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Smith BJ, Guest PC, Martins-de-Souza D. Maximizing Analytical Performance in Biomolecular Discovery with LC-MS: Focus on Psychiatric Disorders. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:25-46. [PMID: 38424029 DOI: 10.1146/annurev-anchem-061522-041154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
In this review, we discuss the cutting-edge developments in mass spectrometry proteomics and metabolomics that have brought improvements for the identification of new disease-based biomarkers. A special focus is placed on psychiatric disorders, for example, schizophrenia, because they are considered to be not a single disease entity but rather a spectrum of disorders with many overlapping symptoms. This review includes descriptions of various types of commonly used mass spectrometry platforms for biomarker research, as well as complementary techniques to maximize data coverage, reduce sample heterogeneity, and work around potentially confounding factors. Finally, we summarize the different statistical methods that can be used for improving data quality to aid in reliability and interpretation of proteomics findings, as well as to enhance their translatability into clinical use and generalizability to new data sets.
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Affiliation(s)
- Bradley J Smith
- 1Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, São Paulo, Brazil;
| | - Paul C Guest
- 1Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, São Paulo, Brazil;
- 2Department of Psychiatry, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- 3Laboratory of Translational Psychiatry, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Daniel Martins-de-Souza
- 1Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, São Paulo, Brazil;
- 4Experimental Medicine Research Cluster, University of Campinas, São Paulo, Brazil
- 5National Institute of Biomarkers in Neuropsychiatry, National Council for Scientific and Technological Development, São Paulo, Brazil
- 6D'Or Institute for Research and Education, São Paulo, Brazil
- 7INCT in Modelling Human Complex Diseases with 3D Platforms (Model3D), São Paulo, Brazil
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2
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Liang Y, Zhang L, Zhang Y. Chromatographic separation of peptides and proteins for characterization of proteomes. Chem Commun (Camb) 2023; 59:270-281. [PMID: 36504223 DOI: 10.1039/d2cc05568f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Characterization of proteomes aims to comprehensively characterize proteins in cells or tissues via two main strategies: (1) bottom-up strategy based on the separation and identification of enzymatic peptides; (2) top-down strategy based on the separation and identification of intact proteins. However, it is challenged by the high complexity of proteomes. Consequently, the improvements in peptide and protein separation technologies for simplifying the sample should be critical. In this feature article, separation columns for peptide and protein separation were introduced, and peptide separation technologies for bottom-up proteomic analysis as well as protein separation technologies for top-down proteomic analysis were summarized. The achievement, recent development, limitation and future trends are discussed. Besides, the outlook on challenges and future directions of chromatographic separation in the field of proteomics was also presented.
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Affiliation(s)
- Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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3
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Lenčo J, Jadeja S, Naplekov DK, Krokhin OV, Khalikova MA, Chocholouš P, Urban J, Broeckhoven K, Nováková L, Švec F. Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial. J Proteome Res 2022; 21:2846-2892. [PMID: 36355445 DOI: 10.1021/acs.jproteome.2c00407] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The performance of the current bottom-up liquid chromatography hyphenated with mass spectrometry (LC-MS) analyses has undoubtedly been fueled by spectacular progress in mass spectrometry. It is thus not surprising that the MS instrument attracts the most attention during LC-MS method development, whereas optimizing conditions for peptide separation using reversed-phase liquid chromatography (RPLC) remains somewhat in its shadow. Consequently, the wisdom of the fundaments of chromatography is slowly vanishing from some laboratories. However, the full potential of advanced MS instruments cannot be achieved without highly efficient RPLC. This is impossible to attain without understanding fundamental processes in the chromatographic system and the properties of peptides important for their chromatographic behavior. We wrote this tutorial intending to give practitioners an overview of critical aspects of peptide separation using RPLC to facilitate setting the LC parameters so that they can leverage the full capabilities of their MS instruments. After briefly introducing the gradient separation of peptides, we discuss their properties that affect the quality of LC-MS chromatograms the most. Next, we address the in-column and extra-column broadening. The last section is devoted to key parameters of LC-MS methods. We also extracted trends in practice from recent bottom-up proteomics studies and correlated them with the current knowledge on peptide RPLC separation.
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Affiliation(s)
- Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Siddharth Jadeja
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Denis K Naplekov
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Oleg V Krokhin
- Department of Internal Medicine, Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, WinnipegR3E 3P4, Manitoba, Canada
| | - Maria A Khalikova
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Petr Chocholouš
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Jiří Urban
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00Brno, Czech Republic
| | - Ken Broeckhoven
- Department of Chemical Engineering (CHIS), Faculty of Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050Brussel, Belgium
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - František Švec
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
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4
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Stejskal K, Jeff ODB, Matzinger M, Dürnberger G, Boychenko A, Jacobs P, Mechtler K. Deep Proteome Profiling with Reduced Carryover Using Superficially Porous Microfabricated nanoLC Columns. Anal Chem 2022; 94:15930-15938. [PMID: 36356180 PMCID: PMC9685595 DOI: 10.1021/acs.analchem.2c01196] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
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In the field of liquid chromatography–mass spectrometry
(LC–MS)-based proteomics, increases in the sampling depth and
proteome coverage have mainly been accomplished by rapid advances
in mass spectrometer technology. The comprehensiveness and quality
of the data that can be generated do, however, also depend on the
performance provided by nano-liquid chromatography (nanoLC) separations.
Proper selection of reversed-phase separation columns can be important
to provide the MS instrument with peptides at the highest possible
concentration and separated at the highest possible resolution. In
the current contribution, we evaluate the use of the prototype generation
2 μPAC nanoLC columns, which use C18-functionalized superficially
porous micropillars as a stationary phase. When compared to traditionally
used fully porous silica stationary phases, more precursors could
be characterized when performing single shot data-dependent LC–MS/MS
analyses of a human cell line tryptic digest. Up to 30% more protein
groups and 60% more unique peptides were identified for short gradients
(10 min) and limited sample amounts (10–100 ng of cell lysate
digest). With LC–MS gradient times of 10, 60, 120, and 180
min, respectively, we identified 2252, 6513, 7382, and 8174 protein
groups with 25, 500, 1000, and 2000 ng of the sample loaded on the
column. Reduction of sample carryover to the next run (up to 2 to
3%) and decreased levels of methionine oxidation (up to 3-fold) were
identified as additional figures of merit. When analyzing a disuccinimidyl
dibutyric urea-crosslinked synthetic library, 29 to 59 more unique
crosslinked peptides could be identified at an experimentally validated
false discovery rate of 1–2%.
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Affiliation(s)
- Karel Stejskal
- IMBA─Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | - Op de Beeck Jeff
- Thermo Fisher Scientific, Technologiepark-Zwijnaarde 82, B-9052 Gent, Belgium
| | - Manuel Matzinger
- IMP─Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
| | - Gerhard Dürnberger
- Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | | | - Paul Jacobs
- Thermo Fisher Scientific, Technologiepark-Zwijnaarde 82, B-9052 Gent, Belgium
| | - Karl Mechtler
- IMP─Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
- IMBA─Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
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5
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Proteomic Discovery and Validation of Novel Fluid Biomarkers for Improved Patient Selection and Prediction of Clinical Outcomes in Alzheimer’s Disease Patient Cohorts. Proteomes 2022; 10:proteomes10030026. [PMID: 35997438 PMCID: PMC9397030 DOI: 10.3390/proteomes10030026] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/13/2022] [Accepted: 07/23/2022] [Indexed: 01/25/2023] Open
Abstract
Alzheimer’s disease (AD) is an irreversible neurodegenerative disease characterized by progressive cognitive decline. The two cardinal neuropathological hallmarks of AD include the buildup of cerebral β amyloid (Aβ) plaques and neurofibrillary tangles of hyperphosphorylated tau. The current disease-modifying treatments are still not effective enough to lower the rate of cognitive decline. There is an urgent need to identify early detection and disease progression biomarkers that can facilitate AD drug development. The current established readouts based on the expression levels of amyloid beta, tau, and phospho-tau have shown many discrepancies in patient samples when linked to disease progression. There is an urgent need to identify diagnostic and disease progression biomarkers from blood, cerebrospinal fluid (CSF), or other biofluids that can facilitate the early detection of the disease and provide pharmacodynamic readouts for new drugs being tested in clinical trials. Advances in proteomic approaches using state-of-the-art mass spectrometry are now being increasingly applied to study AD disease mechanisms and identify drug targets and novel disease biomarkers. In this report, we describe the application of quantitative proteomic approaches for understanding AD pathophysiology, summarize the current knowledge gained from proteomic investigations of AD, and discuss the development and validation of new predictive and diagnostic disease biomarkers.
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6
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Wang C, Liang Y, Yang X, Zhong B, Zhang X, Zhao B, Liang Z, Zhang L, Zhang Y. Surface-Charged Hybrid Monolithic Column for MS-Compatible Peptide Separation with High Peak Capacity and Its Application in Proteomic Analysis. Anal Chem 2022; 94:9525-9529. [PMID: 35762876 DOI: 10.1021/acs.analchem.2c02084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For bottom-up proteomics, peptide separation with high peak capacity under MS-compatible conditions is of vital significance to increase proteome coverage. Herein, a surface-charged ethane-bridged hybrid monolithic column was prepared based on the efficient ring-opening reaction of N-methyl-aza-2,2,4-trimethyl-silacyclopentane after C18-functionalization. The existence of secondary amino groups on the surface was beneficial to reduce the secondary interactions of silanol groups and increase peak capacity for peptide separation with MS-compatible mobile phases (e.g., using 0.1% FA as the mobile phase modifier). Such columns offered a 4-fold increase in peak capacity compared with ethane-bridged hybrid monolithic columns without surface charge modification. By a 100 cm length surface-charged ethane-bridged hybrid capillary column, high peak capacity of 700 was achieved within a 240 min gradient for the separation of Hela tryptic peptides with 0.1% FA-containing mobile phases, under the low backpressure of ∼200 bar. On average, 44493 ± 459 peptides corresponding to 5148 ± 47 proteins were identified from 750 ng Hela tryptic digests. Finally, the surface-charged ethane-bridged hybrid monolithic column was successfully applied in the quantitative proteomic analysis of dopaminergic neuron death model of N-methyl-4-phenylpyridinium iodide induced SH-SY5Y cells. These results demonstrated great promise of such surface-charged ethane-bridged hybrid monolithic columns for bottom-up proteomic analysis in complex samples.
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Affiliation(s)
- Chao Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xue Yang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bowen Zhong
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xiaodan Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Baofeng Zhao
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Zhen Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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7
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Liang Y, Wang C, Liang Z, Zhang L, Zhang Y. C18-Functionalized Amine-Bridged Hybrid Monoliths for Mass Spectrometry-Friendly Peptide Separation and Highly Sensitive Proteomic Analysis. Anal Chem 2022; 94:6084-6088. [PMID: 35404572 DOI: 10.1021/acs.analchem.1c04405] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For proteomic analysis based on mass spectrometry (MS), high-performance peptide separation under MS-friendly conditions is of importance. To this end, a novel kind of amine-bridged hybrid monolith was developed by the sol-gel reaction of bis[3-(trimethoxysilyl)propyl]amine and allyltrimethoxysilane, followed by "thiol-ene" click functionalization of C18 groups. With the secondary amino groups bridged in the framework, the nonspecific adsorption from silanol groups could be decreased, so that peptide peak tailing under MS-friendly conditions was reduced, and half peak width was narrowed. Furthermore, such materials were facilely in situ prepared in the very narrow bore capillary with low backpressure for proteomic analysis of limited amounts of samples. Finally, 16,692 unique peptides corresponding to 3698 protein groups could be averagely identified from 10 ng Hela cell digests in a single 65 min run, and 5257 peptides corresponding to 1062 protein groups could be averagely identified from 200 pg digests in a single 60 min run. Such high sensitivity could be attributed to the decreased nonspecific adsorption, the narrowed peak width, and the miniaturization of the column. It is shown that such monoliths are promising for highly sensitive proteomic analysis, including single-cell proteomics.
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Affiliation(s)
- Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chao Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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8
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Ogata K, Tsai CF, Ishihama Y. Nanoscale Solid-Phase Isobaric Labeling for Multiplexed Quantitative Phosphoproteomics. J Proteome Res 2021; 20:4193-4202. [PMID: 34292731 DOI: 10.1021/acs.jproteome.1c00444] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We established a workflow for highly sensitive multiplexed quantitative phosphoproteomics using a nanoscale solid-phase tandem mass tag (TMT) labeling reactor. Phosphopeptides were first enriched by titanium oxide chromatography and then labeled with isobaric TMT reagents in a StageTip packed with hydrophobic polymer-based sorbents. We found that TMT-labeled singly phosphorylated peptides tend to flow through the titanium oxide column. Therefore, TMT labeling should be performed after the enrichment step from tryptic peptides, resulting in the need for microscale reactions with small amounts of phosphopeptides. Using an optimized protocol for tens to hundreds of nanograms of phosphopeptides, we obtained a nearly 10-fold increase in sensitivity compared to the conventional solution-based TMT protocol. We demonstrate that this nanoscale phosphoproteomics protocol works for 50 μg of HeLa proteins treated with selumetinib, and we successfully quantified the selumetinib-regulated phosphorylated sites on a proteome scale. The MS raw data files have been deposited with the ProteomeXchange Consortium via the jPOST partner repository (https://jpostdb.org) with the data set identifier PXD025536.
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Affiliation(s)
- Kosuke Ogata
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Chia-Feng Tsai
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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9
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Performance of nanoflow liquid chromatography using core-shell particles: A comparison study. J Chromatogr A 2021; 1648:462218. [PMID: 33992996 DOI: 10.1016/j.chroma.2021.462218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/12/2021] [Accepted: 04/26/2021] [Indexed: 01/23/2023]
Abstract
Due to its unique structure, core-shell material has presented significantly improved chromatographic performance in comparison with conventional totally porous material. This has been well demonstrated in the analytical column format, e.g. 4.6 mm i.d. columns. In the proteomics field, there is always a demand for high resolution microseparation tools. In order to explore core-shell material's potential in proteomics-oriented microseparations, we investigated chromatographic performance of core-shell material in a nanoLC format, as well as its resolving power for protein digests. The results show core-shell nanoLC columns have similar van Deemter curves to the totally porous particle-packed nanoLC columns. For 100 µm i.d. capillary columns, the core-shell material does not have significantly better dynamics. However, both core-shell and totally porous particle-packed nanoLC columns have shown high efficiencies: plate heights of ~11 µm, equivalent to 90000 plates per meter, have been achieved with 5 µm particles. Using a 60 cm long core-shell nanoLC column, 72000 plates were realized in an isocratic separation of neutral compounds. For a 15 cm long nanoLC column, a maximum peak capacity of 220 has been achieved in a 5 hour gradient separation of protein digests, indicating the high resolving power of core-shell nanoLC columns. With a standard HeLa cell lysate as the sample, 2546 proteins were identified by using the core-shell nanoLC column, while 2916 proteins were identified by using the totally porous particle-packed nanoLC column. Comparing the two sets of proteomics data, it was found that 1830 proteins were identified by both columns, while 1086 and 716 proteins were uniquely identified by using totally porous and core-shell particle-packed nanoLC columns, respectively, suggesting their complementarity in nanoLC-MS based proteomics.
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10
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How Do the Different Proteomic Strategies Cope with the Complexity of Biological Regulations in a Multi-Omic World? Critical Appraisal and Suggestions for Improvements. Proteomes 2020; 8:proteomes8030023. [PMID: 32899323 PMCID: PMC7564458 DOI: 10.3390/proteomes8030023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
In this second decade of the 21st century, we are lucky enough to have different types of proteomic analyses at our disposal. Furthermore, other functional omics such as transcriptomics have also undergone major developments, resulting in mature tools. However, choice equals questions, and the major question is how each proteomic strategy is fit for which purpose. The aim of this opinion paper is to reposition the various proteomic strategies in the frame of what is known in terms of biological regulations in order to shed light on the power, limitations, and paths for improvement for the different proteomic setups. This should help biologists to select the best-suited proteomic strategy for their purposes in order not to be driven by raw availability or fashion arguments but rather by the best fitness for purpose. In particular, knowing the limitations of the different proteomic strategies helps in interpreting the results correctly and in devising the validation experiments that should be made downstream of the proteomic analyses.
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11
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Affiliation(s)
- Yasushi ISHIHAMA
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University
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12
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Towards a high peak capacity of 130 using nanoflow hydrophilic interaction liquid chromatography. Anal Chim Acta 2019; 1062:147-155. [DOI: 10.1016/j.aca.2019.01.060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 11/21/2022]
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13
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Liang Y, Zhang L, Zhang Y. Well-Defined Materials for High-Performance Chromatographic Separation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:451-473. [PMID: 30939031 DOI: 10.1146/annurev-anchem-061318-114854] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Chromatographic separation has been widely applied in various fields, such as chemical engineering, precision medicine, energy, and biology. Because chromatographic separation is based on differential partitioning between the mobile phase and stationary phase and affected by band dispersion and mass transfer resistance from these two phases, the materials used as the stationary phase play a decisive role in separation performance. In this review, we discuss the design of separation materials to achieve the separation with high efficiency and high resolution and highlight the well-defined materials with uniform pore structure and unique properties. The achievements, recent developments, challenges, and future trends of such materials are discussed. Furthermore, the surface functionalization of separation ma-terials for further improvement of separation performance is reviewed. Finally, future research directions and the challenges of chromatographic separation are presented.
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Affiliation(s)
- Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China;
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China;
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China;
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14
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Iwasaki M, Tabata T, Kawahara Y, Ishihama Y, Nakagawa M. Removal of Interference MS/MS Spectra for Accurate Quantification in Isobaric Tag-Based Proteomics. J Proteome Res 2019; 18:2535-2544. [PMID: 31039306 DOI: 10.1021/acs.jproteome.9b00078] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rapid progress in mass spectrometry (MS) has made comprehensive analyses of the proteome possible, but accurate quantification remains challenging. Isobaric tags for relative and absolute quantification (iTRAQ) is widely used as a tool to quantify proteins expressed in different cell types and various cellular conditions. The quantification precision of iTRAQ is quite high, but the accuracy dramatically decreases in the presence of interference peptides that are coeluted and coisolated with the target peptide. Here, we developed "removal of interference mixture MS/MS spectra (RiMS)" to improve the quantification accuracy of isobaric tag approaches. The presence of spectrum interference is judged by examining the overlap in the elution time of all scanned precursor ions. Removal of this interference decreased protein identification (11% loss) but improved quantification accuracy. Further, RiMS does not require any specialized equipment, such as MS3 instruments or an additional ion separation mode. Finally, we demonstrated that RiMS can be used to quantitatively compare human-induced pluripotent stem cells and human dermal fibroblasts, as it revealed differential protein expressions that reflect the biological characteristics of the cells.
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Affiliation(s)
- Mio Iwasaki
- Center for iPS Cell Research and Application , Kyoto University , Kyoto 606-8507 , Japan
| | - Tsuyoshi Tabata
- Center for iPS Cell Research and Application , Kyoto University , Kyoto 606-8507 , Japan.,Graduate school of Pharmaceutical Sciences , Kyoto University , Kyoto 606-8501 , Japan
| | - Yuka Kawahara
- Center for iPS Cell Research and Application , Kyoto University , Kyoto 606-8507 , Japan
| | - Yasushi Ishihama
- Graduate school of Pharmaceutical Sciences , Kyoto University , Kyoto 606-8501 , Japan
| | - Masato Nakagawa
- Center for iPS Cell Research and Application , Kyoto University , Kyoto 606-8507 , Japan
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15
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Immature and Mature Collagen Crosslinks Quantification Using High-Performance Liquid Chromatography and High-Resolution Mass Spectrometry in Orbitrap™. Methods Mol Biol 2019; 1996:101-111. [PMID: 31127551 DOI: 10.1007/978-1-4939-9488-5_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Different methodologies for collagen quantification have been described in the past. Introduction of mass spectrometry combined with high-performance liquid chromatography (HPLC) is a high-resolution tool, which has generated novel applications in biomedical research. In this study, HPLC coupled to electrospray ionization (ESI) tandem mass spectrometry (HPLC-ESI-MS/MS) was used to characterize tissue samples from AVFs done in rats. These findings helped create a protocol for identifying and quantifying components of immature and mature collagen crosslink moieties. Two different internal standards were used: epinephrine and pyridoxine. Quantification curves were drawn by means of these standards. The goal of the experiment was to achieve accurate quantification with the minimum amount of sample. Time and cost of experiment were considerably minimized. Up to date, this method has not been tested for crosslinking quantification.
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16
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Shishkova E, Hebert AS, Coon JJ. Now, More Than Ever, Proteomics Needs Better Chromatography. Cell Syst 2018; 3:321-324. [PMID: 27788355 DOI: 10.1016/j.cels.2016.10.007] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/07/2016] [Accepted: 10/08/2016] [Indexed: 01/14/2023]
Abstract
From plant research to biomedicine, proteome analysis plays a critical role in many areas of biological inquiry. Steady improvement in mass spectrometer (MS) technology has transformed the speed and depth of proteome analysis. Proteomes of simple organisms can now be sequenced to near completion in just over an hour. Comparable coverage of mammalian proteomes, however, still requires hours or even days of analysis. Here we ask why current technology fails to achieve comprehensive and rapid analysis of the more complex mammalian proteomes. We propose that further advancements in MS technology alone are unlikely to solve this problem and suggest that concomitant improvements in peptide separation technology will be critical.
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Affiliation(s)
- Evgenia Shishkova
- The Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, WI, USA
| | - Alexander S Hebert
- The Genome Center of Wisconsin, University of Wisconsin - Madison, Madison, WI, USA
| | - Joshua J Coon
- The Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, WI, USA; The Genome Center of Wisconsin, University of Wisconsin - Madison, Madison, WI, USA; The Department of Chemistry, University of Wisconsin - Madison, Madison, WI, USA.
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17
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Pfammatter S, Bonneil E, McManus FP, Prasad S, Bailey DJ, Belford M, Dunyach JJ, Thibault P. A Novel Differential Ion Mobility Device Expands the Depth of Proteome Coverage and the Sensitivity of Multiplex Proteomic Measurements. Mol Cell Proteomics 2018; 17:2051-2067. [PMID: 30007914 DOI: 10.1074/mcp.tir118.000862] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/11/2018] [Indexed: 01/17/2023] Open
Abstract
The depth of proteomic analyses is often limited by the overwhelming proportion of confounding background ions that compromise the identification and quantification of low abundance peptides. To alleviate these limitations, we present a new high field asymmetric waveform ion mobility spectrometry (FAIMS) interface that can be coupled to the Orbitrap Tribrid mass spectrometers. The interface provides several advantages over previous generations of FAIMS devices, including ease of operation, robustness, and high ion transmission. Replicate LC-FAIMS-MS/MS analyses (n = 100) of HEK293 protein digests showed stable ion current over extended time periods with uniform peptide identification on more than 10,000 distinct peptides. For complex tryptic digest analyses, the coupling of FAIMS to LC-MS/MS enabled a 30% gain in unique peptide identification compared with non-FAIMS experiments. Improvement in sensitivity facilitated the identification of low abundance peptides, and extended the limit of detection by almost an order of magnitude. The reduction in chimeric MS/MS spectra using FAIMS also improved the precision and the number of quantifiable peptides when using isobaric labeling with tandem mass tag (TMT) 10-plex reagent. We compared quantitative proteomic measurements for LC-MS/MS analyses performed using synchronous precursor selection (SPS) and LC-FAIMS-MS/MS to profile the temporal changes in protein abundance of HEK293 cells following heat shock for periods up to 9 h. FAIMS provided 2.5-fold increase in the number of quantifiable peptides compared with non-FAIMS experiments (30,848 peptides from 2,646 proteins for FAIMS versus 12,400 peptides from 1,229 proteins with SPS). Altogether, the enhancement in ion transmission and duty cycle of the new FAIMS interface extended the depth and comprehensiveness of proteomic analyses and improved the precision of quantitative measurements.
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Affiliation(s)
- Sibylle Pfammatter
- From the ‡Institute for Research in Immunology and Cancer, H3T 1J4, Québec, Canada.,§University of Montréal, Department of Chemistry, H3T 1J4, Québec, Canada
| | - Eric Bonneil
- From the ‡Institute for Research in Immunology and Cancer, H3T 1J4, Québec, Canada
| | - Francis P McManus
- From the ‡Institute for Research in Immunology and Cancer, H3T 1J4, Québec, Canada
| | - Satendra Prasad
- ¶Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Derek J Bailey
- ¶Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Michael Belford
- ¶Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - Pierre Thibault
- From the ‡Institute for Research in Immunology and Cancer, H3T 1J4, Québec, Canada; .,§University of Montréal, Department of Chemistry, H3T 1J4, Québec, Canada
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18
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Dorfer V, Maltsev S, Winkler S, Mechtler K. CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction. J Proteome Res 2018; 17:2581-2589. [PMID: 29863353 PMCID: PMC6079931 DOI: 10.1021/acs.jproteome.7b00836] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coeluting peptides are still a major challenge for the identification and validation of MS/MS spectra, but carry great potential. To tackle these problems, we have developed the here presented CharmeRT workflow, combining a chimeric spectra identification strategy implemented as part of the MS Amanda algorithm with the validation system Elutator, which incorporates a highly accurate retention time prediction algorithm. For high-resolution data sets this workflow identifies 38-64% chimeric spectra, which results in up to 63% more unique peptides compared to a conventional single search strategy.
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Affiliation(s)
- Viktoria Dorfer
- Bioinformatics Research Group , University of Applied Sciences Upper Austria , Softwarepark 11 , 4232 Hagenberg , Austria
| | | | - Stephan Winkler
- Bioinformatics Research Group , University of Applied Sciences Upper Austria , Softwarepark 11 , 4232 Hagenberg , Austria
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19
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Thygesen C, Boll I, Finsen B, Modzel M, Larsen MR. Characterizing disease-associated changes in post-translational modifications by mass spectrometry. Expert Rev Proteomics 2018; 15:245-258. [DOI: 10.1080/14789450.2018.1433036] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Camilla Thygesen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Department of Neuroscience, University of Southern Denmark, Institute of Molecular Medicine, Denmark
| | - Inga Boll
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Bente Finsen
- Department of Neuroscience, University of Southern Denmark, Institute of Molecular Medicine, Denmark
| | - Maciej Modzel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Martin R. Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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20
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Andjelković U, Tufegdžić S, Popović M. Use of monolithic supports for high-throughput protein and peptide separation in proteomics. Electrophoresis 2017; 38:2851-2869. [DOI: 10.1002/elps.201700260] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/02/2017] [Accepted: 09/03/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Uroš Andjelković
- Department of Chemistry-Institute of Chemistry; Technology and Metallurgy; University of Belgrade; Belgrade Serbia
- Department of Biotechnology; University of Rijeka; Rijeka Croatia
| | - Srdjan Tufegdžić
- Department of Chemistry-Institute of Chemistry; Technology and Metallurgy; University of Belgrade; Belgrade Serbia
| | - Milica Popović
- Faculty of Chemistry; University of Belgrade; Belgrade Serbia
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21
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Advances in monolithic silica columns for high-performance liquid chromatography. J Anal Sci Technol 2017. [DOI: 10.1186/s40543-017-0125-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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22
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Bekker-Jensen DB, Kelstrup CD, Batth TS, Larsen SC, Haldrup C, Bramsen JB, Sørensen KD, Høyer S, Ørntoft TF, Andersen CL, Nielsen ML, Olsen JV. An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes. Cell Syst 2017; 4:587-599.e4. [PMID: 28601559 PMCID: PMC5493283 DOI: 10.1016/j.cels.2017.05.009] [Citation(s) in RCA: 308] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/03/2017] [Accepted: 05/11/2017] [Indexed: 01/08/2023]
Abstract
This study investigates the challenge of comprehensively cataloging the complete human proteome from a single-cell type using mass spectrometry (MS)-based shotgun proteomics. We modify a classical two-dimensional high-resolution reversed-phase peptide fractionation scheme and optimize a protocol that provides sufficient peak capacity to saturate the sequencing speed of modern MS instruments. This strategy enables the deepest proteome of a human single-cell type to date, with the HeLa proteome sequenced to a depth of ∼584,000 unique peptide sequences and ∼14,200 protein isoforms (∼12,200 protein-coding genes). This depth is comparable with next-generation RNA sequencing and enables the identification of post-translational modifications, including ∼7,000 N-acetylation sites and ∼10,000 phosphorylation sites, without the need for enrichment. We further demonstrate the general applicability and clinical potential of this proteomics strategy by comprehensively quantifying global proteome expression in several different human cancer cell lines and patient tissue samples. Multi-shot proteomics quantifies the protein levels of 12,200+ genes in HeLa cells This essentially complete HeLa proteome has coverage similar to next-gen RNA-seq Deep coverage of major PTMs is achieved without specific enrichment The approach is extendable to other human cell lines and patient samples
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Affiliation(s)
- Dorte B Bekker-Jensen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Christian D Kelstrup
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
| | - Tanveer S Batth
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Sara C Larsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Christa Haldrup
- Departments of Molecular Medicine and Clinical Medicine, Aarhus University Hospital, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
| | - Jesper B Bramsen
- Departments of Molecular Medicine and Clinical Medicine, Aarhus University Hospital, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
| | - Karina D Sørensen
- Departments of Molecular Medicine and Clinical Medicine, Aarhus University Hospital, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
| | - Søren Høyer
- Institute of Pathology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
| | - Torben F Ørntoft
- Departments of Molecular Medicine and Clinical Medicine, Aarhus University Hospital, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
| | - Claus L Andersen
- Departments of Molecular Medicine and Clinical Medicine, Aarhus University Hospital, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
| | - Michael L Nielsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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23
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Zhao X, Xie X, Sharma S, Tolley LT, Plistil A, Barnett HE, Brisbin MP, Swensen AC, Price JC, Farnsworth PB, Tolley HD, Stearns SD, Lee ML. Compact Ultrahigh-Pressure Nanoflow Capillary Liquid Chromatograph. Anal Chem 2016; 89:807-812. [DOI: 10.1021/acs.analchem.6b03575] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | | | | | - Luke T. Tolley
- Tranxend LLC, 6550 South Millrock
Drive, Suite 200, Salt Lake City, Utah 84121, United States
| | - Alex Plistil
- VICI, Valco Instruments, Houston, Texas 77055, United States
| | - Hal E. Barnett
- VICI, Valco Instruments, Houston, Texas 77055, United States
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24
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Hirata H, Ku WC, Yip AK, Ursekar CP, Kawauchi K, Roy A, Guo AK, Vedula SRK, Harada I, Chiam KH, Ishihama Y, Lim CT, Sawada Y, Sokabe M. MEKK1-dependent phosphorylation of calponin-3 tunes cell contractility. J Cell Sci 2016; 129:3574-3582. [PMID: 27528401 DOI: 10.1242/jcs.189415] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 08/10/2016] [Indexed: 12/30/2022] Open
Abstract
MEKK1 (also known as MAP3K1), which plays a major role in MAPK signaling, has been implicated in mechanical processes in cells, such as migration. Here, we identify the actin-binding protein calponin-3 as a new MEKK1 substrate in the signaling that regulates actomyosin-based cellular contractility. MEKK1 colocalizes with calponin-3 at the actin cytoskeleton and phosphorylates it, leading to an increase in the cell-generated traction stress. MEKK1-mediated calponin-3 phosphorylation is attenuated by the inhibition of myosin II activity, the disruption of actin cytoskeletal integrity and adhesion to soft extracellular substrates, whereas it is enhanced upon cell stretching. Our results reveal the importance of the MEKK1-calponin-3 signaling pathway to cell contractility.
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Affiliation(s)
- Hiroaki Hirata
- Mechanobiology Institute, National University of Singapore, 117411 Singapore
| | - Wei-Chi Ku
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Ai Kia Yip
- A*STAR Bioinformatics Institute, 138671 Singapore
| | | | - Keiko Kawauchi
- Mechanobiology Institute, National University of Singapore, 117411 Singapore
| | - Amrita Roy
- Mechanobiology Institute, National University of Singapore, 117411 Singapore
| | - Alvin Kunyao Guo
- Mechanobiology Institute, National University of Singapore, 117411 Singapore
| | | | - Ichiro Harada
- Locomotive Syndrome Research Institute, Nadogaya Hospital, Kashiwa 277-0032, Japan Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Keng-Hwee Chiam
- Mechanobiology Institute, National University of Singapore, 117411 Singapore A*STAR Bioinformatics Institute, 138671 Singapore
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Chwee Teck Lim
- Mechanobiology Institute, National University of Singapore, 117411 Singapore Department of Biomedical Engineering, National University of Singapore, 117583 Singapore
| | - Yasuhiro Sawada
- Mechanobiology Institute, National University of Singapore, 117411 Singapore Locomotive Syndrome Research Institute, Nadogaya Hospital, Kashiwa 277-0032, Japan Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Masahiro Sokabe
- Mechanobiology Institute, National University of Singapore, 117411 Singapore Mechanobiology Laboratory, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
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25
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Ikegami T, Tanaka N. Recent Progress in Monolithic Silica Columns for High-Speed and High-Selectivity Separations. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:317-342. [PMID: 27306311 DOI: 10.1146/annurev-anchem-071114-040102] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Monolithic silica columns have greater (through-pore size)/(skeleton size) ratios than particulate columns and fixed support structures in a column for chemical modification, resulting in high-efficiency columns and stationary phases. This review looks at how the size range of monolithic silica columns has been expanded, how high-efficiency monolithic silica columns have been realized, and how various methods of silica surface functionalization, leading to selective stationary phases, have been developed on monolithic silica supports, and provides information on the current status of these columns. Also discussed are the practical aspects of monolithic silica columns, including how their versatility can be improved by the preparation of small-sized structural features (sub-micron) and columns (1 mm ID or smaller) and by optimizing reaction conditions for in situ chemical modification with various restrictions, with an emphasis on recent research results for both topics.
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Affiliation(s)
- Tohru Ikegami
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Kyoto 606-8585, Japan;
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26
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Hara T, Desmet G, Baron GV, Minakuchi H, Eeltink S. Effect of polyethylene glycol on pore structure and separation efficiency of silica-based monolithic capillary columns. J Chromatogr A 2016; 1442:42-52. [DOI: 10.1016/j.chroma.2016.03.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/03/2016] [Accepted: 03/04/2016] [Indexed: 10/22/2022]
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27
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Moravcová D, Rantamäki AH, Duša F, Wiedmer SK. Monoliths in capillary electrochromatography and capillary liquid chromatography in conjunction with mass spectrometry. Electrophoresis 2016; 37:880-912. [PMID: 26800083 DOI: 10.1002/elps.201500520] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 12/29/2022]
Abstract
Here, we have reviewed separation studies utilizing monolithic capillary columns for separation of compounds preceding MS analysis. The review is divided in two parts according to the used separation method, namely CEC and capillary LC (cLC). Based on our overview, monolithic CEC-MS technique have been more focused on the syntheses of highly specialized and selective separation phase materials for fast and efficient separation of specific types of analytes. In contrast, monolithic cLC-MS is more widely used and is often employed, for instance, in the analysis of oligonucleotides, metabolites, and peptides and proteins in proteomic studies. While poly(styrene-divinylbenzene)-based and silica-based monolithic capillaries found their place in proteomic analyses, the other laboratory-synthesized monoliths still wait for their wider utilization in routine analyses. The development of new monolithic materials will most likely continue due to the demand of more efficient and rapid separation of increasingly complex samples.
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Affiliation(s)
- Dana Moravcová
- Institute of Analytical Chemistry of the CAS, v. v. i, Brno, Czech Republic
| | | | - Filip Duša
- Institute of Analytical Chemistry of the CAS, v. v. i, Brno, Czech Republic
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28
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Humphrey SJ, James DE, Mann M. Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation. Trends Endocrinol Metab 2015; 26:676-687. [PMID: 26498855 DOI: 10.1016/j.tem.2015.09.013] [Citation(s) in RCA: 339] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/26/2015] [Accepted: 09/28/2015] [Indexed: 12/20/2022]
Abstract
Metabolism research is undergoing a renaissance because many diseases are increasingly recognized as being characterized by perturbations in intracellular metabolic regulation. Metabolic changes can be conferred through changes to the expression of metabolic enzymes, the concentrations of substrates or products that govern reaction kinetics, or post-translational modification (PTM) of the proteins that facilitate these reactions. On the 60th anniversary since its discovery, reversible protein phosphorylation is widely appreciated as an essential PTM regulating metabolism. With the ability to quantitatively measure dynamic changes in protein phosphorylation on a global scale - hereafter referred to as phosphoproteomics - we are now entering a new era in metabolism research, with mass spectrometry (MS)-based proteomics at the helm.
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Affiliation(s)
- Sean J Humphrey
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried 82152, Germany
| | - David E James
- Charles Perkins Centre, School of Molecular Bioscience, Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried 82152, Germany.
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29
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Dimayacyac-Esleta BRT, Tsai CF, Kitata RB, Lin PY, Choong WK, Lin TD, Wang YT, Weng SH, Yang PC, Arco SD, Sung TY, Chen YJ. Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling. Anal Chem 2015; 87:12016-23. [PMID: 26554430 DOI: 10.1021/acs.analchem.5b03639] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Membrane proteins are crucial targets for cancer biomarker discovery and drug development. However, in addition to the inherent challenges of hydrophobicity and low abundance, complete membrane proteome coverage of clinical specimen is usually hindered by the requirement of large amount of starting materials. Toward comprehensive membrane proteomic profiling for small amounts of samples (10 μg), we developed high-pH reverse phase (Hp-RP) combined with stop-and-go extraction tip (StageTip) technique, as a fast (∼15 min.), sensitive, reproducible, high-resolution and multiplexed fractionation method suitable for accurate quantification of the membrane proteome. This approach provided almost 2-fold enhanced detection of peptides encompassing transmembrane helix (TMH) domain, as compared with strong anion exchange (SAX) and strong cation exchange (SCX) StageTip techniques. Almost 5000 proteins (∼60% membrane proteins) can be identified in only 10 μg of membrane protein digests, showing the superior sensitivity of the Hp-RP StageTip approach. The method allowed up to 9- and 6-fold increase in the identification of unique hydrophobic and hydrophilic peptides, respectively. The Hp-RP StageTip method enabled in-depth membrane proteome profiling of 11 lung cancer cell lines harboring different EGFR mutation status, which resulted in the identification of 3983 annotated membrane proteins. This provides the largest collection of reference peptide spectral data for lung cancer membrane subproteome. Finally, relative quantification of membrane proteins between Gefitinib-resistant and -sensitive lung cancer cell lines revealed several up-regulated membrane proteins with key roles in lung cancer progression.
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Affiliation(s)
- Baby Rorielyn T Dimayacyac-Esleta
- Institute of Chemistry, University of the Philippines , Diliman Quezon City 1101, Philippines.,Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Chia-Feng Tsai
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Reta Birhanu Kitata
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan.,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115, Taiwan
| | - Pei-Yi Lin
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Wai-Kok Choong
- Institute of Information Science, Academia Sinica , Taipei 115, Taiwan
| | - Tai-Du Lin
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Department of Biochemical Sciences, National Taiwan University , Taipei 10617, Taiwan
| | - Yi-Ting Wang
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Shao-Hsing Weng
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University , Taipei 10617, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital , Taipei 10617, Taiwan.,National Taiwan University College of Medicine , Taipei 10051, Taiwan.,Institute of Biomedical Science, Academia Sinica , Taipei 115, Taiwan
| | - Susan D Arco
- Institute of Chemistry, University of the Philippines , Diliman Quezon City 1101, Philippines
| | - Ting-Yi Sung
- Institute of Information Science, Academia Sinica , Taipei 115, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan.,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115, Taiwan
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30
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Mitchell CJ, Getnet D, Kim MS, Manda SS, Kumar P, Huang TC, Pinto SM, Nirujogi RS, Iwasaki M, Shaw PG, Wu X, Zhong J, Chaerkady R, Marimuthu A, Muthusamy B, Sahasrabuddhe NA, Raju R, Bowman C, Danilova L, Cutler J, Kelkar DS, Drake CG, Prasad TSK, Marchionni L, Murakami PN, Scott AF, Shi L, Thierry-Mieg J, Thierry-Mieg D, Irizarry R, Cope L, Ishihama Y, Wang C, Gowda H, Pandey A. A multi-omic analysis of human naïve CD4+ T cells. BMC SYSTEMS BIOLOGY 2015; 9:75. [PMID: 26542228 PMCID: PMC4636073 DOI: 10.1186/s12918-015-0225-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 10/28/2015] [Indexed: 12/21/2022]
Abstract
Background Cellular function and diversity are orchestrated by complex interactions of fundamental biomolecules including DNA, RNA and proteins. Technological advances in genomics, epigenomics, transcriptomics and proteomics have enabled massively parallel and unbiased measurements. Such high-throughput technologies have been extensively used to carry out broad, unbiased studies, particularly in the context of human diseases. Nevertheless, a unified analysis of the genome, epigenome, transcriptome and proteome of a single human cell type to obtain a coherent view of the complex interplay between various biomolecules has not yet been undertaken. Here, we report the first multi-omic analysis of human primary naïve CD4+ T cells isolated from a single individual. Results Integrating multi-omics datasets allowed us to investigate genome-wide methylation and its effect on mRNA/protein expression patterns, extent of RNA editing under normal physiological conditions and allele specific expression in naïve CD4+ T cells. In addition, we carried out a multi-omic comparative analysis of naïve with primary resting memory CD4+ T cells to identify molecular changes underlying T cell differentiation. This analysis provided mechanistic insights into how several molecules involved in T cell receptor signaling are regulated at the DNA, RNA and protein levels. Phosphoproteomics revealed downstream signaling events that regulate these two cellular states. Availability of multi-omics data from an identical genetic background also allowed us to employ novel proteogenomics approaches to identify individual-specific variants and putative novel protein coding regions in the human genome. Conclusions We utilized multiple high-throughput technologies to derive a comprehensive profile of two primary human cell types, naïve CD4+ T cells and memory CD4+ T cells, from a single donor. Through vertical as well as horizontal integration of whole genome sequencing, methylation arrays, RNA-Seq, miRNA-Seq, proteomics, and phosphoproteomics, we derived an integrated and comparative map of these two closely related immune cells and identified potential molecular effectors of immune cell differentiation following antigen encounter. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0225-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher J Mitchell
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Derese Getnet
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Srikanth S Manda
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Praveen Kumar
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Tai-Chung Huang
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Sneha M Pinto
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Mio Iwasaki
- Department of Molecular & Cellular BioAnalysis, Kyoto University, Kyoto, Japan.
| | - Patrick G Shaw
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Xinyan Wu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Jun Zhong
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Raghothama Chaerkady
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Arivusudar Marimuthu
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | | | | | - Rajesh Raju
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Caitlyn Bowman
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Ludmila Danilova
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Jevon Cutler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Dhanashree S Kelkar
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Charles G Drake
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Luigi Marchionni
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Peter N Murakami
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
| | - Alan F Scott
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Leming Shi
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA.
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.
| | - Rafael Irizarry
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA.
| | - Leslie Cope
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Yasushi Ishihama
- Department of Molecular & Cellular BioAnalysis, Kyoto University, Kyoto, Japan.
| | - Charles Wang
- Center for Genomics and Division of Microbiology & Molecular Genetics, Loma Linda University, Loma Linda, CA, USA.
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India.
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India. .,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Wakabayashi M, Kyono Y, Sugiyama N, Ishihama Y. Extended Coverage of Singly and Multiply Phosphorylated Peptides from a Single Titanium Dioxide Microcolumn. Anal Chem 2015; 87:10213-21. [DOI: 10.1021/acs.analchem.5b01216] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Masaki Wakabayashi
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29, Yoshida-Shimo-Adachi-Cho,
Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yutaka Kyono
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29, Yoshida-Shimo-Adachi-Cho,
Sakyo-ku, Kyoto, 606-8501, Japan
| | - Naoyuki Sugiyama
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29, Yoshida-Shimo-Adachi-Cho,
Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29, Yoshida-Shimo-Adachi-Cho,
Sakyo-ku, Kyoto, 606-8501, Japan
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Samperi R, Capriotti AL, Cavaliere C, Colapicchioni V, Chiozzi RZ, Laganà A. Food Proteins and Peptides. ADVANCED MASS SPECTROMETRY FOR FOOD SAFETY AND QUALITY 2015. [DOI: 10.1016/b978-0-444-63340-8.00006-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Shiba-Fukushima K, Arano T, Matsumoto G, Inoshita T, Yoshida S, Ishihama Y, Ryu KY, Nukina N, Hattori N, Imai Y. Phosphorylation of mitochondrial polyubiquitin by PINK1 promotes Parkin mitochondrial tethering. PLoS Genet 2014; 10:e1004861. [PMID: 25474007 PMCID: PMC4256268 DOI: 10.1371/journal.pgen.1004861] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/29/2014] [Indexed: 11/18/2022] Open
Abstract
The kinase PINK1 and the E3 ubiquitin (Ub) ligase Parkin participate in mitochondrial quality control. The phosphorylation of Ser65 in Parkin's ubiquitin-like (UBl) domain by PINK1 stimulates Parkin activation and translocation to damaged mitochondria, which induces mitophagy generating polyUb chain. However, Parkin Ser65 phosphorylation is insufficient for Parkin mitochondrial translocation. Here we report that Ser65 in polyUb chain is also phosphorylated by PINK1, and that phosphorylated polyUb chain on mitochondria tethers Parkin at mitochondria. The expression of Tom70MTS-4xUb SE, which mimics phospho-Ser65 polyUb chains on the mitochondria, activated Parkin E3 activity and its mitochondrial translocation. An E3-dead form of Parkin translocated to mitochondria with reduced membrane potential in the presence of Tom70MTS-4xUb SE, whereas non-phospho-polyUb mutant Tom70MTS-4xUb SA abrogated Parkin translocation. Parkin binds to the phospho-polyUb chain through its RING1-In-Between-RING (IBR) domains, but its RING0-linker is also required for mitochondrial translocation. Moreover, the expression of Tom70MTS-4xUb SE improved mitochondrial degeneration in PINK1-deficient, but not Parkin-deficient, Drosophila. Our study suggests that the phosphorylation of mitochondrial polyUb by PINK1 is implicated in both Parkin activation and mitochondrial translocation, predicting a chain reaction mechanism of mitochondrial phospho-polyUb production by which rapid translocation of Parkin is achieved. Parkinson's disease is a neurodegenerative disorder caused by degeneration of the midbrain dopaminergic system in addition to other nervous systems. PINK1 and parkin, which encode mitochondrial protein kinase and cytosolic Ub ligase, respectively, were identified as the genes responsible for the autosomal recessive form of juvenile Parkinson's disease. Activation of PINK1 upon reduction of mitochondrial membrane potential recruits Parkin from the cytosol activating its Ub ligase activity, which ensures removal of damaged mitochondria through mitophagy. However, how PINK1 recruits Parkin to the damaged mitochondria remained unclear. Here, we describe that the phosphorylation of polyUb chain by PINK1 is a key event to recruit Parkin on the mitochondria. Parkin binds to, and is activated by, phospho-polyUb generated by Parkin in collaboration with PINK1. Expression of a phospho-polyUb mimetic protein on mitochondria rescued mitochondrial degeneration caused by loss of PINK1 in Drosophila. Our study suggests the existence of an amplification cascade of Parkin activation and mitochondrial translocation, in which a ‘seed' of phosphorylated polyUb on the mitochondria, generated by PINK1 and Parkin, triggers a chain reaction of Parkin recruitment and activation.
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Affiliation(s)
| | - Taku Arano
- Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Gen Matsumoto
- Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tsuyoshi Inoshita
- Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shigeharu Yoshida
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kwon-Yul Ryu
- Department of Life Science, University of Seoul, Seoul, Korea
| | - Nobuyuki Nukina
- Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo, Japan; Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuzuru Imai
- Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Han J, Ye L, Xu L, Zhou Z, Gao F, Xiao Z, Wang Q, Zhang B. Towards high peak capacity separations in normal pressure nanoflow liquid chromatography using meter long packed capillary columns. Anal Chim Acta 2014; 852:267-73. [DOI: 10.1016/j.aca.2014.09.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 08/31/2014] [Accepted: 09/07/2014] [Indexed: 10/24/2022]
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Abstract
Advances in mass spectrometry (MS) have transformed the scope and impact of protein characterization efforts. Identifying hundreds of proteins from rather simple biological matrices, such as yeast, was a daunting task just a few decades ago. Now, expression of more than half of the estimated ∼20,000 human protein coding genes can be confirmed in record time and from minute sample quantities. Access to proteomic information at such unprecedented depths has been fueled by strides in every stage of the shotgun proteomics workflow-from sample processing to data analysis-and promises to revolutionize our understanding of the causes and consequences of proteome variation.
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36
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Yin X, Liu X, Zhang Y, Yan G, Wang F, Lu H, Shen H, Yang P. Rapid and sensitive profiling and quantification of the human cell line proteome by LC-MS/MS without prefractionation. Proteomics 2014; 14:2008-16. [PMID: 25044409 DOI: 10.1002/pmic.201300510] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 06/11/2014] [Accepted: 07/03/2014] [Indexed: 01/05/2023]
Abstract
In this paper, we demonstrate a rapid and reproducible 1D LC-MS/MS workflow for fast quantitative proteomic research. We have optimized the LC-MS/MS conditions, including digestion and gradient conditions, sample loading amount, and MS parameter settings. As a result, we were able to obtain twice as many protein identifications compared with the LC-MS/MS conditions before optimization. More than 4500 protein groups and 50 000 peptides were identified in less than 8 h without any fractionation. This 1D workflow was then applied to the analysis of the MLN4924 treated/untreated human umbilical vein endothelial cell (HUVEC) samples with label-free quantification. In these experiments, a total of 179 proteins showed a statistically significant expression change after the MLN4924 treatment. Functional analysis showed that these proteins are associated with cell death and survival; gene expression; cell cycle; and DNA replication, recombination, and repair.
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Affiliation(s)
- Xuefei Yin
- Department of Chemistry and Institutes of Biomedical Sciences Shanghai Medical School, Fudan University, Shanghai, P. R. China
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37
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Horie K, Kamakura T, Ikegami T, Wakabayashi M, Kato T, Tanaka N, Ishihama Y. Hydrophilic Interaction Chromatography Using a Meter-Scale Monolithic Silica Capillary Column for Proteomics LC-MS. Anal Chem 2014; 86:3817-24. [DOI: 10.1021/ac4038625] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kanta Horie
- Eisai Co., Ltd, Pharmaceutical Science and Technology
Core Function Unit, Global Formulation Research, Kawashima, Kakamigahara, Gifu 501-6195, Japan
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
| | - Takeo Kamakura
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
| | - Tohru Ikegami
- Department
of Biomolecular Engineering, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Kyoto 606-8585, Japan
| | - Masaki Wakabayashi
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
| | - Takashi Kato
- Eisai Co., Ltd, Pharmaceutical Science and Technology
Core Function Unit, Global Formulation Research, Kawashima, Kakamigahara, Gifu 501-6195, Japan
| | - Nobuo Tanaka
- Department
of Biomolecular Engineering, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Kyoto 606-8585, Japan
- GL Sciences Inc., 237-2
Sayamagahara, Iruma, Saitama 358-0032, Japan
| | - Yasushi Ishihama
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
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38
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Chan AS, Danquah MK, Agyei D, Hartley PG, Zhu Y. A simple microfluidic chip design for fundamental bioseparation. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2014; 2014:175457. [PMID: 24527255 PMCID: PMC3910460 DOI: 10.1155/2014/175457] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 12/12/2013] [Indexed: 06/03/2023]
Abstract
A microchip pressure-driven liquid chromatographic system with a packed column has been designed and fabricated by using poly(dimethylsiloxane) (PDMS). The liquid chromatographic column was packed with mesoporous silica beads of Ia3d space group. Separation of dyes and biopolymers was carried out to verify the performance of the chip. A mixture of dyes (fluorescein and rhodamine B) and a biopolymer mixture (10 kDa Dextran and 66 kDa BSA) were separated and the fluorescence technique was employed to detect the movement of the molecules. Fluorescein molecule was a nonretained species and rhodamine B was attached onto silica surface when dye mixture in deionized water was injected into the microchannel. The retention times for dextran molecule and BSA molecule in biopolymer separation experiment were 45 s and 120 s, respectively. Retention factor was estimated to be 3.3 for dextran and 10.4 for BSA. The selectivity was 3.2 and resolution was 10.7. Good separation of dyes and biopolymers was achieved and the chip design was verified.
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Affiliation(s)
- Alan S. Chan
- CSIRO Materials Science and Engineering, Highett, VIC 3190, Australia
- Department of Chemical Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Michael K. Danquah
- Department of Chemical Engineering, Monash University, Clayton, VIC 3800, Australia
- Department of Chemical Engineering, Curtin University of Technology, Sarawak 98009, Malaysia
| | - Dominic Agyei
- Department of Chemical Engineering, Monash University, Clayton, VIC 3800, Australia
| | | | - Yonggang Zhu
- CSIRO Materials Science and Engineering, Highett, VIC 3190, Australia
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39
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Marino F, Cristobal A, Binai NA, Bache N, Heck AJR, Mohammed S. Characterization and usage of the EASY-spray technology as part of an online 2D SCX-RP ultra-high pressure system. Analyst 2014; 139:6520-8. [DOI: 10.1039/c4an01568a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The EASY-spray technology can now be implemented as a simple online 2D SCX-RP ultra-high pressure system, which allows one to reach deep proteome coverages.
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Affiliation(s)
- Fabio Marino
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
| | - Alba Cristobal
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
| | - Nadine A. Binai
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
| | | | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
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40
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Zhang Z, Wu S, Stenoien DL, Paša-Tolić L. High-throughput proteomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:427-454. [PMID: 25014346 DOI: 10.1146/annurev-anchem-071213-020216] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Mass spectrometry (MS)-based high-throughput proteomics is the core technique for large-scale protein characterization. Due to the extreme complexity of proteomes, sophisticated separation techniques and advanced MS instrumentation have been developed to extend coverage and enhance dynamic range and sensitivity. In this review, we discuss the separation and prefractionation techniques applied for large-scale analysis in both bottom-up (i.e., peptide-level) and top-down (i.e., protein-level) proteomics. Different approaches for quantifying peptides or intact proteins, including label-free and stable-isotope-labeling strategies, are also discussed. In addition, we present a brief overview of different types of mass analyzers and fragmentation techniques as well as selected emerging techniques.
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41
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IWASAKI M, ISHIHAMA Y. Challenges Facing Complete Human Proteome Analysis. CHROMATOGRAPHY 2014. [DOI: 10.15583/jpchrom.2014.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Mio IWASAKI
- Center for iPS Cell Research and Application, Kyoto University
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42
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Liu CC, Deng QL, Fang GZ, Liu HL, Wu JH, Pan MF, Wang S. Ionic liquids monolithic columns for protein separation in capillary electrochromatography. Anal Chim Acta 2013; 804:313-20. [DOI: 10.1016/j.aca.2013.10.037] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 10/11/2013] [Accepted: 10/17/2013] [Indexed: 12/01/2022]
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43
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Rogeberg M, Vehus T, Grutle L, Greibrokk T, Wilson SR, Lundanes E. Separation optimization of long porous-layer open-tubular columns for nano-LC-MS of limited proteomic samples. J Sep Sci 2013; 36:2838-47. [DOI: 10.1002/jssc.201300499] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 05/31/2013] [Accepted: 05/31/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Magnus Rogeberg
- Department of Chemistry; University of Oslo; Blindern Oslo Norway
| | - Tore Vehus
- Department of Chemistry; University of Oslo; Blindern Oslo Norway
| | - Lene Grutle
- Department of Chemistry; University of Oslo; Blindern Oslo Norway
| | - Tyge Greibrokk
- Department of Chemistry; University of Oslo; Blindern Oslo Norway
| | | | - Elsa Lundanes
- Department of Chemistry; University of Oslo; Blindern Oslo Norway
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Zubarev RA. The challenge of the proteome dynamic range and its implications for in-depth proteomics. Proteomics 2013; 13:723-6. [PMID: 23307342 DOI: 10.1002/pmic.201200451] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/22/2012] [Accepted: 12/04/2012] [Indexed: 12/25/2022]
Abstract
The dynamic range of the cellular proteome approaches seven orders of magnitude-from one copy per cell to ten million copies per cell. Since a proteome's abundance distribution represents a nearly symmetric bell-shape curve on the logarithmic copy number scale, detection of half of the expressed cellular proteome, i.e. approximately 5000 proteins, should be a relatively straightforward task with modern mass spectrometric instrumentation that exhibits four orders of magnitude of the dynamic range, while deeper proteome analysis should be progressively more difficult. Indeed, metaanalysis of 15 recent papers that claim detection of >5000 protein groups reveals that the half-proteome analyses currently requires ≈5 h of chromatographic separation, while deeper analyses yield on average ≤20 new proteins per hour of chromatographic gradient. Therefore, a typical proteomics experiment consists of a "high-content" part, with the detection rate of approximately 1000 proteins/h, and a "low-content" tail with much lower rate of discovery and respectively, lower cost efficiency. This result calls for disruptive innovation in deep proteomics analysis.
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Affiliation(s)
- Roman A Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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45
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Ding C, Jiang J, Wei J, Liu W, Zhang W, Liu M, Fu T, Lu T, Song L, Ying W, Chang C, Zhang Y, Ma J, Wei L, Malovannaya A, Jia L, Zhen B, Wang Y, He F, Qian X, Qin J. A fast workflow for identification and quantification of proteomes. Mol Cell Proteomics 2013; 12:2370-80. [PMID: 23669031 DOI: 10.1074/mcp.o112.025023] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The current in-depth proteomics makes use of long chromatography gradient to get access to more peptides for protein identification, resulting in covering of as many as 8000 mammalian gene products in 3 days of mass spectrometer running time. Here we report a fast sequencing (Fast-seq) workflow of the use of dual reverse phase high performance liquid chromatography - mass spectrometry (HPLC-MS) with a short gradient to achieve the same proteome coverage in 0.5 day. We adapted this workflow to a quantitative version (Fast quantification, Fast-quan) that was compatible to large-scale protein quantification. We subjected two identical samples to the Fast-quan workflow, which allowed us to systematically evaluate different parameters that impact the sensitivity and accuracy of the workflow. Using the statistics of significant test, we unraveled the existence of substantial falsely quantified differential proteins and estimated correlation of false quantification rate and parameters that are applied in label-free quantification. We optimized the setting of parameters that may substantially minimize the rate of falsely quantified differential proteins, and further applied them on a real biological process. With improved efficiency and throughput, we expect that the Fast-seq/Fast-quan workflow, allowing pair wise comparison of two proteomes in 1 day may make MS available to the masses and impact biomedical research in a positive way.
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Affiliation(s)
- Chen Ding
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
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46
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Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 986] [Impact Index Per Article: 89.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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47
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Shiba-Fukushima K, Imai Y, Yoshida S, Ishihama Y, Kanao T, Sato S, Hattori N. PINK1-mediated phosphorylation of the Parkin ubiquitin-like domain primes mitochondrial translocation of Parkin and regulates mitophagy. Sci Rep 2012; 2:1002. [PMID: 23256036 PMCID: PMC3525937 DOI: 10.1038/srep01002] [Citation(s) in RCA: 448] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 12/05/2012] [Indexed: 11/09/2022] Open
Abstract
Parkinson's disease genes PINK1 and parkin encode kinase and ubiquitin ligase, respectively. The gene products PINK1 and Parkin are implicated in mitochondrial autophagy, or mitophagy. Upon the loss of mitochondrial membrane potential (ΔΨm), cytosolic Parkin is recruited to the mitochondria by PINK1 through an uncharacterised mechanism – an initial step triggering sequential events in mitophagy. This study reports that Ser65 in the ubiquitin-like domain (Ubl) of Parkin is phosphorylated in a PINK1-dependent manner upon depolarisation of ΔΨm. The introduction of mutations at Ser65 suggests that phosphorylation of Ser65 is required not only for the efficient translocation of Parkin, but also for the degradation of mitochondrial proteins in mitophagy. Phosphorylation analysis of Parkin pathogenic mutants also suggests Ser65 phosphorylation is not sufficient for Parkin translocation. Our study partly uncovers the molecular mechanism underlying the PINK1-dependent mitochondrial translocation and activation of Parkin as an initial step of mitophagy.
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Affiliation(s)
- Kahori Shiba-Fukushima
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
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48
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Rigobello-Masini M, Penteado JCP, Masini JC. Monolithic columns in plant proteomics and metabolomics. Anal Bioanal Chem 2012; 405:2107-22. [DOI: 10.1007/s00216-012-6574-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 11/02/2012] [Accepted: 11/13/2012] [Indexed: 12/16/2022]
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49
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Recent advances in monolithic columns for protein and peptide separation by capillary liquid chromatography. Anal Bioanal Chem 2012. [DOI: 10.1007/s00216-012-6570-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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50
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Yamana R, Iwasaki M, Wakabayashi M, Nakagawa M, Yamanaka S, Ishihama Y. Rapid and Deep Profiling of Human Induced Pluripotent Stem Cell Proteome by One-shot NanoLC–MS/MS Analysis with Meter-scale Monolithic Silica Columns. J Proteome Res 2012; 12:214-21. [DOI: 10.1021/pr300837u] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Ryota Yamana
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mio Iwasaki
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masaki Wakabayashi
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masato Nakagawa
- Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yasushi Ishihama
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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