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Evaluation of Filter, Paramagnetic, and STAGETips Aided Workflows for Proteome Profiling of Symbiodiniaceae Dinoflagellate. Processes (Basel) 2021. [DOI: 10.3390/pr9060983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The integrity of coral reef ecosystems worldwide rests on a fine-tuned symbiotic interaction between an invertebrate and a dinoflagellate microalga from the family Symbiodiniaceae. Recent advances in bottom-up shotgun proteomic approaches and the availability of vast amounts of genetic information about Symbiodiniaceae have provided a unique opportunity to better understand the molecular mechanisms underpinning the interactions of coral-Symbiodiniaceae. However, the resilience of this dinoflagellate cell wall, as well as the presence of polyanionic and phenolics cell wall components, requires the optimization of sample preparation techniques for successful implementation of bottom-up proteomics. Therefore, in this study we compare three different workflows—filter-aided sample preparation (FASP), single-pot solid-phase-enhanced sample preparation (SP3), and stop-and-go-extraction tips (STAGETips, ST)—to develop a high-throughput proteotyping protocol for Symbiodiniaceae algal research. We used the model isolate Symbiodinium tridacnidorum. We show that SP3 outperformed ST and FASP with regard to robustness, digestion efficiency, and contaminant removal, which led to the highest number of total (3799) and unique proteins detected from 23,593 peptides. Most of these proteins were detected with ≥2 unique peptides (73%), zero missed tryptic peptide cleavages (91%), and hydrophilic peptides (>70%). To demonstrate the functionality of this optimized SP3 sample preparation workflow, we examined the proteome of S. tridacnidorum to better understand the molecular mechanism of peridinin-chlorophyll-protein complex (PCP, light harvesting protein) accumulation under low light (LL, 30 μmol photon m−2 s−1). Cells exposed to LL for 7 days upregulated various light harvesting complex (LHCs) proteins through the mevalonate-independent pathway; proteins of this pathway were at 2- to 6-fold higher levels than the control of 120 μmol photon m−2 s−1. Potentially, LHCs which were maintained in an active phosphorylated state by serine/threonine-protein kinase were also upregulated to 10-fold over control. Collectively, our results show that the SP3 method is an efficient high-throughput proteotyping tool for Symbiodiniaceae algal research.
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2
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Bermudez A, Pitteri SJ. Enrichment of Intact Glycopeptides Using Strong Anion Exchange and Electrostatic Repulsion Hydrophilic Interaction Chromatography. Methods Mol Biol 2021; 2271:107-120. [PMID: 33908003 DOI: 10.1007/978-1-0716-1241-5_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Glycosylation is a biologically important and complex protein posttranslational modification. The emergence of glycoproteomic technologies to identify and characterize glycans on proteins has the potential to enable a better understanding the role of glycosylation in biology, disease states, and other areas of interest. In particular, the analysis of intact glycopeptides by mass spectrometry allows information about glycan location and composition to be ascertained. However, such analysis is often complicated by extensive glycan diversity and the low abundance of glycopeptides in a complex mixture relative to nonglycosylated peptides. Enrichment of glycopeptides from a protein enzymatic digest is an effective approach to overcome such challenges. In this chapter, we described a glycopeptide enrichment method combining strong anion exchange, electrostatic repulsion, and hydrophilic interaction chromatography (SAX-ERLIC). Following enzymatic digestion of proteins into peptides, SAX-ERLIC is performed by solid phase extraction to enrich glycopeptides from biological samples with subsequent LC-MS/MS analysis. Glycopeptide data generated using the SAX-ERLIC enrichment yields a high number of total and unique glycopeptide identifications which can be mapped back to proteins. The enrichment strategy is robust, easy to perform, and does not require cleavage of glycans prior to LC-MS/MS analysis.
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Affiliation(s)
- Abel Bermudez
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sharon J Pitteri
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, USA.
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3
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Saadeldin IM, Swelum AAA, Elsafadi M, Mahmood A, Osama A, Shikshaky H, Alfayez M, Alowaimer AN, Magdeldin S. Thermotolerance and plasticity of camel somatic cells exposed to acute and chronic heat stress. J Adv Res 2019; 22:105-118. [PMID: 31969994 PMCID: PMC6965514 DOI: 10.1016/j.jare.2019.11.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 11/05/2019] [Accepted: 11/19/2019] [Indexed: 12/12/2022] Open
Abstract
The Arabian camel is the largest known mammal that can survive in severe hot climatic conditions. We provide the molecular explanation for the thermotolerance of camel granulosa somatic cells after exposure to 45 °C for 2 (acute heat shock) or 20 h (chronic heat shock). The common features of the cellular responses to acute heat stress were the increase of heat shock proteins and DNA repair enzymes expression. Actin polymerization and Rho signaling were critically activated as a cellular defense against heat shock. Cells exposed to chronic heat shock showed altered cell architecture with a decrease in total detected proteins, metabolic enzymes, and cytoskeletal protein expression. Treatment with transforming growth factor beta (TGFβ) pathway inhibitor SB-431542 suppressed the morphological alterations of cells exposed to chronic heat shock. Moreover, during the recovery stage at 38 °C for 24 h, proteomic changes were partially restored with an exponential increase in HSP70 expression, and the cells restored their normal cellular morphology on the 9th day of recovery. Full proteomics data are available via ProteomeXchange with identifier PXD012159. The strategies of cellular defense and tolerance to both thermal conditions reflect the flexible adaptability of camel somatic cells to conserve life under extremely hot conditions.
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Key Words
- Actin
- Anastasis
- CB, Cytochalasin B
- Camel
- GSH, reduced glutathione
- HSPs
- HSPs, heat shock proteins
- IDA, information dependent acquisition
- MDA, malondialdehyde
- Proteomics
- RI, ROCK-inhibitor
- ROCK
- ROCKs, Rho-associated protein kinases
- TGFβ
- TGFβ, transforming growth factor beta
- TIC, total ion chromatography
- Y-27632, ROCK-inhibitor Y-27632
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Affiliation(s)
- Islam M Saadeldin
- Department of Animal Production, College of Food and Agricultural Sciences, King Saud University, 11451 Riyadh, Saudi Arabia.,Department of Physiology, Faculty of Veterinary Medicine, Zagazig University, 44519 Zagazig, Egypt
| | - Ayman Abdel-Aziz Swelum
- Department of Animal Production, College of Food and Agricultural Sciences, King Saud University, 11451 Riyadh, Saudi Arabia.,Department of Theriogenology, Faculty of Veterinary Medicine, Zagazig University, 44519 Zagazig, Egypt
| | - Mona Elsafadi
- Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Amer Mahmood
- Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Aya Osama
- Proteomics and Metabolomics Unit, 57357 Children's Cancer Hospital, Cairo, Egypt
| | - Hassan Shikshaky
- Proteomics and Metabolomics Unit, 57357 Children's Cancer Hospital, Cairo, Egypt
| | - Musaad Alfayez
- Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Saudi Society for Camel Research, King Saud University, Saudi Arabia
| | - Abdullah N Alowaimer
- Department of Animal Production, College of Food and Agricultural Sciences, King Saud University, 11451 Riyadh, Saudi Arabia
| | - Sameh Magdeldin
- Proteomics and Metabolomics Unit, 57357 Children's Cancer Hospital, Cairo, Egypt.,Physiology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
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4
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Yeh TT, Ho MY, Chen WY, Hsu YC, Ku WC, Tseng HW, Chen ST, Chen SF. Comparison of different fractionation strategies for in-depth phosphoproteomics by liquid chromatography tandem mass spectrometry. Anal Bioanal Chem 2019; 411:3417-3424. [PMID: 31011783 DOI: 10.1007/s00216-019-01823-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/18/2019] [Accepted: 04/01/2019] [Indexed: 01/12/2023]
Abstract
Phosphorylation, a major posttranslational modification of proteins, plays an important role in protein activity and cell signaling. However, it is difficult to detect protein phosphorylation because of its low abundance and the fact that the analysis can be hindered by the presence of highly abundant non-phosphoproteins. In order to reduce the sample complexity and improve the efficiency of identification of phosphopeptides, aliphatic hydroxy acid-modified metal oxide chromatography (HAMMOC) was utilized to enrich phosphopeptides from a murine macrophage cell lysate. Strong cation chromatography (SCX), electrostatic repulsion hydrophilic interaction chromatography (ERLIC), and solution isoelectric focusing (sIEF) were investigated in detail for phosphopeptide fractionation strategies followed by liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. A total of 5744 non-redundant phosphopeptides and 2159 phosphoproteins were identified from the cell lysates in three fractionation approaches. The SCX fractionation contained the largest number of phosphoproteins and phosphopeptides that were identified. In addition, 4336, 2064, and 2424 phosphopeptides were identified from SCX-LC-MS/MS, ERLIC-LC-MS/MS, and sIEF-LC/MS-MS, including 2430, 438, and 751 phosphopeptides that were only specifically found in SCX, ERLIC, and sIEF fractionations. In conclusion, these three fractionation strategies demonstrated great complementarity, which greatly improved the efficiency of identification of phosphopeptides and can be suitable for use in in-depth phosphoproteome research. Graphical Abstract.
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Affiliation(s)
- Ting-Ting Yeh
- Department of Chemistry, National Taiwan Normal University, Taipei, 11677, Taiwan
| | - Ming-Yi Ho
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital, Taoyuan, 33305, Taiwan
| | - Wei-Ya Chen
- Department of Chemistry, National Taiwan Normal University, Taipei, 11677, Taiwan
| | - Ya-Chen Hsu
- Department of Chemistry, National Taiwan Normal University, Taipei, 11677, Taiwan
| | - Wei-Chi Ku
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei, 24205, Taiwan
| | - Hsiang-Wen Tseng
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, 31057, Taiwan
| | - Shih-Ta Chen
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, 31057, Taiwan
| | - Sung-Fang Chen
- Department of Chemistry, National Taiwan Normal University, Taipei, 11677, Taiwan.
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5
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Chelius CL, Ribeiro LFC, Huso W, Kumar J, Lincoln S, Tran B, Goo YA, Srivastava R, Harris SD, Marten MR. Phosphoproteomic and transcriptomic analyses reveal multiple functions for Aspergillus nidulans MpkA independent of cell wall stress. Fungal Genet Biol 2019; 125:1-12. [PMID: 30639305 DOI: 10.1016/j.fgb.2019.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/18/2018] [Accepted: 01/04/2019] [Indexed: 12/17/2022]
Abstract
The protein kinase MpkA plays a prominent role in the cell wall integrity signaling (CWIS) pathway, acting as the terminal MAPK activating expression of genes which encode cell wall biosynthetic enzymes and other repair functions. Numerous studies focus on MpkA function during cell wall perturbation. Here, we focus on the role MpkA plays outside of cell wall stress, during steady state growth. In an effort to seek other, as yet unknown, connections to this pathway, an mpkA deletion mutant (ΔmpkA) was subjected to phosphoproteomic and transcriptomic analysis. When compared to the control (isogenic parent of ΔmpkA), there is strong evidence suggesting MpkA is involved with maintaining cell wall strength, branching regulation, and the iron starvation pathway, among others. Particle-size analysis during shake flask growth revealed ΔmpkA mycelia were about 4 times smaller than the control strain and more than 90 cell wall related genes show significantly altered expression levels. The deletion mutant had a significantly higher branching rate than the control and phosphoproteomic results show putative branching-regulation proteins, such as CotA, LagA, and Cdc24, have a significantly different level of phosphorylation. When grown in iron limited conditions, ΔmpkA had no difference in growth rate or production of siderophores, whereas the control strain showed decreased growth rate and increased siderophore production. Transcriptomic data revealed over 25 iron related genes with altered transcript levels. Results suggest MpkA is involved with regulation of broad cellular functions in the absence of stress.
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Affiliation(s)
- Cynthia L Chelius
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD 21250, United States
| | - Liliane F C Ribeiro
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD 21250, United States
| | - Walker Huso
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD 21250, United States
| | - Jyothi Kumar
- Center for Plant Science Innovation and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
| | - Stephen Lincoln
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, United States
| | - Bao Tran
- Mass Spectrometry Center, University of Maryland School of Pharmacy, Baltimore, MD, 21201, United States
| | - Young Ah Goo
- Mass Spectrometry Center, University of Maryland School of Pharmacy, Baltimore, MD, 21201, United States
| | - Ranjan Srivastava
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, United States
| | - Steven D Harris
- Center for Plant Science Innovation and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
| | - Mark R Marten
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD 21250, United States.
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6
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Smith J, Davey G, Polom K, Roviello F, Bones J. Mining the acidic serum proteome utilizing off-gel isoelectric focusing and label free quantitative liquid chromatography mass spectrometry. J Chromatogr A 2018; 1566:32-43. [DOI: 10.1016/j.chroma.2018.06.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/17/2018] [Accepted: 06/18/2018] [Indexed: 12/25/2022]
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7
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Diedrich B, Dengjel J. Insights into autosomal dominant polycystic kidney disease by quantitative mass spectrometry-based proteomics. Cell Tissue Res 2017; 369:41-51. [DOI: 10.1007/s00441-017-2617-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/21/2017] [Indexed: 12/12/2022]
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8
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Davis S, Charles PD, He L, Mowlds P, Kessler BM, Fischer R. Expanding Proteome Coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) Combined with Broad Specificity Proteolysis. J Proteome Res 2017; 16:1288-1299. [PMID: 28164708 PMCID: PMC5363888 DOI: 10.1021/acs.jproteome.6b00915] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The "deep" proteome has been accessible by mass spectrometry for some time. However, the number of proteins identified in cells of the same type has plateaued at ∼8000-10 000 without ID transfer from reference proteomes/data. Moreover, limited sequence coverage hampers the discrimination of protein isoforms when using trypsin as standard protease. Multienzyme approaches appear to improve sequence coverage and subsequent isoform discrimination. Here we expanded proteome and protein sequence coverage in MCF-7 breast cancer cells to an as yet unmatched depth by employing a workflow that addresses current limitations in deep proteome analysis in multiple stages: We used (i) gel-aided sample preparation (GASP) and combined trypsin/elastase digests to increase peptide orthogonality, (ii) concatenated high-pH prefractionation, and (iii) CHarge Ordered Parallel Ion aNalysis (CHOPIN), available on an Orbitrap Fusion (Lumos) mass spectrometer, to achieve 57% median protein sequence coverage in 13 728 protein groups (8949 Unigene IDs) in a single cell line. CHOPIN allows the use of both detectors in the Orbitrap on predefined precursor types that optimizes parallel ion processing, leading to the identification of a total of 179 549 unique peptides covering the deep proteome in unprecedented detail.
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Affiliation(s)
- Simon Davis
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, United Kingdom
| | - Philip D Charles
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, United Kingdom
| | - Lin He
- Bioinformatics Solutions, Inc. , 470 Weber Street North Suite 204, Waterloo, Ontario N2L 6J2, Canada
| | - Peter Mowlds
- Thermo Fisher, Inc. , Stafford House, 1 Boundary Park, Hemel Hampstead HP2 7GE, United Kingdom
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, United Kingdom
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, United Kingdom
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9
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Totten SM, Feasley CL, Bermudez A, Pitteri SJ. Parallel Comparison of N-Linked Glycopeptide Enrichment Techniques Reveals Extensive Glycoproteomic Analysis of Plasma Enabled by SAX-ERLIC. J Proteome Res 2017; 16:1249-1260. [PMID: 28199111 DOI: 10.1021/acs.jproteome.6b00849] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein glycosylation is of increasing interest due to its important roles in protein function and aberrant expression with disease. Characterizing protein glycosylation remains analytically challenging due to its low abundance, ion suppression issues, and microheterogeneity at glycosylation sites, especially in complex samples such as human plasma. In this study, the utility of three common N-linked glycopeptide enrichment techniques is compared using human plasma. By analysis on an LTQ-Orbitrap Elite mass spectrometer, electrostatic repulsion hydrophilic interaction liquid chromatography using strong anion exchange solid-phase extraction (SAX-ERLIC) provided the most extensive N-linked glycopeptide enrichment when compared with multilectin affinity chromatography (M-LAC) and Sepharose-HILIC enrichments. SAX-ERLIC enrichment yielded 191 unique glycoforms across 72 glycosylation sites from 48 glycoproteins, which is more than double that detected using other enrichment techniques. The greatest glycoform diversity was observed in SAX-ERLIC enrichment, with no apparent bias toward specific glycan types. SAX-ERLIC enrichments were additionally analyzed by an Orbitrap Fusion Lumos mass spectrometer to maximize glycopeptide identifications for a more comprehensive assessment of protein glycosylation. In these experiments, 829 unique glycoforms were identified across 208 glycosylation sites from 95 plasma glycoproteins, a significant improvement from the initial method comparison and one of the most extensive site-specific glycosylation analysis in immunodepleted human plasma to date. Data are available via ProteomeXchange with identifier PXD005655.
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Affiliation(s)
- Sarah M Totten
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine , 3155 Porter Drive MC5483, Palo Alto, California 94304, United States
| | - Christa L Feasley
- ThermoFisher Scientific , 1400 Northpoint Parkway Suite 10, West Palm Beach, Florida 33407, United States
| | - Abel Bermudez
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine , 3155 Porter Drive MC5483, Palo Alto, California 94304, United States
| | - Sharon J Pitteri
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine , 3155 Porter Drive MC5483, Palo Alto, California 94304, United States
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10
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Kuljanin M, Dieters-Castator DZ, Hess DA, Postovit LM, Lajoie GA. Comparison of sample preparation techniques for large-scale proteomics. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600337] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/07/2016] [Accepted: 11/07/2016] [Indexed: 01/24/2023]
Affiliation(s)
- Miljan Kuljanin
- Department of Biochemistry; University of Western Ontario; London ON Canada
| | | | - David A. Hess
- Department of Physiology and Pharmacology; University of Western Ontario; London ON Canada
| | - Lynne-Marie Postovit
- Department of Anatomy and Cell Biology; University of Western Ontario; London ON Canada
- Department of Oncology; University of Alberta; Edmonton AB Canada
| | - Gilles A. Lajoie
- Department of Biochemistry; University of Western Ontario; London ON Canada
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Elguoshy A, Magdeldin S, Xu B, Hirao Y, Zhang Y, Kinoshita N, Takisawa Y, Nameta M, Yamamoto K, El-Refy A, El-Fiky F, Yamamoto T. Why are they missing? : Bioinformatics characterization of missing human proteins. J Proteomics 2016; 149:7-14. [PMID: 27535355 DOI: 10.1016/j.jprot.2016.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 07/17/2016] [Accepted: 08/08/2016] [Indexed: 12/19/2022]
Abstract
NeXtProt is a web-based protein knowledge platform that supports research on human proteins. NeXtProt (release 2015-04-28) lists 20,060 proteins, among them, 3373 canonical proteins (16.8%) lack credible experimental evidence at protein level (PE2:PE5). Therefore, they are considered as "missing proteins". A comprehensive bioinformatic workflow has been proposed to analyze these "missing" proteins. The aims of current study were to analyze physicochemical properties, existence and distribution of the tryptic cleavage sites, and to pinpoint the signature peptides of the missing proteins. Our findings showed that 23.7% of missing proteins were hydrophobic proteins possessing transmembrane domains (TMD). Also, forty missing entries generate tryptic peptides were either out of mass detection range (>30aa) or mapped to different proteins (<9aa). Additionally, 21% of missing entries didn't generate any unique tryptic peptides. In silico endopeptidase combination strategy increased the possibility of missing proteins identification. Coherently, using both mature protein database and signal peptidome database could be a promising option to identify some missing proteins by targeting their unique N-terminal tryptic peptide from mature protein database and or C-terminus tryptic peptide from signal peptidome database. In conclusion, Identification of missing protein requires additional consideration during sample preparation, extraction, digestion and data analysis to increase its incidence of identification.
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Affiliation(s)
- Amr Elguoshy
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan; Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo 11682, Egypt
| | - Sameh Magdeldin
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan; Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Bo Xu
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Yoshitoshi Hirao
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Ying Zhang
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Naohiko Kinoshita
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Yusuke Takisawa
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Masaaki Nameta
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Keiko Yamamoto
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Ali El-Refy
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo 11682, Egypt
| | - Fawzy El-Fiky
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo 11682, Egypt
| | - Tadashi Yamamoto
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan.
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12
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Norris EL, Headlam MJ, Dave KA, Smith DD, Bukreyev A, Singh T, Jayakody BA, Chappell KJ, Collins PL, Gorman JJ. Proteoform-Specific Insights into Cellular Proteome Regulation. Mol Cell Proteomics 2016; 15:3297-3320. [PMID: 27451424 PMCID: PMC5054351 DOI: 10.1074/mcp.o116.058438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Indexed: 01/29/2023] Open
Abstract
Knowledge regarding compositions of proteomes at the proteoform level enhances insights into cellular phenotypes. A strategy is described herein for discovery of proteoform-specific information about cellular proteomes. This strategy involved analysis of data obtained by bottom-up mass spectrometry of multiple protein OGE separations on a fraction by fraction basis. The strategy was exemplified using five matched sets of lysates of uninfected and human respiratory syncytial virus-infected A549 cells. Template matching demonstrated that 67.3% of 10475 protein profiles identified focused to narrow pI windows indicative of efficacious focusing. Furthermore, correlation between experimental and theoretical pI gradients indicated reproducible focusing. Based on these observations a proteoform profiling strategy was developed to identify proteoforms, detect proteoform diversity and discover potential proteoform regulation. One component of this strategy involved examination of the focusing profiles for protein groups. A novel concordance analysis facilitated differentiation between proteoforms, including proteoforms generated by alternate splicing and proteolysis. Evaluation of focusing profiles and concordance analysis were applicable to cells from a single and/or multiple biological states. Statistical analyses identified proteoform variation between biological states. Regulation relevant to cellular responses to human respiratory syncytial virus was revealed. Western blotting and Protomap analyses validated the proteoform regulation. Discovery of STAT1, WARS, MX1, and HSPB1 proteoform regulation by human respiratory syncytial virus highlighted the impact of the profiling strategy. Novel truncated proteoforms of MX1 were identified in infected cells and phosphorylation driven regulation of HSPB1 proteoforms was correlated with infection. The proteoform profiling strategy is generally applicable to investigating interactions between viruses and host cells and the analysis of other biological systems.
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Affiliation(s)
| | | | | | - David D Smith
- §Statistics Unit, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Alexander Bukreyev
- ¶Respiratory Virus Section, Laboratory of Infectious Diseases, National Institute for Allergy and Infectious Diseases, NIH, Bethesda, Maryland, and
| | | | | | - Keith J Chappell
- ‖School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Peter L Collins
- ¶Respiratory Virus Section, Laboratory of Infectious Diseases, National Institute for Allergy and Infectious Diseases, NIH, Bethesda, Maryland, and
| | - Jeffrey J Gorman
- From the ‡Protein Discovery Centre and ‖School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
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Magdeldin S, Hirao Y, El Guoshy A, Xu B, Zhang Y, Fujinaka H, Yamamoto K, Yates JR, Yamamoto T. Comprehensive data analysis of human ureter proteome. Data Brief 2016; 6:853-7. [PMID: 26937461 PMCID: PMC4749945 DOI: 10.1016/j.dib.2016.01.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/21/2016] [Accepted: 01/25/2016] [Indexed: 12/04/2022] Open
Abstract
Comprehensive human ureter proteome dataset was generated from OFFGel fractionated ureter samples. Our result showed that among 2217 non-redundant ureter proteins, 751 protein candidates (33.8%) were detected in urine as urinary protein/polypeptide or exosomal protein. On the other hand, comparing ureter protein hits (48) that are not shown in corresponding databases to urinary bladder and prostate human protein atlas databases pinpointed 21 proteins that might be unique to ureter tissue. In conclusion, this finding offers future perspectives for possible identification of ureter disease-associated biomarkers such as ureter carcinoma. In addition, Cytoscape GO annotation was examined on the final ureter dataset to better understand proteins molecular function, biological processes, and cellular component. The ureter proteomic dataset published in this article will provide a valuable resource for researchers working in the field of urology and urine biomarker discovery.
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Affiliation(s)
- Sameh Magdeldin
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan; Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt; Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR11, La Jolla, CA 92037, United States
| | - Yoshitoshi Hirao
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Amr El Guoshy
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan; Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo 11682, Egypt
| | - Bo Xu
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Ying Zhang
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Hidehiko Fujinaka
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Keiko Yamamoto
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR11, La Jolla, CA 92037, United States
| | - Tadashi Yamamoto
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
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14
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Affiliation(s)
- Nicholas M. Riley
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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15
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Magdeldin S, Hirao Y, Elguoshy A, Xu B, Zhang Y, Fujinaka H, Yamamoto K, Yates JR, Yamamoto T. A proteomic glimpse into human ureter proteome. Proteomics 2015; 16:80-4. [PMID: 26442468 PMCID: PMC4737284 DOI: 10.1002/pmic.201500214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/31/2015] [Accepted: 09/28/2015] [Indexed: 12/18/2022]
Abstract
Urine has evolved as one of the most important biofluids in clinical proteomics due to its noninvasive sampling and its stability. Yet, it is used in clinical diagnostics of several disorders by detecting changes in its components including urinary protein/polypeptide profile. Despite the fact that majority of proteins detected in urine are primarily originated from the urogenital (UG) tract, determining its precise source within the UG tract remains elusive. In this article, we performed a comprehensive analysis of ureter proteome to assemble the first unbiased ureter dataset. Next, we compared these data to urine, urinary exosome, and kidney mass spectrometric datasets. Our result concluded that among 2217 nonredundant ureter proteins, 751 protein candidates (33.8%) were detected in urine as urinary protein/polypeptide or exosomal protein. On the other hand, comparing ureter protein hits (48) that are not shown in corresponding databases to urinary bladder and prostate human protein atlas databases pinpointed 21 proteins that might be unique to ureter tissue. In conclusion, this finding offers future perspectives for possible identification of ureter disease-associated biomarkers such as ureter carcinoma. In addition, the ureter proteomic dataset published in this article will provide a valuable resource for researchers working in the field of urology and urine biomarker discovery. All MS data have been deposited in the ProteomeXchange with identifier PXD002620 (http://proteomecentral.proteomexchange.org/dataset/PXD002620).
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Affiliation(s)
- Sameh Magdeldin
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan.,Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismaïlia, Egypt.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, San Diego, CA, USA
| | - Yoshitoshi Hirao
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Amr Elguoshy
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan.,Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Bo Xu
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Ying Zhang
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Hidehiko Fujinaka
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Keiko Yamamoto
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, San Diego, CA, USA
| | - Tadashi Yamamoto
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
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16
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Magdeldin S, Elguoshy A, Yoshida Y, Hirao Y, Xu B, Zhang Y, Yamamoto K, Takimoto H, Fujinaka H, Kinoshita N, Yamamoto T. Complementary Protein and Peptide OFFGEL Fractionation for High-Throughput Proteomic Analysis. Anal Chem 2015; 87:8481-8. [DOI: 10.1021/acs.analchem.5b01911] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Sameh Magdeldin
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
- Department
of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Amr Elguoshy
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
- Biotechnology
Department, Faculty of Agriculture, Al-Azhar University, Cairo 11682, Egypt
| | - Yutaka Yoshida
- Department
of Structural Pathology, Institute of Nephrology, Graduate
School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Yoshitoshi Hirao
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
| | - Bo Xu
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
| | - Ying Zhang
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
| | - Keiko Yamamoto
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
| | - Hiroki Takimoto
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
| | - Hidehiko Fujinaka
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
| | - Naohiko Kinoshita
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
| | - Tadashi Yamamoto
- Biofluid Biomarker
Center, Institute for Research Collaboration and Promotion, Niigata University, Niigata 951-8510, Japan
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17
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Xu Y, Yao B, Shi K, Lu J, Jin Y, Qi B, Li H, Pan S, Chen L, Ma C. Phosphorylation of Serine422 increases the stability and transactivation activities of human Osterix. FEBS Lett 2015; 589:857-64. [PMID: 25728276 DOI: 10.1016/j.febslet.2015.02.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/29/2015] [Accepted: 02/16/2015] [Indexed: 11/19/2022]
Abstract
Osterix (Osx) is an essential regulator for osteoblast differentiation and bone formation. Although phosphorylation has been reported to be involved in the regulation of Osx activity, the precise underlying mechanisms remain to be elucidated. Here we identified S422 as a novel phosphorylation site of Osx and demonstrated that GSK-3β interacted and co-localized with Osx. GSK-3β increased the stability and transactivation activity of Osx through phosphorylation of the newly identified site. These findings expanded our understanding of the mechanisms of posttranslational regulation of Osx and the role of GSK-3β in the control of Osx transactivation activity.
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Affiliation(s)
- Yuexin Xu
- Department of Developmental Genetics, Nanjing Medical University, Hanzhong Road 140, Nanjing 210029, P.R. China
| | - Bing Yao
- Department of Developmental Genetics, Nanjing Medical University, Hanzhong Road 140, Nanjing 210029, P.R. China
| | - Kaikai Shi
- Department of Developmental Genetics, Nanjing Medical University, Hanzhong Road 140, Nanjing 210029, P.R. China
| | - Jianlei Lu
- Department of Developmental Genetics, Nanjing Medical University, Hanzhong Road 140, Nanjing 210029, P.R. China
| | - Yucui Jin
- Department of Developmental Genetics, Nanjing Medical University, Hanzhong Road 140, Nanjing 210029, P.R. China
| | - Bing Qi
- Department of Oral Pathology, Affiliated Hospital of Stomatology, Nanjing Medical University, Hanzhong Road 136, Nanjing 210029, P.R. China
| | - Hongwei Li
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Hanzhong Road 136, Nanjing 210029, P.R. China
| | - Shiyang Pan
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P.R. China
| | - Li Chen
- Molecular Endocrinology Laboratory, Department of Endocrinology, Odense University Hospital, Winslowparken 25. Sal 1, DK-5000 Odense C, Denmark
| | - Changyan Ma
- Department of Developmental Genetics, Nanjing Medical University, Hanzhong Road 140, Nanjing 210029, P.R. China.
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18
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Magdeldin S, Blaser RE, Yamamoto T, Yates JR. Behavioral and proteomic analysis of stress response in zebrafish (Danio rerio). J Proteome Res 2014; 14:943-52. [PMID: 25398274 PMCID: PMC4324451 DOI: 10.1021/pr500998e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
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The
purpose of this study is to determine the behavioral and proteomic
consequences of shock-induced stress in zebrafish (Danio rerio) as a vertebrate model. Here we describe the behavioral effects
of exposure to predictable and unpredictable electric shock, together
with quantitative tandem mass tag isobaric labeling workflow to detect
altered protein candidates in response to shock exposure. Behavioral
results demonstrate a hyperactivity response to electric shock and
a suppression of activity to a stimulus predicting shock. On the basis
of the quantitative changes in protein abundance following shock exposure,
eight proteins were significantly up-regulated (HADHB, hspa8, hspa5,
actb1, mych4, atp2a1, zgc:86709, and zgc:86725). These proteins contribute
crucially in catalytic activities, stress response, cation transport,
and motor activities. This behavioral proteomic driven study clearly
showed that besides the rapid induction of heat shock proteins, other
catalytic enzymes and cation transporters were rapidly elevated as
a mechanism to counteract oxidative stress conditions resulting from
elevated fear/anxiety levels.
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Affiliation(s)
- Sameh Magdeldin
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University , 1-757 Asahimachi-dori, Niigata 951-8510, Japan
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19
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New Proteomic Insights on the Role of NPR-A in Regulating Self-Renewal of Embryonic Stem Cells. Stem Cell Rev Rep 2014; 10:561-72. [DOI: 10.1007/s12015-014-9517-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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