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Karongo R, Horak J, Lämmerhofer M. Comprehensive reversed-phase×chiral two-dimensional liquid chromatography coupled to quadrupole-time-of-flight tandem mass spectrometry with post-first dimension flow splitting for untargeted enantioselective amino acid analysis. J Sep Sci 2023; 46:e2300351. [PMID: 37464972 DOI: 10.1002/jssc.202300351] [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: 05/19/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023]
Abstract
This work describes a comprehensive achiral × chiral two-dimensional liquid chromatography separation for enantioselective amino acid analysis coupled to electrospray ionization-tandem mass spectrometry detection using data-independent acquisition. Flow splitting after the first and second dimension separation was utilized for volumetric flow reduction and for enabling a multi-detector approach (with ultraviolet, fluorescence, charged aerosol, and MS detection), respectively. Derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate provided a chromophore, a fluorophore, and an efficient mass tag for efficient ionization in positive electrospray ionization-mass spectrometry. Chiral columns often have limitations in terms of their chemoselectivity, which may be a problem when complex sample mixtures with structurally related compounds need to be separated. It can be alleviated by a reversed-phase×chiral two-dimensional-liquid chromatography setup, in which the first dimension provides the chemoselectivity and a chiral tandem column constituted of quinine-carbamate derived weak anion-exchanger and zwitterionic ion-exchanger in the second dimension separation of D- and L-amino acid enantiomers. The method was used to control the stereointegrity of the therapeutic peptide octreotide. After hydrolysis, all amino acid constituents were detected with the correct configuration and composition. Some options for flow splitting and integration of destructive detectors in the first dimension separation are outlined.
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Affiliation(s)
- Ryan Karongo
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Tübingen, Germany
| | - Jeannie Horak
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Tübingen, Germany
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich Medical Center, Munich, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Tübingen, Germany
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Lenčo J, Jadeja S, Naplekov DK, Krokhin OV, Khalikova MA, Chocholouš P, Urban J, Broeckhoven K, Nováková L, Švec F. Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial. J Proteome Res 2022; 21:2846-2892. [PMID: 36355445 DOI: 10.1021/acs.jproteome.2c00407] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The performance of the current bottom-up liquid chromatography hyphenated with mass spectrometry (LC-MS) analyses has undoubtedly been fueled by spectacular progress in mass spectrometry. It is thus not surprising that the MS instrument attracts the most attention during LC-MS method development, whereas optimizing conditions for peptide separation using reversed-phase liquid chromatography (RPLC) remains somewhat in its shadow. Consequently, the wisdom of the fundaments of chromatography is slowly vanishing from some laboratories. However, the full potential of advanced MS instruments cannot be achieved without highly efficient RPLC. This is impossible to attain without understanding fundamental processes in the chromatographic system and the properties of peptides important for their chromatographic behavior. We wrote this tutorial intending to give practitioners an overview of critical aspects of peptide separation using RPLC to facilitate setting the LC parameters so that they can leverage the full capabilities of their MS instruments. After briefly introducing the gradient separation of peptides, we discuss their properties that affect the quality of LC-MS chromatograms the most. Next, we address the in-column and extra-column broadening. The last section is devoted to key parameters of LC-MS methods. We also extracted trends in practice from recent bottom-up proteomics studies and correlated them with the current knowledge on peptide RPLC separation.
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Affiliation(s)
- Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Siddharth Jadeja
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Denis K Naplekov
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Oleg V Krokhin
- Department of Internal Medicine, Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, WinnipegR3E 3P4, Manitoba, Canada
| | - Maria A Khalikova
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Petr Chocholouš
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Jiří Urban
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00Brno, Czech Republic
| | - Ken Broeckhoven
- Department of Chemical Engineering (CHIS), Faculty of Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050Brussel, Belgium
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - František Švec
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
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Development of an antibody-free ID-LC MS method for the quantification of procalcitonin in human serum at sub-microgram per liter level using a peptide-based calibration. Anal Bioanal Chem 2021; 413:4707-4725. [PMID: 33987701 DOI: 10.1007/s00216-021-03361-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/03/2021] [Accepted: 04/16/2021] [Indexed: 10/21/2022]
Abstract
The quantification of low abundant proteins in complex matrices by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) remains challenging. A measurement procedure based on optimized antibody-free sample preparation and isotope dilution coupled to LC-MS/MS was developed to quantify procalcitonin (PCT) in human serum at sub-microgram per liter level. A combination of sodium deoxycholate-assisted protein precipitation with acetonitrile, solid-phase extraction, and trypsin digestion assisted with Tween-20 enhanced the method sensitivity. Linearity was established through peptide-based calibration curves in the serum matrix (0.092-5.222 μg/L of PCT) with a good linear fit (R2 ≥ 0.999). Quality control materials spiked with known amounts of protein-based standards were used to evaluate the method's accuracy. The bias ranged from -2.6 to +4.3%, and the intra-day and inter-day coefficients of variations (CVs) were below 2.2% for peptide-based quality controls. A well-characterized correction factor was determined and applied to compensate for digestion incompleteness and material loss before the internal standards spike. Results with metrological traceability to the SI units were established using standard peptide of well-characterized purity determined by peptide impurity corrected amino acid analysis. The validated method enables accurate quantification of PCT in human serum at a limit of quantification down to 0.245 μg/L (bias -1.9%, precision 9.1%). The method was successfully applied to serum samples obtained from patients with sepsis. Interestingly, the PCT concentration reported implementing the isotope dilution LC-MS/MS method was twofold lower than the concentration provided by an immunoassay.
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Uçaktürk E, Başaran AA, Demirel AH. Effect of the Mobile Phase Compositions on the Confirmation Analysis of Some Prohibited Substances in Sport by LC–ESI–MS/MS. Chromatographia 2020. [DOI: 10.1007/s10337-020-03957-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Rebane R, Kruve A, Liigand J, Liigand P, Gornischeff A, Leito I. Ionization efficiency ladders as tools for choosing ionization mode and solvent in liquid chromatography/mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1834-1843. [PMID: 31381213 DOI: 10.1002/rcm.8545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE The choice of mobile phase components and optimal ion source, mainly electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI), is a crucial part in liquid chromatography/mass spectrometry (LC/MS) method development to achieve higher sensitivity and lower detection limits. In this study we demonstrate how to rigorously solve these questions by using ionization efficiency scales. METHODS Four ionization efficiency scales are used: recorded with both APCI and ESI sources and using both methanol- and acetonitrile-containing mobile phases. Each scale contains altogether more than 50 compounds. In addition, measurements with a chromatographic column were also performed. RESULTS We observed a correlation between calibration graph slopes under LC conditions and logIE values in ESI (but not APCI) thereby validating the use of logIE values for choosing the ion source. Most of the studied compounds preferred ESI as an ion source and methanol as mobile organic phase. APCI remains the ion source of choice for polycyclic aromatic hydrocarbons. For APCI, both acetonitrile and methanol provide similar ionization efficiencies with few exceptions. CONCLUSIONS Overall the results of this work give a concise guideline for practitioners in choosing an ion source for LC/MS analysis on the basis of the chemical nature of the analytes.
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Affiliation(s)
- Riin Rebane
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
| | - Anneli Kruve
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
| | - Jaanus Liigand
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
| | - Piia Liigand
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
| | - Artur Gornischeff
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
| | - Ivo Leito
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
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Jaini R, Wang P, Dudareva N, Chapple C, Morgan JA. Targeted Metabolomics of the Phenylpropanoid Pathway in Arabidopsis thaliana using Reversed Phase Liquid Chromatography Coupled with Tandem Mass Spectrometry. PHYTOCHEMICAL ANALYSIS : PCA 2017; 28:267-276. [PMID: 28146307 DOI: 10.1002/pca.2672] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/19/2016] [Accepted: 12/05/2016] [Indexed: 05/07/2023]
Abstract
INTRODUCTION The phenylpropanoid pathway is a source of a diverse group of compounds derived from phenylalanine, many of which are involved in lignin biosynthesis and serve as precursors for the production of valuable compounds, such as coumarins, flavonoids, and lignans. Consequently, recent efforts have been invested in mechanistically understanding monolignol biosynthesis, making the quantification of these metabolites vital. OBJECTIVE To develop an improved and comprehensive analytical method for (i) extensively profiling, and (ii) accurately quantifiying intermediates of the monolignol biosynthetic network, using Arabidopsis thaliana as a model system. METHOD A liquid chromatography-tandem mass spectrometry with electrospray ionization was developed to quantify phenylpropanoid metabolites in Arabidopsis wildtype and cinnamoyl CoA reductase1 (CCR1) deficient lines (ccr1). RESULTS Vortexing at high temperatures (65°C) enhanced release of phenylpropanoids, specifically the more hydrophobic compounds. A pH of 5.3 and ammonium acetate buffer concentration of 2.5 mM resulted in an optimal analyte response across standards. Ion suppression was estimated using standard spike recovery studies for accurate quantitation. The optimized method was used to profile Arabidopsis wildtype and ccr1 stems. An increase in hydroxycinnamic acid derivatives and a decrease in the hydroxycinnamyl aldehydes and alcohols in ccr1 lines, supports a shift of flux from lignin synthesis to other secondary metabolites and phenylpropanoid derivatives. CONCLUSIONS Compared to existing targeted profiling techniques, our method is capable of quantifying a wider range of intermediates (15 out of 22 in WT Arabidopsis stems) at low in vivo concentrations (~50 pmol/g-FW for certain compounds), while requiring minimal sample preparation. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Rohit Jaini
- School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Peng Wang
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Horticulture & Landscape Architecture, West Lafayette, IN, 47907, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - John A Morgan
- School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
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Iannaccone A, Hollingsworth TJ, Koirala D, New DD, Lenchik NI, Beranova-Giorgianni S, Gerling IC, Radic MZ, Giorgianni F. Retinal pigment epithelium and microglia express the CD5 antigen-like protein, a novel autoantigen in age-related macular degeneration. Exp Eye Res 2016; 155:64-74. [PMID: 27989757 DOI: 10.1016/j.exer.2016.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 11/19/2022]
Abstract
We report on a novel autoantigen expressed in human macular tissues, identified following an initial Western blot (WB)-based screening of sera from subjects with age-related macular degeneration (AMD) for circulating auto-antibodies (AAbs) recognizing macular antigens. Immunoprecipitation, 2D-gel electrophoresis (2D-GE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), direct enzyme-linked immunosorbent assays (ELISA), WBs, immunohistochemistry (IHC), human primary and ARPE-19 immortalized cell cultures were used to characterize this novel antigen. An approximately 40-kDa autoantigen in AMD was identified as the scavenger receptor CD5 antigen-like protein (CD5L), also known as apoptosis inhibitor of macrophage (AIM). CD5L/AIM was localized to human RPE by IHC and WB methods and to retinal microglial cells by IHC. ELISAs with recombinant CD5L/AIM on a subset of AMD sera showed a nearly 2-fold higher anti-CD5L/AIM reactivity in AMD vs. Control sera (p = 0.000007). Reactivity ≥0.4 was associated with 18-fold higher odds of having AMD (χ2 = 21.42, p = 0.00063). Circulating CD5L/AIM levels were also nearly 2-fold higher in AMD sera compared to controls (p = 0.0052). The discovery of CD5L/AIM expression in the RPE and in retinal microglial cells adds to the known immunomodulatory roles of these cells in the retina. The discovery of AAbs recognizing CD5L/AIM identifies a possible novel disease biomarker and suggest a potential role for CD5L/AIM in the pathogenesis of AMD in situ. The possible mechanisms via which anti-CD5L/AIM AAbs may contribute to AMD pathogenesis are discussed. In particular, since CD5L is known to stimulate autophagy and to participate in oxidized LDL uptake in macrophages, we propose that anti-CD5L/AIM auto-antibodies may play a role in drusen biogenesis and inflammatory RPE damage in AMD.
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Affiliation(s)
- Alessandro Iannaccone
- University of Tennessee Health Science Center, Department of Ophthalmology, Hamilton Eye Institute, Memphis, TN, USA; Department of Ophthalmology, Duke Eye Center, Duke University School of Medicine, Durham, NC, USA.
| | - T J Hollingsworth
- University of Tennessee Health Science Center, Department of Ophthalmology, Hamilton Eye Institute, Memphis, TN, USA
| | - Diwa Koirala
- University of Tennessee Health Science Center, Department of Ophthalmology, Hamilton Eye Institute, Memphis, TN, USA; University of Tennessee Health Science Center, Department of Pharmaceutical Sciences, Memphis, TN, USA
| | - David D New
- University of Tennessee Health Science Center, Department of Ophthalmology, Hamilton Eye Institute, Memphis, TN, USA
| | - Nataliya I Lenchik
- University of Tennessee Health Science Center, Department of Ophthalmology, Hamilton Eye Institute, Memphis, TN, USA; University of Tennessee Health Science Center, Department of Medicine, Division of Endocrinology, Memphis, TN, USA
| | - Sarka Beranova-Giorgianni
- University of Tennessee Health Science Center, Department of Pharmaceutical Sciences, Memphis, TN, USA
| | - Ivan C Gerling
- University of Tennessee Health Science Center, Department of Medicine, Division of Endocrinology, Memphis, TN, USA
| | - Marko Z Radic
- University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, TN, USA
| | - Francesco Giorgianni
- University of Tennessee Health Science Center, Department of Pharmaceutical Sciences, Memphis, TN, USA
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Hoang K, Pophristic M, Horan AJ, Johnston MV, McEwen CN. High Sensitivity Analysis of Nanoliter Volumes of Volatile and Nonvolatile Compounds using Matrix Assisted Ionization (MAI) Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1590-1596. [PMID: 27349254 DOI: 10.1007/s13361-016-1433-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 06/04/2016] [Accepted: 06/05/2016] [Indexed: 06/06/2023]
Abstract
First results are reported using a simple, fast, and reproducible matrix-assisted ionization (MAI) sample introduction method that provides substantial improvements relative to previously published MAI methods. The sensitivity of the new MAI methods, which requires no laser, high voltage, or nebulizing gas, is comparable to those reported for MALDI-TOF and n-ESI. High resolution full acquisition mass spectra having low chemical background are acquired from low nanoliters of solution using only a few femtomoles of analyte. The limit-of-detection for angiotensin II is less than 50 amol on an Orbitrap Exactive mass spectrometer. Analysis of peptides, including a bovine serum albumin digest, and drugs, including drugs in urine without a purification step, are reported using a 1 μL zero dead volume syringe in which only the analyte solution wetting the walls of the syringe needle is used in the analysis.
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Affiliation(s)
- Khoa Hoang
- University of the Sciences, Philadelphia, PA, USA
| | | | | | | | - Charles N McEwen
- University of the Sciences, Philadelphia, PA, USA.
- MSTM, LLC, Newark, DE, USA.
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Rebane R, Kruve A, Liigand P, Liigand J, Herodes K, Leito I. Establishing Atmospheric Pressure Chemical Ionization Efficiency Scale. Anal Chem 2016; 88:3435-9. [DOI: 10.1021/acs.analchem.5b04852] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Riin Rebane
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
| | - Anneli Kruve
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
| | - Piia Liigand
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
| | - Jaanus Liigand
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
| | - Koit Herodes
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
| | - Ivo Leito
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411, Tartu, Estonia
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Iannaccone A, Giorgianni F, New DD, Hollingsworth TJ, Umfress A, Alhatem AH, Neeli I, Lenchik NI, Jennings BJ, Calzada JI, Satterfield S, Mathews D, Diaz RI, Harris T, Johnson KC, Charles S, Kritchevsky SB, Gerling IC, Beranova-Giorgianni S, Radic MZ. Circulating Autoantibodies in Age-Related Macular Degeneration Recognize Human Macular Tissue Antigens Implicated in Autophagy, Immunomodulation, and Protection from Oxidative Stress and Apoptosis. PLoS One 2015; 10:e0145323. [PMID: 26717306 PMCID: PMC4696815 DOI: 10.1371/journal.pone.0145323] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 12/01/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND We investigated sera from elderly subjects with and without age-related macular degeneration (AMD) for presence of autoantibodies (AAbs) against human macular antigens and characterized their identity. METHODS Sera were collected from participants in the Age-Related Maculopathy Ancillary (ARMA) Study, a cross-sectional investigation ancillary to the Health ABC Study, enriched with participants from the general population. The resulting sample (mean age: 79.2±3.9 years old) included subjects with early to advanced AMD (n = 131) and controls (n = 231). Sera were tested by Western blots for immunoreactive bands against human donor macular tissue homogenates. Immunoreactive bands were identified and graded, and odds ratios (OR) calculated. Based on these findings, sera were immunoprecipitated, and subjected to 2D gel electrophoresis (GE). Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to identify the targets recognized by circulating AAbs seen on 2D-GE, followed by ELISAs with recombinant proteins to confirm LC-MS/MS results, and quantify autoreactivities. RESULTS In AMD, 11 immunoreactive bands were significantly more frequent and 13 were significantly stronger than in controls. Nine of the more frequent bands also showed stronger reactivity. OR estimates ranged between 4.06 and 1.93, and all clearly excluded the null value. Following immunoprecipitation, 2D-GE and LC-MS/MS, five of the possible autoreactivity targets were conclusively identified: two members of the heat shock protein 70 (HSP70) family, HSPA8 and HSPA9; another member of the HSP family, HSPB4, also known as alpha-crystallin A chain (CRYAA); Annexin A5 (ANXA5); and Protein S100-A9, also known as calgranulin B that, when complexed with S100A8, forms calprotectin. ELISA testing with recombinant proteins confirmed, on average, significantly higher reactivities against all targets in AMD samples compared to controls. CONCLUSIONS Consistent with other evidence supporting the role of inflammation and the immune system in AMD pathogenesis, AAbs were identified in AMD sera, including early-stage disease. Identified targets may be mechanistically linked to AMD pathogenesis because the identified proteins are implicated in autophagy, immunomodulation, and protection from oxidative stress and apoptosis. In particular, a role in autophagy activation is shared by all five autoantigens, raising the possibility that the detected AAbs may play a role in AMD via autophagy compromise and downstream activation of the inflammasome. Thus, we propose that the detected AAbs provide further insight into AMD pathogenesis and have the potential to contribute to disease biogenesis and progression.
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Affiliation(s)
- Alessandro Iannaccone
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, United States of America
- * E-mail:
| | - Francesco Giorgianni
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - David D. New
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - T. J. Hollingsworth
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Allison Umfress
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Albert H. Alhatem
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Indira Neeli
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, United States of America
- Department of Microbiology, Immunology & Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Nataliya I. Lenchik
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, United States of America
- Department of Internal Medicine/Endocrinology, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Barbara J. Jennings
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Jorge I. Calzada
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, United States of America
- Charles Retina Institute, Memphis, TN, United States of America
| | - Suzanne Satterfield
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Dennis Mathews
- Eye Specialty Group, Memphis, TN, United States of America
- Southern College of Optometry, Memphis, TN, United States of America
| | - Rocio I. Diaz
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, United States of America
- Charles Retina Institute, Memphis, TN, United States of America
| | - Tamara Harris
- National Institute on Aging, NIH, Bethesda, MD, United States of America
| | - Karen C. Johnson
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Steve Charles
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN, United States of America
- Charles Retina Institute, Memphis, TN, United States of America
| | - Stephen B. Kritchevsky
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, United States of America
- Sticht Center on Aging, Wake Forest University, Winston-Salem, NC, United States of America
| | - Ivan C. Gerling
- Department of Internal Medicine/Endocrinology, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Sarka Beranova-Giorgianni
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Marko Z. Radic
- Department of Microbiology, Immunology & Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States of America
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Proteomics of the human pituitary tissue: bioanalytical methods and applications. Bioanalysis 2015; 6:1989-2003. [PMID: 25158968 DOI: 10.4155/bio.14.132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The pituitary is the central endocrine gland that plays complex regulatory roles in growth, reproduction and metabolism of the body. The human pituitary tissue proteome has been the target of a number of investigations that applied various combinations of advanced separation techniques, mass spectrometry, and bioinformatics tools. This review describes the main features of the bioanalytical workflows used in pituitary proteomics, and summarizes major applications in pituitary proteome mapping, differential protein expression profiling in health and disease, and discovery of post-translational modifications in pituitary proteins.
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Tulipani S, Mora-Cubillos X, Jáuregui O, Llorach R, García-Fuentes E, Tinahones FJ, Andres-Lacueva C. New and Vintage Solutions To Enhance the Plasma Metabolome Coverage by LC-ESI-MS Untargeted Metabolomics: The Not-So-Simple Process of Method Performance Evaluation. Anal Chem 2015; 87:2639-47. [DOI: 10.1021/ac503031d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sara Tulipani
- Biomarkers & Nutrimetabolomic Lab., Nutrition and Food Science Department, XaRTA, INSA, Campus Torribera, Pharmacy Faculty, University of Barcelona, 08028 Barcelona, Spain
- Biomedical Research
Institute (IBIMA), Service of Endocrinology and Nutrition, Malaga
Hospital Complex (Virgen de la Victoria), Campus de Teatinos s/n, University of Malaga, 29071 Malaga, Spain
| | - Ximena Mora-Cubillos
- Biomarkers & Nutrimetabolomic Lab., Nutrition and Food Science Department, XaRTA, INSA, Campus Torribera, Pharmacy Faculty, University of Barcelona, 08028 Barcelona, Spain
| | - Olga Jáuregui
- Scientific and Technological Centres of the University of Barcelona (CCIT-UB), 08028 Barcelona, Spain
| | - Rafael Llorach
- Biomarkers & Nutrimetabolomic Lab., Nutrition and Food Science Department, XaRTA, INSA, Campus Torribera, Pharmacy Faculty, University of Barcelona, 08028 Barcelona, Spain
| | - Eduardo García-Fuentes
- Biomedical Research
Institute (IBIMA), Service of Endocrinology and Nutrition, Hospital
Regional Universitario, Plaza del Hospital Civil s/n, University of Malaga, 29071 Malaga, Spain
- CIBER Fisiopatología
de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Francisco J Tinahones
- Biomedical Research
Institute (IBIMA), Service of Endocrinology and Nutrition, Malaga
Hospital Complex (Virgen de la Victoria), Campus de Teatinos s/n, University of Malaga, 29071 Malaga, Spain
- CIBER Fisiopatología
de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Cristina Andres-Lacueva
- Biomarkers & Nutrimetabolomic Lab., Nutrition and Food Science Department, XaRTA, INSA, Campus Torribera, Pharmacy Faculty, University of Barcelona, 08028 Barcelona, Spain
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13
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Bao J, Krylova SM, Cherney LT, LeBlanc JCY, Pribil P, Johnson PE, Wilson DJ, Krylov SN. Kinetic size-exclusion chromatography with mass spectrometry detection: an approach for solution-based label-free kinetic analysis of protein-small molecule interactions. Anal Chem 2014; 86:10016-20. [PMID: 25275785 DOI: 10.1021/ac503391c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Studying the kinetics of reversible protein-small molecule binding is a major challenge. The available approaches require that either the small molecule or the protein be modified by labeling or immobilization on a surface. Not only can such modifications be difficult to do but also they can drastically affect the kinetic parameters of the interaction. To solve this problem, we present kinetic size-exclusion chromatography with mass spectrometry detection (KSEC-MS), a solution-based label-free approach. KSEC-MS utilizes the ability of size-exclusion chromatography (SEC) to separate any small molecule from any protein-small molecule complex without immobilization and the ability of mass spectrometry (MS) to detect a small molecule without a label. The rate constants of complex formation and dissociation are deconvoluted from the temporal pattern of small molecule elution measured with MS at the exit from the SEC column. This work describes the concept of KSEC-MS and proves it in principle by measuring the rate constants of interaction between carbonic anhydrase and acetazolamide.
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Affiliation(s)
- Jiayin Bao
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University , Toronto, Ontario M3J 1P3, Canada
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14
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Oppliger SR, Münger LH, Nyström L. Rapid and highly accurate detection of steryl glycosides by ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:9410-9419. [PMID: 25175549 DOI: 10.1021/jf501509m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This study describes the development and validation of a fast, accurate, and precise UPLC-Q-TOF-MS method for the analysis of steryl glycosides (SGs). The best combination of separation and sensitivity was obtained with a methanol/water gradient and formic acid as additive, using electrospray ionization (ESI). SGs were detected almost exclusively as sodiated adducts, allowing identification of the intact molecule, including the sugar moiety. The TOF-MS system offered high mass accuracy (1.3 ppm), providing a valuable tool for SG identification. The method was used to quantify single SG species in oat bran and whole wheat, and it was demonstrated that reliable quantification requires accounting for the matrix effect, which may reduce the SG signal by up to 50% in some samples. The level of matrix effect also depends on food matrices with various SG contents, indicating that it should be individually considered for each sample.
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Affiliation(s)
- Selina R Oppliger
- ETH Zurich Institute of Food, Nutrition and Health , Schmelzbergstrasse 9, CH-8092 Zurich, Switzerland
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15
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Dong Q, Giorgianni F, Deng X, Beranova-Giorgianni S, Bridges D, Park EA, Raghow R, Elam MB. Phosphorylation of sterol regulatory element binding protein-1a by protein kinase A (PKA) regulates transcriptional activity. Biochem Biophys Res Commun 2014; 449:449-54. [PMID: 24853806 DOI: 10.1016/j.bbrc.2014.05.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 05/08/2014] [Indexed: 10/25/2022]
Abstract
The counter-regulatory hormone glucagon inhibits lipogenesis via downregulation of sterol regulatory element binding protein 1 (SREBP-1). The effect of glucagon is mediated via protein kinase A (PKA). To determine if SREBP-1 is a direct phosphorylation target of PKA, we conducted mass spectrometry analysis of recombinant n-terminal SREBP-1a following PKA treatment in vitro. This analysis identified serines 331/332 as bona-fide phosphorylation targets of PKA. To determine the functional consequences of phosphorylation at these sites, we constructed mammalian expression vector for both nSREBP-1a and 1c isoforms in which the candidate PKA phosphorylation sites were mutated to active phosphomimetic or non-phosphorylatable amino acids. The transcriptional activity of SREBP was reduced by the phosphomimetic mutation of S332 of nSREBP-1a and the corresponding serine (S308) of nSREBP-1c. This site is a strong candidate for mediating the negative regulatory effect of glucagon on SREBP-1 and lipogenesis.
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Affiliation(s)
- Qingming Dong
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Francesco Giorgianni
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Xiong Deng
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN, USA; Research Service, Veteran's Affairs Medical Center, Memphis, TN, USA
| | - Sarka Beranova-Giorgianni
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Dave Bridges
- Department of Physiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Edwards A Park
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Rajendra Raghow
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN, USA; Research Service, Veteran's Affairs Medical Center, Memphis, TN, USA
| | - Marshall B Elam
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN, USA; Research Service, Veteran's Affairs Medical Center, Memphis, TN, USA.
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16
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Influence of sample and mobile phase composition on peptide retention behaviour and sensitivity in reversed-phase liquid chromatography/mass spectrometry. J Chromatogr A 2013; 1314:199-207. [DOI: 10.1016/j.chroma.2013.09.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 11/20/2022]
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17
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Miyachi A, Murase T, Yamada Y, Osonoi T, Harada KI. Quantitative Analytical Method for Determining the Levels of Gastric Inhibitory Polypeptides GIP1–42 and GIP3–42 in Human Plasma Using LC–MS/MS/MS. J Proteome Res 2013; 12:2690-9. [DOI: 10.1021/pr400069f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Atsushi Miyachi
- Laboratory Management Department, Sanwa Kagaku Kenkyusho Co., Ltd., Mie 511-0406, Japan
| | - Takayo Murase
- Laboratory Management Department, Sanwa Kagaku Kenkyusho Co., Ltd., Mie 511-0406, Japan
| | - Yuichiro Yamada
- Department of Endocrinology
and Diabetes and Geriatric Medicine, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | | | - Ken-ichi Harada
- Graduate School of Environmental
and Human Science and Faculty of Pharmacy, Meijo University, Nagoya, Aichi 468-8503, Japan
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18
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Maurer M, Müller AC, Wagner C, Huber ML, Rudashevskaya EL, Wagner SN, Bennett KL. Combining Filter-Aided Sample Preparation and Pseudoshotgun Technology To Profile the Proteome of a Low Number of Early Passage Human Melanoma Cells. J Proteome Res 2012; 12:1040-8. [DOI: 10.1021/pr301009u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Margarita Maurer
- Division of Immunology, Allergy
and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090
Vienna, Austria
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH Building BT 25.3, A-1090 Vienna, Austria
| | - Christine Wagner
- Division of Immunology, Allergy
and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090
Vienna, Austria
| | - Marie L. Huber
- Division of Immunology, Allergy
and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090
Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH Building BT 25.3, A-1090 Vienna, Austria
| | - Elena L. Rudashevskaya
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH Building BT 25.3, A-1090 Vienna, Austria
| | - Stephan N. Wagner
- Division of Immunology, Allergy
and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090
Vienna, Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH Building BT 25.3, A-1090 Vienna, Austria
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19
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Haura EB, Sacco R, Li J, Müller AC, Grebien F, Superti-Furga G, Bennett KL. Optimisation of Downscaled Tandem Affinity Purifications to Identify Core Protein Complexes. ACTA ACUST UNITED AC 2012; 2:55-68. [PMID: 24077984 DOI: 10.5584/jiomics.v2i1.81] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this study we show that via stable, retroviral-expression of tagged EGFR del (L747-S752 deletion mutant) in the PC9 lung cancer cell line and stable doxycycline-inducible expression of tagged Grb2 using a Flp-mediated recombination HEK293 cell system, the SH-TAP can be downscaled to 5 to 12.5 mg total protein input (equivalent to 0.5 - 1 × 15 cm culture plate or 4 - 8 × 106 cells). The major constituents of the EGFR del complex (USB3B, GRB2, ERRFI, HSP7C, GRP78, HSP71) and the Grb2 complex (ARHG5, SOS1, ARG35, CBL, CBLB, PTPRA, SOS2, DYN2, WIPF2, IRS4) were identified. Adjustment of the quantity of digested protein injected into the mass spectrometer reveals that optimisation is required as high quantities of material led to a decrease in protein sequence coverage and the loss of some interacting proteins. This investigation should aid other researchers in performing tandem affinity purifications in general, and in particular, from low quantities of input material.
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Affiliation(s)
- Eric B Haura
- Department of Thoracic Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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20
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Abstract
Peptides and proteins have been utilized as therapeutic agents for over 40 years. Traditional approaches to quantify these molecules in biological matrices have utilized immunoassay approaches that can be time inefficient, lack assay specificity and have limited analytical ranges. The advances in sample preparation technologies, chromatographic systems and their chemistries, mass spectrometers and their software over the last decade have meant that LC–MS/MS approaches to peptide and protein quantification are feasible and can overcome the problems associated with quantification by immunoassay. In this article we present an overview of the challenges and approaches to overcome them when performing quantitative bioanalysis of peptides and proteins by LC–MS/MS.
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21
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Trufelli H, Palma P, Famiglini G, Cappiello A. An overview of matrix effects in liquid chromatography-mass spectrometry. MASS SPECTROMETRY REVIEWS 2011; 30:491-509. [PMID: 21500246 DOI: 10.1002/mas.20298] [Citation(s) in RCA: 512] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 01/28/2010] [Accepted: 01/28/2010] [Indexed: 05/19/2023]
Abstract
Matrix-dependent signal suppression or enhancement represents a major drawback in quantitative analysis with liquid chromatography coupled to atmospheric pressure ionization mass spectrometry (LC-API-MS). Because matrix effects (ME) might exert a detrimental impact on important method parameters (limit of detection, limit of quantification, linearity, accuracy, and precision), they have to be tested and evaluated during validation procedure. This review gives a detailed description on when these phenomena might be expected, and how they can be evaluated. The major sources of ME are discussed and illustrated with examples from bioanalytical, pharmaceutical, environmental, and food analysis. Because there is no universal solution for ME, the main strategies to overcome these phenomena are described in detail. Special emphasis is devoted to the sample-preparation procedures as well as to the recent improvements on chromatographic and mass spectrometric conditions. An overview of the main calibration techniques to compensate for ME is also presented. All these solutions can be used alone or in combination to retrieve the performance of the LC-MS for a particular matrix-analyte combination.
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Affiliation(s)
- Helga Trufelli
- Dipartimento di Scienze Geologiche, Tecnologie Chimiche e Ambientali, Università degli Studi di Urbino Carlo Bo, Piazza Rinascimento, 6-61029 Urbino, Italy
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22
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Cappiello A, Famiglini G, Palma P, Trufelli H. MATRIX EFFECTS IN LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY. J LIQ CHROMATOGR R T 2010. [DOI: 10.1080/10826076.2010.484314] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Achille Cappiello
- a Dipartimento di Scienze Geologiche , Tecnologie Chimiche e Ambientali a Università degli Studi di Urbino “Carlo Bo” , Urbino , Italy
| | - Giorgio Famiglini
- a Dipartimento di Scienze Geologiche , Tecnologie Chimiche e Ambientali a Università degli Studi di Urbino “Carlo Bo” , Urbino , Italy
| | - Pierangela Palma
- a Dipartimento di Scienze Geologiche , Tecnologie Chimiche e Ambientali a Università degli Studi di Urbino “Carlo Bo” , Urbino , Italy
| | - Helga Trufelli
- a Dipartimento di Scienze Geologiche , Tecnologie Chimiche e Ambientali a Università degli Studi di Urbino “Carlo Bo” , Urbino , Italy
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23
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Comparison between a linear ion trap and a triple quadruple MS in the sensitive detection of large peptides at femtomole amounts on column. J Sep Sci 2010; 33:2478-88. [DOI: 10.1002/jssc.201000157] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Gupta MK, Jang JM, Jung JW, Uhm SJ, Kim KP, Lee HT. Proteomic analysis of parthenogenetic and in vitro fertilized porcine embryos. Proteomics 2009; 9:2846-60. [PMID: 19405025 DOI: 10.1002/pmic.200800700] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteomic data from embryos are essential for the completion of whole proteome catalog due to embryo-specific expression of certain proteins. In this study, using reverse phase LC-MS/MS combined with 1-D SDS-PAGE, we identified 1625 mammalian and 735 Sus scrofa proteins from porcine zygotes that included both cytosolic and membranous proteins. We also found that the global protein profiles of parthenogenetically activated (PA) and in vitro fertilized (IVF) zygotes were similar but differences in expression of individual proteins were also evident. These differences were not due to culture conditions, polyspermy or non-activation of oocytes, as the same culture method was used in both groups, the frequency of polyspermy was 24.3+/-3.0% and the rates of oocyte activation did not differ (p>0.05) between PA and IVF embryos. Consistent with proteomic data, fluorescent Hoechst 33 342 staining and terminal deoxynucleotidyl transferase dUTP nick end labeling assay also revealed that PA embryos were of poor quality as they contained less cells per blastocyst and were more predisposed to apoptosis (p<0.05), although their in vitro development rates were similar. To our knowledge, this is the first report on global peptide sequencing and quantification of protein in PA and IVF embryos by LC-MS/MS that may be useful as a reference map for future studies.
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Affiliation(s)
- Mukesh Kumar Gupta
- Department of Animal Biotechnology, Bio-Organ Research Center, Konkuk University, Hwayang-dong, Gwangjin-Gu, Seoul, South Korea
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25
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Wang X, Nookala S, Narayanan C, Giorgianni F, Beranova-Giorgianni S, McCollum G, Gerling I, Penn JS, Jablonski MM. Proteomic analysis of the retina: removal of RPE alters outer segment assembly and retinal protein expression. Glia 2009; 57:380-92. [PMID: 18803304 PMCID: PMC2653273 DOI: 10.1002/glia.20765] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The mechanisms that regulate the complex physiological task of photoreceptor outer segment assembly remain an enigma. One limiting factor in revealing the mechanism(s) by which this process is modulated is that not all of the role players who participate in this process are known. The purpose of this study was to determine some of the retinal proteins that likely play a critical role in regulating photoreceptor outer segment assembly. To do so, we analyzed and compared the proteome map of tadpole Xenopus laevis retinal pigment epithelium (RPE)-supported retinas containing organized outer segments with that of RPE-deprived retinas containing disorganized outer segments. Solubilized proteins were labeled with CyDye fluors followed by multiplexed two-dimensional separation. The intensity of protein spots and comparison of proteome maps was performed using DeCyder software. Identification of differentially regulated proteins was determined using nanoLC-ESI-MS/MS analysis. We found a total of 27 protein spots, 21 of which were unique proteins, which were differentially expressed in retinas with disorganized outer segments. We predict that in the absence of the RPE, oxidative stress initiates an unfolded protein response. Subsequently, downregulation of several candidate Müller glial cell proteins may explain the inability of photoreceptors to properly fold their outer segment membranes. In this study, we have used identification and bioinformatics assessment of proteins that are differentially expressed in retinas with disorganized outer segments as a first step in determining probable key molecules involved in regulating photoreceptor outer segment assembly.
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Affiliation(s)
- XiaoFei Wang
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN
| | - Suba Nookala
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN
| | | | - Francesco Giorgianni
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN
| | | | - Gary McCollum
- Department of Ophthalmology, Vanderbilt University, Nashville, TN
| | - Ivan Gerling
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN
| | - John S. Penn
- Department of Ophthalmology, Vanderbilt University, Nashville, TN
| | - Monica M. Jablonski
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN
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26
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Polyakov NB, Barylyuk KV, Frankevich VE, Grinkevich VA. Proteomic analysis of heart mitochondria from Bos taurus: I. Application of proteomic methods to identification of transmembrane domains of proteins of the internal mitochondrial membrane. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2009. [DOI: 10.1134/s1068162009010051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Study on the maltooligosaccharide composition of mucilage samples collected along the northern Adriatic coast. Carbohydr Res 2009; 344:120-6. [DOI: 10.1016/j.carres.2008.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Revised: 10/07/2008] [Accepted: 10/09/2008] [Indexed: 11/22/2022]
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28
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van den Broek I, Sparidans RW, Schellens JH, Beijnen JH. Quantitative bioanalysis of peptides by liquid chromatography coupled to (tandem) mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 872:1-22. [DOI: 10.1016/j.jchromb.2008.07.021] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 06/16/2008] [Accepted: 07/12/2008] [Indexed: 12/25/2022]
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29
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Aronov PA, Hall LM, Dettmer K, Stephensen CB, Hammock BD. Metabolic profiling of major vitamin D metabolites using Diels-Alder derivatization and ultra-performance liquid chromatography-tandem mass spectrometry. Anal Bioanal Chem 2008; 391:1917-30. [PMID: 18437365 DOI: 10.1007/s00216-008-2095-8] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 03/20/2008] [Accepted: 03/25/2008] [Indexed: 01/08/2023]
Abstract
Biologically active forms of vitamin D are important analytical targets in both research and clinical practice. The current technology is such that each of the vitamin D metabolites is usually analyzed by individual assay. However, current LC-MS technologies allow the simultaneous metabolic profiling of entire biochemical pathways. The impediment to the metabolic profiling of vitamin D metabolites is the low level of 1alpha,25-dihydroxyvitamin D(3) in human serum (15-60 pg/mL). Here, we demonstrate that liquid-liquid or solid-phase extraction of vitamin D metabolites in combination with Diels-Alder derivatization with the commercially available reagent 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD) followed by ultra-performance liquid chromatography (UPLC)-electrospray/tandem mass spectrometry analysis provides rapid and simultaneous quantification of 1alpha,25-dihydroxyvitamin D(3), 1alpha,25-dihydroxyvitamin D(2), 24R,25-dihydroxyvitamin D(3), 25-hydroxyvitamin D(3) and 25-hydroxyvitamin D(2) in 0.5 mL human serum at a lower limit of quantification of 25 pg/mL. Precision ranged from 1.6-4.8 % and 5-16 % for 25-hydroxyvitamin D(3) and 1alpha,25-dihydroxyvitamin D(3), respectively, using solid-phase extraction.
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Affiliation(s)
- Pavel A Aronov
- Department of Entomology, University of California, Davis, CA, 95616, USA
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30
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Tamvakopoulos C. Mass spectrometry for the quantification of bioactive peptides in biological fluids. MASS SPECTROMETRY REVIEWS 2007; 26:389-402. [PMID: 17160998 DOI: 10.1002/mas.20120] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The study of pharmacologically active peptides is central to the understanding of disease and development of novel therapies. It would be advantageous to monitor the fate of bioactive peptides in biological fluids and tissues following their in vivo administration (exogenous administration) or the modulation of endogenous factors (e.g., peptide hormones) affected by the administration of a pharmacological agent. Measurement of administered compounds (small molecules) in plasma is a mature field. However, measurement of pharmacologically active peptides presents particular problems for quantitative mass spectrometry, including challenges from selectivity and sensitivity perspectives. Current approaches towards peptide quantification in biological fluids include immunoassays and mass spectrometric techniques. Immunoassays, although sensitive, lack the necessary selectivity for distinction between peptide and metabolites. Modified molecules induced by metabolic transformations (e.g., N- or C-terminal truncation of the peptide) might not be differentiated by the antibody used in the assay, leading to cross-reactivity. However, although it is generally accepted that mass spectrometry is an ideal technique for the quantification of trace levels of analytes in biological fluids, immunological techniques are still characterized by better limits of peptide detection. In this review article, novel mass spectrometric approaches and strategies on peptide quantification will be described. The current capabilities and prospects for advances in this critical area of research will be examined.
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Affiliation(s)
- Constantin Tamvakopoulos
- Foundation for Biomedical Research of the Academy of Athens (IIBEAA), Laboratory of Pharmacology-Pharmacotechnology, Athens, Greece 11527.
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31
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Morgenthal K, Wienkoop S, Wolschin F, Weckwerth W. Integrative Profiling of Metabolites and Proteins. Methods Mol Biol 2007; 358:57-75. [PMID: 17035680 DOI: 10.1007/978-1-59745-244-1_4] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Methods such as mRNA expression profiling have provided a vast amount of genomic and transcriptomic information about plants and other organisms. However, there is explicit indication that considerable metabolic control is executed on the metabolite and on the protein level including protein modifications, thereby constituting the phenotypic plasticity. Consequently, the analysis of the molecular phenotype demands the step toward mass spectrometry (MS)-based postgenomic techniques such as metabolomics and proteomics. This chapter describes a straightforward protocol for simultaneously extracting metabolites and proteins from the same biological sample in preparation for MS analysis. Furthermore, protocols for profiling polar metabolites using gas chromatography time-of-flight MS and for shotgun proteomics using liquid chromatography-MS are discussed. A practical course is laid out that outlines all the basic steps, from harvesting to data analysis. These steps enable the correlative study of metabolite and protein dynamics with minimal technical variation. Biological variability of independent samples is exploited for variance analysis and pattern recognition.
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Affiliation(s)
- Katja Morgenthal
- Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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32
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Ashour M, Edrada R, Ebel R, Wray V, Wätjen W, Padmakumar K, Müller WEG, Lin WH, Proksch P. Kahalalide derivatives from the Indian sacoglossan mollusk Elysia grandifolia. JOURNAL OF NATURAL PRODUCTS 2006; 69:1547-53. [PMID: 17125219 DOI: 10.1021/np060172v] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Two new cyclic depsipeptide derivatives, kahalalides R (1) and S (2), together with two known congeners, kahalalides F (3) and D (4), were isolated from the Indian sacoglossan mollusk Elysia grandifolia. The structures of the new compounds were unambiguously established on the basis of NMR spectroscopic (1H, 13C, COSY, HMBC) and mass spectrometric (FABMS, ESIMS, MALDI-TOF/PSD) data, which also included Marfey amino acid analyses. The new derivative kahalalide R was found to exert comparable or even higher cytotoxicity than the potential drug candidate kahalalide F toward the MCF7 human mammary carcinoma cell line.
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Affiliation(s)
- Mohamed Ashour
- Institut für Pharmazeutische Biologie und Biotechnologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, Geb. 26.23, 40225 Düsseldorf, Germany
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Shackman HM, Shou M, Cellar NA, Watson CJ, Kennedy RT. Microdialysis coupled on-line to capillary liquid chromatography with tandem mass spectrometry for monitoring acetylcholine in vivo. J Neurosci Methods 2006; 159:86-92. [PMID: 16876256 DOI: 10.1016/j.jneumeth.2006.06.020] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 06/23/2006] [Accepted: 06/26/2006] [Indexed: 12/01/2022]
Abstract
Capillary liquid chromatography-mass spectrometry (cLC-MS) was coupled on-line to microdialysis sampling to monitor endogenous acetylcholine (ACh) from the rodent brain. In vivo microdialysate sampled at 0.6 microL/min from the striatum of ketamine or chloral hydrate anesthetized rats was loaded onto a sample loop and then injected onto a approximately 5 cm long strong cation exchange (SCX) capillary column. A step gradient was used to separate the analyte from ionization suppressing salts contained in dialysate in 2.4 min. Sampling coupled on-line with cLC-MS allowed for high temporal resolution (data points at 2.4 min intervals), good reproducibility (10-15% relative standard deviation, R.S.D.), and sensitive limits of detection (0.04 nM or 8 amol injected). The method successfully monitored basal and stimulated levels (induced by increased K+ concentrations) of ACh from the anesthetized rat without necessitating perfusion of an acetylcholinesterase (AChE) inhibitor. Absolute and percent basal levels of ACh from rats receiving different anesthetics were also compared.
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Affiliation(s)
- Holly M Shackman
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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Abstract
The pituitary is the central endocrine gland that regulates the functions of various target organs in the human body. Because of the pivotal regulatory role of the pituitary, it is essential to define on a global scale the components of the pituitary protein machinery, including a comprehensive characterization of the post-translational modifications of the pituitary proteins. Of particular interest is the examination of the phosphorylation status of the pituitary in health and disease. Towards the goal of global profiling of pituitary protein phosphorylation, we report here the application of the in-gel IEF-LC-MS/MS approach to the study of the pituitary phosphoproteome. The analytical strategy combined isoelectric focusing in immobilized pH gradient strips with immobilized metal ion affinity chromatography and mass spectrometry. With this method, a total of 50 phosphorylation sites were characterized in 26 proteins. Because the investigation involved primary tissue, the findings provide a direct glimpse into the phosphoprotein machinery operating within the human pituitary tissue microenvironment.
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Affiliation(s)
- Sarka Beranova-Giorgianni
- Charles B. Stout Neuroscience Mass Spectrometry Laboratory, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
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Lanckmans K, Clinckers R, Van Eeckhaut A, Sarre S, Smolders I, Michotte Y. Use of microbore LC-MS/MS for the quantification of oxcarbazepine and its active metabolite in rat brain microdialysis samples. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 831:205-12. [PMID: 16386473 DOI: 10.1016/j.jchromb.2005.12.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2005] [Revised: 10/24/2005] [Accepted: 12/05/2005] [Indexed: 11/18/2022]
Abstract
A microbore LC-MS/MS method is developed and validated for the quantification of the anti-epileptic drug oxcarbazepine (OXC) and its active metabolite 10,11-dihydro-10-hydroxycarbamazepine (MHD) in rat brain microdialysates, together with the internal standard for microdialysis probe calibration, 2-methyl-5H-dibenz(b,f)azepine-5-carboxamide (m-CBZ). The benefits of gradient versus isocratic separation are shown, next to the improved sensitivity resulting from the addition of 0.1% formic acid to the mobile phase. The coupling of microdialysis with ESI-MS requires sample desalting for which column switching was applied. Using weighed regression to calculate the calibration curves (1-1000 ng/mL), the assay was validated in terms of linearity, accuracy and precision, yielding a sensitive (limit of quantification is 1 ng/mL) and selective method for quantification of OXC, MHD and m-CBZ. By applying this method, we were able to determine the extracellular concentrations of OXC and MHD during at least 4h after intraperitoneal (i.p.) administration of 10 mg/kg OXC.
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Affiliation(s)
- Katrien Lanckmans
- Department of Pharmaceutical Chemistry, Drug Analysis and Drug Information, Research Group Experimental Pharmacology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
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Storme ML, Sinnaeve BA, Van Bocxlaer JF. The use of tryptic marker-peptides for the quantitative analysis of Cystatin C. J Sep Sci 2005; 28:1759-63. [PMID: 16224971 DOI: 10.1002/jssc.200500127] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The use of marker-peptides, measured by LC-MS/MS, is investigated for the quantitative analysis of proteins. To that end, cystatin C is chosen as a model protein. It not only functions as a proof of concept protein but the growing interest in cystatin C as a new marker of kidney failure provides a practical application at the same time. The use of trypsin-based proteolysis, to obtain so-called marker-peptides, simplifies the quantification of a protein to the quantification of a single or a number of peptides. Reproducibility of the trypsin proteolysis procedure is vital and has been optimised. A number of the marker-peptides obtained are selected for LC-MS(/MS) analysis. They are completely separated by high-pressure LC allowing maximum selectivity and mass spectrometric multiple reaction monitoring sensitivity. By doing so, linear calibration curves can be obtained for cystatin C over two orders of magnitude. Experiments have been performed on a triple quadrupole mass spectrometer by single ion monitoring (maximum sensitivity) as well as by multiple reaction monitoring (maximum specificity).
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Affiliation(s)
- Michael L Storme
- Laboratory of Medical Biochemistry and Clinical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.
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Sinnaeve BA, Storme ML, Van Bocxlaer JF. Capillary liquid chromatography and tandem mass spectrometry for the quantification of enkephalins in cerebrospinal fluid. J Sep Sci 2005; 28:1779-84. [PMID: 16224973 DOI: 10.1002/jssc.200500114] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A capillary LC-MS/MS system was evaluated for the absolute quantification of enkephalins in cerebrospinal fluid (CSF). On column focusing on a C18 trapping column, in-line with the analytical column, was used for preconcentration. Quantification was performed with a triple quadrupole instrument in the multiple reaction monitoring mode. Weighted linear regression analysis proves to be a good linearity in a dynamic range of two orders of magnitude. The method was validated, yielding calibration curves with correlation coefficients greater than 0.9914. Assay precision and accuracy were evaluated by direct injection of enkephalin fortified artificial CSF (aCSF) samples at three concentration levels. Mean accuracy of analysed concentrations was between 97.63 and 107.6%. LOD and LOQ were assessed at, respectively, 0.5 and 1 pmol/mL. Validation results show that it is feasible, with a capillary LC-MS/MS system, to quantify neuropeptides in the low femtomole range in aCSF. The obtained coefficients of variation, however, indicate that the use of appropriate isotopically labelled internal standards in neuropeptide quantification using narrow bore LC, combined with ESI-MS, may be highly beneficial.
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Affiliation(s)
- Bart A Sinnaeve
- Laboratorium voor Medische Biochemie en Klinische Analyse, Universiteit Gent, Gent, Belgium.
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Molina-Martin M, Marin A, Rivera-Sagredo A, Espada A. Liquid chromatography-mass spectrometry and related techniques for purity assessment in early drug discovery. J Sep Sci 2005; 28:1742-50. [PMID: 16224969 DOI: 10.1002/jssc.200500107] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The combination of HPLC and MS has become the most valuable analytical tool to determine the identity and purity of a drug substance in the drug discovery arena over the past decade. This article describes different LC/MS configurations and their broad applicability to meet the fundamental analytical requirements involved in discovering new drugs. In addition, the value of chemiluminescence nitrogen detection for absolute purity determination and the convenience of CE as an orthogonal separation technique to HPLC are also discussed. In summary, LC/MS-based methodologies that implicate automation, various levels of throughput and open access systems have proved to be an integral part of the drug discovery process. As a result, the paradigm of high-quality/-quantity information is fulfilled in a timely fashion.
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:1110-21. [PMID: 16106339 DOI: 10.1002/jms.809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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