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Sanjai C, Hakkimane SS, Guru BR, Gaonkar SL. A comprehensive review on anticancer evaluation techniques. Bioorg Chem 2024; 142:106973. [PMID: 37984104 DOI: 10.1016/j.bioorg.2023.106973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
The development of effective anticancer strategies and the improvement of our understanding of cancer need analytical tools. Utilizing a variety of analytical approaches while investigating anti-cancer medicines gives us a thorough understanding of the traits and mechanisms concerned to cancer cells, which enables us to develop potent treatments to combat them. The importance of anticancer research may be attributed to various analytical techniques that contributes to the identification of therapeutic targets and the assessment of medication efficacy, which are crucial things in expanding our understanding of cancer biology. The study looks at methods that are often used in cancer research, including cell viability assays, clonogenic assay, flow cytometry, 2D electrophoresis, microarray, immunofluorescence, western blot caspase activation assay, bioinformatics, etc. The fundamentals, applications, and how each technique analytical advances our understanding of cancer are briefly reviewed.
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Affiliation(s)
- Chetana Sanjai
- Department of Biotechnology, Manipal Institute of Technology Bengaluru, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sushruta S Hakkimane
- Department of Biotechnology, Manipal Institute of Technology Bengaluru, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Bharath Raja Guru
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Santosh L Gaonkar
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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2
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Gammelgaard SK, Petersen SB, Haselmann KF, Nielsen PK. Characterization of Insulin Dimers by Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1910-1918. [PMID: 33084334 DOI: 10.1021/jasms.0c00257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
High-molecular weight products (HMWP) are an important critical quality attribute in research and development of insulin biopharmaceuticals. We here demonstrate on two case studies of covalent insulin dimers, induced by Fe2+ incubation or ultraviolet (UV) light stress, that de novo characterization in top-down mass spectrometry (MS) workflows can identify cross-link types and sites. On the MS2 level, electron-transfer/higher-energy collision dissociation (EThcD) efficiently cleaved the interchain disulfide bonds in the dimers to reveal cross-link connectivities between chains. The combined utilization of EThcD and 213 nm ultraviolet photodissociation (UVPD) facilitated identification of the chemical composition of the cross-links. Identification of cross-link sites between chains at residue level was achievable for both dimers with MS3 analysis of MS2 fragments cleaved at the cross-link or additionally the interchain disulfide bonds. UVPD provided identification of cross-link sites in the Fe2+-induced dimer without MS3, while cross-link site identification with MS2 was not possible for the UV light-induced dimer. Thus, using varied multistage approaches, it was discovered that in the UV light-induced dimer, Tyr14 of the A-chain participated in an -O-S- cross-link in which the sulfur was derived either from Cys7 or Cys19 of the B-chain. In the Fe2+-induced dimer, Phe1 from both B-chains were cross-linked through a -CH2-. The UV chromophoric side chain of Phe1 was indicated in the cross-link, explaining why UVPD-MS2 was effective in fragmenting the cross-link and nearby backbone bonds. Our results demonstrated that higher-energy collisional dissociation (HCD), EThcD, and UVPD combined with MS3 were powerful tools for direct de novo characterization of cross-linked insulin dimers.
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Affiliation(s)
- Simon K Gammelgaard
- Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
- Department of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 7, 9220 Aalborg, Denmark
| | - Steffen B Petersen
- Department of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 7, 9220 Aalborg, Denmark
| | - Kim F Haselmann
- Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
| | - Peter Kresten Nielsen
- Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
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3
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Zhu SZ, Zhang L, Zhang J, Guo YL. Arc Plasma-Based Dissociation Device: Fingerprinting Mass Spectrometric Analysis Realized at Atmospheric Condition. Anal Chem 2020; 92:14633-14639. [DOI: 10.1021/acs.analchem.0c03127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Su-zhen Zhu
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Li Zhang
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Jing Zhang
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yin-long Guo
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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Badr KR, Parente‐Rocha JA, Baeza LC, Ficcadori FS, Souza M, Soares CM, Guissoni ACP, Almeida TN, Cardoso DD. Quantitative proteomic analysis of A549 cells infected with human adenovirus type 2. J Med Virol 2019; 91:1239-1249. [DOI: 10.1002/jmv.25439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/30/2019] [Accepted: 02/19/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Kareem R. Badr
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Juliana A. Parente‐Rocha
- Department of Microbiology, Molecular Biology LaboratoryInstitute of Biological Sciences, Federal University of GoiásGoiânia Goiás Brazil
| | - Lilian C. Baeza
- Department of Microbiology, Molecular Biology LaboratoryInstitute of Biological Sciences, Federal University of GoiásGoiânia Goiás Brazil
| | - Fabiola S. Ficcadori
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Menira Souza
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Célia M. Soares
- Department of Microbiology, Molecular Biology LaboratoryInstitute of Biological Sciences, Federal University of GoiásGoiânia Goiás Brazil
| | - Ana Carla P. Guissoni
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Tâmera N. Almeida
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
| | - Divina D. Cardoso
- Department of Microbiology, Human Virology LaboratoryInstitute of Tropical Pathology and Public Health, Federal University of GoiásGoiânia Goiás Brazil
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Abstract
A sizeable proportion of active protein sequences lack structural motifs making them irresolvable by NMR and crystallography. Such intrinsically disordered proteins (IDPs) or regions (IDRs) play a major role in biological mechanisms. They are often involved in cell regulation processes, and by extension can be the perpetrator or signifier of disease. In light of their importance and the shortcomings of conventional methods of biophysical analysis to identify them and to describe their conformational variance, IDPs and IDRs have been termed "the dark proteome." In this chapter we describe the use of ion mobility-mass spectrometry (IM-MS) coupled with electrospray ionization to analyze the conformational diversity of IDPs. Using the LEA protein COR15A as an exemplar system and contrasting it with the behavior of myoglobin, we outline the methods for analyzing an IDP using nanoelectrospray ionization coupled with IM-MS, covering sample preparation, purification; optimization of mass spectrometry conditions and tuning parameters; data collection and analysis. Following this, we detail the use of a "toy" model that provides a predictive framework for the study of all proteins with ESI-IM-MS.
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Parry S, Zhang H, Biggio J, Bukowski R, Varner M, Xu Y, Andrews WW, Saade GR, Esplin MS, Leite R, Ilekis J, Reddy UM, Sadovsky Y, Blair IA. Maternal serum serpin B7 is associated with early spontaneous preterm birth. Am J Obstet Gynecol 2014; 211:678.e1-12. [PMID: 24954659 DOI: 10.1016/j.ajog.2014.06.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/31/2014] [Accepted: 06/16/2014] [Indexed: 11/29/2022]
Abstract
OBJECTIVE We sought to identify serum biomarkers of early spontaneous preterm birth (SPTB) using semiquantitative proteomic analyses. STUDY DESIGN This was a nested case-control study of pregnant women with previous SPTB. Maternal serum was collected at 19-24 and 28-32 weeks' gestation, and analyzed by liquid chromatography-multiple reaction monitoring/mass spectrometry. Targeted and shotgun proteomics identified 31 candidate proteins that were differentially expressed in pooled serum samples from spontaneous preterm (cases [<34 weeks]) and term (controls) deliveries. Candidate protein expression was compared in individual serum samples between cases and controls matched by age and race groups, and clinical site. Protein expression was verified by Western blot in the placenta and fetal membranes from cases and controls. RESULTS Serum samples were available for 35 cases and 35 controls at 19-24 weeks, and 16 cases and 16 controls at 28-32 weeks. One protein, serpin B7, yielded serum concentrations that differed between cases and controls. The mean concentration of serpin B7 at 28-32 weeks was 1.5-fold higher in women with subsequent preterm deliveries compared to controls; there was no difference at 19-24 weeks. Higher levels of serpin B7 at both gestational age windows were associated with a shorter interval to delivery, and higher levels of serpin B7 in samples from 28-32 weeks were associated with a lower gestational age at delivery. Western blotting identified serpin B7 protein in placenta, amnion, and chorion from cases and controls. CONCLUSION Targeted and shotgun serum proteomics analyses associated 1 protein, serpin B7, with early SPTB. Our results require validation in other cohorts and analysis of the possible mechanistic role of serpin B7 in parturition.
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Affiliation(s)
- Samuel Parry
- Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, PA.
| | - Heping Zhang
- Collaborative Center for Statistics in Science, Yale University School of Public Health, New Haven, CT
| | - Joseph Biggio
- Department of Obstetrics and Gynecology, University of Alabama, Birmingham, School of Medicine, Birmingham, AL
| | - Radek Bukowski
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX
| | - Michael Varner
- Department of Obstetrics and Gynecology, University of Utah School of Medicine, Salt Lake City, UT
| | - Yaji Xu
- Collaborative Center for Statistics in Science, Yale University School of Public Health, New Haven, CT
| | - William W Andrews
- Department of Obstetrics and Gynecology, University of Alabama, Birmingham, School of Medicine, Birmingham, AL
| | - George R Saade
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX
| | - M Sean Esplin
- Department of Obstetrics and Gynecology, University of Utah School of Medicine, Salt Lake City, UT
| | - Rita Leite
- Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - John Ilekis
- Pregnancy and Perinatology Branch, Center for Developmental Biology and Perinatal Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD
| | - Uma M Reddy
- Pregnancy and Perinatology Branch, Center for Developmental Biology and Perinatal Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD
| | - Yoel Sadovsky
- Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Ian A Blair
- Center for Cancer Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA
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Qiu B, Wei F, Sun X, Wang X, Duan B, Shi C, Zhang J, Zhang J, Qiu W, Mu W. Measurement of hydroxyproline in collagen with three different methods. Mol Med Rep 2014; 10:1157-63. [PMID: 24858249 DOI: 10.3892/mmr.2014.2267] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 03/31/2014] [Indexed: 11/06/2022] Open
Abstract
Determination of the 4-hydroxy-l-proline (hydroxyproline) concentration may provide useful information for the diagnosis and prognosis of diseases caused by disorders of collagen metabolism. The objective of the present study was to apply liquid chromatography-mass spectrometry (LC-MS) to assess the hydroxyproline concentration. The hydroxyproline concentration in lung and liver tissues measured by LC-MS was compared with values obtained by a colorimetric method, as well as a fluorescence method using high-performance liquid chromatography (HPLC) from previous studies by our group. The determination of the hydroxyproline concentration by LC-MS was improved as compared with that using the colorimetric and HPLC methods, due to its simplicity, high sensitivity (pg level) and short separation time. These results suggested that utilizing the LC-MS method for measuring the hydroxyproline concentration would be advantageous for the diagnosis of diseases associated with abnormalities of collagen metabolism.
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Affiliation(s)
- Bing Qiu
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Fengxiang Wei
- Genetics Laboratory Shenzhen Longgang District Maternity and Child Healthcare Hospital, Shenzhen, Guangdong 518124, P.R. China
| | - Xiuzhi Sun
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Xi Wang
- Department of Gastroenterology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Binhong Duan
- Department of Endocrinology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Chunlin Shi
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Jianying Zhang
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Jiye Zhang
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Wenliang Qiu
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Wenling Mu
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
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8
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Kwon HJ, Kurono S, Kaneko Y, Ohmiya Y, Yasuda K. Analysis of proteins showing differential changes during ATP oscillations in chondrogenesis. Cell Biochem Funct 2014; 32:429-37. [PMID: 24578328 DOI: 10.1002/cbf.3033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 01/02/2014] [Accepted: 01/30/2014] [Indexed: 01/02/2023]
Abstract
Prechondrogenic condensation is a critical step for skeletal pattern formation. Our previous study showed that ATP oscillations play an essential role in prechondrogenic condensation because they induce oscillatory secretion. However, the molecular mechanisms that underlie ATP oscillations remain poorly understood. We examined how differential changes in proteins are implicated in ATP oscillations during chondrogenesis by using liquid chromatography/mass spectrometry. Our analysis showed that a number of proteins involved in ATP synthesis/consumption, catabolic/anabolic processes, actin dynamics, cell migration and adhesion were detected at either the peak or the trough of ATP oscillations, which implies that these proteins have oscillatory expression patterns that are coupled to ATP oscillations. On the basis of the results, we suggest that (1) the oscillatory expression of proteins involved in ATP synthesis/consumption and catabolic/anabolic processes can contribute to the generation or maintenance of ATP oscillations and that (2) the oscillatory expression of proteins involved in actin dynamics, cell migration and adhesion plays key roles in prechondrogenic condensation by inducing collective adhesion and migration in cooperation with ATP oscillations.
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Affiliation(s)
- Hyuck Joon Kwon
- Department of Physical Therapy, College of Health Science, Eulji University, Gyeonggi, South Korea
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9
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Liuni P, Wilson DJ. Understanding and optimizing electrospray ionization techniques for proteomic analysis. Expert Rev Proteomics 2014; 8:197-209. [DOI: 10.1586/epr.10.111] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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10
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Ahmed FE. Utility of mass spectrometry for proteome ana lysis: part I. Conceptual and experimental approaches. Expert Rev Proteomics 2014; 5:841-64. [DOI: 10.1586/14789450.5.6.841] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Williamson YM, Moura H, Simmons K, Whitmon J, Melnick N, Rees J, Woolfitt A, Schieltz DM, Tondella ML, Ades E, Sampson J, Carlone G, Barr JR. A gel-free proteomic-based method for the characterization of Bordetella pertussis clinical isolates. J Microbiol Methods 2012; 90:119-33. [PMID: 22537821 PMCID: PMC5687064 DOI: 10.1016/j.mimet.2012.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 04/04/2012] [Accepted: 04/10/2012] [Indexed: 12/23/2022]
Abstract
Bordetella pertussis (Bp) is the etiologic agent of pertussis or whooping cough, a highly contagious respiratory disease occurring primarily in infants and young children. Although vaccine preventable, pertussis cases have increased over the years leading researchers to re-evaluate vaccine control strategies. Since bacterial outer membrane proteins, comprising the surfaceome, often play roles in pathogenesis and antibody-mediated immunity, three recent Bp circulating isolates were examined using proteomics to identify any potential changes in surface protein expression. Fractions enriched for outer membrane proteins were digested with trypsin and the peptides analyzed by nano liquid chromatography-electrospray ionization-mass spectrometry (nLC-ESI-MS), followed by database analysis to elucidate the surfaceomes of our three Bp isolates. Furthermore, a less labor intensive non-gel based antibody affinity capture technology in conjunction with MS was employed to assess each Bp strains' immunogenic outer membrane proteins. This novel technique is generally applicable allowing for the identification of immunogenic surface expressed proteins on pertussis and other pathogenic bacteria.
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Affiliation(s)
- Yulanda M. Williamson
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Chamblee, Georgia 30341, USA
| | - Hercules Moura
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Chamblee, Georgia 30341, USA
| | - Kaneatra Simmons
- Division of Bacterial Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Jennifer Whitmon
- Division of Bacterial Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Nikkol Melnick
- Division of Bacterial Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Jon Rees
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Chamblee, Georgia 30341, USA
| | - Adrian Woolfitt
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Chamblee, Georgia 30341, USA
| | - David M. Schieltz
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Chamblee, Georgia 30341, USA
| | - Maria L. Tondella
- Division of Bacterial Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Edwin Ades
- Division of Bacterial Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Jacquelyn Sampson
- Division of Bacterial Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - George Carlone
- Division of Bacterial Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - John R. Barr
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Chamblee, Georgia 30341, USA
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Gonzalez-Galarza FF, Lawless C, Hubbard SJ, Fan J, Bessant C, Hermjakob H, Jones AR. A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:431-42. [PMID: 22804616 DOI: 10.1089/omi.2012.0022] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis. In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies. In this article we focus on the review of some of the most popular techniques in the field and present a critical appraisal of several software packages available to process and analyze the data produced. We also describe the importance of community standards to support the wide range of software, which may assist researchers in the analysis of data using different platforms and protocols. It is intended that this review will serve bench scientists both as a useful reference and a guide to the selection and use of different pipelines to perform quantitative proteomics data analysis. We have produced a web-based tool ( http://www.proteosuite.org/?q=other_resources ) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology.
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13
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Gunther NW, Paul M, Nuñez A, Liu Y. pH fractionation and identification of proteins: comparing column chromatofocusing versus liquid isoelectric focusing techniques. J Sep Sci 2012; 35:1399-405. [PMID: 22740249 DOI: 10.1002/jssc.201100865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In proteomic investigations, a number of different separation techniques can be applied to fractionate whole cell proteomes into more manageable fractions for subsequent analysis. In this work, utilizing HPLC and mass spectrometry for protein identification, two different fractionation methods were compared and contrasted to determine the potential of each method for the simple and reproducible fractionation of a bacterial proteome. Column-based chromatofocusing and liquid-based isoelectric focusing both utilized pH gradients to produce similar results in terms of the numbers of proteins successfully identified (402 and 378 proteins) and the consistency of proteins identified from one experiment to the next (<10% change). However, there was limited overlap in the protein sets with <50% of the proteins identified as common between the sets of proteins identified by the different systems. In addition to the numbers of proteins identified and consistency of those identified, the reduced monetary costs of experimentation and increased assay flexibility produced by using isoelectric focusing was considered in order to adopt a system best suited for comparative proteomic projects.
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Affiliation(s)
- Nereus W Gunther
- US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, PA 19038, USA.
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14
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Berkowitz SA, Engen JR, Mazzeo JR, Jones GB. Analytical tools for characterizing biopharmaceuticals and the implications for biosimilars. Nat Rev Drug Discov 2012; 11:527-40. [PMID: 22743980 DOI: 10.1038/nrd3746] [Citation(s) in RCA: 376] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Biologics such as monoclonal antibodies are much more complex than small-molecule drugs, which raises challenging questions for the development and regulatory evaluation of follow-on versions of such biopharmaceutical products (also known as biosimilars) and their clinical use once patent protection for the pioneering biologic has expired. With the recent introduction of regulatory pathways for follow-on versions of complex biologics, the role of analytical technologies in comparing biosimilars with the corresponding reference product is attracting substantial interest in establishing the development requirements for biosimilars. Here, we discuss the current state of the art in analytical technologies to assess three characteristics of protein biopharmaceuticals that regulatory authorities have identified as being important in development strategies for biosimilars: post-translational modifications, three-dimensional structures and protein aggregation.
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Affiliation(s)
- Steven A Berkowitz
- Analytical Development, Biogen Idec, 14 Cambridge Center, Cambridge, Massachusetts 02142, USA
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15
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Doneanu CE, Xenopoulos A, Fadgen K, Murphy J, Skilton SJ, Prentice H, Stapels M, Chen W. Analysis of host-cell proteins in biotherapeutic proteins by comprehensive online two-dimensional liquid chromatography/mass spectrometry. MAbs 2012; 4:24-44. [PMID: 22327428 DOI: 10.4161/mabs.4.1.18748] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Assays for identification and quantification of host-cell proteins (HCPs) in biotherapeutic proteins over 5 orders of magnitude in concentration are presented. The HCP assays consist of two types: HCP identification using comprehensive online two-dimensional liquid chromatography coupled with high resolution mass spectrometry (2D-LC/MS), followed by high-throughput HCP quantification by liquid chromatography, multiple reaction monitoring (LC-MRM). The former is described as a "discovery" assay, the latter as a "monitoring" assay. Purified biotherapeutic proteins (e.g., monoclonal antibodies) were digested with trypsin after reduction and alkylation, and the digests were fractionated using reversed-phase (RP) chromatography at high pH (pH 10) by a step gradient in the first dimension, followed by a high-resolution separation at low pH (pH 2.5) in the second dimension. As peptides eluted from the second dimension, a quadrupole time-of-flight mass spectrometer was used to detect the peptides and their fragments simultaneously by alternating the collision cell energy between a low and an elevated energy (MSE methodology). The MSE data was used to identify and quantify the proteins in the mixture using a proven label-free quantification technique ("Hi3" method). The same data set was mined to subsequently develop target peptides and transitions for monitoring the concentration of selected HCPs on a triple quadrupole mass spectrometer in a high-throughput manner (20 min LC-MRM analysis). This analytical methodology was applied to the identification and quantification of low-abundance HCPs in six samples of PTG1, a recombinant chimeric anti-phosphotyrosine monoclonal antibody (mAb). Thirty three HCPs were identified in total from the PTG1 samples among which 21 HCP isoforms were selected for MRM monitoring. The absolute quantification of three selected HCPs was undertaken on two different LC-MRM platforms after spiking isotopically labeled peptides in the samples. Finally, the MRM quantitation results were compared with TOF-based quantification based on the Hi3 peptides, and the TOF and MRM data sets correlated reasonably well. The results show that the assays provide detailed valuable information to understand the relative contributions of purification schemes to the nature and concentrations of HCP impurities in biopharmaceutical samples, and the assays can be used as generic methods for HCP analysis in the biopharmaceutical industry.
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Wu Q, Yuan H, Zhang L, Zhang Y. Recent advances on multidimensional liquid chromatography-mass spectrometry for proteomics: from qualitative to quantitative analysis--a review. Anal Chim Acta 2012; 731:1-10. [PMID: 22652259 DOI: 10.1016/j.aca.2012.04.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 04/09/2012] [Accepted: 04/09/2012] [Indexed: 02/08/2023]
Abstract
With the acceleration of proteome research, increasing attention has been paid to multidimensional liquid chromatography-mass spectrometry (MDLC-MS) due to its high peak capacity and separation efficiency. Recently, many efforts have been put to improve MDLC-based strategies including "top-down" and "bottom-up" to enable highly sensitive qualitative and quantitative analysis of proteins, as well as accelerate the whole analytical procedure. Integrated platforms with combination of sample pretreatment, multidimensional separations and identification were also developed to achieve high throughput and sensitive detection of proteomes, facilitating highly accurate and reproducible quantification. This review summarized the recent advances of such techniques and their applications in qualitative and quantitative analysis of proteomes.
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Affiliation(s)
- Qi Wu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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An HJ, Lebrilla CB. Structure elucidation of native N- and O-linked glycans by tandem mass spectrometry (tutorial). MASS SPECTROMETRY REVIEWS 2011; 30:560-578. [PMID: 21656841 DOI: 10.1002/mas.20283] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Oligosaccharides play important roles in many biological processes. However, the structural elucidation of oligosaccharides remains a major challenge due to the complexities of their structures. Mass spectrometry provides a powerful method for determining oligosaccharide composition. Tandem mass spectrometry (MS) provides structural information with high sensitivity. Oligosaccharide structures differ from other polymers such as peptides because of the large number of linkage combinations and branching. This complexity makes the analysis of oligosaccharide unique from that of peptides. This tutorial addresses the issue of spectral interpretation of tandem MS under conditions of collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD). The proper interpretation of tandem MS data can provide important structural information on different types of oligosaccharides including O- and N-linked.
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Affiliation(s)
- Hyun Joo An
- Department of Chemistry, University of California, Davis, USA
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18
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García-Cañas V, Simó C, León C, Ibáñez E, Cifuentes A. MS-based analytical methodologies to characterize genetically modified crops. MASS SPECTROMETRY REVIEWS 2011; 30:396-416. [PMID: 21500243 DOI: 10.1002/mas.20286] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2009] [Revised: 11/18/2009] [Accepted: 11/18/2009] [Indexed: 05/09/2023]
Abstract
The development of genetically modified crops has had a great impact on the agriculture and food industries. However, the development of any genetically modified organism (GMO) requires the application of analytical procedures to confirm the equivalence of the GMO compared to its isogenic non-transgenic counterpart. Moreover, the use of GMOs in foods and agriculture faces numerous criticisms from consumers and ecological organizations that have led some countries to regulate their production, growth, and commercialization. These regulations have brought about the need of new and more powerful analytical methods to face the complexity of this topic. In this regard, MS-based technologies are increasingly used for GMOs analysis to provide very useful information on GMO composition (e.g., metabolites, proteins). This review focuses on the MS-based analytical methodologies used to characterize genetically modified crops (also called transgenic crops). First, an overview on genetically modified crops development is provided, together with the main difficulties of their analysis. Next, the different MS-based analytical approaches applied to characterize GM crops are critically discussed, and include "-omics" approaches and target-based approaches. These methodologies allow the study of intended and unintended effects that result from the genetic transformation. This information is considered to be essential to corroborate (or not) the equivalence of the GM crop with its isogenic non-transgenic counterpart.
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Affiliation(s)
- Virginia García-Cañas
- Institute of Industrial Fermentations (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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19
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Wang Y, Lu Q, Wu SL, Karger BL, Hancock WS. Characterization and comparison of disulfide linkages and scrambling patterns in therapeutic monoclonal antibodies: using LC-MS with electron transfer dissociation. Anal Chem 2011; 83:3133-40. [PMID: 21428412 DOI: 10.1021/ac200128d] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The disulfides in three monoclonal antibodies (mAb), the anti-HER2, anti-CD11a, and GLP-1 with IgG4-Fc fusion protein, were completely mapped by LC-MS with the combination of electron-transfer dissociation (ETD) and collision induced dissociation (CID) fragmentation. In addition to mapping the 4 inter- and 12 intrachain disulfides (total 16), the identification of scrambled disulfides in degraded samples (heat-stress) was achieved. The scrambling was likely attributed to an initial breakage between the light (Cys 214) and heavy (Cys 223) chains in anti-HER2, with the same observation found in a similar therapeutic mAb, anti-CD11a. On the other hand, the fusion antibody, with no light chain but containing only two heavy chains, generated much less scrambling under the same heat-stressed conditions. The preferred sites of scrambling were identified, such as the intrachain disulfide for CxxC in the heavy chain, and the C194 of the heavy chain pairing with the terminal Cys residue (C214) in the light chain. The interchain disulfides between the light and heavy chains were weaker than the interchain disulfides between the two heavy chains. The relative high abundance ions observed in ETD provided strong evidence for the linked peptide information, which was particularly useful for the identification of the scrambled disulfides. The use of sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) helped the separation of these misfolded proteins for the determination of scrambled disulfide linkages. This methodology is useful for comparison of disulfide stability generated from different structural designs and providing a new way to determine the scrambling patterns, which could be applied for those seeking to determine unknown disulfide linkages.
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Affiliation(s)
- Yi Wang
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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Chen G, Warrack BM, Goodenough AK, Wei H, Wang-Iverson DB, Tymiak AA. Characterization of protein therapeutics by mass spectrometry: recent developments and future directions. Drug Discov Today 2010; 16:58-64. [PMID: 21093608 DOI: 10.1016/j.drudis.2010.11.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 10/08/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
Abstract
Mass spectrometry (MS) has become a powerful technology in the discovery and development of protein therapeutics in the biopharmaceutical industry. This review article describes recent developments and future trends in the characterization of protein therapeutics using MS. We discuss top-down MS for the characterization of protein modifications, hydrogen/deuterium exchange MS and ion mobility MS methods for higher order protein structure studies. Quantitative analysis of protein therapeutics (in vivo) by MS as an orthogonal approach to immunoassay for pharmacokinetics studies will also be illustrated.
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Affiliation(s)
- Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb Company, PO Box 4000, Princeton, NJ 08543, USA.
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Zmatliková Z, Sedláková P, Lacinová K, Eckhardt A, Pataridis S, Mikšík I. Non-enzymatic posttranslational modifications of bovine serum albumin by oxo-compounds investigated by high-performance liquid chromatography-mass spectrometry and capillary zone electrophoresis-mass spectrometry. J Chromatogr A 2010; 1217:8009-15. [PMID: 20828700 DOI: 10.1016/j.chroma.2010.08.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 08/04/2010] [Accepted: 08/06/2010] [Indexed: 02/05/2023]
Abstract
Non-enzymatic posttranslational modifications of bovine serum albumin (BSA) by various oxo-compounds (glucose, ribose, glyoxal and glutardialdehyde) have been investigated using high-performance liquid chromatography (HPLC) and capillary zone electrophoresis (CZE). Both of these methods used mass spectrometric (MS) detection. Three enzymes (trypsin, pepsin, proteinase K) were used to digest glycated BSA. The extent of modification depended on the selected oxo-compound. Reactivity increased progressively from glucose to glutardialdehyde (glucose<ribose<glyoxal<glutardialdehyde). Carboxymethylation of lysine (CML) was the main type of modification detected. The HPLC/MS method achieved higher coverage and a larger amount of CML was identified compared to CZE/MS.
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Affiliation(s)
- Zdeňka Zmatliková
- Institute of Physiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague 4, Czech Republic
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Kosters H, Wierenga P, Gruppen H. SELDI-TOF-MS as a rapid tool to study food related protein–peptide interactions. Food Hydrocoll 2010. [DOI: 10.1016/j.foodhyd.2010.03.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Piñeiro C, Cañas B, Carrera M. The role of proteomics in the study of the influence of climate change on seafood products. Food Res Int 2010. [DOI: 10.1016/j.foodres.2009.11.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Mass spectrometric analysis of multiple pertussis toxins and toxoids. J Biomed Biotechnol 2010; 2010:942365. [PMID: 20508854 PMCID: PMC2874995 DOI: 10.1155/2010/942365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 03/09/2010] [Indexed: 11/17/2022] Open
Abstract
Bordetella pertussis (Bp) is the causative agent of pertussis, a vaccine preventable disease occurring primarily in children. In recent years, there has been increased reporting of pertussis. Current pertussis vaccines are acellular and consist of Bp proteins including the major virulence factor pertussis toxin (Ptx), a 5-subunit exotoxin. Variation in Ptx subunit amino acid (AA) sequence could possibly affect the immune response. A blind comparative mass spectrometric (MS) analysis of commercially available Ptx as well as the chemically modified toxoid (Ptxd) from licensed vaccines was performed to assess peptide sequence and AA coverage variability as well as relative amounts of Ptx subunits. Qualitatively, there are similarities among the various sources based on AA percent coverages and MS/MS fragmentation profiles. Additionally, based on a label-free mass spectrometry-based quantification method there is differential relative abundance of the subunits among the sources.
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Trimpin S. A perspective on MALDI alternatives-total solvent-free analysis and electron transfer dissociation of highly charged ions by laserspray ionization. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:471-485. [PMID: 20446310 DOI: 10.1002/jms.1737] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Progress in research is hindered by analytical limitations, especially in biological areas in which sensitivity and dynamic range are critical to success. Inherent difficulties of characterization associated with complexity arising from heterogeneity of various materials including topologies (isomeric composition) and insolubility also limit progress. For this reason, we are developing methods for total solvent-free analysis by mass spectrometry consisting of solvent-free ionization followed by solvent-free gas-phase separation. We also recently constructed a novel matrix-assisted laser desorption ionization (MALDI) source that provides a simple, practical and sensitive way of producing highly charged ions by laserspray ionization (LSI) or singly charged ions commonly observed with MALDI by choice of matrix or matrix preparation. This is the first ionization source with such freedom-an extremely powerful analytical 'switch'. Multiply charged LSI ions allow molecules exceeding the mass-to-charge range of the instrument to be observed and permit for the first time electron transfer dissociation fragment ion analysis.
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Affiliation(s)
- Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, MI, USA.
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Ahmed FE. The role of capillary electrophoresis–mass spectrometry to proteome analysis and biomarker discovery. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:1963-81. [DOI: 10.1016/j.jchromb.2009.05.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2008] [Revised: 04/24/2009] [Accepted: 05/10/2009] [Indexed: 01/25/2023]
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Shah SJ, Yu KH, Sangar V, Parry SI, Blair IA. Identification and quantification of preterm birth biomarkers in human cervicovaginal fluid by liquid chromatography/tandem mass spectrometry. J Proteome Res 2009; 8:2407-17. [PMID: 19271751 DOI: 10.1021/pr8010342] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spontaneous preterm birth (PTB) before 37 completed weeks of gestation resulting from preterm labor (PTL) is a leading contributor of perinatal morbidity and mortality. Early identification of at-risk women by reliable screening tests could alleviate this health issue; however, conventional methods such as obstetric history and clinical risk factors, uterine activity monitoring, biochemical markers, and cervical sonography for screening women at risk for PTB have proven unsuccessful in lowering the rate of PTB. Cervicovaginal fluid (CVF) might prove to be a useful, readily available biological fluid for identifying diagnostic PTB biomarkers. Human columnar epithelial endocervical-1 (End1) and vaginal (Vk2) cell secretomes were employed to generate a stable isotope labeled proteome (SILAP) standard to facilitate characterization and relative quantification of proteins present in CVF. The SILAP standard was prepared using stable isotope labeling by amino acids in cell culture (SILAC) of End1 and Vk2 through seven passages. The labeled secreted proteins from both cell lines were combined and characterized by liquid-chromatography-tandem mass spectrometry (LC-MS/MS). In total, 1211 proteins were identified in the End1-Vk2 SILAP standard, with 236 proteins being consistently identified in each of the replicates analyzed. Individual proteins were found to contain <0.5% of the endogenous unlabeled forms. Identified proteins were screened to provide a set of 15 candidates that have either previously been identified as potential PTB biomarkers or could be linked mechanistically to PTB. Stable isotope dilution LC-multiple reaction monitoring (MRM/MS) assays were then developed for conducting relative quantification of the 15 candidate biomarkers in human CVF samples from term and PTB cases. Three proteins were significantly elevated in PTB cases (desmoplakin isoform 1, stratifin, and thrombospondin 1 precursor), providing a foundation for further validation in larger patient cohorts.
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Affiliation(s)
- Sumit J Shah
- Center for Excellence in Environmental Toxicology, Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6160, USA
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Xie H, Gilar M, Gebler JC. Characterization of Protein Impurities and Site-Specific Modifications Using Peptide Mapping with Liquid Chromatography and Data Independent Acquisition Mass Spectrometry. Anal Chem 2009; 81:5699-708. [DOI: 10.1021/ac900468j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hongwei Xie
- Biopharmaceutical Sciences, Waters Corporation, 34 Maple Street, Massachusetts 01757
| | - Martin Gilar
- Biopharmaceutical Sciences, Waters Corporation, 34 Maple Street, Massachusetts 01757
| | - John C. Gebler
- Biopharmaceutical Sciences, Waters Corporation, 34 Maple Street, Massachusetts 01757
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29
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Chen G, Pramanik BN. Application of LC/MS to proteomics studies: current status and future prospects. Drug Discov Today 2009; 14:465-71. [DOI: 10.1016/j.drudis.2009.02.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Revised: 02/02/2009] [Accepted: 02/13/2009] [Indexed: 02/06/2023]
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30
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Blackburn K, Goshe MB. Challenges and strategies for targeted phosphorylation site identification and quantification using mass spectrometry analysis. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 8:90-103. [DOI: 10.1093/bfgp/eln051] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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31
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Bieniossek C, Berger I. Towards eukaryotic structural complexomics. ACTA ACUST UNITED AC 2008; 10:37-46. [PMID: 19009368 DOI: 10.1007/s10969-008-9047-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 10/30/2008] [Indexed: 11/24/2022]
Abstract
Many eukaryotic proteins exist in large multisubunit assemblies and often show compromised folding or activity when their interaction partners are not present. Protein complexes in eukaryotes can contain ten or more subunits with individual polypeptides ranging in size up to several hundred kilodalton, severely restricting the application of conventional cloning strategies and imposing constraints on the choice of the expression host. Modern structural molecular biology often depends on introducing diversity into the specimens under investigation, including mutation, truncation and placement of purification aids. Current recombinant expression methods often require a disproportionate labor investment prior to multiprotein expression, and subsequent to expression and analysis do not provide for rapid revision of the experiment. We have developed reagents and protocols for rapid and flexible multiprotein complex expressions suitable for structural biology, focusing on multigene baculoviral vectors and their recombination mediated assembly. A top priority in protein science is automation. Our strategy can be readily adapted in a robotics setup, for baculovirus/insect cell expression of protein complexes, but likewise also for mammalian or prokaryotic hosts.
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Affiliation(s)
- Christoph Bieniossek
- Institute for Molecular Biology and Biophysics, ETH Hönggerberg, 8093, Zurich, Switzerland
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Hattan SJ, Vestal ML. Novel Three-Dimensional MALDI Plate for Interfacing High-Capacity LC Separations with MALDI-TOF. Anal Chem 2008; 80:9115-23. [DOI: 10.1021/ac8017108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stephen J. Hattan
- Virgin Instruments Corporation, 60 Union Avenue (Suite 1-R), Sudbury, Massachusetts 01776
| | - Marvin L. Vestal
- Virgin Instruments Corporation, 60 Union Avenue (Suite 1-R), Sudbury, Massachusetts 01776
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