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Safari F, Kehelpannala C, Safarchi A, Batarseh AM, Vafaee F. Biomarker Reproducibility Challenge: A Review of Non-Nucleotide Biomarker Discovery Protocols from Body Fluids in Breast Cancer Diagnosis. Cancers (Basel) 2023; 15:2780. [PMID: 37345117 DOI: 10.3390/cancers15102780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
Abstract
Breast cancer has now become the most commonly diagnosed cancer, accounting for one in eight cancer diagnoses worldwide. Non-invasive diagnostic biomarkers and associated tests are superlative candidates to complement or improve current approaches for screening, early diagnosis, or prognosis of breast cancer. Biomarkers detected from body fluids such as blood (serum/plasma), urine, saliva, nipple aspiration fluid, and tears can detect breast cancer at its early stages in a minimally invasive way. The advancements in high-throughput molecular profiling (omics) technologies have opened an unprecedented opportunity for unbiased biomarker detection. However, the irreproducibility of biomarkers and discrepancies of reported markers have remained a major roadblock to clinical implementation, demanding the investigation of contributing factors and the development of standardised biomarker discovery pipelines. A typical biomarker discovery workflow includes pre-analytical, analytical, and post-analytical phases, from sample collection to model development. Variations introduced during these steps impact the data quality and the reproducibility of the findings. Here, we present a comprehensive review of methodological variations in biomarker discovery studies in breast cancer, with a focus on non-nucleotide biomarkers (i.e., proteins, lipids, and metabolites), highlighting the pre-analytical to post-analytical variables, which may affect the accurate identification of biomarkers from body fluids.
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Affiliation(s)
- Fatemeh Safari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
| | - Cheka Kehelpannala
- BCAL Diagnostics Ltd., Suite 506, 50 Clarence St, Sydney, NSW 2000, Australia
- BCAL Dx, The University of Sydney, Sydney Knowledge Hub, Merewether Building, Sydney, NSW 2006, Australia
| | - Azadeh Safarchi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- Microbiomes for One Systems Health, Health and Biosecurity, CSIRO, Westmead, NSW 2145, Australia
| | - Amani M Batarseh
- BCAL Diagnostics Ltd., Suite 506, 50 Clarence St, Sydney, NSW 2000, Australia
- BCAL Dx, The University of Sydney, Sydney Knowledge Hub, Merewether Building, Sydney, NSW 2006, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- UNSW Data Science Hub (uDASH), University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- OmniOmics.ai Pty Ltd., Sydney, NSW 2035, Australia
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2
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Dilmetz BA, Hoffmann P, Condina MR. Quantitative Approach Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-ToF) Mass Spectrometry. Methods Mol Biol 2021; 2228:159-166. [PMID: 33950490 DOI: 10.1007/978-1-0716-1024-4_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Quantitation using mass spectrometry (MS) is a routine approach for multiple analytes, including small molecules and peptides. Electrospray-based MS platforms are typically employed, as they provide highly reproducible outputs for batch processing of multiple samples. Quantitation using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (ToF) mass spectrometry, while less commonly adopted, offers the ability to monitor analytes at significantly higher throughput and lower cost compared with ESI MS. Achieving accurate quantitation using this approach requires the development of appropriate sample preparation, spiking of appropriate internal standards, and acquisition to minimize spot-to-spot variability. Here we describe the preparation of samples for accurate quantitation using MALDI-ToF MS. The methodology presented shows the ability to quantitate perfluorooctanesulfonic acid (PFOS) from contaminated water.
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Affiliation(s)
- Brooke A Dilmetz
- Future Industries Institute, University of South Australia, Adelaide, Australia
| | - Peter Hoffmann
- Future Industries Institute, University of South Australia, Adelaide, Australia
| | - Mark R Condina
- Future Industries Institute, University of South Australia, Adelaide, Australia.
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3
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Koss KM, Tsui C, Unsworth LD. Enzymatic Activity in Fractal Networks of Self-Assembling Peptides. Biomacromolecules 2018; 20:422-434. [DOI: 10.1021/acs.biomac.8b01496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kyle M. Koss
- Department of Chemical and Materials Engineering, University of Alberta, 13-390 Floor - Donadeo Innovation Centre for Engineering
(ICE), 9211-116 Street NW, Edmonton, AB T6G 1H9, Canada
| | - Christopher Tsui
- Department of Chemical and Materials Engineering, University of Alberta, 13-390 Floor - Donadeo Innovation Centre for Engineering
(ICE), 9211-116 Street NW, Edmonton, AB T6G 1H9, Canada
| | - Larry D. Unsworth
- Department of Chemical and Materials Engineering, University of Alberta, 13-390 Floor - Donadeo Innovation Centre for Engineering
(ICE), 9211-116 Street NW, Edmonton, AB T6G 1H9, Canada
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4
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Antimicrobial and proinflammatory effects of two vipericidins. Cytokine 2018; 111:309-316. [DOI: 10.1016/j.cyto.2018.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 09/18/2018] [Accepted: 09/18/2018] [Indexed: 12/27/2022]
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5
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Bilbao A, Gibbons BC, Slysz GW, Crowell KL, Monroe ME, Ibrahim YM, Smith RD, Payne SH, Baker ES. An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 427:91-99. [PMID: 29706793 PMCID: PMC5920534 DOI: 10.1016/j.ijms.2017.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The mass accuracy and peak intensity of ions detected by mass spectrometry (MS) measurements are essential to facilitate compound identification and quantitation. However, high concentration species can yield erroneous results if their ion intensities reach beyond the limits of the detection system, leading to distorted and non-ideal detector response (e.g. saturation), and largely precluding the calculation of accurate m/z and intensity values. Here we present an open source computational method to correct peaks above a defined intensity (saturated) threshold determined by the MS instrumentation such as the analog-to-digital converters or time-to-digital converters used in conjunction with time-of-flight MS. In this method, the isotopic envelope for each observed ion above the saturation threshold is compared to its expected theoretical isotopic distribution. The most intense isotopic peak for which saturation does not occur is then utilized to re-calculate the precursor m/z and correct the intensity, resulting in both higher mass accuracy and greater dynamic range. The benefits of this approach were evaluated with proteomic and lipidomic datasets of varying complexities. After correcting the high concentration species, reduced mass errors and enhanced dynamic range were observed for both simple and complex omic samples. Specifically, the mass error dropped by more than 50% in most cases for highly saturated species and dynamic range increased by 1-2 orders of magnitude for peptides in a blood serum sample.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Erin S Baker
- Corresponding author at: 902 Battelle Blvd., P.O. Box 999, MSIN K8-98, Richland,WA 99352, USA. (E.S. Baker)
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6
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Pekov S, Indeykina M, Popov I, Kononikhin A, Bocharov K, Kozin SA, Makarov AA, Nikolaev E. Application of MALDI-TOF/TOF-MS for relative quantitation of α- and β-Asp7 isoforms of amyloid-β peptide. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2018; 24:141-144. [PMID: 29232976 DOI: 10.1177/1469066717730544] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
It is known that aspartic acid isomerization process plays a role in aging processes and may be used as a marker for aging of natural materials. As for Alzheimer's disease, the most abundant modification in the peptide profile is the aspartate isomerization of amyloid-β. Liquid chromatography-electrospray ionization-mass spectrometry/mass spectrometry-based approaches with Collision Induced Dissociation (CID) or Electron Capture Dissociation (ECD) fragmentation provide a good and precise method for the relative quantitation of iso- to normal amyloid-β peptides but require additional time consuming steps. In this study, MALDI-TOF/TOF-matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry (MS) method was developed as a high-throughput approach for the relative quantitation of the isomerized form of the amyloid-β peptide.
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Affiliation(s)
- Stanislav Pekov
- 1 65014 Moscow Institute of Physics and Technology , Moscow, Russia
- 2 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Maria Indeykina
- 2 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 3 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Igor Popov
- 1 65014 Moscow Institute of Physics and Technology , Moscow, Russia
- 2 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Kononikhin
- 1 65014 Moscow Institute of Physics and Technology , Moscow, Russia
- 2 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Bocharov
- 1 65014 Moscow Institute of Physics and Technology , Moscow, Russia
- 2 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Sergey A Kozin
- 5 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander A Makarov
- 5 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Eugene Nikolaev
- 2 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 3 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Skolkovo Institute of Science and Technology, Skolkovo, Russia
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7
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Smolira A, Hałas S. Direct matrix-assisted laser desorption ionization time-of-flight mass spectrometric analysis of lysozyme contained in hen egg white. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2016; 22:9-17. [PMID: 26863071 DOI: 10.1255/ejms.1403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
As a natural antibacterial peptide, lysozyme (LZ) is widely used in medicine and the food industry. Despite many years of research on this compound, its new antibacterial properties are still to be determined. The primary aim of this work is to demonstrate the application of the matrix-assisted laser desorption ionization (MALDI) time-of-flight mass spectrometric analysis of LZ directly in hen egg white samples without extraction thereof. The egg white samples were kept over 10 weeks at room temperature and measured every week. The resulting positive and negative ion mass spectra were then compared to determine the intensity of the LZ mass peak. Storage of the egg white for over 10 weeks did not influence the LZ mass peak intensity (both positive and negative). It can be concluded that the LZ concentration in the egg white samples did not vary with time. The effect of the matrix/sample ratio on LZ detection was also examined, and it was found to be different in the case of positive and negative ionization. The mass peaks of LZ oligomeric forms were observed in all mass spectra, so the MALDI method could be used in subsequent studies.
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Affiliation(s)
- Anna Smolira
- Mass Spectrometry Laboratory, Institute of Physics, Maria Curie Sklodowska University, Pl. M. Curie-Skłodowskiej 1, 20-031 Lublin, Poland..
| | - Stanisław Hałas
- Mass Spectrometry Laboratory, Institute of Physics, Maria Curie Sklodowska University, Pl. M. Curie- Skłodowskiej 1, 20-031 Lublin, Poland..
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8
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Schopfer LM, Lockridge O, Brimijoin S. Pure human butyrylcholinesterase hydrolyzes octanoyl ghrelin to desacyl ghrelin. Gen Comp Endocrinol 2015; 224:61-8. [PMID: 26073531 DOI: 10.1016/j.ygcen.2015.05.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 05/20/2015] [Accepted: 05/27/2015] [Indexed: 10/23/2022]
Abstract
The ghrelin hormone is a 28 amino acid peptide esterified on serine 3 with octanoic acid. Ghrelin is inactivated by hydrolysis of the ester bond. Previous studies have relied on inhibitors to identify human butyrylcholinesterase (BChE) as the hydrolase in human plasma that converts ghrelin to desacyl ghrelin. The reaction of BChE with ghrelin is unusual because the rate of hydrolysis is very slow and the substrate is ten times larger than standard BChE substrates. These unusual features prompted us to re-examine the reaction, using human BChE preparations that were more than 98% pure. Conversion of ghrelin to desacyl ghrelin was monitored by MALDI TOF mass spectrometry. It was found that 5 different preparations of pure human BChE all hydrolyzed ghrelin, including BChE purified from human plasma, from Cohn fraction IV-4, BChE immunopurified by binding to monoclonals mAb2 and B2 18-5, and recombinant human BChE purified from culture medium. We reasoned that it was unlikely that a common contaminant that could be responsible for ghrelin hydrolysis would appear in all of these preparations. km was <1 μM, and kcat was ~1.4 min(-1). A Michaelis-Menten analysis employing these kinetic values together with serum concentrations of ghrelin and BChE demonstrated that BChE could hydrolyze all of the ghrelin in serum in ~1 h. It was concluded that BChE is physiologically relevant for the hydrolysis of ghrelin.
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Affiliation(s)
- Lawrence M Schopfer
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA.
| | - Oksana Lockridge
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE 68198-5950, USA.
| | - Stephen Brimijoin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.
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9
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Ackermann BL, Berna MJ. Coupling immunoaffinity techniques with MS for quantitative analysis of low-abundance protein biomarkers. Expert Rev Proteomics 2014; 4:175-86. [PMID: 17425454 DOI: 10.1586/14789450.4.2.175] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The field of proteomics is rapidly turning towards targeted mass spectrometry (MS) methods to quantify putative markers or known proteins of biological interest. Historically, the enzyme-linked immunosorbent assay (ELISA) has been used for targeted protein analysis, but, unfortunately, it is limited by the excessive time required for antibody preparation, as well as concerns over selectivity. Despite the ability of proteomics to deliver increasingly quantitative measurements, owing to limited sensitivity, the leads generated are in the microgram per milliliter range. This stands in stark contrast to ELISA, which is capable of quantifying proteins at low picogram per milliliter levels. To bridge this gap, targeted liquid chromatography (LC) tandem MS (MS/MS) analysis of tryptic peptide surrogates using selected reaction monitoring detection has emerged as a viable option for rapid quantification of target proteins. The precision of this approach has been enhanced by the use of stable isotope-labeled peptide internal standards to compensate for variation in recovery and the influence of differential matrix effects. Unfortunately, the complexity of proteinaceous matrices, such as plasma, limits the usefulness of this approach to quantification in the mid-nanogram per milliliter range (medium-abundance proteins). This article reviews the current status of LC/MS/MS using selected reaction monitoring for protein quantification, and specifically considers the use of a single antibody to achieve superior enrichment of either the protein target or the released tryptic peptide. Examples of immunoaffinity-assisted LC/MS/MS are reviewed that demonstrate quantitative analysis of low-abundance proteins (subnanogram per milliliter range). A strategy based on this technology is proposed for the expedited evaluation of novel protein biomarkers, which relies on the synergy created from the complementary nature of MS and ELISA.
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Affiliation(s)
- Bradley L Ackermann
- Eli Lilly & Company, Drug Disposition, Greenfield Laboratories, Greenfield, IN 46140, USA.
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10
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Ahn SH, Bae YJ, Moon JH, Kim MS. Matrix Suppression as a Guideline for Reliable Quantification of Peptides by Matrix-Assisted Laser Desorption Ionization. Anal Chem 2013; 85:8796-801. [DOI: 10.1021/ac401967n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sung Hee Ahn
- Department
of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Yong Jin Bae
- Department
of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Jeong Hee Moon
- Medical
Proteomics Research Center, KRIBB, Daejeon 305-806, Korea
| | - Myung Soo Kim
- Department
of Chemistry, Seoul National University, Seoul 151-742, Korea
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11
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Anderson NL, Razavi M, Pearson TW, Kruppa G, Paape R, Suckau D. Precision of Heavy–Light Peptide Ratios Measured by MALDI-TOF Mass Spectrometry. J Proteome Res 2012; 11:1868-78. [DOI: 10.1021/pr201092v] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- N. Leigh Anderson
- Plasma Proteome Institute, Washington, D.C., United States
- SISCAPA Assay Technologies, Inc., Washington, D.C., United States
| | - Morteza Razavi
- Department of Biochemistry and
Microbiology, University of Victoria, Victoria,
British Columbia, V8W 3P6, Canada
| | - Terry W. Pearson
- SISCAPA Assay Technologies, Inc., Washington, D.C., United States
- Department of Biochemistry and
Microbiology, University of Victoria, Victoria,
British Columbia, V8W 3P6, Canada
| | - Gary Kruppa
- Bruker Daltonics, Billerica, Massachusetts,
United States
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12
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13
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Niklew ML, Hochkirch U, Melikyan A, Moritz T, Kurzawski S, Schlüter H, Ebner I, Linscheid MW. Phosphopeptide Screening Using Nanocrystalline Titanium Dioxide Films as Affinity Matrix-Assisted Laser Desorption Ionization Targets in Mass Spectrometry. Anal Chem 2010; 82:1047-53. [DOI: 10.1021/ac902403m] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marie-Luise Niklew
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany, Analytical Laboratories, Atotech GmbH, Berlin, Germany, and Department of Clinical Chemistry/Central Laboratories, University Medical Center, Hamburg-Eppendorf, Germany
| | - Ulrike Hochkirch
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany, Analytical Laboratories, Atotech GmbH, Berlin, Germany, and Department of Clinical Chemistry/Central Laboratories, University Medical Center, Hamburg-Eppendorf, Germany
| | - Anna Melikyan
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany, Analytical Laboratories, Atotech GmbH, Berlin, Germany, and Department of Clinical Chemistry/Central Laboratories, University Medical Center, Hamburg-Eppendorf, Germany
| | - Thomas Moritz
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany, Analytical Laboratories, Atotech GmbH, Berlin, Germany, and Department of Clinical Chemistry/Central Laboratories, University Medical Center, Hamburg-Eppendorf, Germany
| | - Sandra Kurzawski
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany, Analytical Laboratories, Atotech GmbH, Berlin, Germany, and Department of Clinical Chemistry/Central Laboratories, University Medical Center, Hamburg-Eppendorf, Germany
| | - Hartmut Schlüter
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany, Analytical Laboratories, Atotech GmbH, Berlin, Germany, and Department of Clinical Chemistry/Central Laboratories, University Medical Center, Hamburg-Eppendorf, Germany
| | - Ingo Ebner
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany, Analytical Laboratories, Atotech GmbH, Berlin, Germany, and Department of Clinical Chemistry/Central Laboratories, University Medical Center, Hamburg-Eppendorf, Germany
| | - Michael W. Linscheid
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany, Analytical Laboratories, Atotech GmbH, Berlin, Germany, and Department of Clinical Chemistry/Central Laboratories, University Medical Center, Hamburg-Eppendorf, Germany
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14
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DNA Adduct Formation of 17β-Estradiol in MCF-7 Human Breast Cancer Cells. B KOREAN CHEM SOC 2009. [DOI: 10.5012/bkcs.2009.30.9.2125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Duncan MW, Roder H, Hunsucker SW. Quantitative matrix-assisted laser desorption/ionization mass spectrometry. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 7:355-70. [PMID: 19106161 DOI: 10.1093/bfgp/eln041] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review summarizes the essential characteristics of matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF MS), especially as they relate to its applications in quantitative analysis. Approaches to quantification by MALDI-TOF MS are presented and published applications are critically reviewed.
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Affiliation(s)
- Mark W Duncan
- Division of Endocrinology, Metabolism and Diabetes, School of Medicine, University of Colorado Denver, Mail Stop 8106, 12801 East 17th Avenue, Aurora, CO 80045, USA.
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16
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Szaéjli E, Feheér T, Medzihradszky KF. Investigating the Quantitative Nature of MALDI-TOF MS. Mol Cell Proteomics 2008; 7:2410-8. [DOI: 10.1074/mcp.m800108-mcp200] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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17
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Neubert H, Grace C, Rumpel K, James I. Assessing Immunogenicity in the Presence of Excess Protein Therapeutic Using Immunoprecipitation and Quantitative Mass Spectrometry. Anal Chem 2008; 80:6907-14. [DOI: 10.1021/ac8005439] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | | | - Klaus Rumpel
- Pfizer Global Research and Development, Sandwich, U.K
| | - Ian James
- Pfizer Global Research and Development, Sandwich, U.K
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18
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Abstract
The peptide hormone ghrelin is the only known protein modified with an O-linked octanoyl side group, which occurs on its third serine residue. This modification is crucial for ghrelin's physiological effects including regulation of feeding, adiposity, and insulin secretion. Despite the crucial role for octanoylation in the physiology of ghrelin, the lipid transferase that mediates this novel modification has remained unknown. Here we report the identification and characterization of human GOAT, the ghrelin O-acyl transferase. GOAT is a conserved orphan membrane-bound O-acyl transferase (MBOAT) that specifically octanoylates serine-3 of the ghrelin peptide. Transcripts for both GOAT and ghrelin occur predominantly in stomach and pancreas. GOAT is conserved across vertebrates, and genetic disruption of the GOAT gene in mice leads to complete absence of acylated ghrelin in circulation. The occurrence of ghrelin and GOAT in stomach and pancreas tissues demonstrates the relevance of GOAT in the acylation of ghrelin and further implicates acylated ghrelin in pancreatic function.
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19
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Taylor SW, Sun C, Hsieh A, Andon NL, Ghosh SS. A Sulfated, Phosphorylated 7 kDa Secreted Peptide Characterized by Direct Analysis of Cell Culture Media. J Proteome Res 2008; 7:795-802. [DOI: 10.1021/pr7006686] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Steven W. Taylor
- Amylin Pharmaceuticals, Inc., 9360 Towne Centre Drive, San Diego, California 92121
| | - Chengzao Sun
- Amylin Pharmaceuticals, Inc., 9360 Towne Centre Drive, San Diego, California 92121
| | - Amy Hsieh
- Amylin Pharmaceuticals, Inc., 9360 Towne Centre Drive, San Diego, California 92121
| | - Nancy L. Andon
- Amylin Pharmaceuticals, Inc., 9360 Towne Centre Drive, San Diego, California 92121
| | - Soumitra S. Ghosh
- Amylin Pharmaceuticals, Inc., 9360 Towne Centre Drive, San Diego, California 92121
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20
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Cairns DA, Thompson D, Perkins DN, Stanley AJ, Selby PJ, Banks RE. Proteomic profiling using mass spectrometry – does normalising by total ion current potentially mask some biological differences? Proteomics 2008; 8:21-7. [DOI: 10.1002/pmic.200700598] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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