1
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Cep131 overexpression promotes centrosome amplification and colon cancer progression by regulating Plk4 stability. Cell Death Dis 2019; 10:570. [PMID: 31358734 PMCID: PMC6662699 DOI: 10.1038/s41419-019-1778-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/22/2022]
Abstract
The initiation of centrosome duplication is regulated by the Plk4/STIL/hsSAS-6 axis; however, the involvement of other centrosomal proteins in this process remains unclear. In this study, we demonstrate that Cep131 physically interacts with Plk4 following phosphorylation of residues S21 and T205. Localizing at the centriole, phosphorylated Cep131 has an increased capability to interact with STIL, leading to further activation and stabilization of Plk4 for initiating centrosome duplication. Moreover, we found that Cep131 overexpression resulted in centrosome amplification by excessive recruitment of STIL to the centriole and subsequent stabilization of Plk4, contributing to centrosome amplification. The xenograft mouse model also showed that both centrosome amplification and colon cancer growth were significantly increased by Cep131 overexpression. These findings demonstrate that Cep131 is a novel substrate of Plk4, and that phosphorylation or dysregulated Cep131 overexpression promotes Plk4 stabilization and therefore centrosome amplification, establishing a perspective in understanding a relationship between centrosome amplification and cancer development.
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2
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Ho K, Xiao Q, Fach EM, Hulmes JD, Bethea D, Opiteck GJ, Lu JY, Kayne PS, Hefta SA. Semi-Automated Sample Preparation for Plasma Proteomics. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.jala.2004.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The discovery of new biomarkers will be an essential step to enhance our ability to better diagnose and treat human disease. The proteomics research community has recently increased its use of human blood (plasma/serum) as a sample source for these discoveries. However, while blood is fairly non-invasive and readily available as a specimen, it is not easily analyzed by liquid chromatography (LC)/mass spectrometry (MS), because of its complexity. Therefore, sample preparation is a crucial step prior to the analysis of blood. This sample preparation must also be standardized in order to gain the most information from these valuable samples and to ensure reproducibility. We have designed a semi-automated and highly parallel procedure for the preparation of human plasma samples. Our process takes the samples through eight successive steps before analysis by LC/MS: (1) receipt, (2) reformatting, (3) filtration, (4) depletion, (5) concentration determination and normalization, (6) digestion, (7) extraction, and (8) randomization, triplication, and lyophilization. These steps utilize a number of different liquid handlers and liquid chromatography (LC) systems. This process enhances our ability to discover new biomarkers from human plasma.
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Affiliation(s)
| | - Qing Xiao
- Bristol-Myers Squibb, Clinical Discovery, Clinical Discovery Technologies, Hopewell, NJ
| | - Estelle M. Fach
- Bristol-Myers Squibb, Clinical Discovery, Clinical Discovery Technologies, Hopewell, NJ
| | - Jeffrey D. Hulmes
- Bristol-Myers Squibb, Clinical Discovery, Clinical Discovery Technologies, Hopewell, NJ
| | - Deidra Bethea
- Bristol-Myers Squibb, Clinical Discovery, Clinical Discovery Technologies, Hopewell, NJ
| | - Gregory J. Opiteck
- Bristol-Myers Squibb, Clinical Discovery, Clinical Discovery Technologies, Hopewell, NJ
| | - Joseph Y. Lu
- Bristol-Myers Squibb, Applied Biotechnology, Applied Genomics, Hopewell, NJ
| | - Paul S. Kayne
- Bristol-Myers Squibb, Applied Biotechnology, Applied Genomics, Hopewell, NJ
| | - Stanley A. Hefta
- Bristol-Myers Squibb, Clinical Discovery, Clinical Discovery Technologies, Hopewell, NJ
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3
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Sabbagh B, Mindt S, Neumaier M, Findeisen P. Clinical applications of MS-based protein quantification. Proteomics Clin Appl 2016; 10:323-45. [DOI: 10.1002/prca.201500116] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/18/2015] [Accepted: 12/30/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Bassel Sabbagh
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Sonani Mindt
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Michael Neumaier
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Peter Findeisen
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
- MVZ Labor Dr. Limbach und Kollegen; Heidelberg Germany
- Working Group Proteomics of the German United Society for Clinical Chemistry and Laboratory Medicine e.V. (DGKL); Bonn Germany
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4
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Liu F, Koval M, Ranganathan S, Fanayan S, Hancock WS, Lundberg EK, Beavis RC, Lane L, Duek P, McQuade L, Kelleher NL, Baker MS. Systems Proteomics View of the Endogenous Human Claudin Protein Family. J Proteome Res 2016; 15:339-59. [PMID: 26680015 DOI: 10.1021/acs.jproteome.5b00769] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Claudins are the major transmembrane protein components of tight junctions in human endothelia and epithelia. Tissue-specific expression of claudin members suggests that this protein family is not only essential for sustaining the role of tight junctions in cell permeability control but also vital in organizing cell contact signaling by protein-protein interactions. How this protein family is collectively processed and regulated is key to understanding the role of junctional proteins in preserving cell identity and tissue integrity. The focus of this review is to first provide a brief overview of the functional context, on the basis of the extensive body of claudin biology research that has been thoroughly reviewed, for endogenous human claudin members and then ascertain existing and future proteomics techniques that may be applicable to systematically characterizing the chemical forms and interacting protein partners of this protein family in human. The ability to elucidate claudin-based signaling networks may provide new insight into cell development and differentiation programs that are crucial to tissue stability and manipulation.
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Affiliation(s)
| | - Michael Koval
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, and Department of Cell Biology, Emory University School of Medicine , 205 Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, Georgia 30322, United States
| | | | | | - William S Hancock
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Emma K Lundberg
- SciLifeLab, School of Biotechnology, Royal Institute of Technology (KTH) , SE-171 21 Solna, Stockholm, Sweden
| | - Ronald C Beavis
- Department of Biochemistry and Medical Genetics, University of Manitoba , 744 Bannatyne Avenue, Winnipeg, Manitoba R3E 0W3, Canada
| | - Lydie Lane
- SIB-Swiss Institute of Bioinformatics , CMU - Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Paula Duek
- SIB-Swiss Institute of Bioinformatics , CMU - Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | | | - Neil L Kelleher
- Department of Chemistry, Department of Molecular Biosciences, and Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
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5
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Pleshakova TO, Shumov ID, Ivanov YD, Malsagova KA, Kaysheva AL, Archakov AI. [AFM-based technologies as the way towards the reverse Avogadro number]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 61:239-53. [PMID: 25978390 DOI: 10.18097/pbmc20156102239] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Achievement of the concentration detection limit for proteins at the level of the reverse Avogadro number determines the modern development of proteomics. In this review, the possibility of approximating the reverse Avogadro number by using nanotechnological methods (AFM-based fishing with mechanical and electrical stimulation, nanowire detectors, and other methods) are discussed. The ability of AFM to detect, count, visualize and characterize physico-chemical properties of proteins at concentrations up to 10(-17)-10(-18) M is demonstrated. The combination of AFM-fishing with mass-spectrometry allows the identification of proteins not only in pure solutions, but also in multi-component biological fluids (serum). The possibilities to improve the biospecific fishing efficiency by use of SOMAmers in both AFM and nanowire systems are discussed. The paper also provides criteria for evaluation of the sensitivity of fishing-based detection systems. The fishing efficiency depending on the detection system parameters is estimated. The practical implementation of protein fishing depending on the ratio of the sample solution volume and the surface of the detection system is discussed. The advantages and disadvantages of today's promising nanotechnological protein detection methods implemented on the basis of these schemes.
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Affiliation(s)
| | - I D Shumov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - Yu D Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - A L Kaysheva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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6
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Pleshakova TO, Shumov ID, Ivanov YD, Malsagova KA, Kaysheva AL, Archakov AI. AFM-based technologies as the way towards the reverse Avogadro number. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2015. [DOI: 10.1134/s1990750815030063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Effect of nitric oxide on conformational changes of ovalbumin accompanying self-assembly into non-disease-associated fibrils. Nitric Oxide 2015; 47:1-9. [DOI: 10.1016/j.niox.2015.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 01/29/2015] [Accepted: 02/05/2015] [Indexed: 11/22/2022]
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8
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Use of generic LC–MS/MS assays to characterize atypical PK profile of a biotherapeutic monoclonal antibody. Bioanalysis 2014; 6:3225-35. [DOI: 10.4155/bio.14.167] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background: The fully human monoclonal antibody mAb123, which binds to and neutralizes chemokine motif ligand-21 (CCL21) displays a faster clearance in cynomolgus monkey compared with typical IgG kinetics. A direct and an immunoaffinity LC–MS/MS assays were developed to compare with the previously established ligand-binding assays (LBAs). Results: A strong correlation of LC–MS/MS pharmacokinetic data with LBA data confirmed the rapid drug disposition of mAb123 is an intrinsic property of the molecule, rather than interference of anti-mAb123 antibodies in the LBA. Conclusion: The data illustrate that in cases of unexpected results from LBA, application of orthogonal bioanalytical techniques such as LC–MS/MS can help in in interpretation of pharmacokinetic as determined by LBAs.
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9
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You J, Willcox MD, Madigan MC, Wasinger V, Schiller B, Walsh BJ, Graham PH, Kearsley JH, Li Y. Tear fluid protein biomarkers. Adv Clin Chem 2014; 62:151-96. [PMID: 24772667 DOI: 10.1016/b978-0-12-800096-0.00004-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The tear film covers and protects the ocular surface. It contains various molecules including a large variety of proteins. The protein composition of the tear fluid can change with respect to various local and systemic diseases. Prior to the advent of the proteomic era, tear protein analysis was limited to a few analytical techniques, the most common of which was immunoelectrophoresis, an approach dependent on antibody availability. Using proteomics, hundreds of tear proteins could potentially be identified and subsequently studied. Although detection of low-abundance proteins in the complex tear proteome remains a challenge, advances in sample fractionation and mass spectrometry have greatly enhanced our ability to detect these proteins. With increasing proteomic applications, tears show great potential as biomarkers in the development of clinical assays for various human diseases. In this chapter, we discuss the structure and functions of the tear film and methods for its collection. We also summarize potential tear protein biomarkers identified using proteomic techniques for both ocular and systemic diseases. Finally, modern proteomic techniques for tear biomarker research and future challenges are explored.
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10
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Tam SW, Pirro J, Hinerfeld D. Depletion and fractionation technologies in plasma proteomic analysis. Expert Rev Proteomics 2014; 1:411-20. [PMID: 15966838 DOI: 10.1586/14789450.1.4.411] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This review intends to survey the traditional and current technologies in the depletion and subfractionation of plasma proteins for further analyses. The value of depletion aims to enrich low-abundant proteins by removing highly abundant proteins, such as albumin or immunoglobulin G, from plasma. With this approach, one can examine both the resulting high- and low-abundant protein fractions. The depleted protein population can be further subfractionated based on their isoelectric point ranges, creating a more discrete pool of proteins for detailed post-translational modification studies by methods such as 2D gel electrophoresis and mass spectrometry. The concept of divide to conquer will greatly enhance our ability to identify and characterize low-abundant proteins and cleaved peptides from plasma as important diagnostic markers or potential drug targets. This can potentially reverse the decline in the development of new plasma diagnostic tests.
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Affiliation(s)
- Sun W Tam
- Charles River Proteomic Services, 57 Union Street, Worcester, MA 01608, USA.
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11
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Ackermann BL, Berna MJ. Coupling immunoaffinity techniques with MS for quantitative analysis of low-abundance protein biomarkers. Expert Rev Proteomics 2014; 4:175-86. [PMID: 17425454 DOI: 10.1586/14789450.4.2.175] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The field of proteomics is rapidly turning towards targeted mass spectrometry (MS) methods to quantify putative markers or known proteins of biological interest. Historically, the enzyme-linked immunosorbent assay (ELISA) has been used for targeted protein analysis, but, unfortunately, it is limited by the excessive time required for antibody preparation, as well as concerns over selectivity. Despite the ability of proteomics to deliver increasingly quantitative measurements, owing to limited sensitivity, the leads generated are in the microgram per milliliter range. This stands in stark contrast to ELISA, which is capable of quantifying proteins at low picogram per milliliter levels. To bridge this gap, targeted liquid chromatography (LC) tandem MS (MS/MS) analysis of tryptic peptide surrogates using selected reaction monitoring detection has emerged as a viable option for rapid quantification of target proteins. The precision of this approach has been enhanced by the use of stable isotope-labeled peptide internal standards to compensate for variation in recovery and the influence of differential matrix effects. Unfortunately, the complexity of proteinaceous matrices, such as plasma, limits the usefulness of this approach to quantification in the mid-nanogram per milliliter range (medium-abundance proteins). This article reviews the current status of LC/MS/MS using selected reaction monitoring for protein quantification, and specifically considers the use of a single antibody to achieve superior enrichment of either the protein target or the released tryptic peptide. Examples of immunoaffinity-assisted LC/MS/MS are reviewed that demonstrate quantitative analysis of low-abundance proteins (subnanogram per milliliter range). A strategy based on this technology is proposed for the expedited evaluation of novel protein biomarkers, which relies on the synergy created from the complementary nature of MS and ELISA.
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Affiliation(s)
- Bradley L Ackermann
- Eli Lilly & Company, Drug Disposition, Greenfield Laboratories, Greenfield, IN 46140, USA.
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12
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Wu L, Han DK. Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics. Expert Rev Proteomics 2014; 3:611-9. [PMID: 17181475 DOI: 10.1586/14789450.3.6.611] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Protein profiling using mass spectrometry technology has emerged as a powerful method for analyzing large-scale protein-expression patterns in cells and tissues. However, a number of challenges are present in proteomics research, one of the greatest being the high degree of protein complexity and huge dynamic range of proteins expressed in the complex biological mixtures, which exceeds six orders of magnitude in cells and ten orders of magnitude in body fluids. Since many important signaling proteins have low expression levels, methods to detect the low-abundance proteins in a complex sample are required. This review will focus on the fundamental fractionation and mass spectrometry techniques currently used for large-scale shotgun proteomics research.
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Affiliation(s)
- Linfeng Wu
- University of Connecticut, School of Medicine, Department of Cell Biology, Farmington, Connecticut, CT 06030, USA.
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13
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Bai HX, Liu XH, Yang F, Yang XR, Wang EK. A Prefractionation Method Can Separate Proteomic Proteins into Multigroups by One-step Extraction. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201000140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Park KS, Cha Y, Kim CH, Ahn HJ, Kim D, Ko S, Kim KH, Chang MY, Ko JH, Noh YS, Han YM, Kim J, Song J, Kim JY, Tesar PJ, Lanza R, Lee KA, Kim KS. Transcription elongation factor Tcea3 regulates the pluripotent differentiation potential of mouse embryonic stem cells via the Lefty1-Nodal-Smad2 pathway. Stem Cells 2013; 31:282-92. [PMID: 23169579 DOI: 10.1002/stem.1284] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/25/2012] [Indexed: 01/07/2023]
Abstract
Self-renewal and pluripotency are hallmark properties of pluripotent stem cells, including embryonic stem cells (ESCs) and iPS cells. Previous studies revealed the ESC-specific core transcription circuitry and showed that these core factors (e.g., Oct3/4, Sox2, and Nanog) regulate not only self-renewal but also pluripotent differentiation. However, it remains elusive how these two cell states are regulated and balanced during in vitro replication and differentiation. Here, we report that the transcription elongation factor Tcea3 is highly enriched in mouse ESCs (mESCs) and plays important roles in regulating the differentiation. Strikingly, altering Tcea3 expression in mESCs did not affect self-renewal under nondifferentiating condition; however, upon exposure to differentiating cues, its overexpression impaired in vitro differentiation capacity, and its knockdown biased differentiation toward mesodermal and endodermal fates. Furthermore, we identified Lefty1 as a downstream target of Tcea3 and showed that the Tcea3-Lefty1-Nodal-Smad2 pathway is an innate program critically regulating cell fate choices between self-replication and differentiation commitment. Together, we propose that Tcea3 critically regulates pluripotent differentiation of mESCs as a molecular rheostat of Nodal-Smad2/3 signaling.
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Affiliation(s)
- Kyung-Soon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea.
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15
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Arsene CG, Schulze D, Kratzsch J, Henrion A. High sensitivity mass spectrometric quantification of serum growth hormone by amphiphilic peptide conjugation. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1554-1560. [PMID: 23280743 DOI: 10.1002/jms.3094] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Revised: 08/15/2012] [Accepted: 08/16/2012] [Indexed: 06/01/2023]
Abstract
Amphiphilic peptide conjugation affords a significant increase in sensitivity with protein quantification by electrospray-ionization mass spectrometry. This has been demonstrated for human growth hormone (GH) in serum using N-(3-iodopropyl)-N,N,N-dimethyloctylammonium iodide as derivatizing reagent. The signal enhancement achieved is up to a factor of 5-6 and enables extension of the applicable concentration range down to the very low concentrations (≤ 1.0 µg/L) as encountered with clinical glucose suppression tests for patients with acromegaly. The method has been validated using a set of serum samples spiked with known amounts of recombinant 22 kDa GH in the range of 0.48 to 7.65 µg/L. The coefficient of variation (CV) calculated based on the deviation of results from the expected concentrations was 3.5%. The limit of detection (LoD) was determined as 0.1 µg/L and the limit of quantification (LoQ) as 0.4 µg/L. The potential of the method as a tool in clinical practice has been demonstrated with patient samples of about 1 µg/L.
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Affiliation(s)
- Cristian G Arsene
- Physikalisch-Technische Bundesanstalt, D-38116, Braunschweig, Germany.
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16
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The molecular basis of wound healing processes induced by lithospermi radix: a proteomics and biochemical analysis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2012; 2012:508972. [PMID: 23024692 PMCID: PMC3457683 DOI: 10.1155/2012/508972] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 07/16/2012] [Accepted: 07/18/2012] [Indexed: 12/20/2022]
Abstract
Lithospermi Radix (LR) is an effective traditional Chinese herb in various types of wound healing; however, its mechanism of action remains unknown. A biochemical and proteomic platform was generated to explore the biological phenomena associated with LR and its active component shikonin. We found that both LR ethanol extracts and shikonin are able to promote cell proliferation by up to 25%. The results of proteomic analysis revealed that twenty-two differentially expressed proteins could be identified when fibroblast cells were treated with LR or shikonin. The functions of those proteins are associated with antioxidant activity, antiapoptosis activity, the regulation of cell mobility, the secretion of collagen, the removal of abnormal proteins, and the promotion of cell proliferation, indicating that the efficacy of LR in wound healing may be derived from a synergistic effect on a number of factors induced by the herbal medicine. Furthermore, an animal model confirmed that LR is able to accelerate wound healing on the flank back of the SD rats. Together these findings help to pinpoint the molecular basis of wound healing process induced by LR.
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17
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Lee SW, Kim IJ, Jeong BY, Choi MH, Kim JY, Kwon KH, Lee JW, Yu A, Shin MG. Use of MDLC-DIGE and LC-MS/MS to identify serum biomarkers for complete remission in patients with acute myeloid leukemia. Electrophoresis 2012; 33:1863-72. [DOI: 10.1002/elps.201200047] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Seung-Won Lee
- Department of Anatomy, Chonnam National University Medical School; Gwangju; Korea
| | - In Jae Kim
- Department of Anatomy, Chonnam National University Medical School; Gwangju; Korea
| | - Bo Yoon Jeong
- National Cancer Control Institute; National Cancer Center; Goyang-si; Korea
| | - Mun-Ho Choi
- Department of Computer Science; College of Engineering; Chonnam National University; Gwangju; Korea
| | - Jin Young Kim
- Division of Mass Spectrometry Research; Korea Basic Science Institute; Ochang; Korea
| | - Kyung-Hoon Kwon
- Division of Mass Spectrometry Research; Korea Basic Science Institute; Ochang; Korea
| | - Jae Won Lee
- Department of Statistics; Korea University; Seoul; Korea
| | - Ami Yu
- Department of Statistics; Korea University; Seoul; Korea
| | - Myung-Geun Shin
- Laboratory Medicine; Chonnam National University Medical School; Gwangju; Korea
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18
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Replacing immunoassays with tryptic digestion-peptide immunoaffinity enrichment and LC-MS/MS. Bioanalysis 2012; 4:281-90. [PMID: 22303832 DOI: 10.4155/bio.11.319] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
For decades, immunoassays have provided the framework for protein biomarker studies in clinical medicine and in therapeutic monitoring for drug development. At the same time, investigators have uncovered many issues that make immunoassays unreliable in many human serum and plasma samples. LC-MS/MS after tryptic digestion of proteins is potentially an attractive solution, but the sensitivity of the method is not sufficient to measure many important low-abundance proteins directly. The use of antipeptide antibodies to immunoenrich peptides of interest can improve the sensitivity of the approach, greatly simplify the matrix enabling shortened chromatographic runs, and facilitate the multiplexed quantification of analytes, which could reduce the costs of quantitative protein measurements in complex specimens. We provide an overview of the method and the steps needed to develop an assay. In addition, we review the efforts to make this method generally more applicable.
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19
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Monagle P, Chan AKC, Goldenberg NA, Ichord RN, Journeycake JM, Nowak-Göttl U, Vesely SK. Antithrombotic therapy in neonates and children: Antithrombotic Therapy and Prevention of Thrombosis, 9th ed: American College of Chest Physicians Evidence-Based Clinical Practice Guidelines. Chest 2012; 141:e737S-e801S. [PMID: 22315277 DOI: 10.1378/chest.11-2308] [Citation(s) in RCA: 950] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Neonates and children differ from adults in physiology, pharmacologic responses to drugs, epidemiology, and long-term consequences of thrombosis. This guideline addresses optimal strategies for the management of thrombosis in neonates and children. METHODS The methods of this guideline follow those described in the Methodology for the Development of Antithrombotic Therapy and Prevention of Thrombosis Guidelines: Antithrombotic Therapy and Prevention of Thrombosis, 9th ed: American College of Chest Physicians Evidence-Based Clinical Practice Guidelines. RESULTS We suggest that where possible, pediatric hematologists with experience in thromboembolism manage pediatric patients with thromboembolism (Grade 2C). When this is not possible, we suggest a combination of a neonatologist/pediatrician and adult hematologist supported by consultation with an experienced pediatric hematologist (Grade 2C). We suggest that therapeutic unfractionated heparin in children is titrated to achieve a target anti-Xa range of 0.35 to 0.7 units/mL or an activated partial thromboplastin time range that correlates to this anti-Xa range or to a protamine titration range of 0.2 to 0.4 units/mL (Grade 2C). For neonates and children receiving either daily or bid therapeutic low-molecular-weight heparin, we suggest that the drug be monitored to a target range of 0.5 to 1.0 units/mL in a sample taken 4 to 6 h after subcutaneous injection or, alternatively, 0.5 to 0.8 units/mL in a sample taken 2 to 6 h after subcutaneous injection (Grade 2C). CONCLUSIONS The evidence supporting most recommendations for antithrombotic therapy in neonates and children remains weak. Studies addressing appropriate drug target ranges and monitoring requirements are urgently required in addition to site- and clinical situation-specific thrombosis management strategies.
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Affiliation(s)
- Paul Monagle
- Haematology Department, The Royal Children's Hospital, Department of Paediatrics, The University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Anthony K C Chan
- Department of Pediatrics, McMaster University, Hamilton, ON, Canada
| | - Neil A Goldenberg
- Department of Pediatrics, Section of Hematology/Oncology/Bone Marrow Transplantation and Mountain States Regional Hemophilia and Thrombosis Center, University of Colorado, Aurora, CO
| | - Rebecca N Ichord
- Department of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Janna M Journeycake
- Department of Pediatrics, University of Texas Southwestern Medical Center at Dallas, Dallas, TX
| | - Ulrike Nowak-Göttl
- Thrombosis and Hemostasis Unit, Institute of Clinical Chemistry, University Hospital Kiel, Kiel, Germany
| | - Sara K Vesely
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK.
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A Study of the Wound Healing Mechanism of a Traditional Chinese Medicine, Angelica sinensis, Using a Proteomic Approach. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2012; 2012:467531. [PMID: 22536285 PMCID: PMC3319019 DOI: 10.1155/2012/467531] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 01/19/2012] [Indexed: 11/18/2022]
Abstract
Angelica sinensis (AS) is a traditional Chinese herbal medicine that has been formulated clinically to treat various form of skin trauma and to help wound healing. However, the mechanism by which it works remains a mystery. In this study we have established a new platform to evaluate the pharmacological effects of total AS herbal extracts as well as its major active component, ferulic acid (FA), using proteomic and biochemical analysis. Cytotoxic and proliferation-promoting concentrations of AS ethanol extracts (AS extract) and FA were tested, and then the cell extracts were subject to 2D PAGE analysis. We found 51 differentially expressed protein spots, and these were identified by mass spectrometry. Furthermore, biomolecular assays, involving collagen secretion, migration, and ROS measurements, gave results that are consistent with the proteomic analysis. In this work, we have demonstrated a whole range of pharmacological effects associated with Angelica sinensis that might be beneficial when developing a wound healing pharmaceutical formulation for the herbal medicine.
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Omali NB, Zhao Z, Zhong L, Raftery MJ, Zhu H, Ozkan J, Willcox M. Quantification of protein deposits on silicone hydrogel materials using stable-isotopic labeling and multiple reaction monitoring. BIOFOULING 2012; 28:697-709. [PMID: 22784025 DOI: 10.1080/08927014.2012.702763] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This study was designed to use multiple reaction monitoring (MRM) for accurate quantification of contact lens protein deposits. Worn lenses used with a multipurpose disinfecting solution were collected after wear. Individual contact lenses were extracted and then digested with trypsin. MRM in conjunction with stable-isotope-labeled peptide standards was used for protein quantification. The results show that lysozyme was the major protein detected from both lens types. The amount of protein extracted from contact lenses was affected by the lens material. Except for keratin-1 (0.83 ± 0.61 vs 0.77 ± 0.20, p = 0.81) or proline rich protein-4 (0.11 ± 0.04 vs 0.15 ± 0.12, p = 0.97), the amounts of lysozyme, lactoferrin, or lipocalin-1 extracted from balafilcon A lenses (12.9 ± 9.01, 0.84 ± 0.50 or 2.06 ± 1.6, respectively) were significantly higher than that extracted from senofilcon A lenses (0.88 ± 0.13, 0.50 ± 0.10 or 0.27 ± 0.23, respectively) (p < 0.05). The amount of protein extracted from contact lenses was dependent on both the individual wearer and the contact lens material. This may have implications for the development of clinical responses during lens wear for different people and with different types of contact lenses. The use of MRM-MS is a powerful analytical tool for the quantification of specific proteins from single contact lenses after wear.
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Harbourt DE, Fallon JK, Ito S, Baba T, Ritter JK, Glish GL, Smith PC. Quantification of human uridine-diphosphate glucuronosyl transferase 1A isoforms in liver, intestine, and kidney using nanobore liquid chromatography-tandem mass spectrometry. Anal Chem 2011; 84:98-105. [PMID: 22050083 DOI: 10.1021/ac201704a] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Uridine-disphosphate glucuronosyl transferase (UGT) enzymes catalyze the formation of glucuronide conjugates of phase II metabolism. Methods for absolute quantification of UGT1A1 and UGT1A6 were previously established utilizing stable isotope peptide internal standards with liquid chromatography-tandem mass spectrometry (LC-MS/MS). The current method expands upon this by quantifying eight UGT1A isoforms by nanobore high-performance liquid chromatography (HPLC) coupled with a linear ion trap time-of-flight mass spectrometer platform. Recombinant enzyme digests of each of the isoforms were used to determine assay linearity and detection limits. Enzyme expression level in human liver, kidney, and intestinal microsomal protein was determined by extrapolation from spiked stable isotope standards. Intraday and interday variability was <25% for each of the enzyme isoforms. Enzyme expression varied from 3 to 96 pmol/mg protein in liver and intestinal microsomal protein digests. Expression levels of UGT1A7, 1A8, and 1A10 were below detection limits (<1 pmol/mg protein) in human liver microsome (HLMs). In kidney microsomes the expression of UGT1A3 was below detection limits, but levels of UGT1A4, 1A7, 1A9, and 1A10 protein were higher relative to that of liver, suggesting that renal glucuronidation could be a significant factor in renal elimination of glucuronide conjugates. This novel method allows quantification of all nine UGT1A isoforms, many previously not amenable to measurement with traditional methods such as immunologically based assays. Quantitative measurement of proteins involved in drug disposition, such as the UGTs, significantly improves the ability to evaluate and interpret in vitro and in vivo studies in drug development.
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Affiliation(s)
- David E Harbourt
- Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina 27599, USA
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Austin RJ, Kuestner RE, Chang DK, Madden KR, Martin DB. SILAC compatible strain of Pichia pastoris for expression of isotopically labeled protein standards and quantitative proteomics. J Proteome Res 2011; 10:5251-9. [PMID: 21942632 DOI: 10.1021/pr200551e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The methylotrophic yeast Pichia pastoris is a powerful eukaryotic platform for the production of heterologous protein. Recent publication of the P. pastoris genome has facilitated strain development toward biopharmaceutical and environmental science applications and has advanced the organism as a model system for the study of peroxisome biogenesis and methanol metabolism. Here we report the development of a P. pastoris arg-/lys- auxotrophic strain compatible with SILAC (stable isotope labeling by amino acids in cell culture) proteomic studies, which is capable of generating large quantities of isotopically labeled protein for mass spectrometry-based biomarker measurements. We demonstrate the utility of this strain to produce high purity human serum albumin uniformly labeled with isotopically heavy arginine and lysine. In addition, we demonstrate the first quantitative proteomic analysis of methanol metabolism in P. pastoris, reporting new evidence for a malate-aspartate NADH shuttle mechanism in the organism. This strain will be a useful model organism for the study of metabolism and peroxisome generation.
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Affiliation(s)
- Ryan J Austin
- Institute for Systems Biology, Seattle, WA 98109, USA
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Zhang Y, Li N, Brown PW, Ozer JS, Lai Y. Liquid chromatography/tandem mass spectrometry based targeted proteomics quantification of P-glycoprotein in various biological samples. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:1715-1724. [PMID: 21598331 DOI: 10.1002/rcm.5026] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
P-Glycoprotein (P-gp/ABCB1) is expressed in membrane barriers to exclude pharmacological substrates from cells, and therefore influences the ADME/Tox properties and efficacy of therapeutics. In the present study, a liquid chromatography/tandem mass spectrometry (LC/MS/MS)-mediated targeted proteomics was developed to quantitate P-gp protein. With the aid of in silico predictive tools, a unique 9-mer tryptic peptide of P-gp protein was synthesized (with the stable isotope labeled (SIL) peptide as internal standard) and applied for quantitative LC/MS/MS method development. For LC/MS/MS quantification, the N-glycosylation of the peptide, polymorphism and transmembrane region was intended to be excluded during the peptide selection. The lower limit of quantification was established to be 0.025 nM with the linearity of the standard curve ranging to 20 nM of P-gp signature peptides in the matrix digested surrogate bovine serum albumin. The digestion efficiency, both the accuracy (relative error) and the precision (coefficient of variation) of the method, was verified by using the synthetic quantification peptide and the synthetic surrogate substrate peptide that mimics the sequence of tryptic peptide and associated flanking tryptic cleavage sites at the N- and C-terminals. By applying the method developed, the absolute amounts of human, dog and mouse P-gp (Mdr1a) were quantified in various biological samples. LC/MS/MS-mediated P-gp quantification was achieved as a highly sensitive, selective and reproducible assay and could be directly applicable to many current research needs related to P-gp.
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Affiliation(s)
- Yiqun Zhang
- Pharmacokinetics, Dynamics & Metabolism, Pfizer Global Research & Development Groton Laboratories, Pfizer Inc., Groton, CT 06340, USA
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25
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Whiteaker JR, Lin C, Kennedy J, Hou L, Trute M, Sokal I, Yan P, Schoenherr RM, Zhao L, Voytovich UJ, Kelly-Spratt KS, Krasnoselsky A, Gafken PR, Hogan JM, Jones LA, Wang P, Amon L, Chodosh LA, Nelson PS, McIntosh MW, Kemp CJ, Paulovich AG. A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat Biotechnol 2011; 29:625-34. [PMID: 21685906 PMCID: PMC3232032 DOI: 10.1038/nbt.1900] [Citation(s) in RCA: 279] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 05/20/2011] [Indexed: 01/01/2023]
Abstract
High-throughput technologies can now identify hundreds of candidate protein biomarkers for any disease with relative ease. However, because there are no assays for the majority of proteins and de novo immunoassay development is prohibitively expensive, few candidate biomarkers are tested in clinical studies. We tested whether the analytical performance of a biomarker identification pipeline based on targeted mass spectrometry would be sufficient for data-dependent prioritization of candidate biomarkers, de novo development of assays and multiplexed biomarker verification. We used a data-dependent triage process to prioritize a subset of putative plasma biomarkers from >1,000 candidates previously identified using a mouse model of breast cancer. Eighty-eight novel quantitative assays based on selected reaction monitoring mass spectrometry were developed, multiplexed and evaluated in 80 plasma samples. Thirty-six proteins were verified as being elevated in the plasma of tumor-bearing animals. The analytical performance of this pipeline suggests that it should support the use of an analogous approach with human samples.
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Kollipara S, Agarwal N, Varshney B, Paliwal J. Technological Advancements in Mass Spectrometry and Its Impact on Proteomics. ANAL LETT 2011. [DOI: 10.1080/00032719.2010.520386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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27
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Surface plasmon resonance in doping analysis. Anal Bioanal Chem 2011; 401:389-403. [PMID: 21448606 DOI: 10.1007/s00216-011-4830-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Revised: 02/15/2011] [Accepted: 02/21/2011] [Indexed: 10/18/2022]
Abstract
Doping analysis relies on the determination of prohibited substances that should not be present in the body of an athlete or that should be below a threshold value. In the case of xenobiotics their mere presence is sufficient to establish a doping offence. However, in the case of human biotics the analytical method faces the difficulty of distinguishing between endogenous and exogenous origin. For this purpose ingenious strategies have been implemented, often aided by state-of-the-art technological advancements such as mass spectrometry in all its possible forms. For larger molecules, i.e. protein hormones, the innate structural complexity, the heterogeneous nature, and the extremely low levels in biological fluids have rendered the analytical procedures heavily dependent of immunological approaches. Although approaches these confer specificity and sensitivity to the applications, most rely on the use of two, or even three, antibody incubations with the consequent increment in assay variability. Moreover, the requirement for different antibodies that separately recognise different epitopes in screening and confirmation assays further contributes to differences encountered in either measurement. The development of analytical techniques to measure interactions directly, such as atomic force microscopy, quartz crystal microbalance or surface plasmon resonance, have greatly contributed to the accurate evaluation of molecular interactions in all fields of biology, and expectations are that this will only increase. Here, an overview is provided of surface plasmon resonance, and its particular value in application to the field of doping analysis.
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28
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Halquist MS, Thomas Karnes H. Quantitative liquid chromatography tandem mass spectrometry analysis of macromolecules using signature peptides in biological fluids. Biomed Chromatogr 2010; 25:47-58. [PMID: 21154882 DOI: 10.1002/bmc.1545] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 09/10/2010] [Accepted: 09/14/2010] [Indexed: 01/08/2023]
Abstract
Targeted protein quantification using peptide surrogates has increasingly become important to the validation of biomarker candidates and development of protein therapeutics. These approaches have been proposed and employed as alternatives to immunoassays in biological fluids. Technological advances over the last 20 years in biochemistry and mass spectrometry have prompted the use of peptides as surrogates to quantify enzyme digested proteins using triple quadrupole mass spectrometers. Multiple sample preparation processes are often incorporated to achieve quantification of target proteins using these signature peptides. This review article focuses on these processes or hyphenated techniques for quantification of proteins with peptide surrogates. The most recent advances and strategies involved with hyphenated techniques are discussed.
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Affiliation(s)
- Matthew S Halquist
- Virginia Commonwealth University, Department of Pharmaceutics, PO Box 980533, Richmond, Virginia 980533, USA
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29
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Kim KH, Kamal AHM, Shin KH, Choi JS, Heo HY, Woo SH. Large-scale proteome investigation in wild relatives (A, B, and D genomes) of wheat. Acta Biochim Biophys Sin (Shanghai) 2010; 42:709-16. [PMID: 20810536 DOI: 10.1093/abbs/gmq079] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Large-scale proteomics of three wild relatives of wheat grain (A, B, and D genomes) were analyzed by using multidimensional protein identification technology coupled to liquid chromatography quadruple mass spectrometry. A total of 1568 (peptide match ≥1) and 255 (peptide match ≥2) unique proteins were detected and classified, which represents the most wide-ranging proteomic exploitation to date. The development of standard proteomes exhibiting all of the proteins involved in normal physiology will facilitate the delineation of disease/defense, metabolism, energy metabolism, and protein synthesis. A relative proteome exploration of the expression patterns indicates that proteins are involved in abiotic and biotic stress. Functional category analysis indicates that these differentially expressed proteins are mainly involved in disease/defense (15.38%, 21.26%, and 16.78%), metabolism (8.39%, 12.07%, and 14.09%), energy metabolism (11.19%, 11.49%, and 13.42%), protein synthesis (9.09%, 9.20%, and 8.72%), cell growth and division (9.09%, 4.60%, and 6.04%), cellular organization (4.20%, 5.75%, and 5.37%), development (6.29%, 2.87%, 3.36%), folding and stability (6.29%, 8.62%, and 8.05%), signal transduction (11.19%, 7.47%, and 8.05%), storage protein (4.20%, 1.72%, and 2.01%), transcription (5.59%, 5.17%, and 4.03%), and transport facilitation (1.40%, 1.15%, and 3.36%) in A, B, and D genomes, respectively. Here, we reported genome-specific protein interaction network using Cytoscape software, which provides further insight into the molecular functions and mechanism of biochemical pathways. We provide a promising understanding about the expressed proteins and protein functions. Our approach should be applicable as a marker to assist in breeding or gene transfer for quality and stress research of cultivated wheat.
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Affiliation(s)
- Ki-Hyun Kim
- Department of Crop Science, Chungbuk National University, Cheong-ju, Korea
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30
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Quantification of growth hormone in serum by isotope dilution mass spectrometry. Anal Biochem 2010; 401:228-35. [DOI: 10.1016/j.ab.2010.03.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 02/08/2010] [Accepted: 03/05/2010] [Indexed: 11/21/2022]
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Magparangalan DP, Garrett TJ, Drexler DM, Yost RA. Analysis of Large Peptides by MALDI Using a Linear Quadrupole Ion Trap with Mass Range Extension. Anal Chem 2010; 82:930-4. [DOI: 10.1021/ac9021488] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel P. Magparangalan
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, Department of Medicine, University of Florida, Gainesville, Florida 32610, and Research and Development, Pharmaceutical Candidate Optimization, Discovery Analytical Sciences, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492
| | - Timothy J. Garrett
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, Department of Medicine, University of Florida, Gainesville, Florida 32610, and Research and Development, Pharmaceutical Candidate Optimization, Discovery Analytical Sciences, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492
| | - Dieter M. Drexler
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, Department of Medicine, University of Florida, Gainesville, Florida 32610, and Research and Development, Pharmaceutical Candidate Optimization, Discovery Analytical Sciences, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492
| | - Richard A. Yost
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, Department of Medicine, University of Florida, Gainesville, Florida 32610, and Research and Development, Pharmaceutical Candidate Optimization, Discovery Analytical Sciences, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492
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Makawita S, Diamandis EP. The bottleneck in the cancer biomarker pipeline and protein quantification through mass spectrometry-based approaches: current strategies for candidate verification. Clin Chem 2009; 56:212-22. [PMID: 20007861 DOI: 10.1373/clinchem.2009.127019] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Although robust discovery-phase platforms have resulted in the generation of large numbers of candidate cancer biomarkers, a comparable system for subsequent quantitative assessment and verification of all candidates is lacking. Established immunoassays and available antibodies permit analysis of small subsets of candidates; however, the lack of commercially available reagents, coupled with high costs and lengthy production and purification times, have rendered the large majority of candidates untestable. CONTENT Mass spectrometry (MS), and in particular multiple reaction monitoring (MRM)-MS, has emerged as an alternative technology to immunoassays for quantification of target proteins. Novel biomarkers are expected to be present in serum in the low (microg/L-ng/L) range, but analysis of complex serum or plasma digests by MS has yielded milligram per liter limits of detection at best. The coupling of prior sample purification strategies such as enrichment of target analytes, depletion of high-abundance proteins, and prefractionation, has enabled reliable penetration into the low microgram per liter range. This review highlights prospects for candidate verification through MS-based methods. We first outline the biomarker discovery pipeline and its existing bottleneck; we then discuss various MRM-based strategies for targeted protein quantification, the applicability of such methods for candidate verification, and points of concern. SUMMARY Although it is unlikely that MS-based protein quantification will replace immunoassays in the near future, with the expected improvements in limits of detection and specificity in instrumentation, MRM-based approaches show great promise for alleviating the existing bottleneck to discovery.
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Affiliation(s)
- Shalini Makawita
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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Fortin T, Salvador A, Charrier JP, Lenz C, Bettsworth F, Lacoux X, Choquet-Kastylevsky G, Lemoine J. Multiple Reaction Monitoring Cubed for Protein Quantification at the Low Nanogram/Milliliter Level in Nondepleted Human Serum. Anal Chem 2009; 81:9343-52. [DOI: 10.1021/ac901447h] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- T. Fortin
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - A. Salvador
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - J. P. Charrier
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - C. Lenz
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - F. Bettsworth
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - X. Lacoux
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - G. Choquet-Kastylevsky
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - J. Lemoine
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
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Izrael-Tomasevic A, Phu L, Phung QT, Lill JR, Arnott D. Targeting interferon alpha subtypes in serum: a comparison of analytical approaches to the detection and quantitation of proteins in complex biological matrices. J Proteome Res 2009; 8:3132-40. [PMID: 19351188 DOI: 10.1021/pr900076q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The targeted detection and quantitation of proteins in complex biological fluids such as blood is as analytically challenging as it is crucial for biomedical research. Antibody-based techniques such as the ELISA are the current standards for such measurements, having in favorable cases high specificity and pg/mL detection limits. Long development timelines and susceptibility to cross reactivity have led researchers to investigate mass spectrometric alternatives. The literature contains diverse schemes for sample preparation and multiple platforms for mass spectrometric detection. Critical evaluations of competing technologies are, however, badly needed. Taking closely related subtypes of the pro-inflammatory cytokine interferon alpha as a test case, we compared a sample preparation workflow based on affinity enrichment to one based on generic multidimensional chromatography, and evaluated mass spectrometric techniques using tandem mass spectrometry on low resolution ion traps, high resolution "accurate mass tags," and triple quadrupole selective reaction monitoring. Each workflow and detection method proved capable of detecting and discriminating between these proteins at or below the ng/mL level in human serum. Quantitation by isotope dilution was evaluated using full length protein as the internal standard. Both triple quadrupole selected reaction monitoring and orbitrap selected ion monitoring produced linear calibration curves from 1 ng/mL to 1 microg/mL, with lower limits of quantitation below 5 and 50 ng/mL, respectively.
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Affiliation(s)
- Anita Izrael-Tomasevic
- Protein Chemistry Department, Genentech Inc., South San Francisco, California 94080, USA
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Zhang J, Gonzalez E, Hestilow T, Haskins W, Huang Y. Review of peak detection algorithms in liquid-chromatography-mass spectrometry. Curr Genomics 2009; 10:388-401. [PMID: 20190954 PMCID: PMC2766790 DOI: 10.2174/138920209789177638] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Revised: 05/11/2009] [Accepted: 05/11/2009] [Indexed: 11/22/2022] Open
Abstract
In this review, we will discuss peak detection in Liquid-Chromatography-Mass Spectrometry (LC/MS) from a signal processing perspective. A brief introduction to LC/MS is followed by a description of the major processing steps in LC/MS. Specifically, the problem of peak detection is formulated and various peak detection algorithms are described and compared.
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Affiliation(s)
- Jianqiu Zhang
- Dept. of ECE, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Elias Gonzalez
- Dept. of ECE, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Travis Hestilow
- Dept. of ECE, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - William Haskins
- Dept. of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Yufei Huang
- Dept. of ECE, University of Texas at San Antonio, San Antonio, TX 78249, USA
- Children's Cancer Research Institute, UT Health Science Center, San Antonio, TX 78229, USA
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Lai Y. Identification of interspecies difference in hepatobiliary transporters to improve extrapolation of human biliary secretion. Expert Opin Drug Metab Toxicol 2009; 5:1175-87. [DOI: 10.1517/17425250903127234] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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MRM screening/biomarker discovery with linear ion trap MS: a library of human cancer-specific peptides. BMC Cancer 2009; 9:96. [PMID: 19327145 PMCID: PMC2670839 DOI: 10.1186/1471-2407-9-96] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Accepted: 03/27/2009] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The discovery of novel protein biomarkers is essential in the clinical setting to enable early disease diagnosis and increase survivability rates. To facilitate differential expression analysis and biomarker discovery, a variety of tandem mass spectrometry (MS/MS)-based protein profiling techniques have been developed. For achieving sensitive detection and accurate quantitation, targeted MS screening approaches, such as multiple reaction monitoring (MRM), have been implemented. METHODS MCF-7 breast cancer protein cellular extracts were analyzed by 2D-strong cation exchange (SCX)/reversed phase liquid chromatography (RPLC) separations interfaced to linear ion trap MS detection. MS data were interpreted with the Sequest-based Bioworks software (Thermo Electron). In-house developed Perl-scripts were used to calculate the spectral counts and the representative fragment ions for each peptide. RESULTS In this work, we report on the generation of a library of 9,677 peptides (p < 0.001), representing approximately 1,572 proteins from human breast cancer cells, that can be used for MRM/MS-based biomarker screening studies. For each protein, the library provides the number and sequence of detectable peptides, the charge state, the spectral count, the molecular weight, the parameters that characterize the quality of the tandem mass spectrum (p-value, DeltaM, Xcorr, DeltaCn, Sp, no. of matching a, b, y ions in the spectrum), the retention time, and the top 10 most intense product ions that correspond to a given peptide. Only proteins identified by at least two spectral counts are listed. The experimental distribution of protein frequencies, as a function of molecular weight, closely matched the theoretical distribution of proteins in the human proteome, as provided in the SwissProt database. The amino acid sequence coverage of the identified proteins ranged from 0.04% to 98.3%. The highest-abundance proteins in the cellular extract had a molecular weight (MW)<50,000. CONCLUSION Preliminary experiments have demonstrated that putative biomarkers, that are not detectable by conventional data dependent MS acquisition methods in complex un-fractionated samples, can be reliable identified with the information provided in this library. Based on the spectral count, the quality of a tandem mass spectrum and the m/z values for a parent peptide and its most abundant daughter ions, MRM conditions can be selected to enable the detection of target peptides and proteins.
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Stempfer R, Kubicek M, Lang IM, Christa N, Gerner C. Quantitative assessment of human serum high-abundance protein depletion. Electrophoresis 2009; 29:4316-23. [PMID: 18956433 DOI: 10.1002/elps.200800211] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The aim of this study is to quantify the effectivity of the depletion of human high-abundance serum and plasma proteins for improved protein identification and disease marker candidate discovery and to assess the risk of concomitant removal of relevant marker proteins. 2-DE and bottom-up shotgun MS combining 2-D capillary chromatography with MS/MS were applied in parallel for the analysis of fractions resulting from the depletion procedure. For many proteins the factors of enrichment by the depletion were obvious allowing their enhanced detection and identification upon high-abundance protein depletion. Nano-liquid chromatography linked MS allowed the efficient identification of several low-abundant proteins that were not identified on the 2-DE gels. Resolving the fractions that were eluted from the matrix upon depletion indicated unspecific binding of disease relevant proteins in plasma samples from acute myocardial infarction patients. The unspecific binding to the depletion matrix of inflammatory markers spiked into the serum was found to depend on the type of capturing agent used. Polyclonal avian antibodies (IgY) displayed the least unspecific binding due to the high immunogenicity of mammalian proteins in avian hosts.
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Affiliation(s)
- Rene Stempfer
- Molecular Diagnostics, Life Sciences, Austrian Research Centers GmbH - ARC, Seibersdorf, Austria
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Li N, Palandra J, Nemirovskiy OV, Lai Y. LC−MS/MS Mediated Absolute Quantification and Comparison of Bile Salt Export Pump and Breast Cancer Resistance Protein in Livers and Hepatocytes across Species. Anal Chem 2009; 81:2251-9. [DOI: 10.1021/ac8024009] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Na Li
- Department of Pharmacokinetics, Dynamics, and Drug Metabolism, Pfizer Global Research and Development, St. Louis Laboratories, Pfizer Inc., St. Louis, Missouri 63017
| | - Joe Palandra
- Department of Pharmacokinetics, Dynamics, and Drug Metabolism, Pfizer Global Research and Development, St. Louis Laboratories, Pfizer Inc., St. Louis, Missouri 63017
| | - Olga V. Nemirovskiy
- Department of Pharmacokinetics, Dynamics, and Drug Metabolism, Pfizer Global Research and Development, St. Louis Laboratories, Pfizer Inc., St. Louis, Missouri 63017
| | - Yurong Lai
- Department of Pharmacokinetics, Dynamics, and Drug Metabolism, Pfizer Global Research and Development, St. Louis Laboratories, Pfizer Inc., St. Louis, Missouri 63017
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40
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Jiang H, Wu SL, Karger BL, Hancock WS. Mass spectrometric analysis of innovator, counterfeit, and follow-on recombinant human growth hormone. Biotechnol Prog 2009; 25:207-18. [DOI: 10.1002/btpr.72] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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41
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Fortin T, Salvador A, Charrier JP, Lenz C, Lacoux X, Morla A, Choquet-Kastylevsky G, Lemoine J. Clinical quantitation of prostate-specific antigen biomarker in the low nanogram/milliliter range by conventional bore liquid chromatography-tandem mass spectrometry (multiple reaction monitoring) coupling and correlation with ELISA tests. Mol Cell Proteomics 2008; 8:1006-15. [PMID: 19068476 DOI: 10.1074/mcp.m800238-mcp200] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteomics discovery leads to a list of potential protein biomarkers that have to be subsequently verified and validated with a statistically viable number of patients. Although the most sensitive, the development of an ELISA test is time-consuming when antibodies are not available and need to be conceived. Mass spectrometry analysis driven in quantitative multiple reaction monitoring mode is now appearing as a promising alternative to quantify proteins in biological fluids. However, all the studies published to date describe limits of quantitation in the low microg/ml range when no immunoenrichment of the target protein is applied, whereas the concentration of known clinical biomarkers is usually in the ng/ml range. Using prostate-specific antigen as a model biomarker, we now provide proof of principle that mass spectrometry enables protein quantitation in a concentration range of clinical interest without immunoenrichment. We have developed and optimized a robust sample processing method combining albumin depletion, trypsin digestion, and solid phase extraction of the proteotypic peptides starting from only 100 microl of serum. For analysis, mass spectrometry was coupled to a conventional liquid chromatography system using a 2-mm-internal diameter reverse phase column. This mass spectrometry-based strategy was applied to the quantitation of prostate-specific antigen in sera of patients with either benign prostate hyperplasia or prostate cancer. The quantitation was performed against an external calibration curve by interpolation, and results showed good correlation with existing ELISA tests applied to the same samples. This strategy might now be implemented in any clinical laboratory or certified company for further evaluation of any putative biomarker in the low ng/ml range of serum or plasma.
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Affiliation(s)
- Tanguy Fortin
- R&D Proteomique, bioMérieux SA, 69280 Marcy l'Etoile, France
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Li N, Zhang Y, Hua F, Lai Y. Absolute Difference of Hepatobiliary Transporter Multidrug Resistance-Associated Protein (MRP2/Mrp2) in Liver Tissues and Isolated Hepatocytes from Rat, Dog, Monkey, and Human. Drug Metab Dispos 2008; 37:66-73. [DOI: 10.1124/dmd.108.023234] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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43
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Paulovich AG, Whiteaker JR, Hoofnagle AN, Wang P. The interface between biomarker discovery and clinical validation: The tar pit of the protein biomarker pipeline. Proteomics Clin Appl 2008; 2:1386-1402. [PMID: 20976028 DOI: 10.1002/prca.200780174] [Citation(s) in RCA: 165] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The application of "omics" technologies to biological samples generates hundreds to thousands of biomarker candidates; however, a discouragingly small number make it through the pipeline to clinical use. This is in large part due to the incredible mismatch between the large numbers of biomarker candidates and the paucity of reliable assays and methods for validation studies. We desperately need a pipeline that relieves this bottleneck between biomarker discovery and validation. This paper reviews the requirements for technologies to adequately credential biomarker candidates for costly clinical validation and proposes methods and systems to verify biomarker candidates. Models involving pooling of clinical samples, where appropriate, are discussed. We conclude that current proteomic technologies are on the cusp of significantly affecting translation of molecular diagnostics into the clinic.
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44
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Li N, Nemirovskiy OV, Zhang Y, Yuan H, Mo J, Ji C, Zhang B, Brayman TG, Lepsy C, Heath TG, Lai Y. Absolute quantification of multidrug resistance-associated protein 2 (MRP2/ABCC2) using liquid chromatography tandem mass spectrometry. Anal Biochem 2008; 380:211-22. [DOI: 10.1016/j.ab.2008.05.032] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Revised: 05/19/2008] [Accepted: 05/20/2008] [Indexed: 11/29/2022]
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45
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Kim JC, Kim JY, Yeom SR, Jeong BY, Hwang HZ, Park KJ, Lee SW. 2-D DIGE and MS/MS analysis of protein serum expression in rats housed in concrete and clay cages in winter. Proteomics 2008; 8:3632-44. [DOI: 10.1002/pmic.200700566] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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46
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Kamiie J, Ohtsuki S, Iwase R, Ohmine K, Katsukura Y, Yanai K, Sekine Y, Uchida Y, Ito S, Terasaki T. Quantitative atlas of membrane transporter proteins: development and application of a highly sensitive simultaneous LC/MS/MS method combined with novel in-silico peptide selection criteria. Pharm Res 2008; 25:1469-83. [PMID: 18219561 DOI: 10.1007/s11095-008-9532-4] [Citation(s) in RCA: 388] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Accepted: 01/02/2008] [Indexed: 01/04/2023]
Abstract
PURPOSE To develop an absolute quantification method for membrane proteins, and to construct a quantitative atlas of membrane transporter proteins in the blood-brain barrier, liver and kidney of mouse. METHODS Mouse tissues were digested with trypsin, and mixed with stable isotope labeled-peptide as a quantitative standard. The amounts of transporter proteins were simultaneously determined by liquid chromatography-tandem mass spectrometer (LC/MS/MS). RESULTS The target proteins were digested in-silico, and target peptides for analysis were chosen on the basis of the selection criteria. All of the peptides selected exhibited a detection limit of 10 fmol and linearity over at least two orders of magnitude in the calibration curve for LC/MS/MS analysis. The method was applied to obtain the expression levels of 34 transporters in liver, kidney and blood-brain barrier of mouse. The quantitative values of transporter proteins showed an excellent correlation with the values obtained with existing methods using antibodies or binding molecules. CONCLUSION A sensitive and simultaneous quantification method was developed for membrane proteins. By using this method, we constructed a quantitative atlas of membrane transporter proteins at the blood-brain barrier, liver and kidney in mouse. This technology is expected to have major implications for various fields of biomedical science.
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Affiliation(s)
- Junichi Kamiie
- Division of Membrane Transport and Drug Targeting, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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47
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Zhou H, Dai J, Sheng QH, Li RX, Shieh CH, Guttman A, Zeng R. A fully automated 2-D LC-MS method utilizing online continuous pH and RP gradients for global proteome analysis. Electrophoresis 2008; 28:4311-9. [PMID: 17987634 DOI: 10.1002/elps.200700463] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The conventional 2-D LC-MS/MS setup for global proteome analysis was based on online and offline salt gradients (step and continuous) using strong-cation-exchange chromatography in conjunction with RP chromatography and MS. The use of the online system with step salt elution had the possibility of resulting in peptide overlapping across fractions. The offline mode had the option to operate with continuous salt gradient to decrease peak overlap, but exhibited decreased robustness, lower reproducibility, and sample loss during the process. Due to the extensive washing requirement between the chromatography steps, online continuous gradient was not an option for salt elution. In this report, a fully automated, online, and continuous gradient (pH continuous online gradient, pCOG) 2-D LC-MS/MS system is introduced that provided excellent separation and identification power. The pH gradient-based elution provided more basic peptides than that of salt-based elution. Fraction overlap was significantly minimized by combining pH and continuous gradient elutions. This latter approach also increased sequence coverage and the concomitant confidence level in protein identification. The salt and pH elution-based 2-D LC-MS/MS approaches were compared by analyzing the mouse liver proteome.
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Affiliation(s)
- Hu Zhou
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai, PR China
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Zheng J, Wei C, Leng W, Dong J, Li R, Li W, Wang J, Zhang Z, Jin Q. Membrane subproteomic analysis of Mycobacterium bovis bacillus Calmette-Guérin. Proteomics 2008; 7:3919-31. [PMID: 17922514 DOI: 10.1002/pmic.200700342] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Mycobacterium bovis bacillus Calmette-Guérin (BCG) vaccine has been known for a long time to prevent tuberculosis (TB) worldwide since 1921. Nonetheless, we know little about BCG membrane proteome. In the present study, we utilized alkaline incubation and Triton X-114-based methods to enrich BCG membrane proteins and subsequently digested them using proteolytic enzyme. The recovered peptides were further separated by 2-D LC and identified by ESI-MS/MS. As a result, total 474 proteins were identified, including 78 integral membrane proteins (IMPs). Notably, 18 BCG IMPs were described for the first time in mycobacterium. Further analysis of the 78 IMPs indicated that the theoretical molecular mass distribution of them ranged from 8.06 to 167.86 kDa and pI scores ranged from 4.40 to 11.60. Functional classification revealed that a large proportion of the identified IMPs (67.9%, 53 out of 78) were involved in cell wall and cell processes functional group. In conclusion, here we reported a comprehensive profile of the BCG membrane subproteome. The present investigation may allow the identification of some valuable vaccine and drug target candidates and thus provide basement for future designing of preventive, diagnostic, and therapeutic strategies against TB.
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Affiliation(s)
- Jianhua Zheng
- College of Biological Sciences, China Agricultural University, Beijing, PR China
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49
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Lucitt MB, Price TS, Pizarro A, Wu W, Yocum AK, Seiler C, Pack MA, Blair IA, Fitzgerald GA, Grosser T. Analysis of the zebrafish proteome during embryonic development. Mol Cell Proteomics 2008; 7:981-94. [PMID: 18212345 DOI: 10.1074/mcp.m700382-mcp200] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The model organism zebrafish (Danio rerio) is particularly amenable to studies deciphering regulatory genetic networks in vertebrate development, biology, and pharmacology. Unraveling the functional dynamics of such networks requires precise quantitation of protein expression during organismal growth, which is incrementally challenging with progressive complexity of the systems. In an approach toward such quantitative studies of dynamic network behavior, we applied mass spectrometric methodology and rigorous statistical analysis to create comprehensive, high quality profiles of proteins expressed at two stages of zebrafish development. Proteins of embryos 72 and 120 h postfertilization (hpf) were isolated and analyzed both by two-dimensional (2D) LC followed by ESI-MS/MS and by 2D PAGE followed by MALDI-TOF/TOF protein identification. We detected 1384 proteins from 327,906 peptide sequence identifications at 72 and 120 hpf with false identification rates of less than 1% using 2D LC-ESI-MS/MS. These included only approximately 30% of proteins that were identified by 2D PAGE-MALDI-TOF/TOF. Roughly 10% of all detected proteins were derived from hypothetical or predicted gene models or were entirely unannotated. Comparison of proteins expression by 2D DIGE revealed that proteins involved in energy production and transcription/translation were relatively more abundant at 72 hpf consistent with faster synthesis of cellular proteins during organismal growth at this time compared with 120 hpf. The data are accessible in a database that links protein identifications to existing resources including the Zebrafish Information Network database. This new resource should facilitate the selection of candidate proteins for targeted quantitation and refine systematic genetic network analysis in vertebrate development and biology.
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Affiliation(s)
- Margaret B Lucitt
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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50
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Kulasingam V, Smith CR, Batruch I, Buckler A, Jeffery DA, Diamandis EP. "Product ion monitoring" assay for prostate-specific antigen in serum using a linear ion-trap. J Proteome Res 2008; 7:640-7. [PMID: 18186600 DOI: 10.1021/pr7005999] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While numerous strategies exist for biomarker discovery, the bottleneck to product development and routine use at the clinic is in the verification phase of candidate biomarkers. The aim of this study was to establish a robust and high-throughput product ion monitoring (PIM) assay that is potentially capable of rapidly verifying candidates from discovery phase experiments. Using prostate-specific antigen (PSA), a model biomarker, and a routinely used mass spectrometer for discovery platforms, an ion trap (LTQ, Thermo), the utility of this instrument to perform PIM was explored. The proteotypic doubly charged intact peptide LSEPAELTDAVK ( m/ z 637) fragmenting to m/ z 943 (PAELTDAVK) was monitored. A limit of detection of 10 attomoles with a coefficient of variation (CV) of <20% was obtained for a purified recombinant PSA digest. Immunoextraction of endogenous PSA from serum using a monoclonal antibody on a 96-well microtiter plate, followed by PIM on the LTQ, enabled quantification of PSA down to less than 1 ng/mL with a limit of detection of 0.1 ng/mL and CVs < 20%. Mascot searching and ion ratio confirmation further supported the conclusion that the quantified moiety in serum was the PSA peptide. We conclude that this methodology could be adapted quickly and easily to other candidates, thus providing a much needed technology to bridge the gap between discovery and validation platforms.
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Affiliation(s)
- Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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