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Li M, Zuo J, Yang K, Wang P, Zhou S. Proteomics mining of cancer hallmarks on a single-cell resolution. MASS SPECTROMETRY REVIEWS 2024; 43:1019-1040. [PMID: 37051664 DOI: 10.1002/mas.21842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 11/25/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Dysregulated proteome is an essential contributor in carcinogenesis. Protein fluctuations fuel the progression of malignant transformation, such as uncontrolled proliferation, metastasis, and chemo/radiotherapy resistance, which severely impair therapeutic effectiveness and cause disease recurrence and eventually mortality among cancer patients. Cellular heterogeneity is widely observed in cancer and numerous cell subtypes have been characterized that greatly influence cancer progression. Population-averaged research may not fully reveal the heterogeneity, leading to inaccurate conclusions. Thus, deep mining of the multiplex proteome at the single-cell resolution will provide new insights into cancer biology, to develop prognostic biomarkers and treatments. Considering the recent advances in single-cell proteomics, herein we review several novel technologies with particular focus on single-cell mass spectrometry analysis, and summarize their advantages and practical applications in the diagnosis and treatment for cancer. Technological development in single-cell proteomics will bring a paradigm shift in cancer detection, intervention, and therapy.
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Affiliation(s)
- Maomao Li
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Jing Zuo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ping Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
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2
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Zinzius K, Marchetti GM, Fischer R, Milrad Y, Oltmanns A, Kelterborn S, Yacoby I, Hegemann P, Scholz M, Hippler M. Calredoxin regulates the chloroplast NADPH-dependent thioredoxin reductase in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2023; 193:2122-2140. [PMID: 37474113 PMCID: PMC10602609 DOI: 10.1093/plphys/kiad426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/25/2023] [Accepted: 05/25/2023] [Indexed: 07/22/2023]
Abstract
Calredoxin (CRX) is a calcium (Ca2+)-dependent thioredoxin (TRX) in the chloroplast of Chlamydomonas (Chlamydomonas reinhardtii) with a largely unclear physiological role. We elucidated the CRX functionality by performing in-depth quantitative proteomics of wild-type cells compared with a crx insertional mutant (IMcrx), two CRISPR/Cas9 KO mutants, and CRX rescues. These analyses revealed that the chloroplast NADPH-dependent TRX reductase (NTRC) is co-regulated with CRX. Electron transfer measurements revealed that CRX inhibits NADPH-dependent reduction of oxidized chloroplast 2-Cys peroxiredoxin (PRX1) via NTRC and that the function of the NADPH-NTRC complex is under strict control of CRX. Via non-reducing SDS-PAGE assays and mass spectrometry, our data also demonstrated that PRX1 is more oxidized under high light (HL) conditions in the absence of CRX. The redox tuning of PRX1 and control of the NADPH-NTRC complex via CRX interconnect redox control with active photosynthetic electron transport and metabolism, as well as Ca2+ signaling. In this way, an economic use of NADPH for PRX1 reduction is ensured. The finding that the absence of CRX under HL conditions severely inhibited light-driven CO2 fixation underpins the importance of CRX for redox tuning, as well as for efficient photosynthesis.
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Affiliation(s)
- Karen Zinzius
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Giulia Maria Marchetti
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Ronja Fischer
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Yuval Milrad
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Anne Oltmanns
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Simon Kelterborn
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, 10099 Berlin, Germany
| | - Iftach Yacoby
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, 10099 Berlin, Germany
| | - Martin Scholz
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Michael Hippler
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
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3
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Clases D, Gonzalez de Vega R, Bishop D, Doble P. SEC-ICP-MS and on-line isotope dilution analysis for characterisation and quantification of immunochemical assays. Anal Bioanal Chem 2019; 411:3553-3560. [DOI: 10.1007/s00216-019-01836-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/28/2019] [Accepted: 04/05/2019] [Indexed: 01/08/2023]
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4
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Linscheid MW. Molecules and elements for quantitative bioanalysis: The allure of using electrospray, MALDI, and ICP mass spectrometry side-by-side. MASS SPECTROMETRY REVIEWS 2019; 38:169-186. [PMID: 29603315 DOI: 10.1002/mas.21567] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
To understand biological processes, not only reliable identification, but quantification of constituents in biological processes play a pivotal role. This is especially true for the proteome: protein quantification must follow protein identification, since sometimes minute changes in abundance tell the real tale. To obtain quantitative data, many sophisticated strategies using electrospray and MALDI mass spectrometry (MS) have been developed in recent years. All of them have advantages and limitations. Several years ago, we started to work on strategies, which are principally capable to overcome some of these limits. The fundamental idea is to use elemental signals as a measure for quantities. We began by replacing the radioactive 32 P with the "cold" natural 31 P to quantify modified nucleotides and phosphorylated peptides and proteins and later used tagging strategies for quantification of proteins more generally. To do this, we introduced Inductively Coupled Plasma Mass Spectrometry (ICP-MS) into the bioanalytical workflows, allowing not only reliable and sensitive detection but also quantification based on isotope dilution absolute measurements using poly-isotopic elements. The detection capability of ICP-MS becomes particularly attractive with heavy metals. The covalently bound proteins tags developed in our group are based on the well-known DOTA chelate complex (1,4,7,10-tetraazacyclododecane-N,N',N″,N‴-tetraacetic acid) carrying ions of lanthanoides as metal core. In this review, I will outline the development of this mutual assistance between molecular and elemental mass spectrometry and discuss the scope and limitations particularly of peptide and protein quantification. The lanthanoide tags provide low detection limits, but offer multiplexing capabilities due to the number of very similar lanthanoides and their isotopes. With isotope dilution comes previously unknown accuracy. Separation techniques such as electrophoresis and HPLC were used and just slightly adapted workflows, already in use for quantification in bioanalysis. Imaging mass spectrometry (MSI) with MALDI and laser ablation ICP-MS complemented the range of application in recent years.
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MESH Headings
- Animals
- Chelating Agents/chemistry
- Chromatography, High Pressure Liquid/instrumentation
- Chromatography, High Pressure Liquid/methods
- Heterocyclic Compounds, 1-Ring/chemistry
- Humans
- Lanthanoid Series Elements/chemistry
- Nucleotides/analysis
- Proteins/analysis
- Spectrometry, Mass, Electrospray Ionization/instrumentation
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
- Workflow
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5
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Benda D, Beck S, Linscheid MW. Synthesis and characterization of a new MeCAT reagent containing a photocleavable linker for labeling of proteins and peptides in mass spectrometric analyses. Talanta 2019; 192:197-203. [PMID: 30348378 DOI: 10.1016/j.talanta.2018.09.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/10/2018] [Accepted: 09/14/2018] [Indexed: 11/24/2022]
Abstract
The quantification of proteins and peptides becomes more important besides mere identification in modern life sciences. Therefore, we have developed a new reagent that adds to the known metall-coded affinity tagging strategy employed in molecular and elemental mass spectrometry containing a photocleavable linker. A synthesis route was developed that provides the new reagent in good yields. The stability of the synthesized reagents was assessed under different temperature and illumination conditions. Labeling reactions were carried out at peptide and protein level, while also the fragmentation behavior of labeled peptides was assessed. In additional experiments, the photocleavability of the new reagent was examined. Upon irradiation with ultraviolet light, the photoproducts were liberated and could be used for quantification of labeled peptides.
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Affiliation(s)
- David Benda
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Sebastian Beck
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Michael W Linscheid
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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6
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Bauer M, Remmler D, Dallmann A, Jakubowski N, Börner HG, Panne U, Limberg C. Specific Decoration of a Discrete Bismuth Oxido Cluster by Selected Peptides towards the Design of Metal Tags. Chemistry 2019; 25:759-763. [PMID: 30350473 DOI: 10.1002/chem.201805234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Indexed: 11/12/2022]
Abstract
Metal tags find application in a multitude of biomedical systems and the combination with laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) offers an opportunity for multiplexing. To lay the foundation for an increase of the signal intensities in such processes, we herein present a general approach for efficient functionalization of a well-defined metal oxido cluster [Bi6 O4 (OH)4 (SO3 CF3 )6 (CH3 CN)6 ]⋅2 CH3 CN (1), which can be realized by selecting 7mer peptide sequences via combinatorial means from large one-bead one-compound peptide libraries. Selective cluster-binding peptide sequences (CBS) for 1 were discriminated from non-binders by treatment with H2 S gas to form the reduction product Bi2 S3 , clearly visible to the naked eye. Interactions were further confirmed by NMR experiments. Extension of a binding peptide with a maleimide linker (Mal) introduces the possibility to covalently attach thiol-bearing moieties such as biological probes and for their analysis the presence of the cluster instead of mononuclear entities should lead to an increase of signal intensities in LA-ICP-MS measurements. To prove this, CBS-Mal was covalently bound onto thiol-presenting glass substrates, which then captured 1 effectively, so that LA-ICP-MS measurements demonstrated drastic signal amplification compared to single lanthanide tags.
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Affiliation(s)
- Mona Bauer
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489, Berlin, Germany.,Bundesanstalt für Materialforschung und -prüfung, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Dario Remmler
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489, Berlin, Germany.,Bundesanstalt für Materialforschung und -prüfung, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - André Dallmann
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Norbert Jakubowski
- Bundesanstalt für Materialforschung und -prüfung, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Hans G Börner
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Ulrich Panne
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489, Berlin, Germany.,Bundesanstalt für Materialforschung und -prüfung, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Christian Limberg
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Str. 2, 12489, Berlin, Germany.,IRIS Adlershof, 12489, Berlin, Germany
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7
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Sharar M, Saied EM, Rodriguez MC, Arenz C, Montes-Bayón M, Linscheid MW. Elemental labelling and mass spectrometry for the specific detection of sulfenic acid groups in model peptides: a proof of concept. Anal Bioanal Chem 2017; 409:2015-2027. [DOI: 10.1007/s00216-016-0149-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/04/2016] [Accepted: 12/12/2016] [Indexed: 01/01/2023]
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8
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Highly Sensitive Analysis of Proteins and Metabolites by Metal Tagging Using LC-ICP-MS. Metallomics 2017. [DOI: 10.1007/978-4-431-56463-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Müller L, Traub H, Jakubowski N. Novel Applications of Lanthanoides as Analytical or Diagnostic Tools in the Life Sciences by ICP-MS-based Techniques. PHYSICAL SCIENCES REVIEWS 2016. [DOI: 10.1515/psr-2016-0064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Inductively coupled plasma mass spectrometry (ICP-MS) is a well-established analytical method for multi-elemental analysis in particular for elements at trace and ultra-trace levels. It has found acceptance in various application areas during the last decade. ICP-MS is also more and more applied for detection in the life sciences. For these applications, ICP-MS excels by a high sensitivity, which is independent of the molecular structure of the analyte, a wide linear dynamic range and by excellent multi-element capabilities. Furthermore, methods based on ICP-MS offer simple quantification concepts, for which usually (liquid) standards are applied, low matrix effects compared to other conventional bioanalytical techniques, and relative limits of detection (LODs) in the low pg g−1 range and absolute LODs down to the attomol range.
In this chapter, we focus on new applications where the multi-element capability of ICP-MS is used for detection of lanthanoides or rare earth elements, which are applied as elemental stains or tags of biomolecules and in particular of antibodies.
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10
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Revealing the composition of organic materials in polychrome works of art: the role of mass spectrometry-based techniques. Anal Bioanal Chem 2016; 408:6957-81. [DOI: 10.1007/s00216-016-9862-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/28/2016] [Accepted: 08/03/2016] [Indexed: 10/21/2022]
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11
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He Y, Esteban-Fernández D, Neumann B, Bergmann U, Bierkandt F, Linscheid MW. Application of MeCAT-Click labeling for protein abundance characterization of E. coli after heat shock experiments. J Proteomics 2016; 136:68-76. [DOI: 10.1016/j.jprot.2015.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 12/02/2015] [Accepted: 12/17/2015] [Indexed: 10/22/2022]
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12
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Dallongeville S, Garnier N, Rolando C, Tokarski C. Proteins in Art, Archaeology, and Paleontology: From Detection to Identification. Chem Rev 2015; 116:2-79. [PMID: 26709533 DOI: 10.1021/acs.chemrev.5b00037] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sophie Dallongeville
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Nicolas Garnier
- SARL Laboratoire Nicolas Garnier , 63270 Vic le Comte, France
| | - Christian Rolando
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Caroline Tokarski
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
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13
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Chahrour O, Cobice D, Malone J. Stable isotope labelling methods in mass spectrometry-based quantitative proteomics. J Pharm Biomed Anal 2015; 113:2-20. [PMID: 25956803 DOI: 10.1016/j.jpba.2015.04.013] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 04/05/2015] [Accepted: 04/08/2015] [Indexed: 02/04/2023]
Abstract
Mass-spectrometry based proteomics has evolved as a promising technology over the last decade and is undergoing a dramatic development in a number of different areas, such as; mass spectrometric instrumentation, peptide identification algorithms and bioinformatic computational data analysis. The improved methodology allows quantitative measurement of relative or absolute protein amounts, which is essential for gaining insights into their functions and dynamics in biological systems. Several different strategies involving stable isotopes label (ICAT, ICPL, IDBEST, iTRAQ, TMT, IPTL, SILAC), label-free statistical assessment approaches (MRM, SWATH) and absolute quantification methods (AQUA) are possible, each having specific strengths and weaknesses. Inductively coupled plasma mass spectrometry (ICP-MS), which is still widely recognised as elemental detector, has recently emerged as a complementary technique to the previous methods. The new application area for ICP-MS is targeting the fast growing field of proteomics related research, allowing absolute protein quantification using suitable elemental based tags. This document describes the different stable isotope labelling methods which incorporate metabolic labelling in live cells, ICP-MS based detection and post-harvest chemical label tagging for protein quantification, in addition to summarising their pros and cons.
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Affiliation(s)
| | - Diego Cobice
- Spectroscopy Group, Analytical Services, Almac, UK
| | - John Malone
- Spectroscopy Group, Analytical Services, Almac, UK
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14
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Novel approach for labeling of biopolymers with DOTA complexes using in situ click chemistry for quantification. Talanta 2015; 134:468-475. [DOI: 10.1016/j.talanta.2014.11.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/18/2014] [Accepted: 11/22/2014] [Indexed: 11/21/2022]
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15
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Esteban-Fernández D, El-Khatib AH, Moraleja I, Gómez-Gómez MM, Linscheid MW. Bridging the Gap between Molecular and Elemental Mass Spectrometry: Higher Energy Collisional Dissociation (HCD) Revealing Elemental Information. Anal Chem 2015; 87:1613-21. [DOI: 10.1021/ac5032447] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Diego Esteban-Fernández
- Department
of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor Str. 2, 12489, Berlin, Germany
| | - Ahmed H. El-Khatib
- Department
of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor Str. 2, 12489, Berlin, Germany
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str.
11, 12489, Berlin, Germany
| | - Irene Moraleja
- Department
of Analytical Chemistry, Universidad Complutense de Madrid, Avda. Complutense
s/n, 28040, Madrid, Spain
| | - M. Milagros Gómez-Gómez
- Department
of Analytical Chemistry, Universidad Complutense de Madrid, Avda. Complutense
s/n, 28040, Madrid, Spain
| | - Michael W. Linscheid
- Department
of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor Str. 2, 12489, Berlin, Germany
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16
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Hyrup Møller L, Bahnsen JS, Nielsen HM, Østergaard J, Stürup S, Gammelgaard B. Selenium as an alternative peptide label - comparison to fluorophore-labelled penetratin. Eur J Pharm Sci 2014; 67:76-84. [PMID: 25447743 DOI: 10.1016/j.ejps.2014.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/05/2014] [Indexed: 12/22/2022]
Abstract
In the present study, the impact on peptide properties of labelling peptides with the fluorophore TAMRA or the selenium (Se) containing amino acid SeMet was evaluated. Three differently labelled variants of the cell-penetrating peptide (CPP) penetratin (Pen) were synthesized, PenM(Se), TAMRA-PenM(Se) and TAMRA-Pen. The labelled peptides were characterized in terms of hydrodynamic radius, secondary structure during peptide-membrane interaction, effect on membrane leakage induction, uptake efficiency in HeLa cells. Furthermore, stability of peptides and identities of degradation products in cell media and cell lysate were evaluated. TAMRA-labelling increased the hydrodynamic radius of Pen and PenM(Se) significantly. Labelling with Se caused no or minimal changes in size, secondary structure and membrane leakage induction in concentration levels relevant for cellular uptake studies. Similar degradation patterns of all labelled peptides were observed in HBSS media; degradation was mainly due to oxidation. Cellular uptake was significantly higher for the TAMRA labelled peptides as compared to Se-labelled Pen. Extensive degradation was observed in media during cellular uptake studies, however, in all cell lysates, primarily the intact peptide (PenM(Se), TAMRA-PenM(Se) or TAMRA-Pen) was observed. Selenium labelling caused minimal alteration of the physicochemical properties of the peptide and allowed for absolute quantitative determination of cellular uptake by inductively coupled plasma mass spectrometry. Selenium is thus proposed as a promising alternative label for quantification of peptides in general, altering the properties of the peptide to a minor extent as compared to commonly used peptide labels.
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Affiliation(s)
| | | | | | | | - Stefan Stürup
- Department of Pharmacy, University of Copenhagen, Denmark
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17
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Campanella B, Bramanti E. Detection of proteins by hyphenated techniques with endogenous metal tags and metal chemical labelling. Analyst 2014; 139:4124-53. [DOI: 10.1039/c4an00722k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The absolute and relative quantitation of proteins plays a fundamental role in modern proteomics, as it is the key to understand still unresolved biological questions in medical and pharmaceutical applications.
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Affiliation(s)
- Beatrice Campanella
- National Research Council of Italy
- C.N.R
- Istituto di Chimica dei Composti Organo Metallici-ICCOM-UOS Pisa
- 56124 Pisa, Italy
| | - Emilia Bramanti
- National Research Council of Italy
- C.N.R
- Istituto di Chimica dei Composti Organo Metallici-ICCOM-UOS Pisa
- 56124 Pisa, Italy
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18
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Møller LH, Gabel-Jensen C, Franzyk H, Bahnsen JS, Stürup S, Gammelgaard B. Quantification of pharmaceutical peptides using selenium as an elemental detection label. Metallomics 2014; 6:1639-47. [DOI: 10.1039/c4mt00085d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Se-labelling of pharmaceutical biomolecules provides detailed quantitative and qualitative information on the fate of the biomolecule in cell uptake studies.
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Affiliation(s)
| | | | - Henrik Franzyk
- University of Copenhagen
- Department of Drug Design and Pharmacology
- Denmark
| | | | - Stefan Stürup
- University of Copenhagen
- Department of Pharmacy
- Denmark
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19
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Megger DA, Bracht T, Meyer HE, Sitek B. Label-free quantification in clinical proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1581-90. [DOI: 10.1016/j.bbapap.2013.04.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 03/26/2013] [Accepted: 04/01/2013] [Indexed: 12/31/2022]
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20
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Detection and quantification of proteins and cells by use of elemental mass spectrometry: progress and challenges. Anal Bioanal Chem 2013; 405:5663-70. [DOI: 10.1007/s00216-013-6886-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 02/22/2013] [Accepted: 02/28/2013] [Indexed: 10/27/2022]
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21
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Holste A, Tholey A, Hung CW, Schaumlöffel D. Nano-High-Performance Liquid Chromatography with Online Precleaning Coupled to Inductively Coupled Plasma Mass Spectrometry for the Analysis of Lanthanide-Labeled Peptides in Tryptic Protein Digests. Anal Chem 2013; 85:3064-70. [DOI: 10.1021/ac303618v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Angela Holste
- Université de Pau et des Pays de l’Adour/CNRS UMR 5254,
Laboratoire de Chimie Analytique Bio-Inorganique et Environnement/IPREM,
64053 Pau, France
- Institute for Experimental Medicine−Div. Systematic Proteome Research, Christian-Albrechts-Universität,
24105 Kiel, Germany
| | - Andreas Tholey
- Institute for Experimental Medicine−Div. Systematic Proteome Research, Christian-Albrechts-Universität,
24105 Kiel, Germany
| | - Chien-Wen Hung
- Institute for Experimental Medicine−Div. Systematic Proteome Research, Christian-Albrechts-Universität,
24105 Kiel, Germany
| | - Dirk Schaumlöffel
- Université de Pau et des Pays de l’Adour/CNRS UMR 5254,
Laboratoire de Chimie Analytique Bio-Inorganique et Environnement/IPREM,
64053 Pau, France
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22
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Inductively coupled plasma-MS in drug development: bioanalytical aspects and applications. Bioanalysis 2013; 4:1933-65. [PMID: 22943623 DOI: 10.4155/bio.12.141] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The vast majority of today's modern bioanalytical methods for pharmacokinetic, pharmacodynamic and immunogenicity purposes are based on LC-MS/MS and immunoanalytical approaches. Indeed, these methodologies are suitable for a wide range of molecules from small to large. For a smaller but not insignificant group of compounds, LC-MS/MS is not suitable - or in some cases much less suitable - as a reliable bioanalytical methodology, and inductively coupled plasma (ICP)-MS is a more appropriate methodology. ICP-MS is one of these less widely used techniques in drug development. This methodology is predominantly used for elemental bioanalysis for pharmacokinetics, for imaging purposes, for mass-balance, food-effect and biomarker studies. In addition, in the last couple of years an increasing number of applications has been published, where ICP-MS and its various hyphenations (LC-ICP-MS, CE-ICP-MS) have been used for speciation/metabolism and proteomics studies. Here, the analytical potential, the quantitative bioanalytical aspects, the various modes of operation and the challenges of the application of ICP-MS in life sciences applications are given. This includes an overview of recent applications in this area in scientific literature, the various hyphenation possibilities and their application areas and the analysis of the various sample matrices applicable to these fields. It also provides a brief outlook of where the potential of this technique lies in the future of regulated bioanalysis and drug development.
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23
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Schwarz G, Beck S, Benda D, Linscheid MW. MeCAT – comparing relative quantification of alpha lactalbumin using both molecular and elemental mass spectrometry. Analyst 2013; 138:2449-55. [DOI: 10.1039/c3an36602b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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24
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Messana I, Cabras T, Iavarone F, Vincenzoni F, Urbani A, Castagnola M. Unraveling the different proteomic platforms. J Sep Sci 2012; 36:128-39. [PMID: 23212829 DOI: 10.1002/jssc.201200830] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/05/2012] [Accepted: 10/06/2012] [Indexed: 01/06/2023]
Abstract
This review is addressed to scientists working outside the field of proteomics and wishes to shed a light on the possibility offered by the latest proteomics strategies. Bottom-up and top-down platforms are critically examined outlining advantages and limitations of their application to qualitative and quantitative investigations. Discovery, directed and targeted proteomics as different options for the management of the MS instrument are defined emphasizing their integration in the experimental plan to accomplish meaningful results. The issue of data validation is analyzed and discussed. The most common qualitative proteomic platforms are described, with a particular emphasis on enrichment methods to elucidate PTMs codes (i.e. ubiquitin and histone codes). Label-free and labeled methods for relative and absolute quantification are critically compared. The possible contribution of proteomics platforms to the transition from structural proteomics to functional proteomics (study of the functional connections between different proteins) and to the challenging system biology (integrated study of all the functional cellular functions) is also briefly discussed.
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Affiliation(s)
- Irene Messana
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
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25
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Sanz-Medel A, Montes-Bayón M, Bettmer J, Luisa Fernández-Sanchez M, Ruiz Encinar J. ICP-MS for absolute quantification of proteins for heteroatom-tagged, targeted proteomics. Trends Analyt Chem 2012. [DOI: 10.1016/j.trac.2012.07.020] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Kretschy D, Koellensperger G, Hann S. Elemental labelling combined with liquid chromatography inductively coupled plasma mass spectrometry for quantification of biomolecules: a review. Anal Chim Acta 2012; 750:98-110. [PMID: 23062431 PMCID: PMC3475989 DOI: 10.1016/j.aca.2012.06.040] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 06/23/2012] [Accepted: 06/25/2012] [Indexed: 01/02/2023]
Abstract
This article reviews novel quantification concepts where elemental labelling is combined with flow injection inductively coupled plasma mass spectrometry (FI-ICP-MS) or liquid chromatography inductively coupled plasma mass spectrometry (LC-ICP-MS), and employed for quantification of biomolecules such as proteins, peptides and related molecules in challenging sample matrices. In the first sections an overview on general aspects of biomolecule quantification, as well as of labelling will be presented emphasizing the potential, which lies in such methodological approaches. In this context, ICP-MS as detector provides high sensitivity, selectivity and robustness in biological samples and offers the capability for multiplexing and isotope dilution mass spectrometry (IDMS). Fundamental methodology of elemental labelling will be highlighted and analytical, as well as biomedical applications will be presented. A special focus will lie on established applications underlining benefits and bottlenecks of such approaches for the implementation in real life analysis. Key research made in this field will be summarized and a perspective for future developments including sophisticated and innovative applications will given.
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Affiliation(s)
| | | | - Stephan Hann
- University of Natural Resources and Life Sciences, BOKU Vienna, Department of Chemistry, Division of Analytical Chemistry, Muthgasse 18, A-1190 Vienna, Austria
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27
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Pröfrock D, Prange A. Inductively coupled plasma-mass spectrometry (ICP-MS) for quantitative analysis in environmental and life sciences: a review of challenges, solutions, and trends. APPLIED SPECTROSCOPY 2012; 66:843-68. [PMID: 22800465 DOI: 10.1366/12-06681] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This focal point review provides an overview of recent developments and capabilities of inductively coupled plasma mass spectrometry (ICP-MS) coupled with different separation techniques for applications in the fields of quantitative environmental and bio-analysis. Over the past years numerous technical improvements, which are highlighted in this review, have helped to promote the evolution of ICP-MS to one of the most versatile tools for elemental quantification. In particular, the benefits and possibilities of using state-of-the-art hyphenated ICP-MS approaches for quantitative analysis are demonstrated with a focus on environmental and bio-analytical applications.
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Affiliation(s)
- Daniel Pröfrock
- Helmholtz Zentrum Geesthacht-Zentrum für Material und Küstenforschung, Department Marine Bioanalytical Chemistry, Max-Planck Str. 1, 21502 Geesthacht, Germany.
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28
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Bantscheff M, Lemeer S, Savitski MM, Kuster B. Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal Bioanal Chem 2012; 404:939-65. [PMID: 22772140 DOI: 10.1007/s00216-012-6203-4] [Citation(s) in RCA: 539] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 06/06/2012] [Accepted: 06/15/2012] [Indexed: 02/08/2023]
Abstract
Mass-spectrometry-based proteomics is continuing to make major contributions to the discovery of fundamental biological processes and, more recently, has also developed into an assay platform capable of measuring hundreds to thousands of proteins in any biological system. The field has progressed at an amazing rate over the past five years in terms of technology as well as the breadth and depth of applications in all areas of the life sciences. Some of the technical approaches that were at an experimental stage back then are considered the gold standard today, and the community is learning to come to grips with the volume and complexity of the data generated. The revolution in DNA/RNA sequencing technology extends the reach of proteomic research to practically any species, and the notion that mass spectrometry has the potential to eventually retire the western blot is no longer in the realm of science fiction. In this review, we focus on the major technical and conceptual developments since 2007 and illustrate these by important recent applications.
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29
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Schwarz G, Beck S, Weller MG, Linscheid MW. Comparison of the fragmentation behavior of differentially metal-coded affinity tag (MeCAT)-labeled peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:885-889. [PMID: 22791256 DOI: 10.1002/jms.3036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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30
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Esteban-Fernández D, Ahrends R, Linscheid MW. MeCAT peptide labeling for the absolute quantification of proteins by 2D-LC-ICP-MS. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:760-768. [PMID: 22707168 DOI: 10.1002/jms.3013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Metal-Coded Affinity Tags (MeCAT) reagents were devised for the absolute quantification of labeled proteins and peptides using inductively coupled plasma mass spectrometry (ICP-MS). After the recent publication of quantification approaches for digested proteins, this work presents a multidimensional strategy for the application of MeCAT to samples which require higher chromatographic resolution. Two-dimensional separations based on strong cation exchange (SCX) and reversed-phase (RP) chromatography, were used for the quantification of lysozyme, bovine serum albumin and transferrin after tryptic digestion. The elution protocols were optimized to improve the resolution of the MeCAT-labeled peptides which led to faster elutions in SCX and longer retention times in RP compared with unlabeled peptides. The optimized method provided enough resolution for the samples analyzed. Peptides losses during the whole procedure were studied. Although recoveries of greater than 90% were found in the RP dimension, important global losses in the two-dimensional offline approach forced us to use specific internal standards, in this case MeCAT-labeled standard peptides. External calibration and label-specific isotope dilution analysis (IDA) were tested and compared as possible quantification techniques. While both techniques showed accurate and precise determinations, the label-specific IDA technique resulted in more straightforward measurements and more affordable external calibrations. Finally, simultaneous quantification of three different samples labeled with different lanthanides was successfully performed demonstrating the potential of MeCAT combined with ICP-MS for multiplexing. Electrospray ionization mass spectrometry techniques provided the structural information needed for the identification of the labeled species.
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Affiliation(s)
- Diego Esteban-Fernández
- Department of Chemistry, Laboratory of Applied Analytics and Environmental Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany
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31
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Bergmann U, Ahrends R, Neumann B, Scheler C, Linscheid MW. Application of Metal-Coded Affinity Tags (MeCAT): Absolute Protein Quantification with Top-Down and Bottom-Up Workflows by Metal-Coded Tagging. Anal Chem 2012; 84:5268-75. [DOI: 10.1021/ac203460b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- U. Bergmann
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor-Strasse
2, 12489 Berlin, Germany
- Proteome Factory AG, Magnusstrasse 11, 12489 Berlin, Germany
| | - R. Ahrends
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor-Strasse
2, 12489 Berlin, Germany
| | - B. Neumann
- Proteome Factory AG, Magnusstrasse 11, 12489 Berlin, Germany
| | - C. Scheler
- Proteome Factory AG, Magnusstrasse 11, 12489 Berlin, Germany
| | - M. W. Linscheid
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor-Strasse
2, 12489 Berlin, Germany
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32
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El-Khatib AH, Esteban-Fernández D, Linscheid MW. Dual labeling of biomolecules using MeCAT and DOTA derivatives: application to quantitative proteomics. Anal Bioanal Chem 2012; 403:2255-67. [DOI: 10.1007/s00216-012-5910-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 02/24/2012] [Accepted: 02/27/2012] [Indexed: 10/28/2022]
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33
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Yang XY, Lu J, Sun X, He QY. Application of subproteomics in the characterization of Gram-positive bacteria. J Proteomics 2011; 75:2803-10. [PMID: 22240296 DOI: 10.1016/j.jprot.2011.12.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 12/14/2011] [Accepted: 12/19/2011] [Indexed: 01/13/2023]
Abstract
Gram-positive bacteria cause a series of diseases in human, animals and plants. There has been increasing interest in efforts to investigate pathogenesis of bacteria using multiple "omic" strategies including proteomics. Proteins in different cell fractions of bacteria may play different vital roles in various physiological processes, such as adhesion, invasion, internalization, sensing, respiration, oxidative stress protection and pathogenicity. Subproteomics specifically focuses on the pre-fractionated cellular proteins and thus may be able to characterize more low-abundance molecules that are usually overlooked by the traditional whole-cell proteomics, providing comprehensive information for further investigations. This review intends to outline the current progress, challenges and future development of subproteomics in the characterization of Gram-positive bacteria. This article is part of a Special Issue entitled: Proteomics: The clinical link.
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Affiliation(s)
- Xiao-Yan Yang
- Institute of Life and Health Engineering/National Engineering & Research Center of Genetic Medicine, College of Life Sciences and Technology, Jinan University, Guangzhou 510632, China
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34
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Crotti S, Granzotto C, Cairns WRL, Cescon P, Barbante C. Elemental labeling for the identification of proteinaceous-binding media in art works by ICP-MS. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:1297-1303. [PMID: 22223422 DOI: 10.1002/jms.2021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In the history of art, artists have used many different organic compounds to dissolve pigments and apply them onto a support to obtain a paint layer. Proteins were used with success from the Middle Ages up to the Renaissance, and the traditional protein sources were animal parts (skins, tendons and bones) or milk and eggs. Moreover, some of these materials are commonly used as adhesive. In this paper, the first application of the metallomic analytical technique to the identification of proteins in artworks is reported. Samples were derivatized with DTPA/Eu and the derivatization procedure was evaluated by matrix-assisted laser desorption/ionization time-of-flight before high performance liquid chromatography inductively coupled plasma MS analysis. This study has been carried out on laboratory models prepared in-house for method development, resulting in the correct identification of the different classes of proteinaceous binders typically used. In addition, some unknown paint layer samples have been analyzed demonstrating that the method is applicable to very small sample amounts (0.6 mg), which are compatible with the amount normally available for this kind of analysis. The results obtained demonstrate the effectiveness of the method, suggesting the potential future use as novel diagnostic tool in the scientific study of artworks.
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Affiliation(s)
- S Crotti
- DAIS, Ca' Foscari University of Venice, Dorsoduro 2137, 30123, Venice, Italy
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