1
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Armony G, Brehmer S, Srikumar T, Pfennig L, Zijlstra F, Trede D, Kruppa G, Lefeber DJ, van Gool AJ, Wessels HJCT. The GlycoPaSER Prototype as a Real-Time N-Glycopeptide Identification Tool Based on the PaSER Parallel Computing Platform. Int J Mol Sci 2023; 24:ijms24097869. [PMID: 37175577 PMCID: PMC10178020 DOI: 10.3390/ijms24097869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/13/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Real-time database searching allows for simpler and automated proteomics workflows as it eliminates technical bottlenecks in high-throughput experiments. Most importantly, it enables results-dependent acquisition (RDA), where search results can be used to guide data acquisition during acquisition. This is especially beneficial for glycoproteomics since the wide range of physicochemical properties of glycopeptides lead to a wide range of optimal acquisition parameters. We established here the GlycoPaSER prototype by extending the Parallel Search Engine in Real-time (PaSER) functionality for real-time glycopeptide identification from fragmentation spectra. Glycopeptide fragmentation spectra were decomposed into peptide and glycan moiety spectra using common N-glycan fragments. Each moiety was subsequently identified by a specialized algorithm running in real-time. GlycoPaSER can keep up with the rate of data acquisition for real-time analysis with similar performance to other glycoproteomics software and produces results that are in line with the literature reference data. The GlycoPaSER prototype presented here provides the first proof-of-concept for real-time glycopeptide identification that unlocks the future development of RDA technology to transcend data acquisition.
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Affiliation(s)
- Gad Armony
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Sven Brehmer
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany
| | | | | | - Fokje Zijlstra
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Dennis Trede
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany
| | - Gary Kruppa
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany
| | - Dirk J Lefeber
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alain J van Gool
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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2
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Lesur A, Bernardin F, Koncina E, Letellier E, Kruppa G, Schmit PO, Dittmar G. Quantification of 782 Plasma Peptides by Multiplexed Targeted Proteomics. J Proteome Res 2023. [PMID: 37011904 DOI: 10.1021/acs.jproteome.2c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Blood analysis is one of the foundations of clinical diagnostics. In recent years, the analysis of proteins in blood samples by mass spectrometry has taken a jump forward in terms of sensitivity and the number of identified proteins. The recent development of parallel reaction monitoring with parallel accumulation and serial fragmentation (prm-PASEF) combines ion mobility as an additional separation dimension. This increases the proteome coverage while allowing the use of shorter chromatographic gradients. To demonstrate the method's full potential, we used an isotope-labeled synthetic peptide mix of 782 peptides, derived from 579 plasma proteins, spiked into blood plasma samples with a prm-PASEF measurement allowing the quantification of 565 plasma proteins by targeted proteomics. As a less time-consuming alternative to the prm-PASEF method, we describe guided data independent acquisition (dia)-PASEF (g-dia-PASEF) and compare its application to prm-PASEF for measuring blood plasma. To demonstrate both methods' performance in clinical samples, 20 patient plasma samples from a colorectal cancer (CRC) cohort were analyzed. The analysis identified 14 differentially regulated proteins between the CRC patient and control individual plasma samples. This shows the technique's potential for the rapid and unbiased screening of blood proteins, abolishing the need for the preselection of potential biomarker proteins.
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Affiliation(s)
- Antoine Lesur
- Luxembourg Institute of Health, Strassen L-1445, Luxembourg
| | | | - Eric Koncina
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux L-4367, Luxembourg
| | - Elisabeth Letellier
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux L-4367, Luxembourg
| | - Gary Kruppa
- Bruker Daltonics, Billerica, Massachusetts 01821, United States
| | | | - Gunnar Dittmar
- Luxembourg Institute of Health, Strassen L-1445, Luxembourg
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux L-4367, Luxembourg
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3
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Peng X, Woodhouse I, Hancock G, Parker R, Marx K, Müller J, Salatino S, Partridge T, Nicastri A, Liao H, Kruppa G, Hellner K, Dorrell L, Ternette N. Novel canonical and non-canonical viral antigens extend current targets for immunotherapy of HPV-driven cervical cancer. iScience 2023; 26:106101. [PMID: 36876126 PMCID: PMC9978627 DOI: 10.1016/j.isci.2023.106101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/30/2022] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Current immunotherapeutic approaches for human papillomavirus (HPV)-driven cervical cancer target the viral oncogenes E6 and E7. We report viral canonical and alternative reading frame (ARF)-derived sequences presented on cervical tumor cells, including antigens encoded by the conserved viral gene E1. We confirm immunogenicity of the identified viral peptides in HPV-positive women, and women with cervical intraepithelial neoplasia. We observe consistent transcription of the E1, E6, and E7 genes in 10 primary cervical tumor resections from the four most common high-risk HPV subtypes (HPV16, 18, 31, and 45), suggesting the suitability of E1 as therapeutic target. We finally confirm HLA presentation of canonical peptides derived from E6 and E7, and ARF-derived viral peptides from a reverse-strand transcript spanning the HPV E1 and E2 genes in primary human cervical tumor tissue. Our results extend currently known viral immunotherapeutic targets in cervical cancer and highlight E1 as an important cervical cancer antigen.
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Affiliation(s)
- Xu Peng
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
| | - Isaac Woodhouse
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
| | - Gemma Hancock
- Nuffield Department of Medicine, University of Oxford, OX3 7FZ Oxford, UK
| | - Robert Parker
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Kristina Marx
- Bruker Daltonics, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Julius Müller
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Silvia Salatino
- Wellcome Centre Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Thomas Partridge
- Nuffield Department of Medicine, University of Oxford, OX3 7FZ Oxford, UK
| | - Annalisa Nicastri
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Hanqing Liao
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Gary Kruppa
- Bruker Daltonics, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Karin Hellner
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, John Radcliffe Hospital, OX3 9DU Oxford, UK
| | - Lucy Dorrell
- Nuffield Department of Medicine, University of Oxford, OX3 7FZ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
- Immunocore Ltd., OX14 4RY Abingdon, UK
| | - Nicola Ternette
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
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4
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Mukherjee S, Jankevics A, Busch F, Lubeck M, Zou Y, Kruppa G, Heck AJR, Scheltema RA, Reiding KR. Oxonium Ion-Guided Optimization of Ion Mobility-Assisted Glycoproteomics on the timsTOF Pro. Mol Cell Proteomics 2023; 22:100486. [PMID: 36549589 PMCID: PMC9853368 DOI: 10.1016/j.mcpro.2022.100486] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/15/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Spatial separation of ions in the gas phase, providing information about their size as collisional cross-sections, can readily be achieved through ion mobility. The timsTOF Pro (Bruker Daltonics) series combines a trapped ion mobility device with a quadrupole, collision cell, and a time-of-flight analyzer to enable the analysis of ions at great speed. Here, we show that the timsTOF Pro is capable of physically separating N-glycopeptides from nonmodified peptides and producing high-quality fragmentation spectra, both beneficial for glycoproteomics analyses of complex samples. The glycan moieties enlarge the size of glycopeptides compared with nonmodified peptides, yielding a clear cluster in the mobilogram that, next to increased dynamic range from the physical separation of glycopeptides and nonmodified peptides, can be used to make an effective selection filter for directing the mass spectrometer to analytes of interest. We designed an approach where we (1) focused on a region of interest in the ion mobilogram and (2) applied stepped collision energies to obtain informative glycopeptide tandem mass spectra on the timsTOF Pro:glyco-polygon-stepped collision energy-parallel accumulation serial fragmentation. This method was applied to selected glycoproteins, human plasma- and neutrophil-derived glycopeptides. We show that the achieved physical separation in the region of interest allows for improved extraction of information from the samples, even at shorter liquid chromatography gradients of 15 min. We validated our approach on human neutrophil and plasma samples of known makeup, in which we captured the anticipated glycan heterogeneity (paucimannose, phosphomannose, high mannose, hybrid and complex glycans) from plasma and neutrophil samples at the expected abundances. As the method is compatible with off-the-shelve data acquisition routines and data analysis software, it can readily be applied by any laboratory with a timsTOF Pro and is reproducible as demonstrated by a comparison between two laboratories.
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Affiliation(s)
- Soumya Mukherjee
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Andris Jankevics
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | | | | | - Yang Zou
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Gary Kruppa
- Bruker Daltonik GmbH & Co KG, Bremen, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
| | - Karli R Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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5
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Casasola-LaMacchia A, Seward RJ, Tourdot S, Willetts M, Kruppa G, Agostino MJ, Bergeron G, Ahyi-Amendah N, Ciarla A, Lu Z, Kim HY, Hickling TP, Neubert H. HLAII peptide presentation of infliximab increases when complexed with TNF. Front Immunol 2022; 13:932252. [PMID: 36177046 PMCID: PMC9513746 DOI: 10.3389/fimmu.2022.932252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
CD4+ T-cell activation through recognition of Human Leukocyte Antigen II (HLAII)-presented peptides is a key step in the development of unwanted immune response against biotherapeutics, such as the generation of anti-drug antibodies (ADA). Therefore, the identification of HLAII-presented peptides derived from biotherapeutics is a crucial part of immunogenicity risk assessment and mitigation strategies during drug development. To date, numerous CD4+ T-cell epitopes have been identified by HLAII immunopeptidomics in antibody-based biotherapeutics using either their native or aggregated form. Antibody-target immune complexes have been detected in patients with ADA and are thought to play a role in ADA development by enhancing the presentation of CD4+ T-cell epitopes at the surface of antigen presenting cells (APCs). The aim of this study was to investigate the effect of biotherapeutic antibody-target immune complexes on the HLAII peptide presentation of biotherapeutics in human primary monocyte-derived dendritic cells (DCs). The trimeric tumor necrosis factor (TNF) and its biotherapeutic antagonists infliximab (INFL), adalimumab (ADAL), and a single armed Fab’ were used as a model system. The HLAII immunopeptidome of DCs loaded with antagonists or their immune complexes with TNF was analyzed by trapped ion mobility time-of-flight mass spectrometry (timsTOF MS) leading to the identification of ~ 12,000 unique HLAII-associated peptides per preparation. Anti-TNF sequences were detected at a median of 0.3% of the total immunopeptidome, against a majority background of peptides from endogenous and media-derived proteins. TNF antagonist presentation spanned the variable and constant regions in a widespread manner in both light and heavy chains, consistent with previously discovered HLAII peptides. This investigation extends the collection of observed HLAII peptides from anti-TNF biotherapeutics to include sequences that at least partially span the complementary determining regions (CDRs), such as the LCDR1 for both INFL and ADAL. Although antagonist presentation varied significantly across donors, peptides from both bivalent antagonists INFL and ADAL were more highly presented relative to the Fab’. While TNF immune complexes did not alter overall HLAII presentation, a moderate increase in presentation of a subset of peptide clusters was observed in the case of INFL-TNF, which included HCDR2, HCDR3 and LCDR2 sequences.
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Affiliation(s)
- Andrea Casasola-LaMacchia
- BioMedicine Design, Worldwide Research, Development and Medical, Pfizer Inc., Andover, MA, United States
- *Correspondence: Andrea Casasola-LaMacchia,
| | - Robert Joseph Seward
- BioMedicine Design, Worldwide Research, Development and Medical, Pfizer Inc., Andover, MA, United States
| | - Sophie Tourdot
- BioMedicine Design, Worldwide Research, Development and Medical, Pfizer Inc., Andover, MA, United States
| | | | - Gary Kruppa
- Bruker Daltonics, Billerica, MA, United States
| | | | - Gabrielle Bergeron
- BioMedicine Design, Worldwide Research, Development and Medical, Pfizer Inc., Andover, MA, United States
| | - Nathalie Ahyi-Amendah
- BioMedicine Design, Worldwide Research, Development and Medical, Pfizer Inc., Andover, MA, United States
| | - Andrew Ciarla
- BioMedicine Design, Worldwide Research, Development and Medical, Pfizer Inc., Andover, MA, United States
| | - Zhaojiang Lu
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, MA, United States
| | - Hai-Young Kim
- Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, MA, United States
| | - Timothy P. Hickling
- BioMedicine Design, Worldwide Research, Development and Medical, Pfizer Inc., Andover, MA, United States
| | - Hendrik Neubert
- BioMedicine Design, Worldwide Research, Development and Medical, Pfizer Inc., Andover, MA, United States
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6
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Zhu H, Mellors JS, Chan WC, Thompson JW, Ficarro SB, Tavares I, Bratt AS, Decker J, Krause M, Kruppa G, Buhrlage SJ, Marto JA. On-Chip Preconcentration Microchip Capillary Electrophoresis Based CE-PRM-LIVE for High-Throughput Selectivity Profiling of Deubiquitinase Inhibitors. Anal Chem 2022; 94:9508-9513. [PMID: 35729701 PMCID: PMC10654755 DOI: 10.1021/acs.analchem.2c01337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The family of deubiquitinases (DUBs) comprises ∼100 enzymes that cleave ubiquitin from substrate proteins and thereby regulate key aspects of human physiology. DUBs have recently emerged as disease-relevant and chemically tractable, although currently there are no approved DUB-targeting drugs and most preclinical small molecules are low-potency and/or multitargeted. We paired a novel capillary electrophoresis microchip containing an integrated, "on-chip" C18 bed (SPE-ZipChip) with a TMT version of our recently described PRM-LIVE acquisition scheme on a timsTOF Pro mass spectrometer to facilitate rapid activity-based protein profiling of DUB inhibitors. We demonstrate the ability of the SPE-ZipChip to improve proteome coverage of complex samples as well as the quantitation integrity of CE-PRM-LIVE for TMT labeled samples. These technologies provide a platform to accurately quantify competitive binding of covalent and reversible inhibitors in a multiplexed assay that spans 49 endogenous DUBs in less than 15 min.
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Affiliation(s)
- He Zhu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - J Scott Mellors
- 908 Devices Inc., Boston, Massachusetts 02210, United States
| | - Wai Cheung Chan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - J Will Thompson
- 908 Devices Inc., Boston, Massachusetts 02210, United States
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Isidoro Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Ariana S Bratt
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jens Decker
- Bruker Daltonics GmbH & Co. KG, Bremen 28359, Germany
| | | | - Gary Kruppa
- Bruker S.R.O., District Brno-City 61900 Czech Republic
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
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7
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Loginov DS, Fiala J, Brechlin P, Kruppa G, Novak P. Hydroxyl radical footprinting analysis of a human haptoglobin-hemoglobin complex. Biochim Biophys Acta Proteins Proteom 2022; 1870:140735. [PMID: 34742912 DOI: 10.1016/j.bbapap.2021.140735] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 09/22/2021] [Accepted: 10/26/2021] [Indexed: 10/19/2022]
Abstract
Methods of structural mass spectrometry have become more popular to study protein structure and dynamics. Among them, fast photochemical oxidation of proteins (FPOP) has several advantages such as irreversibility of modifications and more facile determination of the site of modification with single residue resolution. In the present study, FPOP analysis was applied to study the hemoglobin (Hb) - haptoglobin (Hp) complex allowing identification of respective regions altered upon the complex formation. FPOP footprinting using a timsTOF Pro mass spectrometer revealed structural information for 84 and 76 residues in Hp and Hb, respectively, including statistically significant differences in the modification extent below 0.3%. The most affected residues upon complex formation were Met76 and Tyr140 in Hbα, and Tyr280 and Trp284 in Hpβ. The data allowed determination of amino acids directly involved in Hb - Hp interactions and those located outside of the interaction interface yet affected by the complex formation. Also, previously modeled interaction between Hb βTrp37 and Hp βPhe292 was not confirmed by our data. Data are available via ProteomeXchange with identifier PXD021621.
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Affiliation(s)
- Dmitry S Loginov
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic; Orekhovich Institute of Biomedical Chemistry, Pogodinskaja str. 10, 119191 Moscow, Russia.
| | - Jan Fiala
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic; Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Peter Brechlin
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Gary Kruppa
- Bruker s.r.o., Prazakova 60, 619 00, Brno, Czech Republic
| | - Petr Novak
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic.
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8
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Brzhozovskiy A, Kononikhin A, Bugrova AE, Kovalev GI, Schmit PO, Kruppa G, Nikolaev EN, Borchers CH. The Parallel Reaction Monitoring-Parallel Accumulation-Serial Fragmentation (prm-PASEF) Approach for Multiplexed Absolute Quantitation of Proteins in Human Plasma. Anal Chem 2022; 94:2016-2022. [PMID: 35040635 DOI: 10.1021/acs.analchem.1c03782] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mass spectrometry (MS)-based quantitative proteomic methods have become some of the major tools for protein biomarker discovery and validation. The recently developed parallel reaction monitoring-parallel accumulation-serial fragmentation (prm-PASEF) approach on a Bruker timsTOF Pro mass spectrometer allows the addition of ion mobility as a new dimension to LC-MS-based proteomics and increases proteome coverage at a reduced analysis time. In this study, a prm-PASEF approach was used for the multiplexed absolute quantitation of proteins in human plasma using isotope-labeled peptide standards for 125 plasma proteins, over a broad (104-106) dynamic range. Optimization of LC and MS parameters, such as accumulation time and collision energy, resulted in improved sensitivity for more than half of the targets (73 out of 125 peptides) by increasing the signal-to-noise ratio by a factor of up to 10. Overall, 41 peptides showed up to a 2-fold increase in sensitivity, 25 peptides showed up to a 5-fold increase in sensitivity, and 7 peptides showed up to a 10-fold increase in sensitivity. Implementation of the prm-PASEF method allowed absolute protein quantitation (down to 1.13 fmol) in human plasma samples. A comparison of the concentration values of plasma proteins determined by MRM on a QTRAP instrument and by prm-PASEF on a timsTOF Pro revealed an excellent correlation (R2 = 0.97) with a slope of close to 1 (0.99), demonstrating that prm-PASEF is well suited for "absolute" quantitative proteomics.
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Affiliation(s)
- Alexander Brzhozovskiy
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Alexey Kononikhin
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Anna E Bugrova
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia.,Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Grigoriy I Kovalev
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | | | - Gary Kruppa
- Bruker Daltonics, Inc. Billerica, Massachusetts 018215, United States
| | - Evgeny N Nikolaev
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Christoph H Borchers
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia.,Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
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9
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Zhu H, Ficarro SB, Alexander WM, Fleming LE, Adelmant G, Zhang T, Willetts M, Decker J, Brehmer S, Krause M, East MP, Gray NS, Johnson GL, Kruppa G, Marto JA. PRM-LIVE with Trapped Ion Mobility Spectrometry and Its Application in Selectivity Profiling of Kinase Inhibitors. Anal Chem 2021; 93:13791-13799. [PMID: 34606255 DOI: 10.1021/acs.analchem.1c02349] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Parallel reaction monitoring (PRM) has emerged as a popular approach for targeted protein quantification. With high ion utilization efficiency and first-in-class acquisition speed, the timsTOF Pro provides a powerful platform for PRM analysis. However, sporadic chromatographic drift in peptide retention time represents a fundamental limitation for the reproducible multiplexing of targets across PRM acquisitions. Here, we present PRM-LIVE, an extensible, Python-based acquisition engine for the timsTOF Pro, which dynamically adjusts detection windows for reproducible target scheduling. In this initial implementation, we used iRT peptides as retention time standards and demonstrated reproducible detection and quantification of 1857 tryptic peptides from the cell lysate in a 60 min PRM-LIVE acquisition. As an application in functional proteomics, we use PRM-LIVE in an activity-based protein profiling platform to assess binding selectivity of small-molecule inhibitors against 220 endogenous human kinases.
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Affiliation(s)
- He Zhu
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Scott B Ficarro
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, United States
| | - William M Alexander
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Laura E Fleming
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Guillaume Adelmant
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Tinghu Zhang
- Department of Chemical & Systems Biology and ChEM-H, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Matthew Willetts
- Bruker Daltonics Inc, Billerica, Massachusetts 01821, United States
| | - Jens Decker
- Bruker Daltonics GmbH & Co. KG, Bremen 28359, Germany
| | - Sven Brehmer
- Bruker Daltonics GmbH & Co. KG, Bremen 28359, Germany
| | | | - Michael P East
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Nathanael S Gray
- Department of Chemical & Systems Biology and ChEM-H, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Gary L Johnson
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Gary Kruppa
- Bruker S.R.O., District Brno-City 61900, Czech Republic
| | - Jarrod A Marto
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, United States.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
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10
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Loginov DS, Fiala J, Chmelik J, Brechlin P, Kruppa G, Novak P. Correction to "Benefits of Ion Mobility Separation and Parallel Accumulation-Serial Fragmentation Technology on timsTOF Pro for the Needs of Fast Photochemical Oxidation of Protein Analysis". ACS Omega 2021; 6:14726. [PMID: 34124494 PMCID: PMC8190877 DOI: 10.1021/acsomega.1c02648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 06/12/2023]
Abstract
[This corrects the article DOI: 10.1021/acsomega.1c00732.].
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Affiliation(s)
- Dmitry S Loginov
- Institute of Microbiology, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
- Orekhovich Institute of Biomedical Chemistry, Pogodinskaja str. 10, 119191 Moscow, Russia
| | - Jan Fiala
- Faculty of Science, Charles University, Hlavova 8, 128 20 Prague, Czech Republic
| | - Josef Chmelik
- Institute of Microbiology, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
| | - Peter Brechlin
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Gary Kruppa
- Bruker s.r.o., Prazakova 60, 619 00 Brno, Czech Republic
| | - Petr Novak
- Institute of Microbiology, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
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11
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Loginov DS, Fiala J, Chmelik J, Brechlin P, Kruppa G, Novak P. Benefits of Ion Mobility Separation and Parallel Accumulation-Serial Fragmentation Technology on timsTOF Pro for the Needs of Fast Photochemical Oxidation of Protein Analysis. ACS Omega 2021; 6:10352-10361. [PMID: 34056188 PMCID: PMC8153767 DOI: 10.1021/acsomega.1c00732] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/29/2021] [Indexed: 05/07/2023]
Abstract
Fast photochemical oxidation of proteins (FPOP) is a recently developed technique for studying protein folding, conformations, interactions, etc. In this method, hydroxyl radicals, usually generated by KrF laser photolysis of H2O2, are used for irreversible labeling of solvent-exposed side chains of amino acids. Mapping of the oxidized residues to the protein's structure requires pinpointing of modifications using a bottom-up proteomic approach. In this work, a quadrupole time-of-flight (QTOF) mass spectrometer coupled with trapped ion mobility spectrometry (timsTOF Pro) was used for identification of oxidative modifications in a model protein. Multiple modifications on the same residues, including six modifications of histidine, were successfully resolved. Moreover, parallel accumulation-serial fragmentation (PASEF) technology allows successful sequencing of even minor populations of modified peptides. The data obtained indicate a clear improvement of the quality of the FPOP analysis from the viewpoint of the number of identified peptides bearing oxidative modifications and their precise localization. Data are available via ProteomeXchange with identifier PXD020509.
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Affiliation(s)
- Dmitry S. Loginov
- Institute
of Microbiology, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
- Faculty
of Science, Charles University, Hlavova 8, 128 20 Prague, Czech Republic
| | - Jan Fiala
- Orekhovich
Institute of Biomedical Chemistry, Pogodinskaja str. 10, 119191 Moscow, Russia
| | - Josef Chmelik
- Institute
of Microbiology, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
| | - Peter Brechlin
- Bruker
Daltonik GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Gary Kruppa
- Bruker
s.r.o., Prazakova 60, 619 00 Brno, Czech
Republic
| | - Petr Novak
- Institute
of Microbiology, The Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
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12
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Beger RD, Dunn WB, Bandukwala A, Bethan B, Broadhurst D, Clish CB, Dasari S, Derr L, Evans A, Fischer S, Flynn T, Hartung T, Herrington D, Higashi R, Hsu PC, Jones C, Kachman M, Karuso H, Kruppa G, Lippa K, Maruvada P, Mosley J, Ntai I, O'Donovan C, Playdon M, Raftery D, Shaughnessy D, Souza A, Spaeder T, Spalholz B, Tayyari F, Ubhi B, Verma M, Walk T, Wilson I, Witkin K, Bearden DW, Zanetti KA. Towards quality assurance and quality control in untargeted metabolomics studies. Metabolomics 2019; 15:4. [PMID: 30830465 PMCID: PMC6443086 DOI: 10.1007/s11306-018-1460-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022]
Abstract
We describe here the agreed upon first development steps and priority objectives of a community engagement effort to address current challenges in quality assurance (QA) and quality control (QC) in untargeted metabolomic studies. This has included (1) a QA and QC questionnaire responded to by the metabolomics community in 2015 which recommended education of the metabolomics community, development of appropriate standard reference materials and providing incentives for laboratories to apply QA and QC; (2) a 2-day 'Think Tank on Quality Assurance and Quality Control for Untargeted Metabolomic Studies' held at the National Cancer Institute's Shady Grove Campus and (3) establishment of the Metabolomics Quality Assurance and Quality Control Consortium (mQACC) to drive forward developments in a coordinated manner.
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Affiliation(s)
- Richard D Beger
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, USA.
| | - Warwick B Dunn
- School of Biosciences, Phenome Centre Birmingham and Institute for Metabolism and Systems Research, University of Birmingham, Birmingham, B15 2TT, UK.
| | | | | | | | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Leslie Derr
- Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Thomas Flynn
- Food and Drug Administration, Silver Spring, MD, USA
| | - Thomas Hartung
- Johns Hopkins School of Public Health, Baltimore, MD, USA
| | | | | | - Ping-Ching Hsu
- University of Arkansas Medical Sciences, Little Rock, AR, USA
| | - Christina Jones
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | | | | | - Katrice Lippa
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Padma Maruvada
- National Institute of Diabetes and Digestive and Kidney Disorders, Bethesda, MD, USA
| | - Jonathan Mosley
- National Exposure Research Laboratory, US Environmental Protection Agency, Athens, GA, USA
| | | | - Claire O'Donovan
- European Molecular Biology Laboratory -European Bioinformatics Institute, Hinxton, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | - Daniel W Bearden
- National Institute of Standards and Technology, Charleston, SC, USA
- Ichthus Unlimited, LLC, 109, S. 32nd Street, West Des Moines, IA, USA
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13
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Schmit PO, Vialaret J, Wessels HJ, van Gool AJ, Lehmann S, Gabelle A, Wood J, Bern M, Paape R, Suckau D, Kruppa G, Hirtz C. Towards a routine application of Top-Down approaches for label-free discovery workflows. J Proteomics 2018; 175:12-26. [DOI: 10.1016/j.jprot.2017.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 07/14/2017] [Accepted: 08/01/2017] [Indexed: 12/11/2022]
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14
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Razavi M, Johnson LDS, Lum JJ, Kruppa G, Anderson NL, Pearson TW. Quantification of a Proteotypic Peptide from Protein C Inhibitor by Liquid Chromatography–Free SISCAPA-MALDI Mass Spectrometry: Application to Identification of Recurrence of Prostate Cancer. Clin Chem 2013; 59:1514-22. [DOI: 10.1373/clinchem.2012.199786] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND
Biomarker validation remains one of the most challenging constraints to the development of new diagnostic assays. To facilitate biomarker validation, we previously developed a chromatography-free stable isotope standards and capture by antipeptide antibodies (SISCAPA)-MALDI assay allowing rapid, high-throughput quantification of protein analytes in large sample sets. Here we applied this assay to the measurement of a surrogate proteotypic peptide from protein C inhibitor (PCI) in sera from patients with prostate cancer.
METHODS
A 2-plex SISCAPA-MALDI assay for quantification of proteotypic peptides from PCI and soluble transferrin receptor (sTfR) was used to measure these peptides in 159 trypsin-digested sera collected from 51 patients with prostate cancer. These patients had been treated with radiation with or without neoadjuvant androgen deprivation.
RESULTS
Patients who experienced biochemical recurrence of prostate cancer showed decreased serum concentrations of the PCI peptide analyte within 18 months of treatment. The PCI peptide concentrations remained increased in the sera of patients who did not experience cancer recurrence. Prostate-specific antigen concentrations had no predictive value during the same time period.
CONCLUSIONS
The high-throughput, liquid chromatography–free SISCAPA-MALDI assay is capable of rapid quantification of proteotypic PCI and sTfR peptide analytes in complex serum samples. Decreased serum concentrations of the PCI peptide were found to be related to recurrence of prostate cancer in patients treated with radiation with or without hormone therapy. However, a larger cohort of patients will be required for unequivocal validation of the PCI peptide as a biomarker for clinical use.
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Affiliation(s)
- Morteza Razavi
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Lisa DS Johnson
- Trev & Joyce Deeley Research Centre, BC Cancer Agency, Victoria, British Columbia, Canada
| | - Julian J Lum
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
- Trev & Joyce Deeley Research Centre, BC Cancer Agency, Victoria, British Columbia, Canada
| | | | | | - Terry W Pearson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
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15
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Anderson NL, Razavi M, Pearson TW, Kruppa G, Paape R, Suckau D. Precision of Heavy–Light Peptide Ratios Measured by MALDI-TOF Mass Spectrometry. J Proteome Res 2012; 11:1868-78. [DOI: 10.1021/pr201092v] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- N. Leigh Anderson
- Plasma Proteome Institute, Washington, D.C., United States
- SISCAPA Assay Technologies, Inc., Washington, D.C., United States
| | - Morteza Razavi
- Department of Biochemistry and
Microbiology, University of Victoria, Victoria,
British Columbia, V8W 3P6, Canada
| | - Terry W. Pearson
- SISCAPA Assay Technologies, Inc., Washington, D.C., United States
- Department of Biochemistry and
Microbiology, University of Victoria, Victoria,
British Columbia, V8W 3P6, Canada
| | - Gary Kruppa
- Bruker Daltonics, Billerica, Massachusetts,
United States
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16
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17
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Pól J, Vidová V, Kruppa G, Kobliha V, Novák P, Lemr K, Kotiaho T, Kostiainen R, Havlíček V, Volný M. Automated Ambient Desorption−Ionization Platform for Surface Imaging Integrated with a Commercial Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Anal Chem 2009; 81:8479-87. [DOI: 10.1021/ac901368q] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jaroslav Pól
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague, Czech Republic, Division of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Department of Analytical Chemistry, Faculty of Science, Palacký University, Tŕ. Svobody 8, CZ-771 46 Olomouc, Czech Republic, and Laboratory of Analytical Chemistry, Department of Chemistry,
| | - Veronika Vidová
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague, Czech Republic, Division of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Department of Analytical Chemistry, Faculty of Science, Palacký University, Tŕ. Svobody 8, CZ-771 46 Olomouc, Czech Republic, and Laboratory of Analytical Chemistry, Department of Chemistry,
| | - Gary Kruppa
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague, Czech Republic, Division of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Department of Analytical Chemistry, Faculty of Science, Palacký University, Tŕ. Svobody 8, CZ-771 46 Olomouc, Czech Republic, and Laboratory of Analytical Chemistry, Department of Chemistry,
| | - Václav Kobliha
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague, Czech Republic, Division of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Department of Analytical Chemistry, Faculty of Science, Palacký University, Tŕ. Svobody 8, CZ-771 46 Olomouc, Czech Republic, and Laboratory of Analytical Chemistry, Department of Chemistry,
| | - Petr Novák
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague, Czech Republic, Division of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Department of Analytical Chemistry, Faculty of Science, Palacký University, Tŕ. Svobody 8, CZ-771 46 Olomouc, Czech Republic, and Laboratory of Analytical Chemistry, Department of Chemistry,
| | - Karel Lemr
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague, Czech Republic, Division of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Department of Analytical Chemistry, Faculty of Science, Palacký University, Tŕ. Svobody 8, CZ-771 46 Olomouc, Czech Republic, and Laboratory of Analytical Chemistry, Department of Chemistry,
| | - Tapio Kotiaho
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague, Czech Republic, Division of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Department of Analytical Chemistry, Faculty of Science, Palacký University, Tŕ. Svobody 8, CZ-771 46 Olomouc, Czech Republic, and Laboratory of Analytical Chemistry, Department of Chemistry,
| | - Risto Kostiainen
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague, Czech Republic, Division of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Department of Analytical Chemistry, Faculty of Science, Palacký University, Tŕ. Svobody 8, CZ-771 46 Olomouc, Czech Republic, and Laboratory of Analytical Chemistry, Department of Chemistry,
| | - Vladimír Havlíček
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague, Czech Republic, Division of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Department of Analytical Chemistry, Faculty of Science, Palacký University, Tŕ. Svobody 8, CZ-771 46 Olomouc, Czech Republic, and Laboratory of Analytical Chemistry, Department of Chemistry,
| | - Michael Volný
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague, Czech Republic, Division of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Department of Analytical Chemistry, Faculty of Science, Palacký University, Tŕ. Svobody 8, CZ-771 46 Olomouc, Czech Republic, and Laboratory of Analytical Chemistry, Department of Chemistry,
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18
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Baidoo EEK, Benke PI, Neusüss C, Pelzing M, Kruppa G, Leary JA, Keasling JD. Capillary Electrophoresis-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for the Identification of Cationic Metabolites via a pH-Mediated Stacking-Transient Isotachophoretic Method. Anal Chem 2008; 80:3112-22. [DOI: 10.1021/ac800007q] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Takats Z, Kobliha V, Sevcik K, Novak P, Kruppa G, Lemr K, Havlicek V. Characterization of DESI-FTICR mass spectrometry - from ECD to accurate mass tissue analysis. J Mass Spectrom 2008; 43:196-203. [PMID: 17918779 DOI: 10.1002/jms.1285] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Implementation of desorption electrospray ionization (DESI) technique on a 9.4 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer is described. Desorption electrospray technique is capable of the direct investigation of natural samples without any need for sample preparation or chromatographic separation. Since the DESI mass spectra of natural samples are very complex owing to the lack of preseparation or cleanup, the ideal mass spectrometric analyzer for these applications is a high-resolution instrument such as FTICR mass spectrometer. DESI was implemented by constructing an electronically controlled source framework comprising six linear moving stages and one rotating stage. A three-dimensional linear stage was used to accommodate samples, while another 3D linear stage equipped with rotating stage was used as a spray mount. A modified electrosonic sprayer was used as a primary electrospray device. DESI-FTICR setup was characterized with regard to geometrical, electrical and flow conditions using deposited peptide samples in range of 1-100 pmol gross deposited amount on glass and polymer surfaces. Optimized conditions enabled the routine acquisition of DESI-MS spectra on the instrument at 130 000 resolution in the broadband mode and with comparable sensitivity to data reported in the literature. Since the main significance of DESI-FTICR MS is the combination of intact tissue analysis, the capabilities of the technique were demonstrated by analyzing murine liver samples. Presence of lysophospholipids in the liver tissue was tentatively associated with the lipid metabolism taking place in liver. DESI-FTICR is also a promising technique in the field of peptide analysis due to capability of top-down sequencing using electron capture dissociation. As a proof-of-principle experiment, a small synthetic polypeptide containing 36 amino acids was ionized using DESI and was sequenced in the FTICR by means of ECD (electron capture dissociation) fragmentation. Spectra gave almost full sequence information in agreement with the known amino acid sequence of the species.
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Affiliation(s)
- Zoltan Takats
- Semmelweis University, VIII. Ulloi ut 26, 1085 Budapest, Hungary
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20
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Szabolcs A, Kruppa G, Sági J, Ötvös L. Unnatural nucleosides and nucleotides. III. Preparation of 2-14C and 4-14C labelled 5-alkyluracils and 5-alkyl-2′-deoxyuridines. J Labelled Comp Radiopharm 2006. [DOI: 10.1002/jlcr.2580140509] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Robinson NE, Lampi KJ, Speir JP, Kruppa G, Easterling M, Robinson AB. Quantitative measurement of young human eye lens crystallins by direct injection Fourier transform ion cyclotron resonance mass spectrometry. Mol Vis 2006; 12:704-11. [PMID: 16807530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
PURPOSE Human eye lenses at birth are primarily constructed of 12 distinct crystallins and two truncated crystallins. The molecular weights of these 14 proteins vary between about 20,000 and 30,000 Da. The relative amounts of these molecules and their post-synthetic changes with age are of substantial interest in the study of lens biochemistry and lens pathology. Fourier transform mass spectrometry of unfractionated lens homogenates now permits precise quantitative measurement of the relative amounts of lens crystallins. We report herein the measurement of the 14 crystallins in 10 pairs of lenses from humans between the ages of 2 and 300 days. METHODS Eye lenses were obtained from human donors of various ages in the first year of life. These lenses were homogenized in 0.02 M phosphate buffer at pH 7.0 with 0.001 M EDTA, desalted by washing over a 3,000 Da filter, and injected directly into the nanospray source of a hybrid Fourier transform ion cyclotron resonance mass spectrometer, Qq-FT(ICR)MS, equipped with a 12 Tesla magnet. The crystallins were quantitatively ionized and mass analyzed in the ICR cell of the mass spectrometer. The detected signals of all of the isotopic and charge state species for each crystallin were normalized and summed to determine the protein quantities. RESULTS The relative amounts of the 14 crystallins are found to be quite similar from individual to individual at birth. These amounts are in integer ratios to one another that suggest important structural relations within the lens. In two cases, the relative amounts of alphaA- and betaB2-crystallin change proportionally to the logarithm of age during the first year, with alphaA- decreasing and betaB2-crystallin increasing. The changes in alphaA- and betaB2-crystallin are mutually offsetting, with alphaA-crystallin decreasing from 30% to 18% and betaB2-increasing from 12% to 24%. CONCLUSIONS These observations suggest that the human eye lens at birth is constructed of crystallins in which the numbers of crystallin molecules have regular integral relationships to each other. As the lens develops during the first year, some of these relationships change. While the functional significance of the reciprocal decrease in alphaA- and increase in betaB2-crystallin is not known, betaB2-crystallin may substitute for alphaA-crystallin in the lens structures synthesized during the year after birth. Direct injection FT(ICR)MS of unfractionated lens was found to be an excellent method for the quantitative measurement of lens crystallins.
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Affiliation(s)
- Noah E Robinson
- Oregon Institute of Science and Medicine, Cave Junction, OR 97523, USA.
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22
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Rice GE, Georgiou HM, Ahmed N, Shi G, Kruppa G. Translational proteomics: developing a predictive capacity -- a review. Placenta 2006; 27 Suppl A:S76-86. [PMID: 16434096 DOI: 10.1016/j.placenta.2005.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Revised: 10/29/2005] [Accepted: 11/07/2005] [Indexed: 11/27/2022]
Abstract
Over the past decade, proteomics has undergone a rapid development and radiation, diversifying across the biochemical landscape. While no single technique yet delivers complete proteomic coverage, application-specific adaptations afford significant opportunity for discovery and the development of predictive capacity (e.g. surrogate biomarker and clinical diagnostics). Targeted proteomic approaches, protein profiling strategies using affinity capture mass spectrometry and solution array represent realistic opportunities to deliver predictive capacity. The aim of this review is to provide an overview of proteomic technologies and how the outcomes delivered by such platforms may be translated into applications of predictive utility in clinical and basic science. In particular, recent applications in protein/peptide profiling (solid-phase affinity capture mass spectrometry and the targeted approach of antibody arrays) and the opportunities they afford researchers within the discipline of reproductive biology to develop new diagnostic and prognostic tests and surrogate biomarkers to improve the delivery of women's health care are considered.
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Affiliation(s)
- G E Rice
- Department of Translational Proteomics, Baker Heart Research Institute, 75 Commercial Road, Melbourne 3004, Victoria, Australia.
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23
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Robinson NE, Lampi KJ, McIver RT, Williams RH, Muster WC, Kruppa G, Robinson AB. Quantitative measurement of deamidation in lens betaB2-crystallin and peptides by direct electrospray injection and fragmentation in a Fourier transform mass spectrometer. Mol Vis 2005; 11:1211-9. [PMID: 16402021 PMCID: PMC1470883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
PURPOSE Deamidation of lens crystallins and specific deamidation sites have been suggested to be associated with aging and cataracts. However, these studies have been hindered by the lack of suitable quantitative methods of measurement of protein deamidation. We demonstrate herein a method to quantitatively measure deamidation of proteins and peptides without prior sample preparation or separation in order to directly compare the amidated and deamidated forms. We have tested the hypothesis that the 19 mDa mass defect that distinguishes deamidated peptides and proteins from the ordinary natural isotopic species can be utilized for quantitative measurement of their rate and extent of deamidation. The measurement technique used was ion cyclotron resonance Fourier transform mass spectrometry (FTMS), alone with no prior sample preparation or separation. The amidated and deamidated species were recombinantly expressed human eye lens betaB2-crystallins and the peptides GlyIleAsnAlaGly and GlyAsnAsnAsnGly. FTMS measurements of lens proteins from a 1-month-old human donor were also carried out. METHODS Wild type and mutant human eye lens betaB2-crystallins with Gln162 replaced by Glu162 were produced in bacteria, and GlyIleAsnAlaGly and GlyAsnAsnAsnGly were synthesized by Merrifield solid-phase peptide synthesis. The peptides were deamidated in pH 7.4, 37.00 degrees C, 0.15 M Tris-HCl aqueous solution for 18 successive time intervals before analysis. Mutant and wildtype betaB2-crystallin solutions at various compositional percentages were mixed and analyzed. The peptides were introduced by electrospray ionization and immediately analyzed in the ion cyclotron resonance (ICR) Fourier transform mass analyzer. Two mass defect analysis procedures were demonstrated for the proteins. In the first, betaB2-crystallin was introduced into the mass spectrometer by electrospray ionization and the +29 isotopic group was selectively introduced into the ICR mass analyzer, where 14 residue and 18 residue laser-induced fragments were separated and the extent of deamidation determined by mass defect analysis. In the second, betaB2-crystallin was introduced into the mass spectrometer by electrospray ionization and the entire sample was fragmented by collision ionization before introduction into the ICR mass analyzer, where 14 residue fragments were separated and the extent of deamidation determined by mass defect analysis. RESULTS The betaB2-crystallin mass spectra showed a good quantitative dependence upon extent of deamidation. Direct injection by electrospray ionization followed by ion selection and laser fragmentation or by collision fragmentation produced fragments of amidated and deamidated betaB2-crystallin that were appropriate for FTMS quantitative analysis. The two peptides exhibited the expected four deamidation rate curves with acceptable precision. CONCLUSIONS Mass defect FTMS quantitative analysis of protein deamidation, as reported for the first time herein and illustrated with betaB2-crystallin, should prove quite useful. This procedure omits gel separation, chromatography, enzymatic digestion, derivatization, and other procedures that currently add cost and time while degrading quantitative comparison of the amidated and deamidated forms. Mass defect FTMS is also well suited to quantitative deamidation rate studies of peptides. The substantial potential significance of this technique is evident, as example, for lens crystallins where it makes possible quantitative studies of age and disease-dependent deamidation that have heretofore been very difficult. This technique should allow convenient and reliable identification and quantitative measurement of specific deamidation sites that may play a role in aging and cataracts.
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Affiliation(s)
- Noah E Robinson
- Oregon Institute of Science and Medicine, Cave Junction, OR 97523, USA.
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24
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Abstract
Metabolomics, also known as Metabolic Profiling, is an emerging discipline under the umbrella concept of systems biology. The goal of metabolomics is to know and understand the concentrations and fluxes of endogenous metabolites within a living biological system under study. General tools are being developed for the rapid measurement of many metabolites in a single experiment, most of which are mass spectrometric methods. FT-ICR has unique advantages, as a mass spectrometric method, in this regard. Applications of FT-ICR to metabolomics analyses will be discussed and reviewed in the context of the single publication currently available.
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Affiliation(s)
- Stephen C Brown
- Esperion Therapeutics, Inc., Ann Arbor, Michigan 48108, USA.
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25
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McDonald LA, Barbieri LR, Carter GT, Kruppa G, Feng X, Lotvin JA, Siegel MM. FTMS structure elucidation of natural products: application to muraymycin antibiotics using ESI multi-CHEF SORI-CID FTMS(n), the top-down/bottom-up approach, and HPLC ESI capillary-skimmer CID FTMS. Anal Chem 2003; 75:2730-9. [PMID: 12948143 DOI: 10.1021/ac0264731] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The molecular formulas for the structures and substructures of muraymycin antibiotics A1 (C52H90N14O19, MW 1214) and B1 (C49H83N11O18, MW 1113) were determined using electrospray ionization (ESI) Fourier transform mass spectrometry (FTMS). The muraymycin A1 and B1 structures were elucidated by utilizing capillary-skimmer fragmentation with up to five stages of mass spectrometry (MS5). Multi-CHEF, a multiple ion isolation method, was used at each stage of MS(n) to isolate a parent ion and up to four reference ions, for exact-mass calibration. The parent ions were fragmented by SORI-CID and the product ions internally calibrated with average absolute mass errors less than 1 ppm at each stage in the fragmentation processes. Using the top-down/bottom-up approach, the molecular formulas for the antibiotics were determined by summing the elemental formulas of the neutral losses, obtained by measuring the mass differences (<500 Da) between the genetically related sequential parent ion masses in the MS(n) spectra, with the unique elemental formula of the lowest parent ion mass (<500 Da). The structures of 12 additional compounds in the muraymycin complex were elucidated using HPLC ESI capillary-skimmer CID FTMS by correlating their fragmentation patterns with those of muraymycins A1 and B1. Sequential neutral losses of an aminosugar, a valine, a uridine, and an ester fatty acid from the muraymycin parent ions provided diagnostic fragments for characterization.
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Kruppa G, Schnier PD, Tabei K, Van Orden S, Siegel MM. Multiple ion isolation applications in FT-ICR MS: exact-mass MSn internal calibration and purification/interrogation of protein-drug complexes. Anal Chem 2002; 74:3877-86. [PMID: 12175179 DOI: 10.1021/ac020048q] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two new applications using multiple ion isolations in the cell of a Fourier transform-ion cyclotron resonance mass spectrometer equipped with an electrospray ionization source are described. A procedure that uses multiple ion isolations of an analyte and calibrants for internal calibration at each stage in a MSn experiment, under high-resolution exact-mass conditions, for structural characterization/elucidation of angiotensin I and rapamycin is illustrated. Fragment ion mass accuracies < 1.0 ppm are demonstrated and routinely achieved. Purification of a mixture is illustrated by isolating multiple charge states of a protein-drug complex from residual protein for further MSn studies to elucidate the site of covalent drug bonding using IRMPD for a mixture of epidermal growth factor receptor (EGFr) protein and EGFr-drug complex. The procedure developed for multiple ion isolations is referred to as multi-CHEF, multiple correlated harmonic excitation fields, in which tailored waveforms are used to notch out multiple mass regions of a spectrum with minimal off-resonance excitation.
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Affiliation(s)
- Gary Kruppa
- Bruker Daltonics Inc, Billerica, Massachusetts 01821, USA
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27
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Aharoni A, Ric de Vos CH, Verhoeven HA, Maliepaard CA, Kruppa G, Bino R, Goodenowe DB. Nontargeted metabolome analysis by use of Fourier Transform Ion Cyclotron Mass Spectrometry. OMICS 2002; 6:217-34. [PMID: 12427274 DOI: 10.1089/15362310260256882] [Citation(s) in RCA: 355] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Advanced functional genomic tools now allow the parallel and high-throughput analyses of gene and protein expression. Although this information is crucial to our understanding of gene function, it offers insufficient insight into phenotypic changes associated with metabolism. Here we introduce a high-capacity Fourier Transform Ion Cyclotron Mass Spectrometry (FTMS)-based method, capable of nontargeted metabolic analysis and suitable for rapid screening of similarities and dissimilarities in large collections of biological samples (e.g., plant mutant populations). Separation of the metabolites was achieved solely by ultra-high mass resolution; Identification of the putative metabolite or class of metabolites to which it belongs was achieved by determining the elemental composition of the metabolite based upon the accurate mass determination; and relative quantitation was achieved by comparing the absolute intensities of each mass using internal calibration. Crude plant extracts were introduced via direct (continuous flow) injection and ionized by either electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) in both positive or negative ionization modes. We first analyzed four consecutive stages of strawberry fruit development and identified changes in the levels of a large range of masses corresponding to known fruit metabolites. The data also revealed novel information on the metabolic transition from immature to ripe fruit. In another set of experiments, the method was used to track changes in metabolic profiles of tobacco flowers overexpressing a strawberry MYB transcription factor and altered in petal color. Only nine masses appeared different between transgenic and control plants, among which was the mass corresponding to cyanidin-3-rhamnoglucoside, the main flower pigment. The results demonstrate the feasibility and utility of the FTMS approach for a nontargeted and rapid metabolic "fingerprinting," which will greatly speed up current efforts to study the metabolome and derive gene function in any biological system.
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Affiliation(s)
- Asaph Aharoni
- Business Unit Cell Cybernetics, Plant Research International, Wageningen, The Netherlands.
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28
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Abstract
We have identified a human cDNA that is homologous to the chicken kinectin, a putative receptor for the organelle motor kinesin. The human cDNA clone hybridized to a single 4.6-kb mRNA species that codes for a protein of 156 kDa molecular mass. The predicted primary translation product contains an N-terminal transmembrane helix followed by a bipartite nuclear localization sequence and two further C-terminal leucine zipper motifs. In addition, the aminoacid sequence revealed a large region (327-1362) of predicted alpha-helical coiled coils. A monoclonal antibody CT-1 raised against a GST-kinectin fusion protein produced a perinuclear, endoplasmic reticulum-like staining pattern in diverse cell types from different species, indicating evolutionary conservation. Monoclonal antibody CT-1 and anti-chicken kinectin antibodies cross-reacted both in Western blotting and immunoprecipitation with a 160-kDa protein, confirming the antigenic identity of this 160-kDa protein with chicken kinectin. Epitope tagging studies revealed that the nuclear localization sequence motif of kinectin is not functional. Furthermore, a truncated kinesin cDNA lacking the N-terminal hydrophobic domain revealed a nonspecific cytoplasmic staining pattern. Together the data suggest that kinectin is an integral membrane protein anchored in the endoplasmic reticulum via a transmembrane domain.
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Affiliation(s)
- A Fütterer
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität München, Germany
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29
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Kruppa G, Hug P, Liégard A, Rist G, Nesvadba P. Preparation and ESR-Spectroscopical Investigation of Remarkably Persistent Oxoisobenzofuranyl Radicals. Helv Chim Acta 1993. [DOI: 10.1002/hlca.19930760503] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kruppa G, Thoma B, Machleidt T, Wiegmann K, Krönke M. Inhibition of tumor necrosis factor (TNF)-mediated NF-kappa B activation by selective blockade of the human 55-kDa TNF receptor. The Journal of Immunology 1992. [DOI: 10.4049/jimmunol.148.10.3152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The numerous biologic activities of TNF appear mediated by two types of specific cell surface receptors of 55 to 60 kDa (TR55) and 75 to 80 kDa (TR75) molecular mass, respectively. The role of TR55 in the activation of the nuclear transcription factor kappa B (NF-kappa B) was investigated using an antagonistic, mAb, H398, specific for the human TR55. The human leukemic T cell line, Jurkat, which expresses both types of receptors at comparable levels, was used to test for NF-kappa B activation by electrophoretic mobility shift assays using as a probe an oligonucleotide encompassing the two tandemly arranged kappa B sites of the HIV-1 LTR enhancer. mAb H398 is shown to efficiently block not only TNF- but also lymphotoxin-mediated activation of NF-kappa B. Furthermore mAb H398 also impeded TNF- or lymphotoxin-mediated activation of chloramphenicol acetyl transferase gene expression from the HIV-1-LTR as determined by transient transfection assays. These findings indicate that both, induction of NF-kappa B binding to DNA, and transcriptional activity can be efficiently inhibited by selective blockade of TR55. Finally it is shown, that human TR55 confers NF-kappa B inducibility when expressed in the mouse pre-B cell line 70Z/3, which does not respond to TNF in its parental state. Together, the results of this study indicate that TR55 is both necessary and sufficient for mediating TNF activation of NF-kappa B.
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Affiliation(s)
- G Kruppa
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität München, FRG
| | - B Thoma
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität München, FRG
| | - T Machleidt
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität München, FRG
| | - K Wiegmann
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität München, FRG
| | - M Krönke
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität München, FRG
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31
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Kruppa G, Thoma B, Machleidt T, Wiegmann K, Krönke M. Inhibition of tumor necrosis factor (TNF)-mediated NF-kappa B activation by selective blockade of the human 55-kDa TNF receptor. J Immunol 1992; 148:3152-7. [PMID: 1315830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The numerous biologic activities of TNF appear mediated by two types of specific cell surface receptors of 55 to 60 kDa (TR55) and 75 to 80 kDa (TR75) molecular mass, respectively. The role of TR55 in the activation of the nuclear transcription factor kappa B (NF-kappa B) was investigated using an antagonistic, mAb, H398, specific for the human TR55. The human leukemic T cell line, Jurkat, which expresses both types of receptors at comparable levels, was used to test for NF-kappa B activation by electrophoretic mobility shift assays using as a probe an oligonucleotide encompassing the two tandemly arranged kappa B sites of the HIV-1 LTR enhancer. mAb H398 is shown to efficiently block not only TNF- but also lymphotoxin-mediated activation of NF-kappa B. Furthermore mAb H398 also impeded TNF- or lymphotoxin-mediated activation of chloramphenicol acetyl transferase gene expression from the HIV-1-LTR as determined by transient transfection assays. These findings indicate that both, induction of NF-kappa B binding to DNA, and transcriptional activity can be efficiently inhibited by selective blockade of TR55. Finally it is shown, that human TR55 confers NF-kappa B inducibility when expressed in the mouse pre-B cell line 70Z/3, which does not respond to TNF in its parental state. Together, the results of this study indicate that TR55 is both necessary and sufficient for mediating TNF activation of NF-kappa B.
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Affiliation(s)
- G Kruppa
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität München, FRG
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32
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Affiliation(s)
- M Krönke
- Klinische Arbeitsgruppe, Max-Planck-Gesellschaft, Göttingen, F.R.G
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33
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Seliger B, Kruppa G, Schäfer R, Redmond SM, Pfizenmaier K. Gamma interferon regulates long terminal repeat-controlled oncogene expression in transformed mouse fibroblasts at the level of mRNA transcription. J Virol 1988; 62:619-21. [PMID: 3121865 PMCID: PMC250578 DOI: 10.1128/jvi.62.2.619-621.1988] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In transformed NIH 3T3 cells, murine gamma interferon reduces the expression of the long terminal repeat-controlled oncogenes v-mos, c-myc, and v-Ha-ras by a direct effect on the activity of retroviral promoters, as revealed by analyses of RNA half-life and transcriptional activity of retroviral genes as well as by analyses of chloramphenicol acetyltransferase activity in cells transformed with the cat gene under the control of long terminal repeats.
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Affiliation(s)
- B Seliger
- Clinical Research Group Biological Regulation of Host-Tumor Interaction, Max Planck Society, University of Göttingen, Federal Republic of Germany
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34
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Seliger B, Kruppa G, Pfizenmaier K. Murine gamma interferon inhibits v-mos-induced fibroblast transformation via down regulation of retroviral gene expression. J Virol 1987; 61:2567-72. [PMID: 3037117 PMCID: PMC255700 DOI: 10.1128/jvi.61.8.2567-2572.1987] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Expression of the retroviral vector Neor myeloproliferative sarcoma virus (MPSV), which contains the v-mos oncogene and the neomycin resistance gene, leads to neoplastic transformation of mouse fibroblasts. Murine recombinant gamma interferon (IFN-gamma) could revert the neoplastic properties of established Neor MPSV-transformed cell lines to an apparently untransformed phenotype. In the presence of IFN-gamma, the Neor MPSV transformants showed a greater than 97% reduction of cloning efficiency in soft agar, strongly reduced proliferative capacity, and morphological changes. The IFN-gamma-induced phenotypic reversion was preceded by a rapid and selective reduction of all retroviral RNA species, apparently due to IFN-gamma action on the long terminal repeat of Neor MPSV. The mRNA levels of cellular genes either remained unaffected (beta-actin) or were even enhanced (H-2) in IFN-gamma-treated Neor MPSV-transformed cells. Upon removal of IFN-gamma, retroviral gene expression was fully recovered and a gradual reappearance of the transformed phenotype of these cells within 3 weeks was noted. These data show that IFN-gamma can cause a virtually complete, but reversible, inhibition of v-mos-induced neoplastic properties in transformed fibroblasts by selective down regulation of retroviral RNA levels.
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35
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Seliger B, Kruppa G, Pfizenmaier K. Stable expression of a selectable myeloproliferative sarcoma virus in murine T lymphocyte and monocyte cell lines. Immunobiology 1987; 174:313-25. [PMID: 3040583 DOI: 10.1016/s0171-2985(87)80006-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have investigated whether a retroviral vector based on the myeloproliferative sarcoma virus (MPSV) can be expressed in murine T cells and macrophages. This vector (neoR MPSV) carries the dominant selection marker for neomycin resistance (neoR) and the mos oncogene. The murine T cell line BW5147 and the monocytic cell line P388D1 were either transfected with neoR MPSV DNA or infected with neoR MPSV virus. From both lines, neoR cell clones could be established by retroviral infection, but not by calcium-phosphate precipitation-mediated DNA transfection. The efficiency of infection could be increased 60- to 200-fold upon cocultivation of target cells with irradiated neoR MPSV virus-producing cells. All neoR clones showed neoR MPSV specific sequences as revealed by dot blot and Southern blot analysis. The integration and expression of neoR MPSV was stable over a period of now more than 4 months, even in the absence of selection for neomycin resistance. Northern blot analysis showed that neoR clones express full length neoR MPSV. Further, clones of both T cell and monocyte origin were capable to produce infectious virus particles as revealed by focus formation on fibroblasts and conversion of neomycin sensitive fibroblasts to a neomycin resistant phenotype.
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Bartels M, Albert K, Kruppa G, Mann K, Schroth G, Tabarelli S, Zabel M. Fluorinated psychopharmacological agents: noninvasive observation by fluorine-19 nuclear magnetic resonance. Psychiatry Res 1986; 18:197-201. [PMID: 3749381 DOI: 10.1016/0165-1781(86)90106-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Fluorinated psychopharmacological agents were measured with fluorine-19 nuclear magnetic resonance spectroscopy in the brain of intact rats that had been treated with fluphenazine. These in vivo experiments were compared to in vitro measurements of fluphenazine-treated rats. A high-field shift was observed in both in vivo and in vitro measurements. On the basis of the in vitro measurements, fluphenazine concentration in the brains of treated rats was estimated. Our observations demonstrate the feasibility of this technique for determining fluorinated neuroleptics in live mammals.
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Beres J, Bentrude WG, Kruppa G, McKernan PA, Robins RK. Synthesis and antitumor and antiviral activities of a series of 1-beta-D-ribofuranosyl-5-halocytosine (5-halocytidine) cyclic 3',5'-monophosphates. J Med Chem 1985; 28:418-22. [PMID: 2984417 DOI: 10.1021/jm00382a005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A series of 1-beta-ribofuranosyl-5-halocytosine cyclic 3',5'-monophosphates (1-4) has been prepared. Direct halogenation of cytidine 3',5'-monophosphate (cCMP) yielded the Cl, Br, and I compounds while 5-F-cCMP (1) was obtained on cyclization of the 5'-monophosphate. On in vitro testing of 1-4 against L1210 and P388 leukemias, only 1 showed significant low-level activity (ID50 = 3.1 X 10(-4) mmol/L). Derivatives 2-4 were inactive at 10(-1) mmol/L and also proved to have low viral ratings against a series of RNA and DNA virus strains in vitro. By contrast the 5-F-cCMP showed moderate activity against VV, HSV-1, and HSV-2 strains (VR = 0.6-0.9). Both 5-fluorocytidine and 5-fluorocytidine 5'-monophosphate had marked antiviral activity (VR = 1.0-2.1) with the above viruses as well as with parainfluenza virus type 3. The nucleoside and nucleotide also were more active than 5-F-cCMP against L1210 and P388 cells. However, comparison of the cytotoxicities and antiviral ED50 values of 5-F-cCMP, 5-fluorocytidine 5'-monophosphate, and 5-fluorocytidine suggests a potential therapeutic advantage for 5-F-cCMP. Possible rationales for these activities are discussed in terms of 5-F-cCMP and the corresponding 5'-monophosphate as potential prodrugs and as sources, following enzymatic deamination, of cytotoxic 5-fluorouridine or its 5'-monophosphate.
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Albert K, Kruppa G, Zeller KP, Bayer E, Hartmann F. In vivo metabolism of [4-13C]phenacetin in an isolated perfused rat liver measured by continuous flow 13C NMR spectroscopy. Z Naturforsch C Biosci 1984; 39:859-62. [PMID: 6495820 DOI: 10.1515/znc-1984-7-831] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Continuous flow 13C NMR spectroscopy has been used for the first time to monitor the metabolism of a 13C labeled drug in an isolated liver. Continuous and almost immediate information on the metabolite formation could be obtained using 13C labeled phenacetin without alteration of the biological system. The data are consistent with those observed by conventional techniques (HPLC, aliquot 13C NMR measurements). From the biological point of view the sensitivity of continuous flow 13C NMR spectroscopy is still low (10(-3) M). The results presented demonstrate however that non-invasive and non-radioactive real time monitoring of drug metabolism in intact organs is possible.
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Abstract
In a prospective study 1200 sequences of low frequency electrostimulation and ultrasonic therapy have been examined. The basics of the type of currents applied, the therapy scheme and the indication routine are presented. These parameters were kept constant in the course of the 2 years' study. For the treatment 8 different apparatuses were available. The actual current shapes of the generators were measured, the influence of constant-current and constant-voltage output circuits were tested and were discussed in relation to the electrode types.--Advantages and disadvantages of disposable-type, sponge-type, lead-type and vacuum-type electrodes are reported. Treatments were carried out with the current types DF and CP of the diadynamic currents alone, as combined therapy together with ultrasound, as mere ultrasound treatment, as ultrastimulation current, as iontophoresis and galvanic current. The results are compared with comparable examinations by other authors and they are discussed with respect to different influencing factors.
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Kruppa G, Suhr H. Ein einfaches Verfahren zur Bestimmung von Elektronendichten bei plasmachemischen Reaktionen über Impedanz-Messungen. ACTA ACUST UNITED AC 1977. [DOI: 10.1524/zpch.1977.105.3_4.147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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