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Anschütz NH, Gerbig S, Ghezellou P, Silva LMR, Vélez JD, Hermosilla CR, Taubert A, Spengler B. Mass Spectrometry Imaging of In Vitro Cryptosporidium parvum-Infected Cells and Host Tissue. Biomolecules 2023; 13:1200. [PMID: 37627264 PMCID: PMC10452350 DOI: 10.3390/biom13081200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Cryptosporidium parvum is a zoonotic-relevant parasite belonging to the phylum Alveolata (subphylum Apicomplexa). One of the most zoonotic-relevant etiologies of cryptosporidiosis is the species C. parvum, infecting humans, cattle and wildlife. C. parvum-infected intestinal mucosa as well as host cells infected in vitro have not yet been the subject of extensive biochemical investigation. Efficient treatment options or vaccines against cryptosporidiosis are currently not available. Human cryptosporidiosis is currently known as a neglected poverty-related disease (PRD), being potentially fatal in young children or immunocompromised patients. In this study, we used a combination of atmospheric pressure scanning microprobe matrix-assisted laser desorption/ionization (AP-SMALDI) mass spectrometry imaging (MSI) and liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) to determine and locate molecular biomarkers in in vitro C. parvum-infected host cells as well as parasitized neonatal calf intestines. Sections of C. parvum-infected and non-infected host cell pellets and infected intestines were examined to determine potential biomarkers. Human ileocecal adenocarcinoma cells (HCT-8) were used as a suitable in vitro host cell system. More than a thousand different molecular signals were found in both positive- and negative-ion mode, which were significantly increased in C. parvum-infected material. A database search in combination with HPLC-MS/MS experiments was employed for the structural verification of markers. Our results demonstrate some overlap between the identified markers and data obtained from earlier studies on other apicomplexan parasites. Statistically relevant biomarkers were imaged in cell layers of C. parvum-infected and non-infected host cells with 5 µm pixel size and in bovine intestinal tissue with 10 µm pixel size. This allowed us to substantiate their relevance once again. Taken together, the present approach delivers novel metabolic insights on neglected cryptosporidiosis affecting mainly children in developing countries.
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Affiliation(s)
- Nils H. Anschütz
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany; (N.H.A.); (S.G.); (P.G.)
| | - Stefanie Gerbig
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany; (N.H.A.); (S.G.); (P.G.)
| | - Parviz Ghezellou
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany; (N.H.A.); (S.G.); (P.G.)
| | - Liliana M. R. Silva
- Institute of Parasitology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, 35392 Giessen, Germany; (L.M.R.S.); (J.D.V.); (C.R.H.); (A.T.)
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, 2829-511 Caparica, Portugal
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, 7006-554 Évora, Portugal
| | - Juan Diego Vélez
- Institute of Parasitology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, 35392 Giessen, Germany; (L.M.R.S.); (J.D.V.); (C.R.H.); (A.T.)
| | - Carlos R. Hermosilla
- Institute of Parasitology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, 35392 Giessen, Germany; (L.M.R.S.); (J.D.V.); (C.R.H.); (A.T.)
| | - Anja Taubert
- Institute of Parasitology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, 35392 Giessen, Germany; (L.M.R.S.); (J.D.V.); (C.R.H.); (A.T.)
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany; (N.H.A.); (S.G.); (P.G.)
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Kadesch P, Hollubarsch T, Gerbig S, Schneider L, Silva LMR, Hermosilla C, Taubert A, Spengler B. Intracellular Parasites Toxoplasma gondii and Besnoitia besnoiti, Unveiled in Single Host Cells Using AP-SMALDI MS Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1815-1824. [PMID: 32830963 DOI: 10.1021/jasms.0c00043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The obligate intracellular apicomplexan parasites Toxoplasma gondii and Besnoitia besnoiti are important causes of disease in both humans and cattle. To date, effective specific treatments are lacking for both infections. To counteract severe symptoms leading to, e.g., disabilities and even abortion in the case of human toxoplasmosis and bovine besnoitiosis, novel targets are required for development of drugs and vaccines. A promising emerging technique for molecular characterization of organisms is high-resolution atmospheric-pressure scanning microprobe matrix-assisted laser desorption/ionization (AP-SMALDI) mass spectrometry imaging (MSI) which enables semiquantitative visualization of metabolite distributions. MSI was here used to trace and characterize lipid metabolites in primary bovine umbilical vein endothelial cells (BUVECs) upon infection with tachyzoites, an early and pathogenic fast-replicating life stage of T. gondii and B. besnoiti. A cell bulk, derived from noninfected controls and parasite-infected cell pellets, was analyzed by AP-SMALDI MSI in technical and biological triplicates. Multivariate statistical analysis including hierarchical clustering and principle component analysis revealed infection-specific metabolites in both positive- and negative-ion mode, identified by combining database search and LC-MS2 experiments. MSI analyses of host cell monolayers were conducted at 5 μm lateral resolution, allowing single apicomplexan-infected cells to be allocated. This is the first mass spectrometry imaging study on intracellular T. gondii and B. besnoiti infections and the first detailed metabolomic characterization of B. besnoiti tachyzoites. MSI was used here as an efficient tool to discriminate infected from noninfected cells at the single-cell level in vitro.
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Affiliation(s)
- Patrik Kadesch
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Tobias Hollubarsch
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Stefanie Gerbig
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Lars Schneider
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Liliana M R Silva
- Institute of Parasitology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
| | - Carlos Hermosilla
- Institute of Parasitology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
| | - Anja Taubert
- Institute of Parasitology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
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3
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Hage C, Falvo F, Schäfer M, Sinz A. Novel Concepts of MS-Cleavable Cross-linkers for Improved Peptide Structure Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2022-2038. [PMID: 28653243 DOI: 10.1007/s13361-017-1712-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/03/2017] [Accepted: 05/07/2017] [Indexed: 06/07/2023]
Abstract
The chemical cross-linking/mass spectrometry (MS) approach is gaining increasing importance as an alternative method for studying protein conformation and for deciphering protein interaction networks. This study is part of our ongoing efforts to develop innovative cross-linking principles for a facile and efficient assignment of cross-linked products. We evaluate two homobifunctional, amine-reactive, and MS-cleavable cross-linkers regarding their potential for automated analysis of cross-linked products. We introduce the bromine phenylurea (BrPU) linker that possesses a unique structure yielding a distinctive fragmentation pattern on collisional activation. Moreover, BrPU delivers the characteristic bromine isotope pattern and mass defect for all cross-linker-decorated fragments. We compare the fragmentation behavior of the BrPU linker with that of our previously described MS-cleavable TEMPO-Bz linker (which consists of a 2,2,6,6-tetramethylpiperidine-1-oxy moiety connected to a benzyl group) that was developed to perform free-radical-initiated peptide sequencing. Comparative collisional activation experiments (collision-induced dissociation and higher-energy collision-induced dissociation) with both cross-linkers were conducted in negative electrospray ionization mode with an Orbitrap Fusion mass spectrometer using five model peptides. As hypothesized in a previous study, the presence of a cross-linked N-terminal aspartic acid residue seems to be the prerequisite for the loss of an intact peptide from the cross-linked products. As the BrPU linker combines a characteristic mass shift with an isotope signature, it presents a more favorable combination for automated assignment of cross-linked products compared with the TEMPO-Bz linker. ᅟ.
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Affiliation(s)
- Christoph Hage
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Francesco Falvo
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939, Cologne, Germany
- Eurofins Umwelt West GmbH, Vorgebirgsstr. 20, 50389, Wesseling, Germany
| | - Mathias Schäfer
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939, Cologne, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany.
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Iacobucci C, Hage C, Schäfer M, Sinz A. A Novel MS-Cleavable Azo Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2039-2053. [PMID: 28717933 DOI: 10.1007/s13361-017-1744-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/13/2017] [Accepted: 06/15/2017] [Indexed: 06/07/2023]
Abstract
The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers. The ABI-linker possesses an innovative modular scaffold combining the benefits of collisional activation lability with open shell chemistry. This MS-cleavable cross-linker can be efficiently operated via free radical initiated peptide sequencing (FRIPS) in positive ionization mode. Our proof-of-principle study challenges the gas phase behavior of the ABI-linker for the three amino acids, lysine, leucine, and isoleucine, as well as the model peptide thymopentin. The isomeric amino acids leucine and isoleucine could be discriminated by their characteristic side chain fragments. Collisional activation experiments were conducted via positive electrospray ionization (ESI) on two Orbitrap mass spectrometers. The ABI-mediated formation of odd electron product ions in MS/MS and MS3 experiments was evaluated and compared with a previously described azo-based cross-linker. All cross-linked products were amenable to automated analysis by the MeroX software, underlining the future potential of the ABI-linker for structural proteomics studies. Graphical Abstract ᅟ.
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Affiliation(s)
- Claudio Iacobucci
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany.
| | - Christoph Hage
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany
| | - Mathias Schäfer
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Greinstr. 4, D-50939, Kӧln, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany.
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5
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Sadygov RG. Use of singular value decomposition analysis to differentiate phosphorylated precursors in strong cation exchange fractions. Electrophoresis 2014; 35:3498-503. [PMID: 24913822 DOI: 10.1002/elps.201400053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/13/2014] [Accepted: 05/20/2014] [Indexed: 01/26/2023]
Abstract
We studied the use of peak deviations (PDs) for application in phosphoproteomics. Due to the differences in the mass defects, the PDs of samples containing mixtures of phosphorylated and nonphosphorylated peptides show bimodal distributions. The ratios of peak heights accurately predict the phosphoproteome content of a sample. In this work, we apply a signal-processing tool, singular value decomposition, to reveal characteristic features of the phosphorylated, nonphosphorylated, and mixed samples. We show that a simple application of singular value decomposition to the PD matrix (i) detects transitions from mostly phosphorylated samples to mostly nonphosphorylated samples, (ii) reveals modes of low-abundance species in the presence of the high-abundance species (e.g., phosphorylated peptides), and (iii) simplifies the interpretation of the clustering of a covariance matrix obtained from PDs. As the eigenfunctions of the inner-product of the data matrix (made from the PDs) are Hermite functions, we observe a change of sign in the transition from samples enriched in phosphorylated peptides to samples containing fewer phosphorylated peptides. The ordering of the singular values of the data matrix points in the direction of changes to the phosphorylation content. No peptide identifications from a database were used for this study.
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Affiliation(s)
- Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX, USA
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Kalita M, Kasumov T, Brasier AR, Sadygov RG. Use of theoretical peptide distributions in phosphoproteome analysis. J Proteome Res 2013; 12:3207-14. [PMID: 23731183 PMCID: PMC3758224 DOI: 10.1021/pr4003382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The high mass accuracy and resolution of modern mass spectrometers provides new opportunities to employ theoretical peptide distributions in large-scale proteomic studies. We used theoretical distributions to study noise filtering and mass measurement errors and to examine mass-based differentiation of phosphorylated and nonphosphorylated peptides. Only the monoisotopic mass of the experimental precursor ion was necessary for this analysis. We found that peak deviations can be used to characterize the modification states of peptides in a sample. When applied to large-scale proteomic data sets, the peak deviation distribution can be used to filter chemical/electronic noise for singly charged species. Using peak deviation distributions, it is possible to separate the phosphorylated peptides from the nonphosphorylated peptides, enabling evaluation of the phosphoproteome content of a sample. Because this approach is simple, with light computational requirements, the analysis of theoretical peptide distributions has a significant potential for application to phosphoproteome analyses. For our studies we used publicly available data sets from three large-scale proteomic studies.
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Affiliation(s)
- Mridul Kalita
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77573
| | - Takhar Kasumov
- Department of Gastroenterology and Hepatology, Cleveland Clinic, 9500 Euclid, Avenue, Cleveland, OH 44195
| | - Allan R. Brasier
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77573
| | - Rovshan G. Sadygov
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77573
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Mao Y, Zamdborg L, Kelleher NL, Hendrickson CL, Marshall AG. Identification of Phosphorylated Human Peptides by Accurate Mass Measurement Alone. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 308:357-361. [PMID: 22866021 PMCID: PMC3409838 DOI: 10.1016/j.ijms.2011.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
At sufficiently high mass accuracy, it is possible to distinguish phosphorylated from unmodified peptides by mass measurement alone. We examine the feasibility of that idea, tested against a library of all possible in silico tryptic digest peptides from the human proteome database. The overlaps between in silico tryptic digest phosphopeptides generated from known phosphorylated proteins (1-12 sites) and all possible unmodified human peptides are considered for assumed mass error ranges of ±10, ±50, ±100, ±1,000, and ±10,000 ppb. We find that for mass error ±50 ppb, 95% of all phosphorylated human tryptic peptides can be distinguished from nonmodified peptides by accurate mass alone through the entire nominal mass range. We discuss the prospect of on-line LC MS/MS to identify phosphopeptide precursor ions in MS1 for selected dissociation in MS2 to identify the peptide and site(s) of phosphorylation.
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Affiliation(s)
- Yuan Mao
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
| | - Leonid Zamdborg
- Institute for Genomic Biology, 1206 West Gregory Drive, Urbana, IL 61801
| | - Neil L. Kelleher
- Institute for Genomic Biology, 1206 West Gregory Drive, Urbana, IL 61801
| | - Christopher L. Hendrickson
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee Florida 32310-4005, United States
| | - Alan G. Marshall
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee Florida 32310-4005, United States
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Nefedov AV, Sadygov RG. A parallel method for enumerating amino acid compositions and masses of all theoretical peptides. BMC Bioinformatics 2011; 12:432. [PMID: 22059886 PMCID: PMC3270061 DOI: 10.1186/1471-2105-12-432] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 11/07/2011] [Indexed: 11/16/2022] Open
Abstract
Background Enumeration of all theoretically possible amino acid compositions is an important problem in several proteomics workflows, including peptide mass fingerprinting, mass defect labeling, mass defect filtering, and de novo peptide sequencing. Because of the high computational complexity of this task, reported methods for peptide enumeration were restricted to cover limited mass ranges (below 2 kDa). In addition, implementation details of these methods as well as their computational performance have not been provided. The increasing availability of parallel (multi-core) computers in all fields of research makes the development of parallel methods for peptide enumeration a timely topic. Results We describe a parallel method for enumerating all amino acid compositions up to a given length. We present recursive procedures which are at the core of the method, and show that a single task of enumeration of all peptide compositions can be divided into smaller subtasks that can be executed in parallel. The computational complexity of the subtasks is compared with the computational complexity of the whole task. Pseudocodes of processes (a master and workers) that are used to execute the enumerating procedure in parallel are given. We present computational times for our method executed on a computer cluster with 12 Intel Xeon X5650 CPUs (72 cores) running Windows HPC Server. Our method has been implemented as a 32- and 64-bit Windows application using Microsoft Visual C++ and the Message Passing Interface. It is available for download at https://ispace.utmb.edu/users/rgsadygo/Proteomics/ParallelMethod. Conclusion We describe implementation of a parallel method for generating mass distributions of all theoretically possible amino acid compositions.
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Affiliation(s)
- Alexey V Nefedov
- Department of Biochemistry and Molecular Biology, Sealy Center for Molecular Medicine, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
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9
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Ghelis T. Signal processing by protein tyrosine phosphorylation in plants. PLANT SIGNALING & BEHAVIOR 2011; 6:942-51. [PMID: 21628997 PMCID: PMC3257767 DOI: 10.4161/psb.6.7.15261] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 02/22/2011] [Indexed: 05/05/2023]
Abstract
Protein phosphorylation is a reversible post-translational modification controlling many biological processes. Most phosphorylation occurs on serine and threonine, and to a less extend on tyrosine (Tyr). In animals, Tyr phosphorylation is crucial for the regulation of many responses such as growth or differentiation. Only recently with the development of mass spectrometry, it has been reported that Tyr phosphorylation is as important in plants as in animals. The genes encoding protein Tyr kinases and protein Tyr phosphatases have been identified in the Arabidopsis thaliana genome. Putative substrates of these enzymes, and thus Tyr-phosphorylated proteins have been reported by proteomic studies based on accurate mass spectrometry analysis of the phosphopeptides and phosphoproteins. Biochemical approaches, pharmacology and genetic manipulations have indicated that responses to stress and developmental processes involve changes in protein Tyr phosphorylation. The aim of this review is to present an update on Tyr phosphorylation in plants in order to better assess the role of this post-translational modification in plant physiology.
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Affiliation(s)
- Thanos Ghelis
- UPMC Université Paris 06, Sorbonne Universités, UR5 EAC 7180 CNRS, Physiologie Cellulaire et Moléculaire des Plantes, Paris, France.
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10
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Xia Q, Lee MV, Rose CM, Marsh AJ, Hubler SL, Wenger CD, Coon JJ. Characterization and diagnostic value of amino acid side chain neutral losses following electron-transfer dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:255-64. [PMID: 21472585 PMCID: PMC3074364 DOI: 10.1007/s13361-010-0029-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 11/02/2010] [Indexed: 05/14/2023]
Abstract
Using a large set of high mass accuracy and resolution ETD tandem mass spectra, we characterized ETD-induced neutral losses. From these data we deduced the chemical formula for 20 of these losses. Many of them have been previously observed in electron-capture dissociation (ECD) spectra, such as losses of the side chains of arginine, aspartic acid, glutamic acid, glutamine, asparagine, leucine, histidine, and carbamidomethylated cysteine residues. With this information, we examined the diagnostic value of these amino acid-specific losses. Among 1285 peptide-spectrum matches, 92.5% have agreement between neutral loss-derived peptide amino acid composition and the peptide sequences. Moreover, we show that peptides can be uniquely identified by using only the accurate precursor mass and amino acid composition based on neutral losses; the median number of sequence candidates from an accurate mass query is reduced from 21 to 8 by adding side chain loss information. Besides increasing confidence in peptide identification, our findings suggest the potential use of these diagnostic losses in ETD spectra to improve false discovery rate estimation and to enhance the performance of scoring functions in database search algorithms.
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Affiliation(s)
- Qiangwei Xia
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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11
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Römpp A, Guenther S, Schober Y, Schulz O, Takats Z, Kummer W, Spengler B. Histology by mass spectrometry: label-free tissue characterization obtained from high-accuracy bioanalytical imaging. Angew Chem Int Ed Engl 2010; 49:3834-8. [PMID: 20397170 DOI: 10.1002/anie.200905559] [Citation(s) in RCA: 163] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Andreas Römpp
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Schubertstrasse 60, Haus 16, Giessen 35392, Germany
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Palmblad M, van der Burgt YEM, Mostovenko E, Dalebout H, Deelder AM. A novel mass spectrometry cluster for high-throughput quantitative proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1002-1011. [PMID: 20194034 DOI: 10.1016/j.jasms.2010.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 02/01/2010] [Accepted: 02/01/2010] [Indexed: 05/28/2023]
Abstract
We have developed and implemented a novel mass spectrometry (MS) platform combining the advantages of high mass accuracy and resolving power of Fourier transform ion cyclotron resonance (FTICR) with the economy and speed of multiple ion traps for tandem mass spectrometry. The instruments are integrated using novel algorithms and software and work in concert as one system. Using chromatographic time compression, a single expensive FTICR mass spectrometer can match the throughput of multiple relatively inexpensive ion trap instruments. Liquid chromatography (LC)-mass spectrometry data from the two types of spectrometers are aligned and combined to hybrid datasets, from which peptides are identified using accurate mass from the FTICR data and tandem mass spectra from the ion trap data. In addition, the high resolving power and dynamic range of a 12 tesla FTICR also allows precise label-free quantitation. Using two ion traps in parallel with one LC allows simultaneous MS/MS experiments and optimal application of collision induced dissociation and electron-transfer dissociation throughout the chromatographic separation for increased proteome coverage, characterization of post-translational modifications and/or simultaneous measurement in positive and negative ionization mode. An FTICR-ion trap cluster can achieve similar performance and sample throughput as multiple hybrid ion trap-FTICR instruments, but at a lower cost. We here describe the first such FTICR-ion trap cluster, its performance and the idea of chromatographic compression.
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Affiliation(s)
- Magnus Palmblad
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands.
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13
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Römpp A, Guenther S, Schober Y, Schulz O, Takats Z, Kummer W, Spengler B. Massenspektrometrische Histologie: markierungsfreie Gewebecharakterisierung durch hochgenaue bildgebende Bioanalytik. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905559] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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