughput differential proteomic analysis performed primarily not only in human cerebrospinal fluid and serum but also on protein content of other tissues (blood cells, muscles, peripheral nerves, etc.) has been used in the last years to investigate neurodegenerative diseases. Even if the goal for these analyses was mainly the discovery of neurodegenerative disorders biomarkers, the characterization of specific posttranslational modifications (PTMs) and the differential protein expression resulted in being very informative to better define the pathological mechanisms. In this chapter are presented and discussed the positive aspects and challenges of the outcomes of some of our investigations on neurological and neurodegenerative disease, in order to highlight the important role of protein PTMs studies in proteomics-based approaches.
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Affiliation(s)
- Antonio Conti
- Proteome Biochemistry, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Massimo Alessio
- Proteome Biochemistry, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy.
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4
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García-Otero N, Barciela-Alonso MC, Domínguez-González R, Herbello-Hermelo P, Moreda-Piñeiro A, Bermejo-Barrera P. Evaluation of offgel electrophoresis, electrothermal atomic absorption spectroscopy and inductively coupled plasma optical emission spectroscopy for trace metal analysis in marine plankton protein. Microchem J 2015. [DOI: 10.1016/j.microc.2014.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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5
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Conti A, Alessio M. Proteomics for Cerebrospinal Fluid Biomarker Identification in Parkinsons Disease: Methods and Critical Aspects. AIMS MEDICAL SCIENCE 2015. [DOI: 10.3934/medsci.2015.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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6
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Moreda-Piñeiro A, García-Otero N, Bermejo-Barrera P. A review on preparative and semi-preparative offgel electrophoresis for multidimensional protein/peptide assessment. Anal Chim Acta 2014; 836:1-17. [PMID: 24974865 DOI: 10.1016/j.aca.2014.04.053] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 04/23/2014] [Accepted: 04/27/2014] [Indexed: 11/29/2022]
Abstract
Mass spectrometry (MS) techniques are commonly used for protein identification and further analysis of selected protein spots after high resolution 2-D electrophoresis. Complementary gel-free approaches have been developed during the last few years and have shown to be useful tools in modern proteomics. The development and application of various gel-free electrophoresis devices for performing protein fractionation according to the pI differences is therefore a topic of interest. This review describes the current state of isoelectric focusing (IEF) gel-free electrophoresis based on the Agilent offgel 3100 fractionator. The review includes, therefore, (i) an overview on IEF as well as other previous IEF gel-free electrophoresis developments; (ii) offgel fundamentals and future trends; (iii) advantages and disadvantages of current offgel procedures; (iv) requirements of isolated protein pellets for further offgel fractionation; (v) offgel fraction requirements to perform the second dimensional analysis by advance electrophoresis and chromatographic techniques; and (vi) effect of the offgel operating conditions on the stability of metal-protein complexes.
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Affiliation(s)
- Antonio Moreda-Piñeiro
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain.
| | - Natalia García-Otero
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain
| | - Pilar Bermejo-Barrera
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain
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7
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Jha MK, Kim JH, Suk K. Proteome of brain glia: the molecular basis of diverse glial phenotypes. Proteomics 2013; 14:378-98. [PMID: 24124134 DOI: 10.1002/pmic.201300236] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/16/2013] [Accepted: 07/30/2013] [Indexed: 12/11/2022]
Abstract
Several different types of nonneuronal glial cells with diverse phenotypes are present in the CNS, and all have distinct indispensible functions. Although glial cells primarily provide neurons with metabolic and structural support in the healthy brain, they may switch phenotype from a "resting" to a "reactive" state in response to pathological insults. Furthermore, this reactive gliosis is an invariant feature of the pathogeneses of CNS maladies. The glial proteome serves as a signature of glial phenotype, and not only executes physiological functions, but also acts as a molecular mediator of the reactive glial phenotype. The glial proteome is also involved in intra- and intercellular communications as exemplified by glia-glia and neuron-glia interactions. The utilization of authoritative proteomic tools and the bioinformatic analyses have helped to profile the brain glial proteome and explore the molecular mechanisms of diverse glial phenotypes. Furthermore, technologic innovations have equipped the field of "glioproteomics" with refined tools for studies of the expression, interaction, and function of glial proteins in the healthy and in the diseased CNS. Glioproteomics is expected to contribute to the elucidation of the molecular mechanisms of CNS pathophysiology and to the discovery of biomarkers and theragnostic targets in CNS disorders.
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Affiliation(s)
- Mithilesh Kumar Jha
- Department of Pharmacology, Brain Science & Engineering Institute, Kyungpook National University School of Medicine, Daegu, South Korea
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8
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García-Otero N, Barciela-Alonso MC, Moreda-Piñeiro A, Bermejo-Barrera P. Study of extraction procedures for protein analysis in plankton samples by OFFGEL electrophoresis hyphenated with Lab-on-a-chip technology. Talanta 2013; 115:631-41. [DOI: 10.1016/j.talanta.2013.05.066] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/24/2013] [Accepted: 05/30/2013] [Indexed: 11/29/2022]
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9
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Sample loading influences studies comparing isoelectric focusing vs. strong cation exchange peptide fractionation. J Chromatogr A 2013; 1307:207-8. [DOI: 10.1016/j.chroma.2013.06.080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/26/2013] [Accepted: 06/30/2013] [Indexed: 01/28/2023]
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10
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Ma C, Zhao X, Han H, Tong W, Zhang Q, Qin P, Chang C, Peng B, Ying W, Qian X. N-linked glycoproteome profiling of human serum using tandem enrichment and multiple fraction concatenation. Electrophoresis 2013; 34:2440-50. [DOI: 10.1002/elps.201200662] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/05/2013] [Accepted: 03/08/2013] [Indexed: 11/08/2022]
Affiliation(s)
| | - Xinyuan Zhao
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
| | - Huanhuan Han
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
| | - Wei Tong
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
| | - Qi Zhang
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
| | - Peibin Qin
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
| | - Cheng Chang
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
| | - Bo Peng
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
| | - Wantao Ying
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
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11
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Millioni R, Franchin C, Tessari P, Polati R, Cecconi D, Arrigoni G. Pros and cons of peptide isolectric focusing in shotgun proteomics. J Chromatogr A 2013; 1293:1-9. [PMID: 23639126 DOI: 10.1016/j.chroma.2013.03.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 02/03/2023]
Abstract
In shotgun proteomics, protein mixtures are proteolytically digested before tandem mass spectrometry (MS/MS) analysis. Biological samples are generally characterized by a very high complexity, therefore a step of peptides fractionation before the MS analysis is essential. This passage reduces the sample complexity and increases its compatibility with the sampling performance of the instrument. Among all the existing approaches for peptide fractionation, isoelectric focusing has several peculiarities that are theoretically known but practically rarely exploited by the proteomics community. The main aim of this review is to draw the readers' attention to these unique qualities, which are not accessible with other common approaches, and that represent important tools to increase confidence in the identification of proteins and some post-translational modifications. The general characteristics of different methods to perform peptide isoelectric focusing with natural and artificial pH gradients, the existing instrumentation, and the informatics tools available for isoelectric point calculation are also critically described. Finally, we give some general conclusions on this strategy, underlying its principal limitations.
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Affiliation(s)
- Renato Millioni
- Department of Medicine, University of Padova, Via Giustiniani 2, 35121 Padova, Italy; Proteomics Center of Padova University, VIMM and Padova University Hospital, Via G. Orus 2/B, 35129 Padova, Italy.
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12
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Apori AA, Brozynski MN, El-Sayed IH, Herr AE. Microfluidic Validation of Diagnostic Protein Markers for Spontaneous Cerebrospinal Fluid Rhinorrhea. J Proteome Res 2013; 12:1254-65. [DOI: 10.1021/pr300928p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Akwasi A. Apori
- Department
of Bioengineering, University of California—Berkeley, Berkeley,
California
| | - Martina N. Brozynski
- Department
of Bioengineering, University of California—Berkeley, Berkeley,
California
| | - Ivan H. El-Sayed
- Department of
Otolaryngology, University of California—San Francisco, San
Francisco, California
| | - Amy E. Herr
- Department
of Bioengineering, University of California—Berkeley, Berkeley,
California
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13
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Ho JH, Lee OK, Fu YJ, Shih HT, Tseng CY, Chung CC, Han CL, Chen YJ. An iTRAQ proteomic study reveals an association between diet-induced enhanced fatty acid metabolism and the development of glucose intolerance in prediabetic mice. J Proteome Res 2013; 12:1120-33. [PMID: 23316967 DOI: 10.1021/pr300662j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
High-fat diet (HFD)-induced glucose intolerance and insulin resistance increases the chances of developing type-2 diabetes and cardiovascular disease. To study the mechanism(s) by which a HFD impairs glucose tolerance, we used a quantitative proteomic platform that integrated pI-based OFFGEL fractionation and iTRAQ labeling to profile the temporal changes in adipose membrane protein expression in mice fed a HFD for up to 8 months. Within 2 months of starting the diet, the mice adipose and liver tissues accumulated fat droplets, which contributed to subsequent insulin resistance and glucose intolerance within 6 months. The membrane proteomic delineation of such phenotypic expression resulted in quantification of 1713 proteins with 266, 343, and 125 differentially expressed proteins in 2-, 6-, and 8-month HFD-fed versus control mice, respectively. Pathway analysis of these differentially expressed proteins revealed the interplay between upregulation of fatty acid metabolism and downregulation of glucose metabolism. Substantial upregulation of adipose and liver carnitine palmitoyltransferase (Cpt) 1, the rate-limiting enzyme in the transport of long-chain fatty acids into mitochondria, occurred by 2 months. The increase in hepatic Cpt 1a expression was associated with a progressive decrease in glucose uptake as evidenced by downregulation of the liver glucose transporter protein (Glut) 2. Loss of glycogen storage was found in those hepatocytes full of fat droplets. Intriguingly, skeletal muscle Cpt 1b expression was unaltered by the HFD, whereas skeletal muscle Glut 4 and tyrosine phosphoryated insulin receptor substrate 1 (p-IRS1) were substantially upregulated at the same time as abnormal glucose metabolism developed in adipose and liver tissues. This study defines some of the molecular mechanisms as well as the relationship among adipose tissue, liver and skeletal muscle during development of HFD-induced glucose intolerance in vivo and identifies Cpt 1 as a potential drug target for the control or prevention of diabetes.
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Affiliation(s)
- Jennifer H Ho
- Graduate Institute of Clinical Medicine, Taipei Medical University, Taipei, Taiwan
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14
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Stoyanov A. IEF-based multidimensional applications in proteomics: Toward higher resolution. Electrophoresis 2012; 33:3281-90. [DOI: 10.1002/elps.201200221] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 08/20/2012] [Accepted: 08/21/2012] [Indexed: 01/08/2023]
Affiliation(s)
- Alexander Stoyanov
- Department of Pathology and Anatomical Sciences; University of Missouri; Columbia; MO; USA
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15
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Jafari M, Primo V, Smejkal GB, Moskovets EV, Kuo WP, Ivanov AR. Comparison of in-gel protein separation techniques commonly used for fractionation in mass spectrometry-based proteomic profiling. Electrophoresis 2012; 33:2516-26. [PMID: 22899259 PMCID: PMC4234072 DOI: 10.1002/elps.201200031] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Fractionation of complex samples at the cellular, subcellular, protein, or peptide level is an indispensable strategy to improve the sensitivity in mass spectrometry-based proteomic profiling. This study revisits, evaluates, and compares the most common gel-based protein separation techniques i.e. 1D SDS-PAGE, 1D preparative SDS-PAGE, IEF-IPG, and 2D-PAGE in their performance as fractionation approaches in nano LC-ESI-MS/MS analysis of a mixture of protein standards and mitochondrial extracts isolated from rat liver. This work demonstrates that all the above techniques provide complementary protein identification results, but 1D SDS-PAGE and IEF-IPG had the highest number of identifications. The IEF-IPG technique resulted in the highest average number of detected peptides per protein. The 2D-PAGE was evaluated as a protein fractionation approach. This work shows that the recovery of proteins and resulting proteolytic digests is highly dependent on the total volume of the gel matrix. The performed comparison of the fractionation techniques demonstrates the potential of a combination of orthogonal 1D SDS-PAGE and IEF-IPG for the improved sensitivity of profiling without significant decrease in throughput.
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Affiliation(s)
- Mohieddin Jafari
- HSPH Proteomics Resource, Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, USA
- School of Paramedical Science, Shahid Beheshti University of Medical Science, Tehran, Iran
- School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Vincent Primo
- Harvard Catalyst, The Harvard Clinical and Translational Science Center, Laboratory for Innovative Translational Technologies, Boston, MA, USA
| | - Gary B. Smejkal
- Harvard Catalyst, The Harvard Clinical and Translational Science Center, Laboratory for Innovative Translational Technologies, Boston, MA, USA
| | | | - Winston P. Kuo
- Harvard Catalyst, The Harvard Clinical and Translational Science Center, Laboratory for Innovative Translational Technologies, Boston, MA, USA
- Harvard School of Dental Medicine, Department of Developmental Biology, Boston, MA, USA
| | - Alexander R. Ivanov
- HSPH Proteomics Resource, Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, USA
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16
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Duša F, Křenková J, Moravcová D, Kahle V, Šlais K. Divergent-flow isoelectric focusing for separation and preparative analysis of peptides. Electrophoresis 2012; 33:1687-94. [DOI: 10.1002/elps.201100587] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Jana Křenková
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
| | - Dana Moravcová
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
| | - Vladislav Kahle
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
| | - Karel Šlais
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
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17
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Cao Z, Tang HY, Wang H, Liu Q, Speicher DW. Systematic comparison of fractionation methods for in-depth analysis of plasma proteomes. J Proteome Res 2012; 11:3090-100. [PMID: 22536952 DOI: 10.1021/pr201068b] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Discovery and validation of plasma biomarkers are quite challenging because of the high complexity and wide dynamic range of the plasma proteome. Current plasma protein profiling strategies usually use major protein immunodepletion and nanoLC-MS/MS as the first and final analytical steps, respectively, but additional fractionation is needed to detect and quantify low-abundance disease biomarkers. In this study, the performances of 1-D SDS-PAGE, peptide isoelectrofocusing, and peptide high pH reverse-phase chromatography for fractionation of immunodepleted human plasma were systematically compared by evaluating protein coverage, peptide resolution, and capacity to detect known low-abundance proteins. Trade-offs between increasing the number of fractions to improve proteome coverage and resulting decreases in throughput also were assessed. High pH reverse-phase HPLC exhibited the highest peptide resolution and yielded the best depth of analysis with detection of the largest number of known low-abundance proteins for a given level of fractionation. Another advantage of using high pH reverse-phase fractionation rather than 1-D SDS gels is that all fractionation steps except for abundant protein depletion occur at the peptide level, making this strategy more compatible with quantitative biomarker validation methods such as stable isotope dilution multiple reaction monitoring.
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Affiliation(s)
- Zhijun Cao
- Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute , Philadelphia, Pennsylvania, United States
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18
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Boschetti E, Chung MCM, Righetti PG. "The quest for biomarkers": are we on the right technical track? Proteomics Clin Appl 2011; 6:22-41. [PMID: 22213582 DOI: 10.1002/prca.201100039] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 10/01/2011] [Accepted: 11/15/2011] [Indexed: 12/19/2022]
Abstract
The discovery phase of biomarkers of diagnostic or therapeutic interest started a decade ago with the very rapid development of proteomic investigations. In spite of the development of innovative technologies and multiple approaches, the "harvest" is still modest. Various reasons justified the encountered difficulties and most of them have been circumvented by specific sample treatments or dedicated analytical approaches. Nevertheless, the situation of very modest biomarker discovery level did not change much. This review intends to specifically analyze the main approaches used for biomarker discovery phase and evaluate related advantages and disadvantages. Thus, preliminary sample treatments such as fractionation, depletion and reduction of dynamic concentration range will critically be discussed and then the main differential expression investigation methods analyzed. Combinations of technologies are also discussed along with possible proposals to federate associations of complementary technologies for better chances of success.
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Affiliation(s)
- Egisto Boschetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milano, Italy.
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19
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Pourhaghighi MR, Karzand M, Girault HH. Orthogonality of Two-Dimensional Separations Based on Conditional Entropy. Anal Chem 2011; 83:7676-81. [DOI: 10.1021/ac2017772] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mohammad Reza Pourhaghighi
- Laboratoire d’Electrochimie Physique et Analytique, Station 6, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Mohammad Karzand
- Information Theory Laboratory, Station 14, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Hubert H. Girault
- Laboratoire d’Electrochimie Physique et Analytique, Station 6, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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20
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Zeng Y, Shao D, Fang Y. On-Line Two-Dimension Liquid Chromatography for the Analysis of Ingredients in the Medicinal Preparation of Coptis Chinensis Franch. ANAL LETT 2011. [DOI: 10.1080/00032719.2010.526261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Krishnan S, Gaspari M, Corte AD, Bianchi P, Crescente M, Cerletti C, Torella D, Indolfi C, de Gaetano G, Donati MB, Rotilio D, Cuda G. OFFgel-based multidimensional LC-MS/MS approach to the cataloguing of the human platelet proteome for an interactomic profile. Electrophoresis 2011; 32:686-95. [DOI: 10.1002/elps.201000592] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 12/13/2010] [Accepted: 12/26/2010] [Indexed: 11/05/2022]
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22
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Mun J, Kim YH, Yu J, Bae J, Noh DY, Yu MH, Lee C. A proteomic approach based on multiple parallel separation for the unambiguous identification of an antibody cognate antigen. Electrophoresis 2011; 31:3428-36. [PMID: 20872419 DOI: 10.1002/elps.201000136] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Autoantibodies obtained from cancer patients have been identified as useful tools for cancer diagnostics, prognostics, and as potential targets for immunotherapy. Serological proteome analysis in combination with 2-DE is a classic strategy for identification of tumor-associated antigens in the serum of cancer patients. However, serological proteome analysis cannot always indicate the true antigen out of a complex proteome identified from a single protein spot because the most abundant protein is not always the most antigenic. To address this problem, we utilized multiple parallel separation (MPS) for proteome separation. The common identities present in the fractions obtained using different separation methods were regarded as the true antigens. The merit of our MPS technique was validated using anti-ARPC2 and anti-PTEN antibodies. Next, we applied the MPS technique for the identification of glycyl-tRNA synthetase as the cognate antigen for an autoantibody that was overexpressed in the plasma of breast cancer patients. These results reveal that MPS can unambiguously identify an antibody cognate antigen by reducing false-positives. Therefore, MPS could be used for the characterization of diagnostic antibodies raised in laboratory animals as well as autoantibodies isolated from diseased patients.
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Affiliation(s)
- Joohee Mun
- Functional Proteomics Center, Korea Institute of Science and Technology, Seongbuk, Seoul, Republic of Korea
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23
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Ly L, Wasinger VC. Protein and peptide fractionation, enrichment and depletion: Tools for the complex proteome. Proteomics 2011; 11:513-34. [DOI: 10.1002/pmic.201000394] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 10/03/2010] [Accepted: 10/18/2010] [Indexed: 12/28/2022]
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24
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Vaezzadeh AR, Briscoe AC, Steen H, Lee RS. One-step sample concentration, purification, and albumin depletion method for urinary proteomics. J Proteome Res 2010; 9:6082-9. [PMID: 20923230 DOI: 10.1021/pr100924s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Workflows in urinary proteomics studies are often complex and require many steps to enrich, purify, deplete, and separate the complex mixture. Many of these methods are laborious, are time-consuming, and have the potential for error. Although individual steps of these methods have been previously studied, their downstream compatibilities with fractionation technologies such as off-gel electrophoresis have not been investigated. We developed a one-step sample preparation workflow that simultaneously (i) concentrates proteins, (ii) purifies by removing salts and other low molecular weight compounds, and (iii) depletes (albumin) from urine samples. This simple and robust workflow can be multiplexed and is compatible with a diverse range of downstream multidimensional separation technologies. Additionally, because of its high reproducibility and flexibility in processing samples with different volumes and concentrations, it has the potential to be used for standardization of urinary proteomics studies, as well as for studying other body fluids of similar complexity.
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Affiliation(s)
- Ali R Vaezzadeh
- Department of Urology, Harvard Medical School, Boston, Massachusetts 02115, USA
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25
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Cologna SM, Russell WK, Lim PJ, Vigh G, Russell DH. Combining isoelectric point-based fractionation, liquid chromatography and mass spectrometry to improve peptide detection and protein identification. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1612-1619. [PMID: 20537905 PMCID: PMC2927729 DOI: 10.1016/j.jasms.2010.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 03/17/2010] [Accepted: 04/14/2010] [Indexed: 05/29/2023]
Abstract
The off-line coupling of an isoelectric trapping device termed membrane separated wells for isoelectric focusing and trapping (MSWIFT) to mass spectrometry-based proteomic studies is described. The MSWIFT is a high capacity, high-throughput, mass spectrometry-compatible isoelectric trapping device that provides isoelectric point (pI)-based separations of complex mixtures of peptides. In MSWIFT, separation and analyte trapping are achieved by migrating the peptide ions through membranes having fixed pH values until the peptide pI is bracketed by the pH values of adjacent membranes. The pH values of the membranes can be tuned, thus affording a high degree of experimental flexibility. Specific advantages of using MSWIFT for sample prefractionation include: (1) small sample volumes (approximately 200 microL), (2) customized membranes over a large pH range, (3) flexibility in the number of desired fractions, (4) membrane compatibility with a variety of solvents systems, and (5) resulting fractions do not require sample cleanup before MS analysis. Here, we demonstrate the utility of MSWIFT for mass spectrometry-based detection of peptides in improving dynamic range and the reduction of ion suppression effects for high-throughput separations of tryptic peptides.
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Affiliation(s)
| | | | | | | | - David H. Russell
- Address reprint requests to: Professor David H. Russell, Department of Chemistry, Texas A&M University, PO BOX 30012, College Station, TX 77842, Fax: (979) 845-9485, Phone: (979) 845-3345,
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26
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Wetterhall M, Zuberovic A, Hanrieder J, Bergquist J. Assessment of the partitioning capacity of high abundant proteins in human cerebrospinal fluid using affinity and immunoaffinity subtraction spin columns. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:1519-30. [PMID: 20444656 DOI: 10.1016/j.jchromb.2010.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 04/01/2010] [Accepted: 04/01/2010] [Indexed: 11/18/2022]
Abstract
The performance of three different affinity and immunoaffinity subtraction spin columns was investigated for the removal of the most abundant proteins in human cerebrospinal fluid (CSF). A pool of human CSF was processed with the spin columns and both the bound and flow through fractions were compared with each other and with intact CSF using 1D gel electrophoresis and nanoLC-MALDI-TOF/TOF-MS analysis. MASCOT MS/MS ionscores were compared before and after processing with the columns. The non-specific co-removal of proteins bound to the high abundant proteins, so called "sponge effect" was also examined for each spin column. The reproducibility of one of the spin columns, ProteomeLab IgY-12 proteome partitioning spin column, was further investigated by isobaric tags for relative and absolute quantification (iTRAQ) labeling and MS/MS analysis. Overall, 173 unique proteins were identified on a 95% MudPIT confidence scoring level. For all three spin columns, the number of proteins identified and their MASCOT scores were increased up to 10 times. The largest degree of non-specific protein removal was observed for a purely affinity based albumin removal column, where 28 other proteins also were present. The ProteomeLab IgY-12 proteome partitioning spin column showed very high reproducibility when combined with iTRAQ labeling and MS/MS analysis. The combined relative standard deviation (R.S.D.) for the high abundant protein removal, iTRAQ labeling and nanoLC-MALDI-TOF/TOF-MS analysis was less than 17.5%.
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Affiliation(s)
- Magnus Wetterhall
- Department of Physical and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
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Arrey TN, Rietschel B, Papasotiriou DG, Bornemann S, Baeumlisberger D, Karas M, Meyer B. Approaching the Complexity of Elastase-Digested Membrane Proteomes Using Off-Gel IEF/nLC-MALDI-MS/MS. Anal Chem 2010; 82:2145-9. [DOI: 10.1021/ac902776h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tabiwang N. Arrey
- Cluster of Excellence, “Macromolecular Complexes”, Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Benjamin Rietschel
- Cluster of Excellence, “Macromolecular Complexes”, Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Dimitrios G. Papasotiriou
- Cluster of Excellence, “Macromolecular Complexes”, Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Sandra Bornemann
- Cluster of Excellence, “Macromolecular Complexes”, Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Dominic Baeumlisberger
- Cluster of Excellence, “Macromolecular Complexes”, Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Michael Karas
- Cluster of Excellence, “Macromolecular Complexes”, Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Bjoern Meyer
- Cluster of Excellence, “Macromolecular Complexes”, Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
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28
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Fang Y, Robinson DP, Foster LJ. Quantitative Analysis of Proteome Coverage and Recovery Rates for Upstream Fractionation Methods in Proteomics. J Proteome Res 2010; 9:1902-12. [DOI: 10.1021/pr901063t] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuan Fang
- Centre for High-Throughput Biology, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Dale P. Robinson
- Centre for High-Throughput Biology, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J. Foster
- Centre for High-Throughput Biology, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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29
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Elschenbroich S, Ignatchenko V, Sharma P, Schmitt-Ulms G, Gramolini AO, Kislinger T. Peptide separations by on-line MudPIT compared to isoelectric focusing in an off-gel format: application to a membrane-enriched fraction from C2C12 mouse skeletal muscle cells. J Proteome Res 2010; 8:4860-9. [PMID: 19670906 DOI: 10.1021/pr900318k] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
High-resolution peptide separation is pivotal for successful shotgun proteomics. The need for capable techniques propels invention and improvement of ever more sophisticated approaches. Recently, Agilent Technologies has introduced the OFFGEL fractionator, which conducts peptide separation by isoelectric focusing in an off-gel setup. This platform has been shown to accomplish high resolution of peptides for diverse sample types, yielding valuable advantages over comparable separation techniques. In this study, we deliver the first comparison of the newly emerging OFFGEL approach to the well-established on-line MudPIT platform. Samples from a membrane-enriched fraction isolated from murine C2C12 cells were subjected to replicate analysis by OFFGEL (12 fractions, pH 3-10) followed by RP-LC-MS/MS or 12-step on-line MudPIT. OFFGEL analyses yielded 1398 proteins (identified by 10,269 peptides), while 1428 proteins (11,078 peptides) were detected with the MudPIT approach. Thus, our data shows that both platforms produce highly comparable results in terms of protein/peptide identifications and reproducibility for the sample type analyzed. We achieve more accurate peptide focusing after OFFGEL fractionation with 88% of all peptides binned to a single fraction, as compared to 61% of peptides detected in only one step in MudPIT analyses. Our study suggests that both platforms are equally capable of high quality peptide separation of a sample with medium complexity, rendering them comparably valuable for comprehensive proteomic analyses.
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30
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Dayon L, Turck N, Kienle S, Schulz-Knappe P, Hochstrasser DF, Scherl A, Sanchez JC. Isobaric Tagging-Based Selection and Quantitation of Cerebrospinal Fluid Tryptic Peptides with Reporter Calibration Curves. Anal Chem 2010; 82:848-58. [DOI: 10.1021/ac901854k] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Loïc Dayon
- Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, and Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
| | - Natacha Turck
- Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, and Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
| | - Stefan Kienle
- Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, and Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
| | - Peter Schulz-Knappe
- Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, and Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
| | - Denis F. Hochstrasser
- Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, and Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
| | - Alexander Scherl
- Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, and Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
| | - Jean-Charles Sanchez
- Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, and Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
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31
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Hood BL, Stewart NA, Conrads TP. Development of High-Throughput Mass Spectrometry–Based Approaches for Cancer Biomarker Discovery and Implementation. Clin Lab Med 2009; 29:115-38. [DOI: 10.1016/j.cll.2009.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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