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Ivanov MV, Bubis JA, Gorshkov V, Tarasova IA, Levitsky LI, Solovyeva EM, Lipatova AV, Kjeldsen F, Gorshkov MV. DirectMS1Quant: Ultrafast Quantitative Proteomics with MS/MS-Free Mass Spectrometry. Anal Chem 2022; 94:13068-13075. [PMID: 36094425 DOI: 10.1021/acs.analchem.2c02255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, we presented the DirectMS1 method of ultrafast proteome-wide analysis based on minute-long LC gradients and MS1-only mass spectra acquisition. Currently, the method provides the depth of human cell proteome coverage of 2500 proteins at a 1% false discovery rate (FDR) when using 5 min LC gradients and 7.3 min runtime in total. While the standard MS/MS approaches provide 4000-5000 protein identifications within a couple of hours of instrumentation time, we advocate here that the higher number of identified proteins does not always translate into better quantitation quality of the proteome analysis. To further elaborate on this issue, we performed a one-on-one comparison of quantitation results obtained using DirectMS1 with three popular MS/MS-based quantitation methods: label-free (LFQ) and tandem mass tag quantitation (TMT), both based on data-dependent acquisition (DDA) and data-independent acquisition (DIA). For comparison, we performed a series of proteome-wide analyses of well-characterized (ground truth) and biologically relevant samples, including a mix of UPS1 proteins spiked at different concentrations into an Echerichia coli digest used as a background and a set of glioblastoma cell lines. MS1-only data was analyzed using a novel quantitation workflow called DirectMS1Quant developed in this work. The results obtained in this study demonstrated comparable quantitation efficiency of 5 min DirectMS1 with both TMT and DIA methods, yet the latter two utilized a 10-20-fold longer instrumentation time.
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Affiliation(s)
- Mark V Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Julia A Bubis
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Irina A Tarasova
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Lev I Levitsky
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Elizaveta M Solovyeva
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Anastasiya V Lipatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Frank Kjeldsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
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Combination of Derivatization–HPLC–MS and Enzymatic Hydrolysis–Edman Degradation for Amino Acid Sequence and Configuration of Polymyxin B Components. Chromatographia 2021. [DOI: 10.1007/s10337-021-04091-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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3
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Ivanov MV, Bubis JA, Gorshkov V, Tarasova IA, Levitsky LI, Lobas AA, Solovyeva EM, Pridatchenko ML, Kjeldsen F, Gorshkov MV. DirectMS1: MS/MS-Free Identification of 1000 Proteins of Cellular Proteomes in 5 Minutes. Anal Chem 2020; 92:4326-4333. [DOI: 10.1021/acs.analchem.9b05095] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Mark V. Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Julia A. Bubis
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Irina A. Tarasova
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Lev I. Levitsky
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Anna A. Lobas
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Elizaveta M. Solovyeva
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Marina L. Pridatchenko
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Frank Kjeldsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Mikhail V. Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141700 Dolgoprudny, Russia
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4
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Reese HR, Shanahan CC, Proulx C, Menegatti S. Peptide science: A "rule model" for new generations of peptidomimetics. Acta Biomater 2020; 102:35-74. [PMID: 31698048 DOI: 10.1016/j.actbio.2019.10.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023]
Abstract
Peptides have been heavily investigated for their biocompatible and bioactive properties. Though a wide array of functionalities can be introduced by varying the amino acid sequence or by structural constraints, properties such as proteolytic stability, catalytic activity, and phase behavior in solution are difficult or impossible to impart upon naturally occurring α-L-peptides. To this end, sequence-controlled peptidomimetics exhibit new folds, morphologies, and chemical modifications that create new structures and functions. The study of these new classes of polymers, especially α-peptoids, has been highly influenced by the analysis, computational, and design techniques developed for peptides. This review examines techniques to determine primary, secondary, and tertiary structure of peptides, and how they have been adapted to investigate peptoid structure. Computational models developed for peptides have been modified to predict the morphologies of peptoids and have increased in accuracy in recent years. The combination of in vitro and in silico techniques have led to secondary and tertiary structure design principles that mirror those for peptides. We then examine several important developments in peptoid applications inspired by peptides such as pharmaceuticals, catalysis, and protein-binding. A brief survey of alternative backbone structures and research investigating these peptidomimetics shows how the advancement of peptide and peptoid science has influenced the growth of numerous fields of study. As peptide, peptoid, and other peptidomimetic studies continue to advance, we will expect to see higher throughput structural analyses, greater computational accuracy and functionality, and wider application space that can improve human health, solve environmental challenges, and meet industrial needs. STATEMENT OF SIGNIFICANCE: Many historical, chemical, and functional relations draw a thread connecting peptides to their recent cognates, the "peptidomimetics". This review presents a comprehensive survey of this field by highlighting the width and relevance of these familial connections. In the first section, we examine the experimental and computational techniques originally developed for peptides and their morphing into a broader analytical and predictive toolbox. The second section presents an excursus of the structures and properties of prominent peptidomimetics, and how the expansion of the chemical and structural diversity has returned new exciting properties. The third section presents an overview of technological applications and new families of peptidomimetics. As the field grows, new compounds emerge with clear potential in medicine and advanced manufacturing.
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5
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Götze S, Stallforth P. Structure elucidation of bacterial nonribosomal lipopeptides. Org Biomol Chem 2020; 18:1710-1727. [DOI: 10.1039/c9ob02539a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We provide a summary of the tools, which allow elucidate the structures of nonribosomal lipopetides.
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Affiliation(s)
- Sebastian Götze
- Department of Paleobiotechnology
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
| | - Pierre Stallforth
- Department of Paleobiotechnology
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
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6
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Hurtado Silva M, Berry IJ, Strange N, Djordjevic SP, Padula MP. Terminomics Methodologies and the Completeness of Reductive Dimethylation: A Meta-Analysis of Publicly Available Datasets. Proteomes 2019; 7:proteomes7020011. [PMID: 30934878 PMCID: PMC6631386 DOI: 10.3390/proteomes7020011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 12/30/2022] Open
Abstract
Methods for analyzing the terminal sequences of proteins have been refined over the previous decade; however, few studies have evaluated the quality of the data that have been produced from those methodologies. While performing global N-terminal labelling on bacteria, we observed that the labelling was not complete and investigated whether this was a common occurrence. We assessed the completeness of labelling in a selection of existing, publicly available N-terminomics datasets and empirically determined that amine-based labelling chemistry does not achieve complete labelling and potentially has issues with labelling amine groups at sequence-specific residues. This finding led us to conduct a thorough review of the historical literature that showed that this is not an unexpected finding, with numerous publications reporting incomplete labelling. These findings have implications for the quantitation of N-terminal peptides and the biological interpretations of these data.
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Affiliation(s)
- Mariella Hurtado Silva
- Proteomics Core Facility and School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
| | - Iain J Berry
- Proteomics Core Facility and School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
- The ithree Institute, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
| | - Natalie Strange
- Proteomics Core Facility and School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
| | - Steven P Djordjevic
- The ithree Institute, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
| | - Matthew P Padula
- Proteomics Core Facility and School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
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Novel, efficient, facile, and comprehensive protocol for post-column amino acid analysis of icatibant acetate containing natural and unnatural amino acids using the QbD approach. Amino Acids 2018; 51:295-309. [DOI: 10.1007/s00726-018-2665-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023]
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Ivanov MV, Tarasova IA, Levitsky LI, Solovyeva EM, Pridatchenko ML, Lobas AA, Bubis JA, Gorshkov MV. MS/MS-Free Protein Identification in Complex Mixtures Using Multiple Enzymes with Complementary Specificity. J Proteome Res 2017; 16:3989-3999. [DOI: 10.1021/acs.jproteome.7b00365] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mark V. Ivanov
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow
Institute
of Physics and Technology (State University), 9 Institutsky Per. Dolgoprudny, Moscow 141700, Russia
| | - Irina A. Tarasova
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
| | - Lev I. Levitsky
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow
Institute
of Physics and Technology (State University), 9 Institutsky Per. Dolgoprudny, Moscow 141700, Russia
| | - Elizaveta M. Solovyeva
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow
Institute
of Physics and Technology (State University), 9 Institutsky Per. Dolgoprudny, Moscow 141700, Russia
| | - Marina L. Pridatchenko
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
| | - Anna A. Lobas
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow
Institute
of Physics and Technology (State University), 9 Institutsky Per. Dolgoprudny, Moscow 141700, Russia
| | - Julia A. Bubis
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow
Institute
of Physics and Technology (State University), 9 Institutsky Per. Dolgoprudny, Moscow 141700, Russia
| | - Mikhail V. Gorshkov
- V.L.
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow
Institute
of Physics and Technology (State University), 9 Institutsky Per. Dolgoprudny, Moscow 141700, Russia
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9
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Moruz L, Käll L. Peptide retention time prediction. MASS SPECTROMETRY REVIEWS 2017; 36:615-623. [PMID: 26799864 DOI: 10.1002/mas.21488] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 11/12/2015] [Indexed: 06/05/2023]
Abstract
Most methods for interpreting data from shotgun proteomics experiments are to large degree dependent on being able to predict properties of peptide-ions. Often such predicted properties are limited to molecular mass and fragment spectra, but here we put focus on a perhaps underutilized property, a peptide's chromatographic retention time. We review a couple of different principles of retention time prediction,and their applications within computational proteomics. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:615-623, 2017.
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Affiliation(s)
- Luminita Moruz
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology - KTH, Stockholm, Sweden
| | - Lukas Käll
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology - KTH, Stockholm, Sweden
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10
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Ivanov MV, Levitsky LI, Lobas AA, Panic T, Laskay ÜA, Mitulovic G, Schmid R, Pridatchenko ML, Tsybin YO, Gorshkov MV. Empirical Multidimensional Space for Scoring Peptide Spectrum Matches in Shotgun Proteomics. J Proteome Res 2014; 13:1911-20. [DOI: 10.1021/pr401026y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Mark V. Ivanov
- Institute
for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow Institute of Physics and Technology (State University), Inststitutskii per., 9, Dolgoprudny 141700, Moscow region, Russia
| | - Lev I. Levitsky
- Institute
for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow Institute of Physics and Technology (State University), Inststitutskii per., 9, Dolgoprudny 141700, Moscow region, Russia
| | - Anna A. Lobas
- Institute
for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow Institute of Physics and Technology (State University), Inststitutskii per., 9, Dolgoprudny 141700, Moscow region, Russia
| | - Tanja Panic
- Medical University of Vienna, Spitalgasse 23, Vienna 1090, Austria
| | - Ünige A. Laskay
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 2 av. Forel, Lausanne 1015, Switzerland
| | - Goran Mitulovic
- Medical University of Vienna, Spitalgasse 23, Vienna 1090, Austria
| | - Rainer Schmid
- Medical University of Vienna, Spitalgasse 23, Vienna 1090, Austria
| | - Marina L. Pridatchenko
- Institute
for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
| | - Yury O. Tsybin
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 2 av. Forel, Lausanne 1015, Switzerland
| | - Mikhail V. Gorshkov
- Institute
for Energy Problems of Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
- Moscow Institute of Physics and Technology (State University), Inststitutskii per., 9, Dolgoprudny 141700, Moscow region, Russia
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Qiao X, Wang R, Yan H, Wang T, Zhao Q, Zhang L, Zhang Y. Development of a novel imidazolium-based aromatic quaternary ammonium tag: synthesis and application to the efficient analysis of cysteinyl-peptides by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:256-264. [PMID: 24375876 DOI: 10.1002/rcm.6785] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 10/30/2013] [Accepted: 11/12/2013] [Indexed: 06/03/2023]
Abstract
RATIONALE Chemical derivatization is a very promising technique for improving analysis of peptides by mass spectrometry (MS). In this study, a novel kind of imidazolium-based aromatic quaternary ammonium tag, 1-[3-[(2-iodo-1-oxoethyl)amino]propyl]-3-butylimidazolium bromide (IPBI), designed with strong gas-phase basicity and a permanent positive charge, was firstly synthesized and further used for derivatization of cysteinyl-peptides with improved ionization efficiency and higher charge states. METHODS Both the model peptides and tryptic digests of proteins were used to evaluate the effect of IPBI derivatization on the MS performance of the derivatized peptides, and the results were further compared with the commonly used iodoacetamide (IAA) tag. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF)-MS and electrospray ionization (ESI)-MS were used to evaluate the ionization efficiency and charge states of the derivatized peptides. RESULTS With model peptides as samples, a nearly 100% derivatization efficiency and superior stability were achieved via IPBI derivatization. By further analysis of both standard peptides and tryptic protein digests, the ionization efficiency and charge states of IPBI-derivatized peptides could be remarkably improved. For example, for protein bovine serum albumin, compared with the commercial available IAA tag, the identification efficiency of cysteinyl-peptides was increased about 67% by combining with IPBI derivatization. CONCLUSIONS The results indicated that the novel tag is an effective derivatization reagent for cysteinyl-peptide identification. We hope it could be further used for high-efficiency cysteinyl-peptide identification in proteome research, especially those with low abundance and poor ionization efficiency.
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Affiliation(s)
- Xiaoqiang Qiao
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province & College of Pharmaceutical Sciences, Hebei University, Baoding, 071002, China
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12
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Ait-Belkacem R, Berenguer C, Villard C, Ouafik L, Figarella-Branger D, Chinot O, Lafitte D. MALDI imaging and in-source decay for top-down characterization of glioblastoma. Proteomics 2014; 14:1290-301. [PMID: 24376047 DOI: 10.1002/pmic.201300329] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/27/2013] [Accepted: 10/04/2013] [Indexed: 01/15/2023]
Abstract
Glioblastoma multiforme is one of the most common intracranial tumors encountered in adults. This tumor of very poor prognosis is associated with a median survival rate of approximately 14 months. One of the major issues to better understand the biology of these tumors and to optimize the therapy is to obtain the molecular structure of glioblastoma. MALDI molecular imaging enables location of molecules in tissues without labeling. However, molecular identification in situ is not an easy task. In this paper, we used MALDI imaging coupled to in-source decay to characterize markers of this pathology. We provided MALDI molecular images up to 30 μm spatial resolution of mouse brain tissue sections. MALDI images showed the heterogeneity of the glioblastoma. In the various zones and at various development stages of the tumor, using our top-down strategy, we identified several proteins. These proteins play key roles in tumorigenesis. Particular attention was given to the necrotic area with characterization of hemorrhage, one of the most important poor prognosis factors in glioblastoma.
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