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Teunissen CE, Kimble L, Bayoumy S, Bolsewig K, Burtscher F, Coppens S, Das S, Gogishvili D, Fernandes Gomes B, Gómez de San José N, Mavrina E, Meda FJ, Mohaupt P, Mravinacová S, Waury K, Wojdała AL, Abeln S, Chiasserini D, Hirtz C, Gaetani L, Vermunt L, Bellomo G, Halbgebauer S, Lehmann S, Månberg A, Nilsson P, Otto M, Vanmechelen E, Verberk IMW, Willemse E, Zetterberg H. Methods to Discover and Validate Biofluid-Based Biomarkers in Neurodegenerative Dementias. Mol Cell Proteomics 2023; 22:100629. [PMID: 37557955 PMCID: PMC10594029 DOI: 10.1016/j.mcpro.2023.100629] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023] Open
Abstract
Neurodegenerative dementias are progressive diseases that cause neuronal network breakdown in different brain regions often because of accumulation of misfolded proteins in the brain extracellular matrix, such as amyloids or inside neurons or other cell types of the brain. Several diagnostic protein biomarkers in body fluids are being used and implemented, such as for Alzheimer's disease. However, there is still a lack of biomarkers for co-pathologies and other causes of dementia. Such biofluid-based biomarkers enable precision medicine approaches for diagnosis and treatment, allow to learn more about underlying disease processes, and facilitate the development of patient inclusion and evaluation tools in clinical trials. When designing studies to discover novel biofluid-based biomarkers, choice of technology is an important starting point. But there are so many technologies to choose among. To address this, we here review the technologies that are currently available in research settings and, in some cases, in clinical laboratory practice. This presents a form of lexicon on each technology addressing its use in research and clinics, its strengths and limitations, and a future perspective.
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Affiliation(s)
- Charlotte E Teunissen
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands.
| | - Leighann Kimble
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; KIN Center for Digital Innovation, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Sherif Bayoumy
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Katharina Bolsewig
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Felicia Burtscher
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Salomé Coppens
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; National Measurement Laboratory at LGC, Teddington, United Kingdom
| | - Shreyasee Das
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; ADx NeuroSciences, Gent, Belgium
| | - Dea Gogishvili
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Bárbara Fernandes Gomes
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Nerea Gómez de San José
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Neurology, University of Ulm, Ulm, Germany
| | - Ekaterina Mavrina
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; KIN Center for Digital Innovation, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Francisco J Meda
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Pablo Mohaupt
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; LBPC-PPC, IRMB CHU Montpellier, INM INSERM, Université de Montpellier, Montpellier, France
| | - Sára Mravinacová
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Katharina Waury
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Anna Lidia Wojdała
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Section of Neurology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Sanne Abeln
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Davide Chiasserini
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Section of Physiology and Biochemistry, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Christophe Hirtz
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; LBPC-PPC, IRMB CHU Montpellier, INM INSERM, Université de Montpellier, Montpellier, France
| | - Lorenzo Gaetani
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Section of Neurology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Lisa Vermunt
- Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Giovanni Bellomo
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Section of Neurology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Steffen Halbgebauer
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Neurology, University of Ulm, Ulm, Germany; German Center for Neurodegenerative Diseases (DZNE e.V.), Ulm, Germany
| | - Sylvain Lehmann
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; LBPC-PPC, IRMB CHU Montpellier, INM INSERM, Université de Montpellier, Montpellier, France
| | - Anna Månberg
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Peter Nilsson
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Markus Otto
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Neurology, University of Ulm, Ulm, Germany; Department of Neurology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Eugeen Vanmechelen
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; ADx NeuroSciences, Gent, Belgium
| | - Inge M W Verberk
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Eline Willemse
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Henrik Zetterberg
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden; Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK; Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China; Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Jia H, Dantuluri S, Margulies S, Smith V, Lever R, Allers T, Koh J, Chen S, Maupin-Furlow JA. RecJ3/4-aRNase J form a Ubl-associated nuclease complex functioning in survival against DNA damage in Haloferax volcanii. mBio 2023; 14:e0085223. [PMID: 37458473 PMCID: PMC10470531 DOI: 10.1128/mbio.00852-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/02/2023] [Indexed: 09/02/2023] Open
Abstract
Nucleases are strictly regulated and often localized in the cell to avoid the uncontrolled degradation of DNA and RNA. Here, a new type of nuclease complex, composed of RecJ3, RecJ4, and aRNase J, was identified through its ATP-dependent association with the ubiquitin-like SAMP1 and AAA-ATPase Cdc48a. The complex was discovered in Haloferax volcanii, an archaeon lacking an RNA exosome. Genetic analysis revealed aRNase J to be essential and RecJ3, RecJ4, and Cdc48a to function in the recovery from DNA damage including genotoxic agents that generate double-strand breaks. The RecJ3:RecJ4:aRNase J complex (isolated in 2:2:1 stoichiometry) functioned primarily as a 3'-5' exonuclease in hydrolyzing RNA and ssDNA, with the mechanism non-processive for ssDNA. aRNase J could also be purified as a homodimer that catalyzed endoribonuclease activity and, thus, was not restricted to the 5'-3' exonuclease activity typical of aRNase J homologs. Moreover, RecJ3 and RecJ4 could be purified as a 560-kDa subcomplex in equimolar subunit ratio with nuclease activities mirroring the full RecJ3/4-aRNase J complex. These findings prompted reconstitution assays that suggested RecJ3/4 could suppress, alter, and/or outcompete the nuclease activities of aRNase J. Based on the phenotypic results, this control mechanism of aRNase J by RecJ3/4 is not necessary for cell growth but instead appears important for DNA repair. IMPORTANCE Nucleases are critical for various cellular processes including DNA replication and repair. Here, a dynamic type of nuclease complex is newly identified in the archaeon Haloferax volcanii, which is missing the canonical RNA exosome. The complex, composed of RecJ3, RecJ4, and aRNase J, functions primarily as a 3'-5' exonuclease and was discovered through its ATP-dependent association with the ubiquitin-like SAMP1 and Cdc48a. aRNase J alone forms a homodimer that has endonuclease function and, thus, is not restricted to 5'-3' exonuclease activity typical of other aRNase J enzymes. RecJ3/4 appears to suppress, alter, and/or outcompete the nuclease activities of aRNase J. While aRNase J is essential for growth, RecJ3/4, Cdc48a, and SAMPs are important for recovery against DNA damage. These biological distinctions may correlate with the regulated nuclease activity of aRNase J in the RecJ3/4-aRNaseJ complex.
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Affiliation(s)
- Huiyong Jia
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Swathi Dantuluri
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Shae Margulies
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Victoria Smith
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Rebecca Lever
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Sixue Chen
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
- Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, Florida, USA
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
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3
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Révész Á, Hevér H, Steckel A, Schlosser G, Szabó D, Vékey K, Drahos L. Collision energies: Optimization strategies for bottom-up proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:1261-1299. [PMID: 34859467 DOI: 10.1002/mas.21763] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 06/07/2023]
Abstract
Mass-spectrometry coupled to liquid chromatography is an indispensable tool in the field of proteomics. In the last decades, more and more complex and diverse biochemical and biomedical questions have arisen. Problems to be solved involve protein identification, quantitative analysis, screening of low abundance modifications, handling matrix effect, and concentrations differing by orders of magnitude. This led the development of more tailored protocols and problem centered proteomics workflows, including advanced choice of experimental parameters. In the most widespread bottom-up approach, the choice of collision energy in tandem mass spectrometric experiments has outstanding role. This review presents the collision energy optimization strategies in the field of proteomics which can help fully exploit the potential of MS based proteomics techniques. A systematic collection of use case studies is then presented to serve as a starting point for related further scientific work. Finally, this article discusses the issue of comparing results from different studies or obtained on different instruments, and it gives some hints on methodology transfer between laboratories based on measurement of reference species.
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Affiliation(s)
- Ágnes Révész
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Helga Hevér
- Chemical Works of Gedeon Richter Plc, Budapest, Hungary
| | - Arnold Steckel
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gitta Schlosser
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dániel Szabó
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Károly Vékey
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
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4
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Maxwell CB, Sandhu JK, Cao TH, McCann GP, Ng LL, Jones DJL. The Edge Effect in High-Throughput Proteomics: A Cautionary Tale. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37155737 DOI: 10.1021/jasms.3c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In order for mass spectrometry to continue to grow as a platform for high-throughput clinical and translational research, careful consideration must be given to quality control by ensuring that the assay performs reproducibly and accurately and precisely. In particular, the throughput required for large cohort clinical validation in biomarker discovery and diagnostic screening has driven the growth of multiplexed targeted liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) assays paired with sample preparation and analysis in multiwell plates. However, large scale MS-based proteomics studies are often plagued by batch effects: sources of technical variation in the data, which can arise from a diverse array of sources such as sample preparation batches, different reagent lots, or indeed MS signal drift. These batch effects can confound the detection of true signal differences, resulting in incorrect conclusions being drawn about significant biological effects or lack thereof. Here, we present an intraplate batch effect termed the edge effect arising from temperature gradients in multiwell plates, commonly reported in preclinical cell culture studies but not yet reported in a clinical proteomics setting. We present methods herein to ameliorate the phenomenon including proper assessment of heating techniques for multiwell plates and incorporation of surrogate standards, which can normalize for intraplate variation.
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Affiliation(s)
- Colleen B Maxwell
- The Leicester van Geest MultiOmics Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Jatinderpal K Sandhu
- The Leicester van Geest MultiOmics Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Thong H Cao
- The Leicester van Geest MultiOmics Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Gerry P McCann
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Leong L Ng
- The Leicester van Geest MultiOmics Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Donald J L Jones
- The Leicester van Geest MultiOmics Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
- Leicester Cancer Research Centre, RKCSB, University of Leicester, Leicester LE2 7LX, United Kingdom
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5
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Huang J, Qi Y, Zeng X, Huang W, Chen D. Simultaneous quantification of plasma immunoglobulin subclasses for assessment of maternal and fetal immune response during pregnancy. J Chromatogr A 2022; 1673:463096. [DOI: 10.1016/j.chroma.2022.463096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/19/2022] [Accepted: 04/28/2022] [Indexed: 11/29/2022]
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Mohanty I, Moore SG, Biggs JS, Freeman CJ, Gaul DA, Garg N, Agarwal V. Stereochemical Assignment and Absolute Abundance of Nonproteinogenic Amino Acid Homoarginine in Marine Sponges. ACS OMEGA 2021; 6:33200-33205. [PMID: 34901671 PMCID: PMC8656204 DOI: 10.1021/acsomega.1c05685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/16/2021] [Indexed: 06/14/2023]
Abstract
Together with arginine, the nonproteinogenic amino acid homoarginine is a substrate for the production of vasodilator nitric oxide in the human body. In marine sponges, homoarginine has been postulated to serve as a precursor for the biosynthesis of pyrrole-imidazole alkaloid and bromotyrosine alkaloid classes of natural products. The absolute abundance of homoarginine, its abundance relative to arginine, and its stereochemical assignment in marine sponges are not known. Here, using stable isotope dilution mass spectrometry, we quantify the absolute abundances of homoarginine and arginine in marine sponges. We find that the abundance of homoarginine is highly variable and can far exceed the concentration of arginine, even in sponges where incorporation of homoarginine in natural products cannot be rationalized. The [homoarginine]/[arginine] ratio in marine sponges is greater than that in human analytes. By derivatization of sponge extracts with Marfey's reagent and comparison with authentic standards, we determine the l-isomer of homoarginine to be exclusively present in sponges. Our results shed light on the presence of the high abundance of homoarginine in marine sponge metabolomes and provide the foundation to investigate the biosynthetic routes and physiological roles of this nonproteinogenic amino acid in sponge physiology.
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Affiliation(s)
- Ipsita Mohanty
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Samuel G. Moore
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Jason S. Biggs
- University
of Guam Marine Laboratory, UOG Station, Mangilao, Guam 96923, United States
| | - Christopher J. Freeman
- Department
of Biology, College of Charleston, Charleston, South Carolina 29424, United States
- Smithsonian
Marine Station, Ft. Pierce, Florida 34949, United States
| | - David A. Gaul
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Neha Garg
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Vinayak Agarwal
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- School
of Biological Sciences, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
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7
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Wheeler JX, Thelwell C, Rigsby P, Whiting G. Quantitation of thrombin-activatable fibrinolysis inhibitor in human plasma by isotope dilution mass spectrometry. Anal Biochem 2021; 638:114413. [PMID: 34644544 DOI: 10.1016/j.ab.2021.114413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022]
Abstract
Measurement of Thrombin-activatable fibrinolysis inhibitor (TAFI) in human plasma is dependent on reproducible assays. To date, standards for measuring TAFI are frequently calibrated relative to pooled normal human plasma and arbitrarily assigned a potency of 100% TAFI, despite variation in TAFI concentrations between plasma pools. Alternatively, TAFI calibrators can be assigned a value in SI units but the approach used for value assignment is not consistent and furthermore, if purified TAFI is used to determine TAFI concentration in plasma, may be adversely affected by matrix effects. A TAFI plasma standard in mass units with traceability to the SI unit of mass is desirable. We report here the establishment of a quantitative mass spectrometry method for TAFI in plasma. Traceability is obtained by reference to calibrators that consist of blank plasma spiked with a defined amount of purified TAFI, value assigned by amino acid analysis. The calibrators are run alongside the samples, using the same preparation steps and conditions; an acetonitrile assisted tryptic digestion and multi-dimensional liquid chromatography (LC) separation followed by SRM-MS analysis. We measured the TAFI quantitatively in human plasma with reproducibility, reliability and precision, and demonstrated the applicability of this approach for value assigning a common reference standard.
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Affiliation(s)
- Jun X Wheeler
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, EN6 3QG, UK
| | - Craig Thelwell
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, EN6 3QG, UK
| | - Peter Rigsby
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, EN6 3QG, UK
| | - Gail Whiting
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, EN6 3QG, UK.
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8
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Recent advances in proteomics and its implications in pituitary endocrine disorders. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140700. [PMID: 34303023 DOI: 10.1016/j.bbapap.2021.140700] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 07/03/2021] [Accepted: 07/15/2021] [Indexed: 12/15/2022]
Abstract
Pituitary adenoma is considered as one of the most frequent intracranial tumors having salient impact on human health such as mass effects, hypopituitarism and visual defects etc. During the past few decades, there has been enormous advancement in mass spectrometry (MS)-based proteomics. However, very little is known about the molecular pathogenesis of pituitary adenomas in the context of proteomics. In this review article, we have focused on the provenance of pituitary tumors and their pathogenesis with the help of MS-based proteomics approaches. Recent advancements in quantitative proteomic approaches are outlined here that would be useful in the near pituitary adenoma proteomics research. This review discusses the enormous potential of pituitary adenomas research through proteomics with a common aim of deciphering disease pathobiology and identifying the work done in studying pituitary tumors during past decade.
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9
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Sá JDO, Trino LD, Oliveira AK, Lopes AFB, Granato DC, Normando AGC, Santos ES, Neves LX, Carnielli CM, Paes Leme AF. Proteomic approaches to assist in diagnosis and prognosis of oral cancer. Expert Rev Proteomics 2021; 18:261-284. [PMID: 33945368 DOI: 10.1080/14789450.2021.1924685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Oral squamous cell carcinoma (OSCC) ranks among the top 10 leading causes of cancer worldwide, with 5-year survival rate of about 50%, high lymph node metastasis, and relapse rates. The OSCC diagnosis, prognosis, and treatment are mostly based on the clinical TNM classification. There is an urgent need for the discovery of biomarkers and therapeutic targets to assist in the clinical decision-making process.Areas covered: We summarize proteomic studies of the OSCC tumor, immune microenvironment, potential liquid biopsy sites, and post-translational modifications trying to retrieve information in the discovery and verification or (pre)validation phases. The search strategy was based on the combination of MeSH terms and expert refinement.Expert opinion: Untargeted combined with targeted proteomics are strategies that provide reliable and reproducible quantitation of proteins and are the methods of choice of many groups worldwide. Undoubtedly, proteomics has been contributing to the understanding of OSCC progression and uncovers potential candidates as biomarker or therapeutic targets. Nevertheless, none of these targets are available in the clinical practice yet. The scientific community needs to overcome the limitations by investing in robust experimental designs to strengthen the value of the findings, leveraging the translation of knowledge, and further supporting clinical decisions.
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Affiliation(s)
- Jamile De Oliveira Sá
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil.,Departamento De Diagnóstico Oral, Faculdade De Odontologia De Piracicaba, Universidade Estadual De Campinas (UNICAMP), Piracicaba, Brazil
| | - Luciana Daniele Trino
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Ana Karina Oliveira
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Ariane Fidelis Busso Lopes
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Daniela Campos Granato
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Ana Gabriela Costa Normando
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil.,Departamento De Diagnóstico Oral, Faculdade De Odontologia De Piracicaba, Universidade Estadual De Campinas (UNICAMP), Piracicaba, Brazil
| | - Erison Santana Santos
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil.,Departamento De Diagnóstico Oral, Faculdade De Odontologia De Piracicaba, Universidade Estadual De Campinas (UNICAMP), Piracicaba, Brazil
| | - Leandro Xavier Neves
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Carolina Moretto Carnielli
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Adriana Franco Paes Leme
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
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10
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Bian J, Sze YH, Tse DYY, To CH, McFadden SA, Lam CSY, Li KK, Lam TC. SWATH Based Quantitative Proteomics Reveals Significant Lipid Metabolism in Early Myopic Guinea Pig Retina. Int J Mol Sci 2021; 22:4721. [PMID: 33946922 PMCID: PMC8124159 DOI: 10.3390/ijms22094721] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 12/14/2022] Open
Abstract
Most of the previous myopic animal studies employed a single-candidate approach and lower resolution proteomics approaches that were difficult to detect minor changes, and generated limited systems-wide biological information. Hence, a complete picture of molecular events in the retina involving myopic development is lacking. Here, to investigate comprehensive retinal protein alternations and underlying molecular events in the early myopic stage, we performed a data-independent Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) based proteomic analysis coupled with different bioinformatics tools in pigmented guinea pigs after 4-day lens-induced myopia (LIM). Myopic eyes compared to untreated contralateral control eyes caused significant changes in refractive error and choroid thickness (p < 0.05, n = 5). Relative elongation of axial length and the vitreous chamber depth were also observed. Using pooled samples from all individuals (n = 10) to build a species-specific retinal ion library for SWATH analysis, 3202 non-redundant proteins (with 24,616 peptides) were identified at 1% global FDR. For quantitative analysis, the 10 individual retinal samples (5 pairs) were analyzed using a high resolution Triple-TOF 6600 mass spectrometry (MS) with technical replicates. In total, 37 up-regulated and 21 down-regulated proteins were found significantly changed after LIM treatment (log2 ratio (T/C) > 0.26 or < -0.26; p ≤ 0.05). Data are accepted via ProteomeXchange with identifier PXD025003. Through Ingenuity Pathways Analysis (IPA), "lipid metabolism" was found as the top function associated with the differentially expressed proteins. Based on the protein abundance and peptide sequences, expression patterns of two regulated proteins (SLC6A6 and PTGES2) identified in this pathway were further successfully validated with high confidence (p < 0.05) using a novel Multiple Reaction Monitoring (MRM) assay on a QTRAP 6500+ MS. In summary, through an integrated discovery and targeted proteomic approach, this study serves as the first report to detect and confirm novel retinal protein changes and significant biological functions in the early LIM mammalian guinea pigs. The study provides new workflow and insights for further research to myopia control.
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Affiliation(s)
- Jingfang Bian
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Ying-Hon Sze
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Dennis Yan-Yin Tse
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - Chi-Ho To
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - Sally A. McFadden
- School of Psychology, College of Engineering, Science and the Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Carly Siu-Yin Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - King-Kit Li
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Thomas Chuen Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen 518052, China
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11
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Révész Á, Milley MG, Nagy K, Szabó D, Kalló G, Csősz É, Vékey K, Drahos L. Tailoring to Search Engines: Bottom-Up Proteomics with Collision Energies Optimized for Identification Confidence. J Proteome Res 2020; 20:474-484. [PMID: 33284634 PMCID: PMC7786379 DOI: 10.1021/acs.jproteome.0c00518] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Bottom-up
proteomics relies on identification of peptides from
tandem mass spectra, usually via matching against sequence databases.
Confidence in a peptide–spectrum match can be characterized
by a score value given by the database search engines, and it depends
on the information content and the quality of the spectrum. The latter
are influenced by experimental parameters, of which the collision
energy is the most important one in the case of collision-induced
dissociation. We examined how the identification score of the Byonic
and Andromeda (MaxQuant) engines varies with collision energy for
more than a thousand individual peptides from a HeLa tryptic digest
on a QTof instrument. We thereby extended our earlier study on Mascot
scores and corroborated its findings on the potential bimodal nature
of this energy dependence. Optimal energies as a function of m/z show comparable linear trends for the
three engines. On the basis of peptide-level results, we designed
methods with one or two liquid chromatography–tandem mass spectrometry
(LC-MS/MS) runs and various collision energy settings and assessed
their practical performance in peptide and protein identification
from the HeLa standard sample. A 10–40% gain in various measures,
such as the number of identified proteins or sequence coverage, was
obtained over the factory default settings. Best performing methods
differ for the three engines, suggesting that the experimental parameters
should be fine-tuned to the choice of the engine. We also recommend
a simple approach and provide reference data to ease the transfer
of the optimized methods to other mass spectrometers relevant for
proteomics. We demonstrate the utility of this approach on an Orbitrap
instrument. Data sets can be accessed via the MassIVE repository (MSV000086379).
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Affiliation(s)
- Ágnes Révész
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - Márton Gyula Milley
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - Kinga Nagy
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - Dániel Szabó
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary.,Faculty of Science, Institute of Chemistry, Hevesy György PhD School of Chemistry, ELTE, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Gergő Kalló
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Éva Csősz
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Károly Vékey
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
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12
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Han Y, Cheng L, Sun W. Analysis of Protein-Protein Interaction Networks through Computational Approaches. Protein Pept Lett 2020; 27:265-278. [PMID: 31692419 DOI: 10.2174/0929866526666191105142034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/08/2019] [Accepted: 09/26/2019] [Indexed: 01/02/2023]
Abstract
The interactions among proteins and genes are extremely important for cellular functions. Molecular interactions at protein or gene levels can be used to construct interaction networks in which the interacting species are categorized based on direct interactions or functional similarities. Compared with the limited experimental techniques, various computational tools make it possible to analyze, filter, and combine the interaction data to get comprehensive information about the biological pathways. By the efficient way of integrating experimental findings in discovering PPIs and computational techniques for prediction, the researchers have been able to gain many valuable data on PPIs, including some advanced databases. Moreover, many useful tools and visualization programs enable the researchers to establish, annotate, and analyze biological networks. We here review and list the computational methods, databases, and tools for protein-protein interaction prediction.
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Affiliation(s)
- Ying Han
- Cardiovascular Department, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Weiju Sun
- Cardiovascular Department, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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13
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Challenges and Opportunities in Clinical Applications of Blood-Based Proteomics in Cancer. Cancers (Basel) 2020; 12:cancers12092428. [PMID: 32867043 PMCID: PMC7564506 DOI: 10.3390/cancers12092428] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The traditional approach in identifying cancer related protein biomarkers has focused on evaluation of a single peptide/protein in tissue or circulation. At best, this approach has had limited success for clinical applications, since multiple pathological tumor pathways may be involved during initiation or progression of cancer which diminishes the significance of a single candidate protein/peptide. Emerging sensitive proteomic based technologies like liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics can provide a platform for evaluating serial serum or plasma samples to interrogate secreted products of tumor–host interactions, thereby revealing a more “complete” repertoire of biological variables encompassing heterogeneous tumor biology. However, several challenges need to be met for successful application of serum/plasma based proteomics. These include uniform pre-analyte processing of specimens, sensitive and specific proteomic analytical platforms and adequate attention to study design during discovery phase followed by validation of discovery-level signatures for prognostic, predictive, and diagnostic cancer biomarker applications. Abstract Blood is a readily accessible biofluid containing a plethora of important proteins, nucleic acids, and metabolites that can be used as clinical diagnostic tools in diseases, including cancer. Like the on-going efforts for cancer biomarker discovery using the liquid biopsy detection of circulating cell-free and cell-based tumor nucleic acids, the circulatory proteome has been underexplored for clinical cancer biomarker applications. A comprehensive proteome analysis of human serum/plasma with high-quality data and compelling interpretation can potentially provide opportunities for understanding disease mechanisms, although several challenges will have to be met. Serum/plasma proteome biomarkers are present in very low abundance, and there is high complexity involved due to the heterogeneity of cancers, for which there is a compelling need to develop sensitive and specific proteomic technologies and analytical platforms. To date, liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics has been a dominant analytical workflow to discover new potential cancer biomarkers in serum/plasma. This review will summarize the opportunities of serum proteomics for clinical applications; the challenges in the discovery of novel biomarkers in serum/plasma; and current proteomic strategies in cancer research for the application of serum/plasma proteomics for clinical prognostic, predictive, and diagnostic applications, as well as for monitoring minimal residual disease after treatments. We will highlight some of the recent advances in MS-based proteomics technologies with appropriate sample collection, processing uniformity, study design, and data analysis, focusing on how these integrated workflows can identify novel potential cancer biomarkers for clinical applications.
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14
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Leuchsenring AB, Karlsson C, Bundgaard L, Malmström J, Heegaard PMH. Targeted mass spectrometry for Serum Amyloid A (SAA) isoform profiling in sequential blood samples from experimentally Staphylococcus aureus infected pigs. J Proteomics 2020; 227:103904. [PMID: 32702520 DOI: 10.1016/j.jprot.2020.103904] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/19/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022]
Abstract
Serum amyloid A (SAA) is a well-described acute phase protein induced during the acute phase response (APR) to infection. Four isoform specific genes are found in most mammals. Depending on species, SAA3 and SAA4 are generally preferentially expressed extrahepatically whereas SAA1 and SAA2 are hepatic isoforms dominating the SAA serum pool. Little is known about how specific infections affect the serum SAA isoform profile, as SAA isoform discriminating antibodies are not generally available. An antibody independent, quantitative targeted MS method (Selected Reaction Monitoring, SRM) based on available information on porcine SAA isoform genes was developed and used to profile SAA in serum samples from pigs experimentally infected with Staphylococcus aureus (Sa). While results suggest SAA2 as the main circulating porcine SAA isoform, induced around 10 times compared to non-infected controls, total SAA serum concentrations reached only around 4 μg/mL, much lower than established previously by immunoassays. This might suggest that SAA isoform variants not detected by the SRM method might be present in porcine serum. The assay allows monitoring host responses to experimental infections, infectious diseases and inflammation states in the pig at an unprecedented level of detail. It can also be used in a non-calibrated (relative quantification) format. SIGNIFICANCE: We developed an SRM MS method which for the first time allowed the specific quantification of each of the circulating porcine SAA isoforms (SAA2, SAA3, SAA4). It was found that SAA2 is the dominating circulating isoform of SAA in the pig and that, during the acute phase response to Sa infection SAA2, SAA3 and SAA4 are induced approx. 10, 15 and 2 times, respectively. Absolute levels of the isoforms as determined by SRM MS were much lower than reported previously for total SAA quantified by immunosassays, suggesting the existence of hitherto non-described SAA variants. SRM MS holds great promise for the study of the basic biology of SAA isoforms with the potential to study an even broader range of SAA variants.
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Affiliation(s)
- Anna Barslund Leuchsenring
- Department of Biotechnology and Biomedicine, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Christofer Karlsson
- Department of Clinical Sciences, Lund, Division of Infection Medicine, Lund University, BMC, Lund, Sweden
| | - Louise Bundgaard
- Department of Biotechnology and Biomedicine, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Johan Malmström
- Department of Clinical Sciences, Lund, Division of Infection Medicine, Lund University, BMC, Lund, Sweden
| | - Peter M H Heegaard
- Department of Biotechnology and Biomedicine, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark.
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15
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Unraveling the Composition of Insecticidal Crystal Proteins in Bacillus thuringiensis: a Proteomics Approach. Appl Environ Microbiol 2020; 86:AEM.00476-20. [PMID: 32276971 DOI: 10.1128/aem.00476-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/23/2020] [Indexed: 01/04/2023] Open
Abstract
Bacillus thuringiensis (Bt) is the most widely used active ingredient for biological insecticides. The composition of δ-endotoxins (Cry and Cyt proteins) in the parasporal crystal determines the toxicity profile of each Bt strain. However, a reliable method for their identification and quantification has not been available, due to the high sequence identity of the genes that encode the δ-endotoxins and the toxins themselves. Here, we have developed an accurate and reproducible mass spectrometry-based method (liquid chromatography-tandem mass spectrometry-multiple reaction monitoring [LC-MS/MS-MRM]) using isotopically labeled proteotypic peptides for each protein in a particular mixture to determine the relative proportion of each δ-endotoxin within the crystal. To validate the method, artificial mixtures containing Cry1Aa, Cry2Aa, and Cry6Aa were analyzed. Determination of the relative abundance of proteins (in molarity) with our method was in good agreement with the expected values. This method was then applied to the most common commercial Bt-based products, DiPel DF, XenTari GD, VectoBac 12S, and Novodor, in which between three and six δ-endotoxins were identified and quantified in each product. This novel approach is of great value for the characterization of Bt-based products, not only providing information on host range, but also for monitoring industrial crystal production and quality control and product registration for Bt-based insecticides.IMPORTANCE Bacillus thuringiensis (Bt)-based biological insecticides are used extensively to control insect pests and vectors of human diseases. Bt-based products provide greater specificity and biosafety than broad-spectrum synthetic insecticides. The biological activity of this bacterium resides in spores and crystals comprising complex mixtures of toxic proteins. We developed and validated a fast, accurate, and reproducible method for quantitative determination of the crystal components of Bt-based products. This method will find clear applications in the improvement of various aspects of the industrial production process of Bt. An important aspect of the production of Bt-based insecticides is its quality control. By specifically quantifying the relative proportion of each of the toxins that make up the crystal, our method represents the most consistent and repeatable evaluation procedure in the quality control of different batches produced in successive fermentations. This method can also contribute to the design of specific culture media and fermentation conditions that optimize Bt crystal composition across a range of Bt strains that target different pestiferous insects. Quantitative information on crystal composition should also prove valuable to phytosanitary product registration authorities that oversee the safety and efficacy of crop protection products.
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16
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Trötschel C, Hamzeh H, Alvarez L, Pascal R, Lavryk F, Bönigk W, Körschen HG, Müller A, Poetsch A, Rennhack A, Gui L, Nicastro D, Strünker T, Seifert R, Kaupp UB. Absolute proteomic quantification reveals design principles of sperm flagellar chemosensation. EMBO J 2020; 39:e102723. [PMID: 31880004 PMCID: PMC7024835 DOI: 10.15252/embj.2019102723] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 11/19/2022] Open
Abstract
Cilia serve as cellular antennae that translate sensory information into physiological responses. In the sperm flagellum, a single chemoattractant molecule can trigger a Ca2+ rise that controls motility. The mechanisms underlying such ultra-sensitivity are ill-defined. Here, we determine by mass spectrometry the copy number of nineteen chemosensory signaling proteins in sperm flagella from the sea urchin Arbacia punctulata. Proteins are up to 1,000-fold more abundant than the free cellular messengers cAMP, cGMP, H+ , and Ca2+ . Opto-chemical techniques show that high protein concentrations kinetically compartmentalize the flagellum: Within milliseconds, cGMP is relayed from the receptor guanylate cyclase to a cGMP-gated channel that serves as a perfect chemo-electrical transducer. cGMP is rapidly hydrolyzed, possibly via "substrate channeling" from the channel to the phosphodiesterase PDE5. The channel/PDE5 tandem encodes cGMP turnover rates rather than concentrations. The rate-detection mechanism allows continuous stimulus sampling over a wide dynamic range. The textbook notion of signal amplification-few enzyme molecules process many messenger molecules-does not hold for sperm flagella. Instead, high protein concentrations ascertain messenger detection. Similar mechanisms may occur in other small compartments like primary cilia or dendritic spines.
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Affiliation(s)
- Christian Trötschel
- Fakultät für Biologie und BiotechnologieRuhr‐Universität BochumBochumGermany
| | - Hussein Hamzeh
- Center of Advanced European Studies and Research (caesar), Molecular Sensory SystemsBonnGermany
- Marine Biological LaboratoryWoods HoleMAUSA
| | - Luis Alvarez
- Center of Advanced European Studies and Research (caesar), Molecular Sensory SystemsBonnGermany
| | - René Pascal
- Center of Advanced European Studies and Research (caesar), Molecular Sensory SystemsBonnGermany
| | - Fedir Lavryk
- Center of Advanced European Studies and Research (caesar), Molecular Sensory SystemsBonnGermany
| | - Wolfgang Bönigk
- Center of Advanced European Studies and Research (caesar), Molecular Sensory SystemsBonnGermany
| | - Heinz G Körschen
- Center of Advanced European Studies and Research (caesar), Molecular Sensory SystemsBonnGermany
| | - Astrid Müller
- Center of Advanced European Studies and Research (caesar), Molecular Sensory SystemsBonnGermany
| | - Ansgar Poetsch
- Fakultät für Biologie und BiotechnologieRuhr‐Universität BochumBochumGermany
- Present address:
Center for Marine and Molecular BiotechnologyQNLMQindaoChina
- Present address:
College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Andreas Rennhack
- Center of Advanced European Studies and Research (caesar), Molecular Sensory SystemsBonnGermany
| | - Long Gui
- Departments of Cell Biology and BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Daniela Nicastro
- Departments of Cell Biology and BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Timo Strünker
- Center of Advanced European Studies and Research (caesar), Molecular Sensory SystemsBonnGermany
- Marine Biological LaboratoryWoods HoleMAUSA
- Center of Reproductive Medicine and AndrologyUniversity Hospital MünsterMünsterGermany
| | - Reinhard Seifert
- Center of Advanced European Studies and Research (caesar), Molecular Sensory SystemsBonnGermany
- Marine Biological LaboratoryWoods HoleMAUSA
| | - U Benjamin Kaupp
- Center of Advanced European Studies and Research (caesar), Molecular Sensory SystemsBonnGermany
- Marine Biological LaboratoryWoods HoleMAUSA
- Life& Medical Sciences Institute (LIMES)University of BonnBonnGermany
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17
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Quantitative mass spectrometry-based proteomics in the era of model-informed drug development: Applications in translational pharmacology and recommendations for best practice. Pharmacol Ther 2019; 203:107397. [DOI: 10.1016/j.pharmthera.2019.107397] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/29/2019] [Indexed: 02/08/2023]
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18
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Relative quantitation of endogenous proteins by quadrupole-time of flight and tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1106-1107:11-18. [PMID: 30615973 DOI: 10.1016/j.jchromb.2018.12.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 11/23/2018] [Accepted: 12/16/2018] [Indexed: 01/17/2023]
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19
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Woods AG, Sokolowska I, Ngounou Wetie AG, Channaveerappa D, Dupree EJ, Jayathirtha M, Aslebagh R, Wormwood KL, Darie CC. Mass Spectrometry for Proteomics-Based Investigation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:1-26. [DOI: 10.1007/978-3-030-15950-4_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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Révész Á, Rokob TA, Jeanne Dit Fouque D, Turiák L, Memboeuf A, Vékey K, Drahos L. Selection of Collision Energies in Proteomics Mass Spectrometry Experiments for Best Peptide Identification: Study of Mascot Score Energy Dependence Reveals Double Optimum. J Proteome Res 2018; 17:1898-1906. [PMID: 29607649 DOI: 10.1021/acs.jproteome.7b00912] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Collision energy is a key parameter determining the information content of beam-type collision induced dissociation tandem mass spectrometry (MS/MS) spectra, and its optimal choice largely affects successful peptide and protein identification in MS-based proteomics. For an MS/MS spectrum, quality of peptide match based on sequence database search, often characterized in terms of a single score, is a complex function of spectrum characteristics, and its collision energy dependence has remained largely unexplored. We carried out electrospray ionization-quadrupole-time of flight (ESI-Q-TOF)-MS/MS measurements on 2807 peptides from tryptic digests of HeLa and E. coli at 21 different collision energies. Agglomerative clustering of the resulting Mascot score versus energy curves revealed that only few of them display a single, well-defined maximum; rather, they feature either a broad plateau or two clear peaks. Nonlinear least-squares fitting of one or two Gaussian functions allowed the characteristic energies to be determined. We found that the double peaks and the plateaus in Mascot score can be associated with the different energy dependence of b- and y-type fragment ion intensities. We determined that the energies for optimum Mascot scores follow separate linear trends for the unimodal and bimodal cases with rather large residual variance even after differences in proton mobility are taken into account. This leaves room for experiment optimization and points to the possible influence of further factors beyond m/ z.
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Affiliation(s)
| | | | - Dany Jeanne Dit Fouque
- UMR CNRS 6521, CEMCA , Université de Bretagne Occidentale , 6 Av. Le Gorgeu , 29238 Brest Cedex 3 , France
| | | | - Antony Memboeuf
- UMR CNRS 6521, CEMCA , Université de Bretagne Occidentale , 6 Av. Le Gorgeu , 29238 Brest Cedex 3 , France
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21
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Integrated SWATH-based and targeted-based proteomics provide insights into the retinal emmetropization process in guinea pig. J Proteomics 2018; 181:1-15. [PMID: 29572162 DOI: 10.1016/j.jprot.2018.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 03/12/2018] [Accepted: 03/19/2018] [Indexed: 01/13/2023]
Abstract
Myopia is generally regarded as a failure of normal emmetropization process, however, its underlying molecular mechanisms are unclear. To investigate the retinal protein profile changes during emmetropization, we studied differential protein expressions of ocular growth in young guinea pigs at 3 and 21 days old respectively, when significant axial elongation was detected (P < 0.001, n = 10). Independent pooled retinal samples of both eyes were subjected to SWATH mass spectrometry (MS) followed by bioinformatics analysis using cloud-based platforms. A comprehensive retina SWATH ion-library consisting of 3138 (22,871) unique proteins (peptides) at 1% FDR was constructed. 40 proteins were found to be significantly up-regulated and 8 proteins down-regulated during emmetropization (≥log2 of 0.43 with ≥2 peptides matched per protein; P < 0.05). Using pathway analysis, the most significant pathway identifiable was 'phototransduction' (P = 1.412e-4). Expression patterns of 7 proteins identified in this pathway were further validated and confirmed (P < 0.05) with high-resolution Multiple Reaction Monitoring (MRM-HR) MS. Combining discovery and targeted proteomics approaches, this study for the first time comprehensively profiled protein changes in the guinea pig retina during normal emmetropization-associated eye growth. The findings of this study are also relevant to the myopia development, which is the result of failed emmetropization. SIGNIFICANCE Myopia is considered as a failure of emmetropization. However, the underlying biochemical mechanism of emmetropization, a visually guided process in which eye grows towards the optimal optical state of clear vision during early development, is not well understood. Retina is known as the key tissue to regulate this active eye growth. we studied eye growth of young guinea pigs and harvested their retinal tissues. A comprehensive SWATH ion library with identification of a total 3138 unique proteins were established, in which 48 proteins exhibited significant differential expressions between 3 and 21 days old. After MRM-HR confirmation, 'phototransduction' were found as the most active pathway during emmetropic eye growth. This study is the first in discovering key retinal protein players and pathways which are presumably orchestrated by biological mechanism(s) underlying emmetropization.
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22
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Lanucara F, Lam C, Mann J, Monie TP, Colombo SAP, Holman SW, Boyd J, Dange MC, Mann DA, White MRH, Eyers CE. Dynamic phosphorylation of RelA on Ser42 and Ser45 in response to TNFα stimulation regulates DNA binding and transcription. Open Biol 2017; 6:rsob.160055. [PMID: 27466442 PMCID: PMC4967822 DOI: 10.1098/rsob.160055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 07/01/2016] [Indexed: 12/14/2022] Open
Abstract
The NF-κB signalling module controls transcription through a network of protein kinases such as the IKKs, as well as inhibitory proteins (IκBs) and transcription factors including RelA/p65. Phosphorylation of the NF-κB subunits is critical for dictating system dynamics. Using both non-targeted discovery and quantitative selected reaction monitoring-targeted proteomics, we show that the cytokine TNFα induces dynamic multisite phosphorylation of RelA at a number of previously unidentified residues. Putative roles for many of these phosphorylation sites on RelA were predicted by modelling of various crystal structures. Stoichiometry of phosphorylation determination of Ser45 and Ser42 revealed preferential early phosphorylation of Ser45 in response to TNFα. Quantitative analyses subsequently confirmed differential roles for pSer42 and pSer45 in promoter-specific DNA binding and a role for both of these phosphosites in regulating transcription from the IL-6 promoter. These temporal dynamics suggest that RelA-mediated transcription is likely to be controlled by functionally distinct NF-κB proteoforms carrying different combinations of modifications, rather than a simple ‘one modification, one effect’ system.
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Affiliation(s)
- Francesco Lanucara
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Connie Lam
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Jelena Mann
- Fibrosis Laboratory, Liver Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Tom P Monie
- MRC Human Nutrition Research, University of Cambridge, Cambridge CB2 1GA, UK
| | - Stefano A P Colombo
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Stephen W Holman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - James Boyd
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Manohar C Dange
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Derek A Mann
- Fibrosis Laboratory, Liver Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Michael R H White
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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23
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Development of a UHPLC-MS/MS (SRM) method for the quantitation of endogenous glucagon and dosed GLP-1 from human plasma. Bioanalysis 2017; 9:733-751. [PMID: 28488894 DOI: 10.4155/bio-2017-0021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
AIM The performance of glucagon and GLP-1 immunoassays is often poor, but few sensitive LC-MS/MS methods exist as alternatives. EXPERIMENTAL A multiplexed LC-MS/MS method using a 2D extraction technique was developed. RESULTS The method was established for the quantitation of endogenous glucagon (LLOQ: 15 pg/ml) and dosed GLP-1 (LLOQ: 25 pg/ml) in human plasma, and is the first such method avoiding immunoenrichment. Specificity of endogenous glucagon quantitation was assured using a novel approach with a supercharging mobile phase additive to access a sensitive qualifier SRM. Endogenous glucagon concentrations were within the expected range, and showed good reproducibility after extended sample storage. A cross-validation against established immunoassays using physiological study samples demonstrated some similarities between methods. CONCLUSION The LC-MS/MS method offers a viable alternative to immunoassays for quantitation of endogenous glucagon, dosed glucagon and/or dosed GLP-1.
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24
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Bennett RJ, Simpson DM, Holman SW, Ryan S, Brownridge P, Eyers CE, Colyer J, Beynon RJ. DOSCATs: Double standards for protein quantification. Sci Rep 2017; 7:45570. [PMID: 28368040 PMCID: PMC5377311 DOI: 10.1038/srep45570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/27/2017] [Indexed: 12/12/2022] Open
Abstract
The two most common techniques for absolute protein quantification are based on either mass spectrometry (MS) or on immunochemical techniques, such as western blotting (WB). Western blotting is most often used for protein identification or relative quantification, but can also be deployed for absolute quantification if appropriate calibration standards are used. MS based techniques offer superior data quality and reproducibility, but WB offers greater sensitivity and accessibility to most researchers. It would be advantageous to apply both techniques for orthogonal quantification, but workflows rarely overlap. We describe DOSCATs (DOuble Standard conCATamers), novel calibration standards based on QconCAT technology, to unite these platforms. DOSCATs combine a series of epitope sequences concatenated with tryptic peptides in a single artificial protein to create internal tryptic peptide standards for MS as well as an intact protein bearing multiple linear epitopes. A DOSCAT protein was designed and constructed to quantify five proteins of the NF-κB pathway. For three target proteins, protein fold change and absolute copy per cell values measured by MS and WB were in excellent agreement. This demonstrates that DOSCATs can be used as multiplexed, dual purpose standards, readily deployed in a single workflow, supporting seamless quantitative transition from MS to WB.
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Affiliation(s)
- Richard J Bennett
- Centre for Proteome Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
| | - Deborah M Simpson
- Centre for Proteome Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
| | - Stephen W Holman
- Centre for Proteome Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
| | - Sheila Ryan
- Institute of Ageing and Chronic Disease, The Apex Building, 6 West Derby St., Liverpool L7 8TX, UK
| | - Philip Brownridge
- Centre for Proteome Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
| | - Claire E Eyers
- Centre for Proteome Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
| | - John Colyer
- Badrilla Ltd. Leeds Innovation Centre, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Liverpool L69 7ZB, UK
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25
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Pottiez G, Yang L, Stewart T, Song N, Aro P, Galasko DR, Quinn JF, Peskind ER, Shi M, Zhang J. Mass-Spectrometry-Based Method To Quantify in Parallel Tau and Amyloid β 1-42 in CSF for the Diagnosis of Alzheimer's Disease. J Proteome Res 2017; 16:1228-1238. [PMID: 28112948 DOI: 10.1021/acs.jproteome.6b00829] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alzheimer's disease (AD), the most common form of dementia, afflicts about 50 million people worldwide. Currently, AD diagnosis is primarily based on psychological evaluation and can only be confirmed post-mortem. Reliable and objective biomarkers for prognosis and diagnosis have been sought for years. Together, tau and amyloid β 1-42 (Aβ42) in cerebrospinal fluid (CSF) have been shown to provide good diagnostic sensitivity and specificity. Additionally, phosphorylated forms of tau, such as tau pS181, have also shown promising results. However, the measurement of such markers currently relies on antibody-based immunoassays that have shown variability, leading to discrepant results across laboratories. To date, mass spectrometry methods developed to evaluate CSF tau and Aβ42 are not compatible. We present in this article the development of a mass-spectrometry-based method of quantification for CSF tau and Aβ42 in parallel. The absolute concentrations of tau and Aβ42 we measured are on average 50 ng/mL (7-130 ng/mL) and 7.1 ng/mL (3-13 ng/mL), respectively. Analyses of CSF tau and Aβ42, in a cohort of patients with AD, mild cognitive impairment, and healthy controls (30 subjects), provide significant group differences evaluated with ROC curves (AUC(control-AD) and AUC(control-MCI) = 1, AUC(MCI-AD) = 0.76), with at least equivalent diagnostic utility to immunoassay measurements in the same sample set. Finally, a significant and negative correlation was found between the tau and Aβ peptides ratio and the disease severity.
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Affiliation(s)
- Gwënaël Pottiez
- Department of Pathology, School of Medicine, University of Washington , Seattle, Washington 98104, United States
| | - Li Yang
- Department of Pathology, School of Medicine, University of Washington , Seattle, Washington 98104, United States
| | - Tessandra Stewart
- Department of Pathology, School of Medicine, University of Washington , Seattle, Washington 98104, United States
| | - Ning Song
- Department of Pathology, School of Medicine, University of Washington , Seattle, Washington 98104, United States
| | - Patrick Aro
- Department of Pathology, School of Medicine, University of Washington , Seattle, Washington 98104, United States
| | - Douglas R Galasko
- Department of Neurosciences, University of California at San Diego , San Diego, California 92093, United States
| | - Joseph F Quinn
- Department of Neurology, Oregon Health and Science University , Portland, Oregon 97239, United States.,Portland VA Medical Center , Portland, Oregon 97239, United States
| | - Elaine R Peskind
- Northwest Network VISN-20 Mental Illness Research, Education, and Clinical Center, VA Puget Sound Health Care System , Seattle, Washington 98108, United States.,Department of Psychiatry and Behavioral Sciences, University of Washington , Seattle, Washington 98195, United States
| | - Min Shi
- Department of Pathology, School of Medicine, University of Washington , Seattle, Washington 98104, United States
| | - Jing Zhang
- Department of Pathology, School of Medicine, University of Washington , Seattle, Washington 98104, United States.,Department of Pathology, Peking University Health Science Centre and Third Hospital , Beijing 100083, China
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26
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Peggion C, Massimino ML, Biancotto G, Angeletti R, Reggiani C, Sorgato MC, Bertoli A, Stella R. Absolute quantification of myosin heavy chain isoforms by selected reaction monitoring can underscore skeletal muscle changes in a mouse model of amyotrophic lateral sclerosis. Anal Bioanal Chem 2017; 409:2143-2153. [PMID: 28078418 DOI: 10.1007/s00216-016-0160-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/05/2016] [Accepted: 12/15/2016] [Indexed: 01/08/2023]
Abstract
Skeletal muscle fibers contain different isoforms of myosin heavy chain (MyHC) that define distinctive contractile properties. In light of the muscle capacity to adapt MyHC expression to pathophysiological conditions, a rapid and quantitative assessment of MyHC isoforms in small muscle tissue quantities would represent a valuable diagnostic tool for (neuro)muscular diseases. As past protocols did not meet these requirements, in the present study we applied a targeted proteomic approach based on selected reaction monitoring that allowed the absolute quantification of slow and fast MyHC isoforms in different mouse skeletal muscles with high reproducibility. This mass-spectrometry-based method was validated also in a pathological specimen, by comparison of the MyHC expression profiles in different muscles from healthy mice and a genetic mouse model of amyotrophic lateral sclerosis (ALS) expressing the SOD1(G93A) mutant. This analysis showed that terminally ill ALS mice have a fast-to-slow shift in the fiber type composition of the tibialis anterior and gastrocnemius muscles, as previously reported. These results will likely open the way to accurate and rapid diagnoses of human (neuro)muscular diseases by the proposed method. Graphical Abstract Methods for myosin heavy chain (MyHC) quantification: a comparison of classical methods and selected reaction monitoring (SRM)-based mass spectrometry approaches.
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Affiliation(s)
- Caterina Peggion
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, 35131, Padua, PD, Italy
| | - Maria Lina Massimino
- CNR Neuroscience Institute, University of Padua, Via Ugo Bassi 58/B, 35131, Padua, PD, Italy
| | - Giancarlo Biancotto
- Department of Chemistry, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università, 10, 35020, Legnaro, PD, Italy
| | - Roberto Angeletti
- Department of Chemistry, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università, 10, 35020, Legnaro, PD, Italy
| | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, 35131, Padua, PD, Italy
| | - Maria Catia Sorgato
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, 35131, Padua, PD, Italy.,CNR Neuroscience Institute, University of Padua, Via Ugo Bassi 58/B, 35131, Padua, PD, Italy
| | - Alessandro Bertoli
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, 35131, Padua, PD, Italy.
| | - Roberto Stella
- Department of Chemistry, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università, 10, 35020, Legnaro, PD, Italy.
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27
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Holman SW, Hammond DE, Simpson DM, Waters J, Hurst JL, Beynon RJ. Protein turnover measurement using selected reaction monitoring-mass spectrometry (SRM-MS). PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0362. [PMID: 27644981 PMCID: PMC5031629 DOI: 10.1098/rsta.2015.0362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/23/2016] [Indexed: 05/28/2023]
Abstract
Protein turnover represents an important mechanism in the functioning of cells, with deregulated synthesis and degradation of proteins implicated in many diseased states. Therefore, proteomics strategies to measure turnover rates with high confidence are of vital importance to understanding many biological processes. In this study, the more widely used approach of non-targeted precursor ion signal intensity (MS1) quantification is compared with selected reaction monitoring (SRM), a data acquisition strategy that records data for specific peptides, to determine if improved quantitative data would be obtained using a targeted quantification approach. Using mouse liver as a model system, turnover measurement of four tricarboxylic acid cycle proteins was performed using both MS1 and SRM quantification strategies. SRM outperformed MS1 in terms of sensitivity and selectivity of measurement, allowing more confident determination of protein turnover rates. SRM data are acquired using cheaper and more widely available tandem quadrupole mass spectrometers, making the approach accessible to a larger number of researchers than MS1 quantification, which is best performed on high mass resolution instruments. SRM acquisition is ideally suited to focused studies where the turnover of tens of proteins is measured, making it applicable in determining the dynamics of proteins complexes and complete metabolic pathways.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Stephen W Holman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Dean E Hammond
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Deborah M Simpson
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - John Waters
- Mammalian Behaviour and Evolution Group, Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
| | - Jane L Hurst
- Mammalian Behaviour and Evolution Group, Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
| | - Robert J Beynon
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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28
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Stella R, Barrucci F, Angeletti R, James P, Montesissa C, Biancotto G. Targeted proteomics for the indirect detection of dexamethasone treatment in bovines. Anal Bioanal Chem 2016; 408:8343-8353. [DOI: 10.1007/s00216-016-9951-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/01/2016] [Accepted: 09/15/2016] [Indexed: 01/08/2023]
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29
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Jarnuczak AF, Lee DCH, Lawless C, Holman SW, Eyers CE, Hubbard SJ. Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics. J Proteome Res 2016; 15:2945-59. [PMID: 27454336 DOI: 10.1021/acs.jproteome.6b00048] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Quantitative mass spectrometry-based proteomics of complex biological samples remains challenging in part due to the variability and charge competition arising during electrospray ionization (ESI) of peptides and the subsequent transfer and detection of ions. These issues preclude direct quantification from signal intensity alone in the absence of a standard. A deeper understanding of the governing principles of peptide ionization and exploitation of the inherent ionization and detection parameters of individual peptides is thus of great value. Here, using the yeast proteome as a model system, we establish the concept of peptide F-factor as a measure of detectability, closely related to ionization efficiency. F-factor is calculated by normalizing peptide precursor ion intensity by absolute abundance of the parent protein. We investigated F-factor characteristics in different shotgun proteomics experiments, including across multiple ESI-based LC-MS platforms. We show that F-factors mirror previously observed physicochemical predictors as peptide detectability but demonstrate a nonlinear relationship between hydrophobicity and peptide detectability. Similarly, we use F-factors to show how peptide ion coelution adversely affects detectability and ionization. We suggest that F-factors have great utility for understanding peptide detectability and gas-phase ion chemistry in complex peptide mixtures, selection of surrogate peptides in targeted MS studies, and for calibration of peptide ion signal in label-free workflows. Data are available via ProteomeXchange with identifier PXD003472.
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Affiliation(s)
- Andrew F Jarnuczak
- Faculty of Biology, Medicine and Health, University of Manchester , Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Dave C H Lee
- Faculty of Biology, Medicine and Health, University of Manchester , Second Floor, Wolfson Molecular Imaging Centre, 27 Palatine Road, Withington, Manchester, M20 3JL, United Kingdom
| | - Craig Lawless
- Faculty of Biology, Medicine and Health, University of Manchester , Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Stephen W Holman
- Centre for Proteome Research, University of Liverpool , Department of Biochemistry, Institute of Integrative Biology, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Claire E Eyers
- Centre for Proteome Research, University of Liverpool , Department of Biochemistry, Institute of Integrative Biology, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Simon J Hubbard
- Faculty of Biology, Medicine and Health, University of Manchester , Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
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30
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Mackenzie RJ, Lawless C, Holman SW, Lanthaler K, Beynon RJ, Grant CM, Hubbard SJ, Eyers CE. Absolute protein quantification of the yeast chaperome under conditions of heat shock. Proteomics 2016; 16:2128-40. [PMID: 27252046 PMCID: PMC4996341 DOI: 10.1002/pmic.201500503] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 05/05/2016] [Accepted: 05/31/2016] [Indexed: 11/10/2022]
Abstract
Chaperones are fundamental to regulating the heat shock response, mediating protein recovery from thermal-induced misfolding and aggregation. Using the QconCAT strategy and selected reaction monitoring (SRM) for absolute protein quantification, we have determined copy per cell values for 49 key chaperones in Saccharomyces cerevisiae under conditions of normal growth and heat shock. This work extends a previous chemostat quantification study by including up to five Q-peptides per protein to improve confidence in protein quantification. In contrast to the global proteome profile of S. cerevisiae in response to heat shock, which remains largely unchanged as determined by label-free quantification, many of the chaperones are upregulated with an average two-fold increase in protein abundance. Interestingly, eight of the significantly upregulated chaperones are direct gene targets of heat shock transcription factor-1. By performing absolute quantification of chaperones under heat stress for the first time, we were able to evaluate the individual protein-level response. Furthermore, this SRM data was used to calibrate label-free quantification values for the proteome in absolute terms, thus improving relative quantification between the two conditions. This study significantly enhances the largely transcriptomic data available in the field and illustrates a more nuanced response at the protein level.
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Affiliation(s)
- Rebecca J Mackenzie
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK.,Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK
| | - Craig Lawless
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK
| | - Stephen W Holman
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK
| | - Karin Lanthaler
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK
| | - Chris M Grant
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK
| | - Simon J Hubbard
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK
| | - Claire E Eyers
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK
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31
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Streng AS, de Boer D, Bouwman FG, Mariman EC, Scholten A, van Dieijen-Visser MP, Wodzig WK. Development of a targeted selected ion monitoring assay for the elucidation of protease induced structural changes in cardiac troponin T. J Proteomics 2016; 136:123-32. [DOI: 10.1016/j.jprot.2015.12.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 12/08/2015] [Accepted: 12/29/2015] [Indexed: 12/14/2022]
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32
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Holman SW, McLean L, Eyers CE. RePLiCal: A QconCAT Protein for Retention Time Standardization in Proteomics Studies. J Proteome Res 2016; 15:1090-102. [PMID: 26775667 DOI: 10.1021/acs.jproteome.5b00988] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study introduces a new reversed-phase liquid chromatography retention time (RT) standard, RePLiCal (Reversed-phase liquid chromatography calibrant), produced using QconCAT technology. The synthetic protein contains 27 lysine-terminating calibrant peptides, meaning that the same complement of standards can be generated using either Lys-C or trypsin-based digestion protocols. RePLiCal was designed such that each constituent peptide is unique with respect to all eukaryotic proteomes, thereby enabling integration into a wide range of proteomic analyses. RePLiCal has been benchmarked against three commercially available peptide RT standard kits and outperforms all in terms of LC gradient coverage. RePLiCal also provides a higher number of calibrant points for chromatographic retention time standardization and normalization. The standard provides stable RTs over long analysis times and can be readily transferred between different LC gradients and nUHPLC instruments. Moreover, RePLiCal can be used to predict RTs for other peptides in a timely manner. Furthermore, it is shown that RePLiCal can be used effectively to evaluate trapping column performance for nUHPLC instruments using trap-elute configurations, to optimize gradients to maximize peptide and protein identification rates, and to recalibrate the m/z scale of mass spectrometry data post-acquisition.
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Affiliation(s)
- Stephen W Holman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Lynn McLean
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Crown Street, Liverpool L69 7ZB, United Kingdom
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33
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Rogniaux H, Pavlovic M, Lupi R, Lollier V, Joint M, Mameri H, Denery S, Larré C. Allergen relative abundance in several wheat varieties as revealed via a targeted quantitative approach using MS. Proteomics 2016; 15:1736-45. [PMID: 25764008 DOI: 10.1002/pmic.201400416] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 02/13/2015] [Accepted: 03/02/2015] [Indexed: 12/18/2022]
Abstract
Food allergy has become a major health issue in developed countries, therefore there is an urgent need to develop analytical methods able to detect and quantify with a good sensitivity and reliability some specific allergens in complex food matrices. In this paper, we present a targeted MS/MS approach to compare the relative abundance of the major recognized wheat allergens in the salt-soluble (albumin/globulin) fraction of wheat grains. Twelve allergens were quantified in seven wheat varieties, selected from three Triticum species: T. aestivum (bread wheat), T. durum (durum wheat), and T. monococcum. The allergens were monitored from one or two proteotypic peptides and their relative abundance was deduced from the intensity of one fragment measured in MS/MS. Whereas the abundance of some of the targeted allergens was quite stable across the genotypes, others like alpha-amylase inhibitors showed clear differences according to the wheat species, in accordance with the results of earlier functional studies. This study enriches the scarce knowledge available on allergens content in wheat genotypes, and brings new perspectives for food safety and plant breeding.
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Affiliation(s)
- Hélène Rogniaux
- INRA UR1268 Biopolymers Interactions Assemblies, Nantes, France
| | - Marija Pavlovic
- INRA UR1268 Biopolymers Interactions Assemblies, Nantes, France
| | - Roberta Lupi
- INRA UR1268 Biopolymers Interactions Assemblies, Nantes, France
| | | | - Mathilde Joint
- INRA UR1268 Biopolymers Interactions Assemblies, Nantes, France
| | - Hamza Mameri
- INRA UR1268 Biopolymers Interactions Assemblies, Nantes, France
| | - Sandra Denery
- INRA UR1268 Biopolymers Interactions Assemblies, Nantes, France
| | - Colette Larré
- INRA UR1268 Biopolymers Interactions Assemblies, Nantes, France
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Lawless C, Holman SW, Brownridge P, Lanthaler K, Harman VM, Watkins R, Hammond DE, Miller RL, Sims PFG, Grant CM, Eyers CE, Beynon RJ, Hubbard SJ. Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring. Mol Cell Proteomics 2016; 15:1309-22. [PMID: 26750110 PMCID: PMC4824857 DOI: 10.1074/mcp.m115.054288] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Indexed: 11/06/2022] Open
Abstract
Defining intracellular protein concentration is critical in molecular systems biology. Although strategies for determining relative protein changes are available, defining robust absolute values in copies per cell has proven significantly more challenging. Here we present a reference data set quantifying over 1800 Saccharomyces cerevisiae proteins by direct means using protein-specific stable-isotope labeled internal standards and selected reaction monitoring (SRM) mass spectrometry, far exceeding any previous study. This was achieved by careful design of over 100 QconCAT recombinant proteins as standards, defining 1167 proteins in terms of copies per cell and upper limits on a further 668, with robust CVs routinely less than 20%. The selected reaction monitoring-derived proteome is compared with existing quantitative data sets, highlighting the disparities between methodologies. Coupled with a quantification of the transcriptome by RNA-seq taken from the same cells, these data support revised estimates of several fundamental molecular parameters: a total protein count of ∼100 million molecules-per-cell, a median of ∼1000 proteins-per-transcript, and a linear model of protein translation explaining 70% of the variance in translation rate. This work contributes a “gold-standard” reference yeast proteome (including 532 values based on high quality, dual peptide quantification) that can be widely used in systems models and for other comparative studies.
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Affiliation(s)
- Craig Lawless
- From the ‡Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Stephen W Holman
- §Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Philip Brownridge
- §Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Karin Lanthaler
- From the ‡Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Victoria M Harman
- §Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Rachel Watkins
- From the ‡Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Dean E Hammond
- §Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Rebecca L Miller
- §Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Paul F G Sims
- From the ‡Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Christopher M Grant
- From the ‡Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Claire E Eyers
- §Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Robert J Beynon
- §Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Simon J Hubbard
- From the ‡Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK;
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35
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Couchman L, Jones DJL, Moniz CF. The use of turbulent flow chromatography for rapid, on-line analysis of tryptic digests. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:2140-2146. [PMID: 26467226 DOI: 10.1002/rcm.7371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/19/2015] [Accepted: 08/21/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Following digestion of proteins with trypsin, digests are typically subjected to further 'clean-up' prior to liquid chromatography/mass spectometry (LC/MS) analysis, in order to reduce the complexity of the digested matrix, as well as helping to remove residual denaturants and reduction/alkylation reagents prior to injection onto the analytical HPLC column. Often, this is carried out using off-line techniques, and is not ideally suited to high-throughput workloads, for example in clinical laboratories. METHODS Bovine serum albumin (BSA) was used as a model protein. Following denaturation with urea, reduction/alkylation, and digestion with trypsin, the analytical recovery of a selection of proteotypic BSA peptides was assessed using a two-dimensional, turbulent flow chromatography method. Peptides were identified using a Q Exactive™ mass spectometer operating in full-scan mode. RESULTS Total analysis time (including the on-line sample clean-up) was 15 min per injection. Aside from the most hydrophilic peptide selected, ATEEQLK, recovery using the turbulent flow chromatography systems was greater than 30% for all remaining peptides (N = 17), and exceeded 50% for 12 of the 18 peptides studied. There was a broad correlation between the hydrophobicity factor and the observed recovery. CONCLUSIONS This study suggests that turbulent flow chromatography offers a rapid, on-line alternative to solid-phase extraction for the analysis of peptide digests by LC/MS. A wide range of column chemistries are available, and the technique can be further optimised for analyses which are targetted to specific peptides. As with turbulent flow chromatography for small-molecule workflows, this approach may be ideally suited to high-throughput applications, such as those which are emerging from within clinical laboratories.
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Affiliation(s)
- L Couchman
- Viapath Analytics, Department of Clinical Biochemistry, King's College Hospital, Denmark Hill, London, SE5 9RS, UK
- Department of Cancer Studies, Leicester Royal Infirmary, University of Leicester, Leicester, LE2 7LX, UK
| | - D J L Jones
- Department of Cancer Studies, Leicester Royal Infirmary, University of Leicester, Leicester, LE2 7LX, UK
| | - C F Moniz
- Department of Clinical Biochemistry, King's College Hospital, Denmark Hill, London, SE5 9RS, UK
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36
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Huang PY, Mactier S, Armacki N, Giles Best O, Belov L, Kaufman KL, Pascovici D, Mulligan SP, Christopherson RI. Protein profiles distinguish stable and progressive chronic lymphocytic leukemia. Leuk Lymphoma 2015; 57:1033-43. [DOI: 10.3109/10428194.2015.1094692] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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37
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Heaney LM, Jones DJL, Mbasu RJ, Ng LL, Suzuki T. High mass accuracy assay for trimethylamine N-oxide using stable-isotope dilution with liquid chromatography coupled to orthogonal acceleration time of flight mass spectrometry with multiple reaction monitoring. Anal Bioanal Chem 2015; 408:797-804. [DOI: 10.1007/s00216-015-9164-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/20/2015] [Accepted: 10/29/2015] [Indexed: 02/06/2023]
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38
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Kalló G, Chatterjee A, Tóth M, Rajnavölgyi É, Csutak A, Tőzsér J, Csősz É. Relative quantification of human β-defensins by a proteomics approach based on selected reaction monitoring. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1623-1631. [PMID: 26467114 DOI: 10.1002/rcm.7259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 06/16/2015] [Accepted: 06/21/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE A targeted proteomics method based on selected reaction monitoring (SRM) is a relevant approach for the analysis of multiple analytes in biological samples. Defensins are phylogenetically conserved small antimicrobial peptides contributing to innate host defense and exhibiting low immunogenicity, resistance to proteolysis and a broad range of antimicrobial activities. The goal of the present study was to develop and optimize SRM-based targeted proteomics methods for the detection of human β-defensins 1-4 in various biological fluids. METHODS An SRM-based targeted proteomics method was developed and validated for the detection of human β-defensins 1-4. The supernatants of resting and IL-1β-stimulated Caco2, HT-29 and SW-1116 colonic epithelial cells (CEC), cell lysates of CECs and tear samples of human healthy individuals were analyzed and the feasibility of the developed method was validated by ELISA and dot-blot analysis complemented by RT-qPCR. RESULTS Our results demonstrate that the developed SRM method offers an alternative approach for the cost-effective and rapid analysis of human β-defensins in samples with biological relevance. CONCLUSIONS A semi-quantitative targeted mass spectrometry method was developed and validated for the relative quantification of β-defensins 1-4 in cell culture supernatants and body fluid analyses.
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Affiliation(s)
- Gergő Kalló
- Department of Biochemistry and Molecular Biology, Proteomics Core Facility, Faculty of Medicine, University of Debrecen, Egyetem ter. 1, 4010, Debrecen, Hungary
| | - Arunima Chatterjee
- Department of Immunology, Faculty of Medicine, University of Debrecen, Egyetem ter. 1, 4010, Debrecen, Hungary
| | - Márta Tóth
- Department of Immunology, Faculty of Medicine, University of Debrecen, Egyetem ter. 1, 4010, Debrecen, Hungary
| | - Éva Rajnavölgyi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Egyetem ter. 1, 4010, Debrecen, Hungary
| | - Adrienne Csutak
- Department of Ophthalmology, Faculty of Medicine, University of Debrecen, Egyetem ter. 1, 4010, Debrecen, Hungary
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Proteomics Core Facility, Faculty of Medicine, University of Debrecen, Egyetem ter. 1, 4010, Debrecen, Hungary
| | - Éva Csősz
- Department of Biochemistry and Molecular Biology, Proteomics Core Facility, Faculty of Medicine, University of Debrecen, Egyetem ter. 1, 4010, Debrecen, Hungary
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39
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Sunagar K, Morgenstern D, Reitzel AM, Moran Y. Ecological venomics: How genomics, transcriptomics and proteomics can shed new light on the ecology and evolution of venom. J Proteomics 2015; 135:62-72. [PMID: 26385003 DOI: 10.1016/j.jprot.2015.09.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/02/2015] [Accepted: 09/09/2015] [Indexed: 01/18/2023]
Abstract
Animal venom is a complex cocktail of bioactive chemicals that traditionally drew interest mostly from biochemists and pharmacologists. However, in recent years the evolutionary and ecological importance of venom is realized as this trait has direct and strong influence on interactions between species. Moreover, venom content can be modulated by environmental factors. Like many other fields of biology, venom research has been revolutionized in recent years by the introduction of systems biology approaches, i.e., genomics, transcriptomics and proteomics. The employment of these methods in venom research is known as 'venomics'. In this review we describe the history and recent advancements of venomics and discuss how they are employed in studying venom in general and in particular in the context of evolutionary ecology. We also discuss the pitfalls and challenges of venomics and what the future may hold for this emerging scientific field.
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Affiliation(s)
- Kartik Sunagar
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - David Morgenstern
- Proteomics Resource Center, Langone Medical Center, New York University, New York, USA.
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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40
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Abstract
The increasing acceptance that proteins may exert multiple functions in the cell brings with it new analytical challenges that will have an impact on the field of proteomics. Many proteomics workflows begin by destroying information about the interactions between different proteins, and the reduction of a complex protein mixture to constituent peptides also scrambles information about the combinatorial potential of post-translational modifications. To bring the focus of proteomics on to the domain of protein moonlighting will require novel analytical and quantitative approaches.
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41
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Large-scale label-free phosphoproteomics: from technology to data interpretation. Bioanalysis 2015; 6:2403-20. [PMID: 25384593 DOI: 10.4155/bio.14.188] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein phosphorylation plays a central role in the dynamic intracellular signaling and the control of biochemical pathways in all living cells. Recent advances in high-performance MS/MS-based technology make the large-scale identification and quantification of phosphorylation sites possible. Here, we review the full data generation pipeline, starting from sample preparation methods and LC-MS detection procedures, through to data processing and analysis software tools that facilitate the systematic comparative profiling of thousands of phosphoproteins in different biological specimens in a single experiment. We emphasize current challenges and promising avenues for the mechanistic interpretation and visualization of global phosphorylation networks and their relevance to human health and disease.
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42
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Al Feteisi H, Achour B, Rostami-Hodjegan A, Barber J. Translational value of liquid chromatography coupled with tandem mass spectrometry-based quantitative proteomics forin vitro–in vivoextrapolation of drug metabolism and transport and considerations in selecting appropriate techniques. Expert Opin Drug Metab Toxicol 2015; 11:1357-69. [DOI: 10.1517/17425255.2015.1055245] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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43
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Qi D, Lawless C, Teleman J, Levander F, Holman SW, Hubbard S, Jones AR. Representation of selected-reaction monitoring data in the mzQuantML data standard. Proteomics 2015; 15:2592-6. [PMID: 25884107 PMCID: PMC4692094 DOI: 10.1002/pmic.201400281] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 03/02/2015] [Accepted: 04/14/2015] [Indexed: 11/06/2022]
Abstract
The mzQuantML data standard was designed to capture the output of quantitative software in proteomics, to support submissions to public repositories, development of visualization software and pipeline/modular approaches. The standard is designed around a common core that can be extended to support particular types of technique through the release of semantic rules that are checked by validation software. The first release of mzQuantML supported four quantitative proteomics techniques via four sets of semantic rules: (i) intensity-based (MS(1) ) label free, (ii) MS(1) label-based (such as SILAC or N(15) ), (iii) MS(2) tag-based (iTRAQ or tandem mass tags), and (iv) spectral counting. We present an update to mzQuantML for supporting SRM techniques. The update includes representing the quantitative measurements, and associated meta-data, for SRM transitions, the mechanism for inferring peptide-level or protein-level quantitative values, and support for both label-based or label-free SRM protocols, through the creation of semantic rules and controlled vocabulary terms. We have updated the specification document for mzQuantML (version 1.0.1) and the mzQuantML validator to ensure that consistent files are produced by different exporters. We also report the capabilities for production of mzQuantML files from popular SRM software packages, such as Skyline and Anubis.
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Affiliation(s)
- Da Qi
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Craig Lawless
- The Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Johan Teleman
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden.,Bioinformatics Infrastructure for Life Sciences (BILS), Lund University, Lund, Sweden
| | - Stephen W Holman
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Simon Hubbard
- The Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Andrew R Jones
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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44
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Absolute quantification of podocalyxin, a potential biomarker of glomerular injury in human urine, by liquid chromatography–mass spectrometry. J Chromatogr A 2015; 1397:81-5. [DOI: 10.1016/j.chroma.2015.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/20/2015] [Accepted: 04/01/2015] [Indexed: 12/30/2022]
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45
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López-Villar E, Martos-Moreno GÁ, Chowen JA, Okada S, Kopchick JJ, Argente J. A proteomic approach to obesity and type 2 diabetes. J Cell Mol Med 2015; 19:1455-70. [PMID: 25960181 PMCID: PMC4511345 DOI: 10.1111/jcmm.12600] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/02/2015] [Indexed: 12/13/2022] Open
Abstract
The incidence of obesity and type diabetes 2 has increased dramatically resulting in an increased interest in its biomedical relevance. However, the mechanisms that trigger the development of diabetes type 2 in obese patients remain largely unknown. Scientific, clinical and pharmaceutical communities are dedicating vast resources to unravel this issue by applying different omics tools. During the last decade, the advances in proteomic approaches and the Human Proteome Organization have opened and are opening a new door that may be helpful in the identification of patients at risk and to improve current therapies. Here, we briefly review some of the advances in our understanding of type 2 diabetes that have occurred through the application of proteomics. We also review, in detail, the current improvements in proteomic methodologies and new strategies that could be employed to further advance our understanding of this pathology. By applying these new proteomic advances, novel therapeutic and/or diagnostic protein targets will be discovered in the obesity/Type 2 diabetes area.
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Affiliation(s)
- Elena López-Villar
- Departments of Endocrinology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain.,Oncohematology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Gabriel Á Martos-Moreno
- Departments of Endocrinology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Investigación La Princesa, Madrid, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie A Chowen
- Departments of Endocrinology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Investigación La Princesa, Madrid, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Shigeru Okada
- Edison Biotechnology Institute, Ohio University, Konneker Research Laboratories, Athens, OH, USA.,Department of Pediatrics, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - John J Kopchick
- Edison Biotechnology Institute, Ohio University, Konneker Research Laboratories, Athens, OH, USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH, USA.,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - Jesús Argente
- Departments of Endocrinology and Pediatrics, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Investigación La Princesa, Madrid, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
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46
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Hill RC, Calle EA, Dzieciatkowska M, Niklason LE, Hansen KC. Quantification of extracellular matrix proteins from a rat lung scaffold to provide a molecular readout for tissue engineering. Mol Cell Proteomics 2015; 14:961-73. [PMID: 25660013 PMCID: PMC4390273 DOI: 10.1074/mcp.m114.045260] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/06/2015] [Indexed: 01/20/2023] Open
Abstract
The use of extracellular matrix (ECM) scaffolds, derived from decellularized tissues for engineered organ generation, holds enormous potential in the field of regenerative medicine. To support organ engineering efforts, we developed a targeted proteomics method to extract and quantify extracellular matrix components from tissues. Our method provides more complete and accurate protein characterization than traditional approaches. This is accomplished through the analysis of both the chaotrope-soluble and -insoluble protein fractions and using recombinantly generated stable isotope labeled peptides for endogenous protein quantification. Using this approach, we have generated 74 peptides, representing 56 proteins to quantify protein in native (nondecellularized) and decellularized lung matrices. We have focused on proteins of the ECM and additional intracellular proteins that are challenging to remove during the decellularization procedure. Results indicate that the acellular lung scaffold is predominantly composed of structural collagens, with the majority of these proteins found in the insoluble ECM, a fraction that is often discarded using widely accepted proteomic methods. The decellularization procedure removes over 98% of intracellular proteins evaluated and retains, to varying degrees, proteoglycans and glycoproteins of the ECM. Accurate characterization of ECM proteins from tissue samples will help advance organ engineering efforts by generating a molecular readout that can be correlated with functional outcome to drive the next generation of engineered organs.
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Affiliation(s)
- Ryan C Hill
- ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045
| | | | - Monika Dzieciatkowska
- ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045
| | - Laura E Niklason
- §Department of Biomedical Engineering and Anesthesiology, ¶Yale University, New Haven, CT 06519
| | - Kirk C Hansen
- ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045,
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47
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Kuharev J, Navarro P, Distler U, Jahn O, Tenzer S. In-depth evaluation of software tools for data-independent acquisition based label-free quantification. Proteomics 2015; 15:3140-51. [PMID: 25545627 DOI: 10.1002/pmic.201400396] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/22/2014] [Accepted: 12/17/2014] [Indexed: 12/21/2022]
Abstract
Label-free quantification (LFQ) based on data-independent acquisition workflows currently experiences increasing popularity. Several software tools have been recently published or are commercially available. The present study focuses on the evaluation of three different software packages (Progenesis, synapter, and ISOQuant) supporting ion mobility enhanced data-independent acquisition data. In order to benchmark the LFQ performance of the different tools, we generated two hybrid proteome samples of defined quantitative composition containing tryptically digested proteomes of three different species (mouse, yeast, Escherichia coli). This model dataset simulates complex biological samples containing large numbers of both unregulated (background) proteins as well as up- and downregulated proteins with exactly known ratios between samples. We determined the number and dynamic range of quantifiable proteins and analyzed the influence of applied algorithms (retention time alignment, clustering, normalization, etc.) on quantification results. Analysis of technical reproducibility revealed median coefficients of variation of reported protein abundances below 5% for MS(E) data for Progenesis and ISOQuant. Regarding accuracy of LFQ, evaluation with synapter and ISOQuant yielded superior results compared to Progenesis. In addition, we discuss reporting formats and user friendliness of the software packages. The data generated in this study have been deposited to the ProteomeXchange Consortium with identifier PXD001240 (http://proteomecentral.proteomexchange.org/dataset/PXD001240).
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Affiliation(s)
- Jörg Kuharev
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Pedro Navarro
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Olaf Jahn
- Proteomics Group, Max-Planck-Institute of Experimental Medicine, Göttingen, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
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48
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Pieroni L, Levi Mortera S, Greco V, Sirolli V, Ronci M, Felaco P, Fucci G, De Fulviis S, Massoud R, Condò S, Capria A, Di Daniele N, Bernardini S, Urbani A, Bonomini M. Biocompatibility assessment of haemodialysis membrane materials by proteomic investigations. MOLECULAR BIOSYSTEMS 2015; 11:1633-43. [DOI: 10.1039/c5mb00058k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We examine and compare the protein adsorption capacity and coagulation profiles of different haemodialysis membrane biomaterials.
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49
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Yılmaz ZB, Kofahl B, Beaudette P, Baum K, Ipenberg I, Weih F, Wolf J, Dittmar G, Scheidereit C. Quantitative dissection and modeling of the NF-κB p100-p105 module reveals interdependent precursor proteolysis. Cell Rep 2014; 9:1756-1769. [PMID: 25482563 DOI: 10.1016/j.celrep.2014.11.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 10/20/2014] [Accepted: 11/08/2014] [Indexed: 12/26/2022] Open
Abstract
The mechanisms that govern proteolytic maturation or complete destruction of the precursor proteins p100 and p105 are fundamental to homeostasis and activation of NF-κB; however, they remain poorly understood. Using mass-spectrometry-based quantitative analysis of noncanonical LTβR-induced signaling, we demonstrate that stimulation induces simultaneous processing of both p100 and p105. The precursors not only form hetero-oligomers but also interact with the ATPase VCP/p97, and their induced proteolysis strictly depends on the signal response domain (SRD) of p100, suggesting that the SRD-targeting proteolytic machinery acts in cis and in trans. Separation of cellular pools by isotope labeling revealed synchronous dynamics of p105 and p100 proteolysis. The generation of p50 and p52 from their precursors depends on functional VCP/p97. We have developed quantitative mathematical models that describe the dynamics of the system and predict that p100-p105 complexes are signal responsive.
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Affiliation(s)
- Zekiye Buket Yılmaz
- Signal Transduction Laboratory, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
| | - Bente Kofahl
- Mathematical Modeling Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Patrick Beaudette
- Signal Transduction Laboratory, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany; Mass Spectrometry Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Katharina Baum
- Mathematical Modeling Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Inbal Ipenberg
- Signal Transduction Laboratory, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Falk Weih
- Leibniz-Institute for Age Research-Fritz-Lipmann-Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Jana Wolf
- Mathematical Modeling Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Gunnar Dittmar
- Mass Spectrometry Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Claus Scheidereit
- Signal Transduction Laboratory, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
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Iliuk AB, Arrington JV, Tao WA. Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications. Electrophoresis 2014; 35:3430-40. [PMID: 24890697 PMCID: PMC4250476 DOI: 10.1002/elps.201400153] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/29/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022]
Abstract
Phosphoproteomics is the systematic study of one of the most common protein modifications in high throughput with the aim of providing detailed information of the control, response, and communication of biological systems in health and disease. Advances in analytical technologies and strategies, in particular the contributions of high-resolution mass spectrometers, efficient enrichments of phosphopeptides, and fast data acquisition and annotation, have catalyzed dramatic expansion of signaling landscapes in multiple systems during the past decade. While phosphoproteomics is an essential inquiry to map high-resolution signaling networks and to find relevant events among the apparently ubiquitous and widespread modifications of proteome, it presents tremendous challenges in separation sciences to translate it from discovery to clinical practice. In this mini-review, we summarize the analytical tools currently utilized for phosphoproteomic analysis (with focus on MS), progresses made on deciphering clinically relevant kinase-substrate networks, MS uses for biomarker discovery and validation, and the potential of phosphoproteomics for disease diagnostics and personalized medicine.
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Affiliation(s)
- Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | | | - Weiguo Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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