151
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Takemori N, Takemori A, Matsuoka K, Morishita R, Matsushita N, Aoshima M, Takeda H, Sawasaki T, Endo Y, Higashiyama S. High-throughput synthesis of stable isotope-labeled transmembrane proteins for targeted transmembrane proteomics using a wheat germ cell-free protein synthesis system. MOLECULAR BIOSYSTEMS 2014; 11:361-5. [PMID: 25431973 DOI: 10.1039/c4mb00556b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a wheat germ cell-free protein synthesis system, we developed a high-throughput method for the synthesis of stable isotope-labeled full-length transmembrane proteins as proteoliposomes to mimic the in vivo environment, and we successfully constructed an internal standard library for targeted transmembrane proteomics by using mass spectrometry.
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152
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Absolute protein quantification of clinically relevant cytochrome P450 enzymes and UDP-glucuronosyltransferases by mass spectrometry-based targeted proteomics. J Pharm Biomed Anal 2014; 100:393-401. [DOI: 10.1016/j.jpba.2014.08.016] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/30/2014] [Accepted: 08/10/2014] [Indexed: 11/20/2022]
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153
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Ronsein GE, Pamir N, von Haller PD, Kim DS, Oda MN, Jarvik GP, Vaisar T, Heinecke JW. Parallel reaction monitoring (PRM) and selected reaction monitoring (SRM) exhibit comparable linearity, dynamic range and precision for targeted quantitative HDL proteomics. J Proteomics 2014; 113:388-99. [PMID: 25449833 DOI: 10.1016/j.jprot.2014.10.017] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/30/2014] [Accepted: 10/16/2014] [Indexed: 10/24/2022]
Abstract
UNLABELLED High-density lipoprotein (HDL), a lipid nanoparticle containing many different low abundance proteins, is an attractive target for clinical proteomics because its compositional heterogeneity is linked to its cardioprotective effects. Selected reaction monitoring (SRM) is currently the method of choice for targeted quantification of proteins in such a complex biological matrix. However, model system studies suggest that parallel reaction monitoring (PRM) is more specific than SRM because many product ions can be used to confirm the identity of a peptide. We therefore compared PRM and SRM for their abilities to quantify proteins in HDL, using (15)N-labeled apolipoprotein A-I (HDL's most abundant protein) as the internal standard. PRM and SRM exhibited comparable linearity, dynamic range, precision, and repeatability for protein quantification of HDL. Moreover, the single internal standard protein performed as well as protein-specific peptide internal standards when quantifying 3 different proteins. Importantly, PRM and SRM yielded virtually identical quantitative results for 26 proteins in HDL isolated from 44 subjects. Because PRM requires less method development than SRM and is potentially more specific, our observations indicate that PRM in concert with a single isotope-labeled protein is a promising new strategy for quantifying HDL proteins in translational studies. BIOLOGICAL SIGNIFICANCE HDL, a complex matrix composed of lipids and proteins, is implicated in cardioprotection. Its cholesterol content correlates inversely with cardiovascular disease and it is the current metric to assess cardiovascular risk. However, the cholesterol content does not capture HDL's complexity and heterogeneity. Devising metrics that better capture HDL's cardioprotective effects, we developed an optimized method for quantification of HDL proteome, using PRM in concert with a single labeled protein as internal standard. The availability of a method that increases sample throughput without compromising the reproducibility, sensitivity, and accuracy could therefore point to better risk assessment for CVD or other diseases.
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Affiliation(s)
| | - Nathalie Pamir
- Departments of Medicine, University of Washington, Seattle, WA 98109, USA
| | | | - Daniel S Kim
- Departments of Medicine, University of Washington, Seattle, WA 98109, USA; Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Michael N Oda
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Gail P Jarvik
- Departments of Medicine, University of Washington, Seattle, WA 98109, USA; Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Tomas Vaisar
- Departments of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Jay W Heinecke
- Departments of Medicine, University of Washington, Seattle, WA 98109, USA
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154
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Otto A, Becher D, Schmidt F. Quantitative proteomics in the field of microbiology. Proteomics 2014; 14:547-65. [PMID: 24376008 DOI: 10.1002/pmic.201300403] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/15/2013] [Accepted: 12/06/2013] [Indexed: 12/11/2022]
Abstract
Quantitative proteomics has become an indispensable analytical tool for microbial research. Modern microbial proteomics covers a wide range of topics in basic and applied research from in vitro characterization of single organisms to unravel the physiological implications of stress/starvation to description of the proteome content of a cell at a given time. With the techniques available, ranging from classical gel-based procedures to modern MS-based quantitative techniques, including metabolic and chemical labeling, as well as label-free techniques, quantitative proteomics is today highly successful in sophisticated settings of high complexity such as host-pathogen interactions, mixed microbial communities, and microbial metaproteomics. In this review, we will focus on the vast range of techniques practically applied in current research with an introduction of the workflows used for quantitative comparisons, a description of the advantages/disadvantages of the various methods, reference to hallmark publications and presentation of applications in current microbial research.
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Affiliation(s)
- Andreas Otto
- Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Germany
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155
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Bundgaard L, Jacobsen S, Dyrlund TF, Sørensen MA, Harman VM, Beynon RJ, Brownridge PJ, Petersen LJ, Bendixen E. Development of a Method for Absolute Quantification of Equine Acute Phase Proteins Using Concatenated Peptide Standards and Selected Reaction Monitoring. J Proteome Res 2014; 13:5635-47. [DOI: 10.1021/pr500607s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Louise Bundgaard
- Department
of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Højbakkegaard Allé 5, Taastrup 2630, Denmark
- Department
of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Gustav Wieds Vej 10c, Aarhus 8000, Denmark
| | - Stine Jacobsen
- Department
of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Højbakkegaard Allé 5, Taastrup 2630, Denmark
| | - Thomas F. Dyrlund
- Department
of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Gustav Wieds Vej 10c, Aarhus 8000, Denmark
| | - Mette Aa. Sørensen
- Department
of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Højbakkegaard Allé 5, Taastrup 2630, Denmark
| | - Victoria M. Harman
- Protein
Function Group, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Robert J. Beynon
- Protein
Function Group, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Philip J. Brownridge
- Protein
Function Group, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Lars J. Petersen
- Department
of Nuclear Medicine, Clinical Cancer Research Center, Aalborg University Hospital, Hobrovej 18-22, Aalborg 9000, Denmark
- Department
of Clinical Medicine, Aalborg University Hospital, Sdr. Skovvej 11, Aalborg 9000, Denmark
| | - Emøke Bendixen
- Department
of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Gustav Wieds Vej 10c, Aarhus 8000, Denmark
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156
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González-Antuña A, Rodríguez-González P, Ohlendorf R, Henrion A, Delatour V, García Alonso JI. Determination of Cystatin C in human serum by isotope dilution mass spectrometry using mass overlapping peptides. J Proteomics 2014; 112:141-55. [PMID: 25230103 DOI: 10.1016/j.jprot.2014.09.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/21/2014] [Accepted: 09/04/2014] [Indexed: 12/23/2022]
Abstract
UNLABELLED We propose a peptide-based isotope dilution mass spectrometry approach for Cystatin C determination in human serum samples, a clinical marker for renal status for which backup by a mass spectrometry based primary method has been missing so far. In contrast to common protocols, the isotope labelled version of the proteotypic signature peptide is designed such as keeping the isotopic difference as little as possible with respect to the peptide released from the protein. Peptides labelled in two (13)C atoms are added to the serum samples just before proteolysis. After two steps of chromatographic purification the sample is measured by selected reaction monitoring using a LC-MS/MS. Resolution of the first quadrupole is reduced to transmit the whole parent ion cluster to the collision cell for monitoring accurate isotopic distributions of the molecular fragments. Molar fractions of labelled and natural abundance peptides are directly obtained from the experimental mass spectra of the in-cell fragment ions. Thus, the natural abundance protein concentration is obtained from the fragment-ion spectrum of the sample without resorting to extra calibration runs. Applicability of the approach is demonstrated by the measurement of the serum concentration of Cystatin C in Reference Material ERM R-DA471/IFCC and real samples. BIOLOGICAL SIGNIFICANCE Cystatin C is used as an alternative marker instead of, or in combination with creatinine for non-invasive determination of glomerular filtration rates. Advantages advocating in favour of Cystatin C in diagnosis of chronic kidney diseases are the lower variability of its serum level and, particularly, virtual independence on sex, age and muscle mass. However, in order to capitalize, accuracy of measurement has to be in proportion with the predictive power of the marker. Though there are label-free methods available for screening purposes or high-throughput analysis, achieving high levels of reliability and accuracy in quantitative proteomics takes reference to isotope labelled materials. Present routine assays (mainly nephelometry, turbidimetry and ligand-binding assays) are known to leave improvement to be desired in that respect. Absolute quantification based on enzymatic signature-peptides provides a method principle establishing traceability to the International System of Units on the level of primary methods. The kind of technique is capable, by this way, of high accuracy value-assignment to matrix materials needed for calibration of present routine assays, where not completely replacing them. Cystatin C measurement by isotope dilution mass spectrometry is developed in this study with the aim of making available this tool to support diagnostics of kidney function in the same way.
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Affiliation(s)
- Ana González-Antuña
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Pablo Rodríguez-González
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain.
| | - Rudiger Ohlendorf
- Physikalisch-Technische Bundesanstalt, Bundesallee 100, D-38116 Braunschweig, Germany
| | - André Henrion
- Physikalisch-Technische Bundesanstalt, Bundesallee 100, D-38116 Braunschweig, Germany
| | - Vincent Delatour
- Laboratoire National de Métrologie et d'Essais (LNE), Paris, France(1)
| | - J Ignacio García Alonso
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
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157
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Drabovich AP, Martínez-Morillo E, Diamandis EP. Toward an integrated pipeline for protein biomarker development. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:677-86. [PMID: 25218201 DOI: 10.1016/j.bbapap.2014.09.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/08/2014] [Accepted: 09/04/2014] [Indexed: 01/06/2023]
Abstract
Protein biomarker development is a multidisciplinary task involving basic, translational and clinical research. Integration of multidisciplinary efforts in a single pipeline is challenging, but crucial to facilitate rational discovery of protein biomarkers and alleviate existing disappointments in the field. In this review, we discuss in detail individual phases of biomarker development pipeline, such as biomarker candidate identification, verification and validation. We focus on mass spectrometry as a principal technique for protein identification and quantification, and discuss complementary -omics approaches for selection of biomarker candidates. Proteomic samples, protein-based clinical laboratory tests and limitations of biomarker development are reviewed in detail, and critical assessment of all phases of biomarker development pipeline is provided. This article is part of a Special Issue entitled: Medical Proteomics.
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Affiliation(s)
- Andrei P Drabovich
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
| | | | - Eleftherios P Diamandis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
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158
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Pichlo M, Bungert-Plümke S, Weyand I, Seifert R, Bönigk W, Strünker T, Kashikar ND, Goodwin N, Müller A, Pelzer P, Van Q, Enderlein J, Klemm C, Krause E, Trötschel C, Poetsch A, Kremmer E, Kaupp UB, Körschen HG, Collienne U. High density and ligand affinity confer ultrasensitive signal detection by a guanylyl cyclase chemoreceptor. J Cell Biol 2014; 206:541-57. [PMID: 25135936 PMCID: PMC4137060 DOI: 10.1083/jcb.201402027] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 07/15/2014] [Indexed: 12/28/2022] Open
Abstract
Guanylyl cyclases (GCs), which synthesize the messenger cyclic guanosine 3',5'-monophosphate, control several sensory functions, such as phototransduction, chemosensation, and thermosensation, in many species from worms to mammals. The GC chemoreceptor in sea urchin sperm can decode chemoattractant concentrations with single-molecule sensitivity. The molecular and cellular underpinnings of such ultrasensitivity are not known for any eukaryotic chemoreceptor. In this paper, we show that an exquisitely high density of 3 × 10(5) GC chemoreceptors and subnanomolar ligand affinity provide a high ligand-capture efficacy and render sperm perfect absorbers. The GC activity is terminated within 150 ms by dephosphorylation steps of the receptor, which provides a means for precise control of the GC lifetime and which reduces "molecule noise." Compared with other ultrasensitive sensory systems, the 10-fold signal amplification by the GC receptor is surprisingly low. The hallmarks of this signaling mechanism provide a blueprint for chemical sensing in small compartments, such as olfactory cilia, insect antennae, or even synaptic boutons.
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Affiliation(s)
- Magdalena Pichlo
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
| | - Stefanie Bungert-Plümke
- Marine Biological Laboratory, Woods Hole, MA 02543 Institute of Complex Systems (ICS-4), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ingo Weyand
- Marine Biological Laboratory, Woods Hole, MA 02543 Institute of Complex Systems (ICS-4), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Reinhard Seifert
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
| | - Wolfgang Bönigk
- Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Timo Strünker
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
| | - Nachiket Dilip Kashikar
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543 Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton BN1 9QG, England, UK
| | - Normann Goodwin
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543 Babraham Institute, Cambridge CB22 3AT, England, UK
| | - Astrid Müller
- Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Patric Pelzer
- Marine Biological Laboratory, Woods Hole, MA 02543 Department of Functional Neuroanatomy, Institute of Anatomy and Cell Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Qui Van
- III. Physikalisches Institut, Universität Göttingen, 37077 Göttingen, Germany
| | - Jörg Enderlein
- III. Physikalisches Institut, Universität Göttingen, 37077 Göttingen, Germany
| | - Clementine Klemm
- Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Eberhard Krause
- Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | | | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum. 44801 Bochum, Germany
| | - Elisabeth Kremmer
- Institut für Molekulare Immunologie, Helmholtz-Zentrum München, 81377 München, Germany
| | - U Benjamin Kaupp
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
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159
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Yang W, Kernstock R, Simmons N, Alak A. Guanidinated protein internal standard for immunoaffinity-liquid chromatography/tandem mass spectrometry quantitation of protein therapeutics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:1489-1500. [PMID: 24861599 DOI: 10.1002/rcm.6924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 04/14/2014] [Accepted: 04/15/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE A protein internal standard (IS) is essential and superior to a peptide IS to achieve reproducible results in the quantitation of protein therapeutics using immunoaffinity-liquid chromatography/tandem mass spectrometry (LC/MS/MS). Guanidination has been used as a protein post-modification technique for more than half a century. A decade ago, the modification was applied to lysine-ending peptides to enhance their MALDI responses and peptide sequencing coverage. However, rarely has tryptic digestion of guanidinated proteins been investigated, likely due to the early conclusion that trypsin did not hydrolyze peptide bonds involving homoarginine in guanidinated proteins. In this study, the opposite was observed. Guanidinated lysine residues of proteins did not hinder the access of trypsin allowing for proteolytic digestion. Based on this observation, a new concept of internal standard, named Guanidinated Protein Internal Standard (GP-IS), was proposed for LC/MS/MS quantitation of protein therapeutics. METHODS The GP-IS is prepared by treating a portion of the therapeutic protein (analyte) with guanidine to convert arginine residues in the protein into homoarginine residues. After tryptic digestion, the GP-IS produces a series of homoarginine-ending peptides plus another series of arginine-ending peptides. One of the homoarginine-ending peptides, which corresponds to the analyte surrogate (lysine-ending) peptide, was chosen as a peptide internal standard (GP-PIS) for LC/MS/MS quantitation. RESULTS Using this GP-IS approach, a sensitive and robust immunoaffinity-LC/MS/MS assay was developed and fully validated with a linearity range from 10 to 1000 ng/mL using 200 μL of human serum for the quantitation of an Astellas protein drug in clinical development. CONCLUSIONS The proposed strategy allows LC/MS/MS to play an ever-increasing role in bioanalytical support for protein therapeutics development because of its capability of completely tracking all variations from the beginning to the end of sample analysis, easier preparation compared to isotope-labeled protein-IS, and greater flexibility for changing to alternate analyte surrogate peptides.
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Affiliation(s)
- Wenchu Yang
- Bioanalysis-US, Astellas Research Institute of America, Skokie, IL, 60077, USA
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160
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Percy AJ, Yang J, Chambers AG, Simon R, Hardie DB, Borchers CH. Multiplexed MRM with Internal Standards for Cerebrospinal Fluid Candidate Protein Biomarker Quantitation. J Proteome Res 2014; 13:3733-3747. [DOI: 10.1021/pr500317d] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew J. Percy
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Juncong Yang
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Andrew G. Chambers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Romain Simon
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Darryl B. Hardie
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Christoph H. Borchers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
- Department
of Biochemistry and Microbiology, University of Victoria, Petch Building
Room 207, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
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161
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Pritchard C, Groves KJ, Biesenbruch S, O’Connor G, Ashcroft AE, Arsene C, Schulze D, Quaglia M. Quantification of Human Growth Hormone in Serum with a Labeled Protein as an Internal Standard: Essential Considerations. Anal Chem 2014; 86:6525-32. [DOI: 10.1021/ac501032q] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Caroline Pritchard
- LGC, Queens Road, Teddington, London TW11
0LY, United Kingdom
- Astbury
Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Kate J. Groves
- LGC, Queens Road, Teddington, London TW11
0LY, United Kingdom
| | | | - Gavin O’Connor
- LGC, Queens Road, Teddington, London TW11
0LY, United Kingdom
| | - Alison E. Ashcroft
- Astbury
Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Cristian Arsene
- Physikalisch-Technische Bundesanstalt, Bundesallee
100, 38116 Braunschweig, Germany
| | - Dirk Schulze
- Physikalisch-Technische Bundesanstalt, Bundesallee
100, 38116 Braunschweig, Germany
| | - Milena Quaglia
- LGC, Queens Road, Teddington, London TW11
0LY, United Kingdom
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162
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163
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Qiu X, Zhang H, Lai Y. Quantitative targeted proteomics for membrane transporter proteins: method and application. AAPS JOURNAL 2014; 16:714-26. [PMID: 24830943 DOI: 10.1208/s12248-014-9607-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/05/2014] [Indexed: 01/04/2023]
Abstract
Although global proteomics has shown promise for discovery of many new proteins, biomarkers, protein modifications, and polymorphisms, targeted proteomics is emerging in the proteomics research field as a complement to untargeted shotgun proteomics, particularly when a determined set of low-abundance functional proteins need to be measured. The function and expression of proteins related to drug absorption, distribution, metabolism, and excretion (ADME) such as cytochrome P450 enzymes and membrane transporters are of great interest in biopharmaceutical research. Since the variation in ADME-related protein expression is known to be a major complicating factor encountered during in vitro-in vivo and in vivo-in vivo extrapolations (IVIVE), the accurate quantification of the ADME proteins in complex biological systems becomes a fundamental element in establishing IVIVE for pharmacokinetic predictions. In this review, we provide an overview of relevant methodologies followed by a summary of recent applications encompassing mass spectrometry-based targeted quantifications of membrane transporters.
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Affiliation(s)
- Xi Qiu
- Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey, 08543, USA
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164
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Farrokhi V, McShane AJ, Nemati R, Yao X. Stable isotope dilution mass spectrometry for membrane transporter quantitation. AAPS JOURNAL 2014; 15:1222-31. [PMID: 24022320 DOI: 10.1208/s12248-013-9529-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/16/2013] [Indexed: 11/30/2022]
Abstract
This review provides an introduction to stable isotope dilution mass spectrometry (MS) and its emerging applications in the analysis of membrane transporter proteins. Various approaches and application examples, for the generation and use of quantitation reference standards—either stable isotope-labeled peptides or proteins—are discussed as they apply to the MS quantitation of membrane proteins. Technological considerations for the sample preparation of membrane transporter proteins are also presented.
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165
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166
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Zhao C, Trudeau B, Xie H, Prostko J, Fishpaugh J, Ramsay C. Epitope mapping and targeted quantitation of the cardiac biomarker troponin by SID-MRM mass spectrometry. Proteomics 2014; 14:1311-21. [PMID: 24596168 DOI: 10.1002/pmic.201300150] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 02/05/2014] [Accepted: 02/27/2014] [Indexed: 11/09/2022]
Abstract
The absolute quantitation of the targeted protein using MS provides a promising method to evaluate/verify biomarkers used in clinical diagnostics. In this study, a cardiac biomarker, troponin I (TnI), was used as a model protein for method development. The epitope peptide of TnI was characterized by epitope excision followed with LC/MS/MS method and acted as the surrogate peptide for the targeted protein quantitation. The MRM-based MS assay using a stable internal standard that improved the selectivity, specificity, and sensitivity of the protein quantitation. Also, plasma albumin depletion and affinity enrichment of TnI by anti-TnI mAb-coated microparticles reduced the sample complexity, enhanced the dynamic range, and further improved the detecting sensitivity of the targeted protein in the biological matrix. Therefore, quantitation of TnI, a low abundant protein in human plasma, has demonstrated the applicability of the targeted protein quantitation strategy through its epitope peptide determined by epitope mapping method.
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Affiliation(s)
- Cheng Zhao
- Research Analytical Chemistry, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL, USA
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167
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Edfors F, Boström T, Forsström B, Zeiler M, Johansson H, Lundberg E, Hober S, Lehtiö J, Mann M, Uhlen M. Immunoproteomics using polyclonal antibodies and stable isotope-labeled affinity-purified recombinant proteins. Mol Cell Proteomics 2014; 13:1611-24. [PMID: 24722731 DOI: 10.1074/mcp.m113.034140] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The combination of immuno-based methods and mass spectrometry detection has great potential in the field of quantitative proteomics. Here, we describe a new method (immuno-SILAC) for the absolute quantification of proteins in complex samples based on polyclonal antibodies and stable isotope-labeled recombinant protein fragments to allow affinity enrichment prior to mass spectrometry analysis and accurate quantification. We took advantage of the antibody resources publicly available from the Human Protein Atlas project covering more than 80% of all human protein-coding genes. Epitope mapping revealed that a majority of the polyclonal antibodies recognized multiple linear epitopes, and based on these results, a semi-automated method was developed for peptide enrichment using polyclonal antibodies immobilized on protein A-coated magnetic beads. A protocol based on the simultaneous multiplex capture of more than 40 protein targets showed that approximately half of the antibodies enriched at least one functional peptide detected in the subsequent mass spectrometry analysis. The approach was further developed to also generate quantitative data via the addition of heavy isotope-labeled recombinant protein fragment standards prior to trypsin digestion. Here, we show that we were able to use small amounts of antibodies (50 ng per target) in this manner for efficient multiplex analysis of quantitative levels of proteins in a human HeLa cell lysate. The results suggest that polyclonal antibodies generated via immunization of recombinant protein fragments could be used for the enrichment of target peptides to allow for rapid mass spectrometry analysis taking advantage of a substantial reduction in sample complexity. The possibility of building up a proteome-wide resource for immuno-SILAC assays based on publicly available antibody resources is discussed.
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Affiliation(s)
- Fredrik Edfors
- From the ‡Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Tove Boström
- ¶Department of Proteomics, KTH - Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Björn Forsström
- From the ‡Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Marlis Zeiler
- ‖Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Henrik Johansson
- **Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, SE-171 21 Stockholm, Sweden
| | - Emma Lundberg
- From the ‡Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Sophia Hober
- ¶Department of Proteomics, KTH - Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Janne Lehtiö
- **Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, SE-171 21 Stockholm, Sweden
| | - Matthias Mann
- ‖Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Mathias Uhlen
- From the ‡Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden; ¶Department of Proteomics, KTH - Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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168
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Nouri-Nigjeh E, Zhang M, Ji T, Yu H, An B, Duan X, Balthasar J, Johnson RW, Qu J. Effects of calibration approaches on the accuracy for LC-MS targeted quantification of therapeutic protein. Anal Chem 2014; 86:3575-84. [PMID: 24611550 PMCID: PMC3982980 DOI: 10.1021/ac5001477] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
LC–MS
provides a promising alternative to ligand-binding
assays for quantification of therapeutic proteins and biomarkers.
As LC–MS methodology is based on the analysis of proteolytic
peptides, calibration approaches utilizing various calibrators and
internal standards (I.S.) have been developed. A comprehensive assessment
of the accuracy and reliability of these approaches is essential but
has yet been reported. Here we performed a well-controlled and systematic
comparative study using quantification of monoclonal-antibody in plasma
as the model system. Method development utilized a high-throughput
orthogonal-array-optimization, and two sensitive and stable signature-peptides
(SP) from different domains were selected based on extensive evaluations
in plasma matrix. With the purities of all protein/peptide standards
corrected by quantitative amino acid analysis (AAA), five calibration
approaches using stable-isotope-labeled (SIL) I.S. were thoroughly
compared, including those at peptide, extended-peptide, and protein
levels and two “hybrid” approaches (i.e., protein calibrator
with SIL-peptide or SIL-extended-peptide I.S.). These approaches were
further evaluated in parallel for a 15 time point, preclinical pharmacokinetic
study. All methods showed good precision (CV% < 20%). When examined
with protein-spiked plasma QC, peptide-level calibration exhibited
severe negative biases (−23 to −62%), highly discordant
results between the two SP (deviations of 38–56%), and misleading
pharmacokinetics assessments. Extended-peptide calibration showed
significant improvements but still with unacceptable accuracy. Conversely,
protein-level and the two hybrid calibrations achieved good quantitative
accuracy (error < 10%), concordant results by two SP (deviations
< 15%), and correct pharmacokinetic parameters. Hybrid approaches
were found to provide a cost-effective means for accurate quantification
without the costly SIL-protein. Other key findings include (i) using
two SP provides a versatile gauge for method reliability; (ii) evaluation
of peptide stability in the matrix before SP selection is critical;
and (iii) using AAA to verify purities of protein/peptide calibrators
ensures accurate quantitation. These results address fundamental calibration
issues that have not been adequately investigated in published studies
and will provide valuable guidelines for the “fit for purpose”
development of accurate LC–MS assays for therapeutic proteins
and biomarkers in biological matrices.
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Affiliation(s)
- Eslam Nouri-Nigjeh
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York , Amherst, NY 14260, United States
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169
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Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics 2014; 13:907-17. [PMID: 24443746 PMCID: PMC3945918 DOI: 10.1074/mcp.m113.036095] [Citation(s) in RCA: 431] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/14/2014] [Indexed: 12/25/2022] Open
Abstract
Adoption of targeted mass spectrometry (MS) approaches such as multiple reaction monitoring (MRM) to study biological and biomedical questions is well underway in the proteomics community. Successful application depends on the ability to generate reliable assays that uniquely and confidently identify target peptides in a sample. Unfortunately, there is a wide range of criteria being applied to say that an assay has been successfully developed. There is no consensus on what criteria are acceptable and little understanding of the impact of variable criteria on the quality of the results generated. Publications describing targeted MS assays for peptides frequently do not contain sufficient information for readers to establish confidence that the tests work as intended or to be able to apply the tests described in their own labs. Guidance must be developed so that targeted MS assays with established performance can be made widely distributed and applied by many labs worldwide. To begin to address the problems and their solutions, a workshop was held at the National Institutes of Health with representatives from the multiple communities developing and employing targeted MS assays. Participants discussed the analytical goals of their experiments and the experimental evidence needed to establish that the assays they develop work as intended and are achieving the required levels of performance. Using this "fit-for-purpose" approach, the group defined three tiers of assays distinguished by their performance and extent of analytical characterization. Computational and statistical tools useful for the analysis of targeted MS results were described. Participants also detailed the information that authors need to provide in their manuscripts to enable reviewers and readers to clearly understand what procedures were performed and to evaluate the reliability of the peptide or protein quantification measurements reported. This paper presents a summary of the meeting and recommendations.
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Affiliation(s)
- Steven A. Carr
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | - Bruno Domon
- ‖Luxembourg Clinical Proteomics Center, Luxembourg
| | | | | | | | - Ruth Hüttenhain
- ¶¶Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- ‖‖University of California San Francisco, California
| | | | | | - Tao Liu
- Pacific Northwest National Laboratory, Richland, Washington
| | | | - DR Mani
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | | | | | - Ruedi Aebersold
- ¶¶Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | | | | | - Emily Boja
- National Cancer Institute, NIH Bethesda, Maryland
| | | | | | | | | | - Daniel Chan
- Johns Hopkins University, Baltimore, Maryland
| | - Hasmik Keshishian
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Eric Kuhn
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Jerry S.H. Lee
- National Cancer Institute, NIH Bethesda, Maryland
- Johns Hopkins University, Baltimore, Maryland
| | | | - Robert Moritz
- **Institute for Systems Biology, Seattle, Washington
| | | | | | | | | | | | | | | | - Gordon Whiteley
- Liedos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research
| | - Arun Wiita
- ‖‖University of California San Francisco, California
| | - Susan Weintraub
- University of Texas Health Science Center, San Antonio, Texas
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170
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Application and challenges in using LC–MS assays for absolute quantitative analysis of therapeutic proteins in drug discovery. Bioanalysis 2014; 6:859-79. [DOI: 10.4155/bio.14.36] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
As more protein therapeutics enter the drug-discovery pipeline, the traditional ligand-binding assay (LBA) faces additional challenges to meet the rapid and diverse bioanalytical needs in the early drug-discovery stage. The high specificity and sensitivity afforded by LC–MS, along with its rapid method development, is proving invaluable for the analysis of protein therapeutics in support of drug discovery. LC–MS not only serves as a quantitative tool to complement LBA in drug discovery, it also provides structural details at a molecular level, which are used to address issues that cannot be resolved using LBA alone. This review will describe the key benefits and applications, as well as the techniques and challenges for applying LC–MS to support protein quantification in drug discovery.
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171
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172
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Trauchessec M, Jaquinod M, Bonvalot A, Brun V, Bruley C, Ropers D, de Jong H, Garin J, Bestel-Corre G, Ferro M. Mass spectrometry-based workflow for accurate quantification of Escherichia coli enzymes: how proteomics can play a key role in metabolic engineering. Mol Cell Proteomics 2014; 13:954-68. [PMID: 24482123 DOI: 10.1074/mcp.m113.032672] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Metabolic engineering aims to design high performance microbial strains producing compounds of interest. This requires systems-level understanding; genome-scale models have therefore been developed to predict metabolic fluxes. However, multi-omics data including genomics, transcriptomics, fluxomics, and proteomics may be required to model the metabolism of potential cell factories. Recent technological advances to quantitative proteomics have made mass spectrometry-based quantitative assays an interesting alternative to more traditional immuno-affinity based approaches. This has improved specificity and multiplexing capabilities. In this study, we developed a quantification workflow to analyze enzymes involved in central metabolism in Escherichia coli (E. coli). This workflow combined full-length isotopically labeled standards with selected reaction monitoring analysis. First, full-length (15)N labeled standards were produced and calibrated to ensure accurate measurements. Liquid chromatography conditions were then optimized for reproducibility and multiplexing capabilities over a single 30-min liquid chromatography-MS analysis. This workflow was used to accurately quantify 22 enzymes involved in E. coli central metabolism in a wild-type reference strain and two derived strains, optimized for higher NADPH production. In combination with measurements of metabolic fluxes, proteomics data can be used to assess different levels of regulation, in particular enzyme abundance and catalytic rate. This provides information that can be used to design specific strains used in biotechnology. In addition, accurate measurement of absolute enzyme concentrations is key to the development of predictive kinetic models in the context of metabolic engineering.
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Affiliation(s)
- Mathieu Trauchessec
- Commisariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Recherches en Technologie et Sciences pour le Vivant (iRTSV), Biologie à Grande Echelle, F-38054 Grenoble, France
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173
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Li KW, Jimenez CR. Synapse proteomics: current status and quantitative applications. Expert Rev Proteomics 2014; 5:353-60. [DOI: 10.1586/14789450.5.2.353] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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174
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Percy AJ, Byrns S, Chambers AG, Borchers CH. Targeted quantitation of CVD-linked plasma proteins for biomarker verification and validation. Expert Rev Proteomics 2014; 10:567-78. [DOI: 10.1586/14789450.2013.856763] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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175
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Di Michele M, Van Geet C, Freson K. Recent advances in platelet proteomics. Expert Rev Proteomics 2014; 9:451-66. [DOI: 10.1586/epr.12.31] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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176
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Wu Q, Shan Y, Qu Y, Jiang H, Yuan H, Liu J, Zhang S, Liang Z, Zhang L, Zhang Y. Improved accuracy for label-free absolute quantification of proteome by combining the absolute protein expression profiling algorithm and summed tandem mass spectrometric total ion current. Analyst 2014; 139:138-46. [DOI: 10.1039/c3an01738a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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177
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Villanueva J, Carrascal M, Abian J. Isotope dilution mass spectrometry for absolute quantification in proteomics: Concepts and strategies. J Proteomics 2014; 96:184-99. [DOI: 10.1016/j.jprot.2013.11.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 12/25/2022]
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178
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Macleod AK, Zang T, Riches Z, Henderson CJ, Wolf CR, Huang JTJ. A targeted in vivo SILAC approach for quantification of drug metabolism enzymes: regulation by the constitutive androstane receptor. J Proteome Res 2013; 13:866-74. [PMID: 24303842 PMCID: PMC3923450 DOI: 10.1021/pr400897t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The modulation of drug metabolism enzyme (DME) expression by therapeutic agents is a central mechanism of drug-drug interaction and should be assessed as early as possible in preclinical drug development. Direct measurement of DME levels is typically achieved by Western blotting, qPCR, or microarray, but these techniques have their limitations; antibody cross-reactivity among highly homologous subfamilies creates ambiguity, while discordance between mRNA and protein expression undermines observations. The aim of this study was to design a simple targeted workflow by combining in vivo SILAC and label-free proteomics approaches for quantification of DMEs in mouse liver, facilitating a rapid and comprehensive evaluation of metabolic potential at the protein level. A total of 197 peptides, representing 51 Phase I and Phase II DMEs, were quantified by LC-MS/MS using targeted high resolution single ion monitoring (tHR/SIM) with a defined mass-to-charge and retention time window for each peptide. In a constitutive androstane receptor (Car) activated mouse model, comparison of tHR/SIM-in vivo SILAC with Western blotting for analysis of the expression of cytochromes P450 was favorable, with agreement in fold-change values between methods. The tHR/SIM-in vivo SILAC approach therefore permits the robust analysis of multiple DME in a single protein sample, with clear utility for the assessment of the drug-drug interaction potential of candidate therapeutic compounds.
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Affiliation(s)
- A Kenneth Macleod
- Jacqui Wood Cancer Centre, Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee , James Arrott Drive, Dundee DD1 9SY, Scotland
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179
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Genomic and post-genomic leads toward regulation of spermatogenesis. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:409-22. [DOI: 10.1016/j.pbiomolbio.2013.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 01/08/2013] [Indexed: 01/15/2023]
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180
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Targeted selected reaction monitoring mass spectrometric immunoassay for insulin-like growth factor 1. PLoS One 2013; 8:e81125. [PMID: 24278387 PMCID: PMC3836743 DOI: 10.1371/journal.pone.0081125] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 10/09/2013] [Indexed: 11/30/2022] Open
Abstract
Insulin-like growth factor 1 (IGF1) is an important biomarker of human growth disorders that is routinely analyzed in clinical laboratories. Mass spectrometry-based workflows offer a viable alternative to standard IGF1 immunoassays, which utilize various pre-analytical preparation strategies. In this work we developed an assay that incorporates a novel sample preparation method for dissociating IGF1 from its binding proteins. The workflow also includes an immunoaffinity step using antibody-derivatized pipette tips, followed by elution, trypsin digestion, and LC-MS/MS separation and detection of the signature peptides in a selected reaction monitoring (SRM) mode. The resulting quantitative mass spectrometric immunoassay (MSIA) exhibited good linearity in the range of 1 to 1,500 ng/mL IGF1, intra- and inter-assay precision with CVs of less than 10%, and lowest limits of detection of 1 ng/mL. The linearity and recovery characteristics of the assay were also established, and the new method compared to a commercially available immunoassay using a large cohort of human serum samples. The IGF1 SRM MSIA is well suited for use in clinical laboratories.
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181
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van den Broek I, Smit NPM, Romijn FPHTM, van der Laarse A, Deelder AM, van der Burgt YEM, Cobbaert CM. Evaluation of interspecimen trypsin digestion efficiency prior to multiple reaction monitoring-based absolute protein quantification with native protein calibrators. J Proteome Res 2013; 12:5760-74. [PMID: 24168082 DOI: 10.1021/pr400763d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Implementation of quantitative clinical chemistry proteomics (qCCP) requires targeted proteomics approaches, usually involving bottom-up multiple reaction monitoring-mass spectrometry (MRM-MS) with stable-isotope labeled standard (SIS) peptides, to move toward more accurate measurements. Two aspects of qCCP that deserve special attention are (1) proper calibration and (2) the assurance of consistent digestion. Here, we describe the evaluation of tryptic digestion efficiency by monitoring various signature peptides, missed cleavages, and modifications during proteolysis of apolipoprotein A-I and B in normo- and hypertriglyceridemic specimens. Absolute quantification of apolipoprotein A-I and B was performed by LC-MRM-MS with SIS peptide internal standards at two time points (4 and 20 h), using three native protein calibrators. Comparison with an immunoturbidimetric assay revealed recoveries of 99.4 ± 6.5% for apolipoprotein A-I and 102.6 ± 7.2% for apolipoprotein B after 4 h of trypsin digestion. Protein recoveries after 20 h trypsin incubation equaled 95.9 ± 6.9% and 106.0 ± 10.0% for apolipoproteins A-I and B, respectively. In conclusion, the use of metrologically traceable, native protein calibrators looks promising for accurate quantification of apolipoprotein A-I and B. Selection of rapidly formed peptides, that is, with no or minor missed cleavages, and the use of short trypsin incubation times for these efficiently cleaved peptides are likely to further reduce the variability introduced by trypsin digestion and to improve the traceability of test results to reach the desirable analytical performance for clinical chemistry application.
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Affiliation(s)
- Irene van den Broek
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center (LUMC) , Albinusdreef 2, 2333 ZA, Leiden, the Netherlands
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182
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Wilffert D, Reis CR, Hermans J, Govorukhina N, Tomar T, de Jong S, Quax WJ, van de Merbel NC, Bischoff R. Antibody-Free LC-MS/MS Quantification of rhTRAIL in Human and Mouse Serum. Anal Chem 2013; 85:10754-60. [DOI: 10.1021/ac4017902] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel Wilffert
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, Antonius
Deusinglaan 1, Groningen, 9713 AV The Netherlands
| | - Carlos R. Reis
- Pharmaceutical
Biology, Department of Pharmacy, University of Groningen, Antonius
Deusinglaan 1, Groningen, 9713 AV The Netherlands
| | - Jos Hermans
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, Antonius
Deusinglaan 1, Groningen, 9713 AV The Netherlands
| | - Natalia Govorukhina
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, Antonius
Deusinglaan 1, Groningen, 9713 AV The Netherlands
| | - Tushar Tomar
- Department
of Gynecologic Oncology, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, Groningen, 9713 GZ The Netherlands
| | - Steven de Jong
- Department
of Medical Oncology, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, Groningen, 9713 GZ The Netherlands
| | - Wim J. Quax
- Pharmaceutical
Biology, Department of Pharmacy, University of Groningen, Antonius
Deusinglaan 1, Groningen, 9713 AV The Netherlands
| | - Nico C. van de Merbel
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, Antonius
Deusinglaan 1, Groningen, 9713 AV The Netherlands
- PRA, Bioanalytical Laboratory, Westerbrink 3, Assen, 9405 BJ The Netherlands
| | - Rainer Bischoff
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, Antonius
Deusinglaan 1, Groningen, 9713 AV The Netherlands
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183
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Pre-analytical and analytical variability in absolute quantitative MRM-based plasma proteomic studies. Bioanalysis 2013; 5:2837-56. [DOI: 10.4155/bio.13.245] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Quantitative plasma proteomics, through the use of targeted MRM-MS and isotopically labeled standards, is emerging as a popular technique to address biological- and biomedical-centered queries. High precision and accuracy are essential in such measurements, particularly in protein biomarker research where translation to the clinic is sought. Standardized procedures and routine performance evaluation of all stages of the workflow (both pre-analytical and analytical) are therefore imperative to satisfy these requisites and enable high inter-laboratory reproducibility and transferability. In this review, we first discuss the pre-analytical and analytical variables that can affect the precision and accuracy of ‘absolute’ quantitative plasma proteomic measurements. Proposed strategies to limit such variability will then be highlighted and unmet needs for future exploration will be noted. Although there is no way to conduct a truly comprehensive review on this broad, rapidly changing topic, we have highlighted key aspects and included references to review articles on various sub-topics.
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184
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Deracinois B, Flahaut C, Duban-Deweer S, Karamanos Y. Comparative and Quantitative Global Proteomics Approaches: An Overview. Proteomes 2013; 1:180-218. [PMID: 28250403 PMCID: PMC5302699 DOI: 10.3390/proteomes1030180] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/08/2013] [Accepted: 10/08/2013] [Indexed: 01/14/2023] Open
Abstract
Proteomics became a key tool for the study of biological systems. The comparison between two different physiological states allows unravelling the cellular and molecular mechanisms involved in a biological process. Proteomics can confirm the presence of proteins suggested by their mRNA content and provides a direct measure of the quantity present in a cell. Global and targeted proteomics strategies can be applied. Targeted proteomics strategies limit the number of features that will be monitored and then optimise the methods to obtain the highest sensitivity and throughput for a huge amount of samples. The advantage of global proteomics strategies is that no hypothesis is required, other than a measurable difference in one or more protein species between the samples. Global proteomics methods attempt to separate quantify and identify all the proteins from a given sample. This review highlights only the different techniques of separation and quantification of proteins and peptides, in view of a comparative and quantitative global proteomics analysis. The in-gel and off-gel quantification of proteins will be discussed as well as the corresponding mass spectrometry technology. The overview is focused on the widespread techniques while keeping in mind that each approach is modular and often recovers the other.
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Affiliation(s)
- Barbara Deracinois
- Université Lille Nord de France, Lille F-59000, France.
- Université d'Artois, LBHE, Lens F-62307, France.
- IMPRT-IFR114, Lille F-59000, France.
| | - Christophe Flahaut
- Université Lille Nord de France, Lille F-59000, France.
- Université d'Artois, LBHE, Lens F-62307, France.
- IMPRT-IFR114, Lille F-59000, France.
| | - Sophie Duban-Deweer
- Université Lille Nord de France, Lille F-59000, France.
- Université d'Artois, LBHE, Lens F-62307, France.
- IMPRT-IFR114, Lille F-59000, France.
| | - Yannis Karamanos
- Université Lille Nord de France, Lille F-59000, France.
- Université d'Artois, LBHE, Lens F-62307, France.
- IMPRT-IFR114, Lille F-59000, France.
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185
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Bronsema KJ, Bischoff R, van de Merbel NC. High-Sensitivity LC-MS/MS Quantification of Peptides and Proteins in Complex Biological Samples: The Impact of Enzymatic Digestion and Internal Standard Selection on Method Performance. Anal Chem 2013; 85:9528-35. [DOI: 10.1021/ac4015116] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kees J. Bronsema
- Analytical Biochemistry, Department
of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Bioanalytical
Laboratory, PRA, Early Development Services, Westerbrink 3, 9405 BJ, Assen, The Netherlands
| | - Rainer Bischoff
- Analytical Biochemistry, Department
of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Nico C. van de Merbel
- Analytical Biochemistry, Department
of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Bioanalytical
Laboratory, PRA, Early Development Services, Westerbrink 3, 9405 BJ, Assen, The Netherlands
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186
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Hoshi Y, Uchida Y, Tachikawa M, Inoue T, Ohtsuki S, Terasaki T. Quantitative Atlas of Blood–Brain Barrier Transporters, Receptors, and Tight Junction Proteins in Rats and Common Marmoset. J Pharm Sci 2013; 102:3343-55. [DOI: 10.1002/jps.23575] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 04/10/2013] [Accepted: 04/12/2013] [Indexed: 01/16/2023]
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187
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Schmid AW, Fauvet B, Moniatte M, Lashuel HA. Alpha-synuclein post-translational modifications as potential biomarkers for Parkinson disease and other synucleinopathies. Mol Cell Proteomics 2013; 12:3543-58. [PMID: 23966418 DOI: 10.1074/mcp.r113.032730] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The development of novel therapies against neurodegenerative disorders requires the ability to detect their early, presymptomatic manifestations in order to enable treatment before irreversible cellular damage occurs. Precocious signs indicative of neurodegeneration include characteristic changes in certain protein levels, which can be used as diagnostic biomarkers when they can be detected in fluids such as blood plasma or cerebrospinal fluid. In the case of synucleinopathies, cerebrospinal alpha-synuclein (α-syn) has attracted great interest as a potential biomarker; however, there is ongoing debate regarding the association between cerebrospinal α-syn levels and neurodegeneration in Parkinson disease and synucleinopathies. Post-translational modifications (PTMs) have emerged as important determinants of α-syn's physiological and pathological functions. Several PTMs are enriched within Lewy bodies and exist at higher levels in α-synucleinopathy brains, suggesting that certain modified forms of α-syn might be more relevant biomarkers than the total α-syn levels. However, the quantification of PTMs in bodily fluids poses several challenges. This review describes the limitations of current immunoassay-based α-syn quantification methods and highlights how these limitations can be overcome using novel mass-spectrometry-based assays. In addition, we describe how advances in chemical synthesis, which have enabled the preparation of α-syn proteins that are site-specifically modified at single or multiple residues, can facilitate the development of more accurate assays for detecting and quantifying α-syn PTMs in health and disease.
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Affiliation(s)
- Adrien W Schmid
- Proteomics Core Facility, School of Life Sciences, Station 19, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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188
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Blankley RT, Fisher C, Westwood M, North R, Baker PN, Walker MJ, Williamson A, Whetton AD, Lin W, McCowan L, Roberts CT, Cooper GJS, Unwin RD, Myers JE. A label-free selected reaction monitoring workflow identifies a subset of pregnancy specific glycoproteins as potential predictive markers of early-onset pre-eclampsia. Mol Cell Proteomics 2013; 12:3148-59. [PMID: 23897580 DOI: 10.1074/mcp.m112.026872] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Pre-eclampsia (PE) is a serious complication of pregnancy with potentially life threatening consequences for both mother and baby. Presently there is no test with the required performance to predict which healthy first-time mothers will go on to develop PE. The high specificity, sensitivity, and multiplexed nature of selected reaction monitoring holds great potential as a tool for the verification and validation of putative candidate biomarkersfor disease states. Realization of this potential involves establishing a high throughput, cost effective, reproducible sample preparation workflow. We have developed a semi-automated HPLC-based sample preparation workflow before a label-free selected reaction monitoring approach. This workflow has been applied to the search for novel predictive biomarkers for PE. To discover novel candidate biomarkers for PE, we used isobaric tagging to identify several potential biomarker proteins in plasma obtained at 15 weeks gestation from nulliparous women who later developed PE compared with pregnant women who remained healthy. Such a study generates a number of "candidate" biomarkers that require further testing in larger patient cohorts. As proof-of-principle, two of these proteins were taken forward for verification in a 100 women (58 PE, 42 controls) using label-free SRM. We obtained reproducible protein quantitation across the 100 samples and demonstrated significant changes in protein levels, even with as little as 20% change in protein concentration. The SRM data correlated with a commercial ELISA, suggesting that this is a robust workflow suitable for rapid, affordable, label-free verification of which candidate biomarkers should be taken forward for thorough investigation. A subset of pregnancy-specific glycoproteins (PSGs) had value as novel predictive markers for PE.
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Affiliation(s)
- Richard T Blankley
- Maternal and Fetal Health Research Centre, Institute of Human Development, The University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
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189
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Beck A, Diemer H, Ayoub D, Debaene F, Wagner-Rousset E, Carapito C, Van Dorsselaer A, Sanglier-Cianférani S. Analytical characterization of biosimilar antibodies and Fc-fusion proteins. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2013.02.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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190
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Hopfgartner G, Lesur A, Varesio E. Analysis of biopharmaceutical proteins in biological matrices by LC-MS/MS II. LC-MS/MS analysis. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2013.03.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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191
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Craft GE, Chen A, Nairn AC. Recent advances in quantitative neuroproteomics. Methods 2013; 61:186-218. [PMID: 23623823 PMCID: PMC3891841 DOI: 10.1016/j.ymeth.2013.04.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 03/29/2013] [Accepted: 04/13/2013] [Indexed: 01/07/2023] Open
Abstract
The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson's disease and Alzheimer's disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed light on a number of aspects of neuroscience that relates to normal brain function as well as of the changes in protein expression and regulation that occurs in neuropsychiatric and neurodegenerative disorders.
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Affiliation(s)
- George E Craft
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
| | - Anshu Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
| | - Angus C Nairn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
- Yale/NIDA Neuroproteomics Center, Yale University School of Medicine, New Haven, CT, 06508
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192
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Zhao Y, Brasier AR. Applications of selected reaction monitoring (SRM)-mass spectrometry (MS) for quantitative measurement of signaling pathways. Methods 2013; 61:313-22. [PMID: 23410677 PMCID: PMC3763905 DOI: 10.1016/j.ymeth.2013.02.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 01/30/2013] [Accepted: 02/01/2013] [Indexed: 01/12/2023] Open
Abstract
Quantitative measurement of the major regulatory proteins in signaling networks poses several technical challenges, including low abundance, the presence of post-translational modifications (PTMs), and the lack of suitable affinity detection reagents. Using the innate immune response (IIR) as a model signaling pathway, we illustrate the approach of stable isotope dilution (SID)-selected reaction monitoring (SRM)-mass spectrometry (MS) assays for quantification of low abundance signaling proteins. A work flow for SID-SRM-MS assay development is established for proteins with experimentally observed MS spectra and for those without. Using the interferon response factor (IRF)-3 transcription factor as an example, we illustrate the steps in high responding signature peptide identification, SID-SRM-MS assay optimization, and evaluation. SRM assays for normalization of IIR abundance to invariant housekeeping proteins are presented. We provide an example of SID-SRM assay development for post-translational modification (PTM) detection using an activating phospho-Ser modified NF-κB/RelA transcription factor, and describe challenges inherent in PTM-SID-SRM-MS assay development. Application of highly qualified quantitative, SID-SRM-MS assays will enable a systems-level approach to understanding the dynamics and kinetics of signaling in host cells, such as the IIR.
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Affiliation(s)
- Yingxin Zhao
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX, USA
- Departments of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Translational Science, University of Texas Medical Branch, Galveston, TX, USA
| | - Allan R. Brasier
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX, USA
- Departments of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Translational Science, University of Texas Medical Branch, Galveston, TX, USA
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193
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Percy AJ, Chambers AG, Yang J, Borchers CH. Multiplexed MRM-based quantitation of candidate cancer biomarker proteins in undepleted and non-enriched human plasma. Proteomics 2013; 13:2202-15. [DOI: 10.1002/pmic.201200316] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 02/06/2013] [Accepted: 03/26/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Andrew J. Percy
- University of Victoria - Genome British Columbia Proteomics Centre; Vancouver Island Technology Park; Victoria BC Canada
| | - Andrew G. Chambers
- University of Victoria - Genome British Columbia Proteomics Centre; Vancouver Island Technology Park; Victoria BC Canada
| | - Juncong Yang
- University of Victoria - Genome British Columbia Proteomics Centre; Vancouver Island Technology Park; Victoria BC Canada
| | - Christoph H. Borchers
- University of Victoria - Genome British Columbia Proteomics Centre; Vancouver Island Technology Park; Victoria BC Canada
- Department of Biochemistry and Microbiology; University of Victoria; Victoria BC Canada
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194
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van den Broek I, Niessen WM, van Dongen WD. Bioanalytical LC–MS/MS of protein-based biopharmaceuticals. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 929:161-79. [DOI: 10.1016/j.jchromb.2013.04.030] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/15/2013] [Accepted: 04/20/2013] [Indexed: 12/18/2022]
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195
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Metrology for metalloproteins—where are we now, where are we heading? Anal Bioanal Chem 2013; 405:5697-723. [DOI: 10.1007/s00216-013-6933-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/18/2013] [Accepted: 03/19/2013] [Indexed: 01/10/2023]
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196
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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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197
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A review on recent developments in mass spectrometry instrumentation and quantitative tools advancing bacterial proteomics. Appl Microbiol Biotechnol 2013; 97:4749-62. [DOI: 10.1007/s00253-013-4897-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 03/29/2013] [Accepted: 04/03/2013] [Indexed: 10/26/2022]
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198
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Kim JS, Lee Y, Lee MY, Shin J, Han JM, Yang EG, Yu MH, Kim S, Hwang D, Lee C. Multiple reaction monitoring of multiple low-abundance transcription factors in whole lung cancer cell lysates. J Proteome Res 2013; 12:2582-96. [PMID: 23586733 DOI: 10.1021/pr3011414] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lung cancer-related transcription factors (TFs) were identified by integrating previously reported genomic, transcriptomic, and proteomic data and were quantified by multiple reaction monitoring (MRM) in various cell lines. All experiments were performed without affinity depletion or subfractionation of cell lysates. Since the target proteins were expected to be present in low abundance, we experimentally optimized MRM transition parameters with chemically synthesized peptides. Quantitation was based on stable isotope-labeled standard peptides (SIS peptides). Out of 288 MRM measurements (36 peptides representing 28 TFs × 8 cell lines), 241 were successfully obtained within a quantitation limit of 15 amol, 221 measurements (91.7%) showed coefficients of variation (CVs) of ≤ 20%, and 149 (61.8%) showed CVs of ≤ 10%, quantifying as low as 19.4 amol/μg protein for STAT2 with a CV of 6.3% in an A549 cell. Comparisons between MRM measurements and levels of the corresponding mRNAs revealed linear, nonlinear, or no relationship between protein and mRNA levels, indicating the need for an MRM assay. An integrative analysis of MRM and gene expression profiles from doxorubicin-resistant H69AR and sensitive H69 cells further showed that 14 differentially expressed TFs, such as STAT1 and SMAD4, regulated genes associated with drug resistance and cell differentiation-related processes. Thus, the analytical performance of MRM for the quantitation of low abundance TFs suggests its usefulness for biological application.
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Affiliation(s)
- Jun Seok Kim
- Theragnosis Research Center, Korea Institute of Science and Technology, Seoul, Korea
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199
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Simicevic J, Schmid AW, Gilardoni PA, Zoller B, Raghav SK, Krier I, Gubelmann C, Lisacek F, Naef F, Moniatte M, Deplancke B. Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nat Methods 2013; 10:570-6. [PMID: 23584187 DOI: 10.1038/nmeth.2441] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 03/14/2013] [Indexed: 02/06/2023]
Abstract
The cellular abundance of transcription factors (TFs) is an important determinant of their regulatory activities. Deriving TF copy numbers is therefore crucial to understanding how these proteins control gene expression. We describe a sensitive selected reaction monitoring-based mass spectrometry assay that allowed us to determine the copy numbers of up to ten proteins simultaneously. We applied this approach to profile the absolute levels of key TFs, including PPARγ and RXRα, during terminal differentiation of mouse 3T3-L1 pre-adipocytes. Our analyses revealed that individual TF abundance differs dramatically (from ∼250 to >300,000 copies per nucleus) and that their dynamic range during differentiation can vary up to fivefold. We also formulated a DNA binding model for PPARγ based on TF copy number, binding energetics and local chromatin state. This model explains the increase in PPARγ binding sites during the final differentiation stage that occurs despite a concurrent saturation in PPARγ copy number.
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Affiliation(s)
- Jovan Simicevic
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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200
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Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 979] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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