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Chong L, Hsu CC, Zhu Y. Advances in mass spectrometry-based phosphoproteomics for elucidating abscisic acid signaling and plant responses to abiotic stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6547-6557. [PMID: 35959917 DOI: 10.1093/jxb/erac324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stresses have significant impacts on crop yield and quality. Even though significant efforts during the past decade have been devoted to uncovering the core signaling pathways associated with the phytohormone abscisic acid (ABA) and abiotic stress in plants, abiotic stress signaling mechanisms in most crops remain largely unclear. The core components of the ABA signaling pathway, including early events in the osmotic stress-induced phosphorylation network, have recently been elucidated in Arabidopsis with the aid of phosphoproteomics technologies. We now know that SNF1-related kinases 2 (SnRK2s) are not only inhibited by the clade A type 2C protein phosphatases (PP2Cs) through dephosphorylation, but also phosphorylated and activated by upstream mitogen-activated protein kinase kinase kinases (MAP3Ks). Through describing the course of studies to elucidate abiotic stress and ABA signaling, we will discuss how we can take advantage of the latest innovations in mass-spectrometry-based phosphoproteomics and structural proteomics to boost our investigation of plant regulation and responses to ABA and abiotic stress.
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Affiliation(s)
- Leelyn Chong
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Chuan-Chih Hsu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Sanya Institute of Henan University, Sanya, Hainan, China
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Thongboonkerd V, Chaiyarit S. Gel-Based and Gel-Free Phosphoproteomics to Measure and Characterize Mitochondrial Phosphoproteins. Curr Protoc 2022; 2:e390. [PMID: 35275445 DOI: 10.1002/cpz1.390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mitochondrion is a key intracellular organelle regulating metabolic processes, oxidative stress, energy production, calcium homeostasis, and cell survival. Protein phosphorylation plays an important role in regulating mitochondrial functions and cellular signaling pathways. Dysregulation of protein phosphorylation status can cause protein malfunction and abnormal signal transduction, leading to organ dysfunction and disease. Investigating the mitochondrial phosphoproteins is therefore crucial to better understand the molecular and pathogenic mechanisms of many metabolic disorders. Conventional analyses of phosphoproteins, for instance, via western blotting, can be done only for proteins for which specific antibodies to their phosphorylated forms are available. Moreover, such an approach is not suitable for large-scale study of phosphoproteins. Currently, proteomics represents an important tool for large-scale analysis of proteins and their post-translational modifications, including phosphorylation. Here, we provide step-by-step protocols for the proteomics analysis of mitochondrial phosphoproteins (the phosphoproteome), using renal tubular cells as an example. These protocols include methods to effectively isolate mitochondria and to validate the efficacy of mitochondrial enrichment as well as its purity. We also provide detailed protocols for performing both gel-based and gel-free phosphoproteome analyses. The gel-based analysis involves two-dimensional gel electrophoresis and phosphoprotein-specific staining, followed by protein identification via mass spectrometry, whereas the gel-free approach is based on in-solution mass spectrometric identification of specific phosphorylation sites and residues. In all, these approaches allow large-scale analyses of mitochondrial phosphoproteins that can be applied to other cells and tissues of interest. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Mitochondrial isolation/purification from renal tubular cells Support Protocol: Validation of enrichment efficacy and purity of mitochondrial isolation Basic Protocol 2: Gel-based phosphoproteome analysis Basic Protocol 3: Gel-free phosphoproteome analysis.
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Affiliation(s)
- Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sakdithep Chaiyarit
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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Gao Y, Liu S, Jia Q, Wu L, Yuan D, Li EY, Feng Q, Wang G, Palli SR, Wang J, Li S. Juvenile hormone membrane signaling phosphorylates USP and thus potentiates 20-hydroxyecdysone action in Drosophila. Sci Bull (Beijing) 2022; 67:186-197. [PMID: 36546012 DOI: 10.1016/j.scib.2021.06.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 01/06/2023]
Abstract
Juvenile hormone (JH) and 20-hydroxyecdysone (20E) coordinately regulate development and metamorphosis in insects. Two JH intracellular receptors, methoprene-tolerant (Met) and germ-cell expressed (Gce), have been identified in the fruit fly Drosophila melanogaster. To investigate JH membrane signaling pathway without the interference from JH intracellular signaling, we characterized phosphoproteome profiles of the Met gce double mutant in the absence or presence of JH in both chronic and acute phases. Functioning through a potential receptor tyrosine kinase and phospholipase C pathway, JH membrane signaling activated protein kinase C (PKC) which phosphorylated ultraspiracle (USP) at Ser35, the PKC phosphorylation site required for the maximal action of 20E through its nuclear receptor complex EcR-USP. The uspS35A mutant, in which Ser was replaced with Ala at position 35 by genome editing, showed decreased expression of Halloween genes that are responsible for ecdysone biosynthesis and thus attenuated 20E signaling that delayed developmental timing. The uspS35A mutant also showed lower Yorkie activity that reduced body size. Altogether, JH membrane signaling phosphorylates USP at Ser35 and thus potentiates 20E action that regulates the normal fly development. This study helps better understand the complex JH signaling network.
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Affiliation(s)
- Yue Gao
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China; Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou 514779, China
| | - Suning Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Qiangqiang Jia
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Lixian Wu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Dongwei Yuan
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Emma Y Li
- International Department, The Affiliated High School of South China Normal University, Guangzhou 510631, China
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Guirong Wang
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Subba R Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington 40546, USA
| | - Jian Wang
- Department of Entomology, University of Maryland, College Park 20742, USA.
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China; Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou 514779, China.
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Sitapara R, Lam TT, Gandjeva A, Tuder RM, Zisman LS. Phosphoproteomic analysis of lung tissue from patients with pulmonary arterial hypertension. Pulm Circ 2021; 11:20458940211031109. [PMID: 34966541 PMCID: PMC8711668 DOI: 10.1177/20458940211031109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 06/18/2021] [Indexed: 11/29/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is a rare disorder associated with high
morbidity and mortality despite currently available treatments. We compared the
phosphoproteome of lung tissue from subjects with idiopathic PAH (iPAH) obtained
at the time of lung transplant with control lung tissue. The mass
spectrometry-based analysis found 60,428 phosphopeptide features from which 6622
proteins were identified. Within the subset of identified proteins there were
1234 phosphopeptides with q < 0.05, many of which are
involved in immune regulation, angiogenesis, and cell proliferation. Most
notably there was a marked relative increase in phosphorylated (S378) IKZF3
(Aiolos), a zinc finger transcription factor that plays a key role in lymphocyte
regulation. In vitro phosphorylation assays indicated that GSK3 alpha and/or
GSK3 beta could phosphorylate IKZF3 at S378. Western blot analysis demonstrated
increased pIKZF3 in iPAH lungs compared to controls. Immunohistochemistry
demonstrated phosphorylated IKZF3 in lymphocytes surrounding severely
hypertrophied pulmonary arterioles. In situ hybrization showed gene expression
in lymphocyte aggregates in PAH samples. A BCL2 reporter assay showed that IKZF3
increased BCL2 promoter activity and demonstrated the potential role of
phosphorylation of IKZF3 in the regulation of BCL mediated transcription. Kinase
network analysis demonstrated potentially important regulatory roles of casein
kinase 2, cyclin-dependent kinase 1 (CDK1), mitogen-associated protein kinases
(MAPKs), and protein kinases (PRKs) in iPAH. Bioinformatic analysis demonstrated
enrichment of RhoGTPase signaling and the potential importance of cGMP-dependent
protein kinase 1 (PRKG). In conclusion, this unbiased phosphoproteomic analysis
demonstrated several novel targets regulated by kinase networks in iPAH, and
reinforced the potential role of immune regulation in the pathogenesis of iPAH.
The identified up- and down-regulated phosphoproteins have potential to serve as
biomarkers for PAH and to provide new insights for therapeutic strategies.
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Affiliation(s)
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, Yale University, New Haven, CT, USA.,MS & Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT, USA
| | - Aneta Gandjeva
- Program in Translational Lung Research, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Rubin M Tuder
- Program in Translational Lung Research, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Lawrence S Zisman
- Rensselaer Center for Translational Research Inc., Troy, NY, USA.,Pulmokine Inc., Troy, NY, USA
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Quantitative Phosphoproteomic Comparison of Lens Proteins in Highly Myopic Cataract and Age-Related Cataract. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6668845. [PMID: 34055996 PMCID: PMC8130905 DOI: 10.1155/2021/6668845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/23/2021] [Accepted: 04/02/2021] [Indexed: 11/17/2022]
Abstract
Purpose To investigate and compare the lens phosphoproteomes in patients with highly myopic cataract (HMC) or age-related cataract (ARC). Methods In this study, we undertook a comparative phosphoproteome analysis of the lenses from patients with HMC or ARC. Intact lenses from ARC and HMC patients were separated into the cortex and nucleus. After protein digestion, the phosphopeptides were quantitatively analyzed with TiO2 enrichment and liquid chromatography-mass spectrometry. The potential functions of different phosphopeptides were assessed by Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Results In total, 522 phosphorylation sites in 164 phosphoproteins were identified. The number of phosphorylation sites was significantly higher in the cortex than in the nucleus, in both ARC and HMC lenses. The differentially phosphorylated peptides in the lens cortex and nucleus in HMC eyes were significantly involved in the glutathione metabolism pathway. The KEGG pathway enrichment analysis indicated that the differences in phosphosignaling mediators between the ARC and HMC lenses were associated with glycolysis and the level of phosphorylated phosphoglycerate kinase 1 was lower in HMC lenses than in ARC lenses. Conclusions We provide an overview of the differential phosphoproteomes of HMC and ARC lenses that can be used to clarify the molecular mechanisms underlying their different phenotypes.
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Pan DY, Zeng XQ, Ma GF, Gao J, Li N, Miao Q, Lian JJ, Zhou H, Xu LL, Chen SY. Label-free quantitative proteomic analysis identifies CTNNB1 as a direct target of FOXP3 in gastric cancer cells. Oncol Lett 2018; 15:7655-7660. [PMID: 29740487 PMCID: PMC5934717 DOI: 10.3892/ol.2018.8277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 02/15/2018] [Indexed: 12/20/2022] Open
Abstract
Forkhead box protein 3 (FOXP3) is expressed in numerous types of tumor cell and is associated with tumor progression and prognosis. A previous study reported that FOXP3 inhibited cellular proliferation and induced apoptosis of gastric cancer (GC) cells by activating the apoptosis signaling pathway. In the present study, label-free quantitative proteomic analysis and chromatin immunoprecipitation-polymerase chain reaction (ChIP-PCR) was performed to investigate the mechanism by which the anticancer role of FOXP3 was mediated and the proteins that with which it may interact. Label-free quantitative proteomic analysis was used to screen for proteins differentially expressed between FOXP3-overexpressing GC (AF) and vector (ANC) cells. Catenin β1 (CTNNB1) was one of the proteins that exhibited the greatest difference between AF and ANC among 3,313 proteins identified by liquid chromatography with tandem mass spectrometry analysis. The expression of CTNNB1 was evaluated by reverse transcription-quantitative PCR and western blotting. The association between FOXP3 and CTNNB1 was confirmed by ChIP-PCR in AGS cells. The changes in expression of epithelial-mesenchymal transition-associated proteins were analyzed by western blotting. The level of FOXP3 expression was positively associated with CTNNB1 and E-cadherin expression, but not with vimentin and N-cadherin expression. FOXP3 positively regulates CTNNB1 and binds to it directly. Along with the upregulation of glycogen synthase kinase 3β (GSK3β), which was also a protein whose expression was found to change significantly in proteomic analysis and has a key role in the Wnt pathway. This association is an attractive and novel hypothesis for the mechanism by which FOXP3 inhibits the invasion and metastasis of GC cells.
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Affiliation(s)
- Du-Yi Pan
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Xiao-Qing Zeng
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Gui-Fen Ma
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Jing Gao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P.R. China
| | - Na Li
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Qing Miao
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Jing-Jing Lian
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Hu Zhou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P.R. China
| | - Li-Li Xu
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Shi-Yao Chen
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
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Acylation of Superoxide Dismutase 1 (SOD1) at K122 Governs SOD1-Mediated Inhibition of Mitochondrial Respiration. Mol Cell Biol 2017; 37:MCB.00354-17. [PMID: 28739857 DOI: 10.1128/mcb.00354-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/11/2017] [Indexed: 12/24/2022] Open
Abstract
In this study, we employed proteomics to identify mechanisms of posttranslational regulation on cell survival signaling proteins. We focused on Cu-Zn superoxide dismutase (SOD1), which protects cells from oxidative stress. We found that acylation of K122 on SOD1, while not impacting SOD1 catalytic activity, suppressed the ability of SOD1 to inhibit mitochondrial metabolism at respiratory complex I. We found that deacylase depletion increased K122 acylation on SOD1, which blocked the suppression of respiration in a K122-dependent manner. In addition, we found that acyl-mimicking mutations at K122 decreased SOD1 accumulation in mitochondria, initially hinting that SOD1 may inhibit respiration directly within the intermembrane space (IMS). However, surprisingly, we found that forcing the K122 acyl mutants into the mitochondria with an IMS-targeting tag did not recover their ability to suppress respiration. Moreover, we found that suppressing or boosting respiration levels toggled SOD1 in or out of the mitochondria, respectively. These findings place SOD1-mediated inhibition of respiration upstream of its mitochondrial localization. Lastly, deletion-rescue experiments show that a respiration-defective mutant of SOD1 is also impaired in its ability to rescue cells from toxicity caused by SOD1 deletion. Together, these data suggest a previously unknown interplay between SOD1 acylation, metabolic regulation, and SOD1-mediated cell survival.
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Analyses of PDE-regulated phosphoproteomes reveal unique and specific cAMP-signaling modules in T cells. Proc Natl Acad Sci U S A 2017. [PMID: 28634298 DOI: 10.1073/pnas.1703939114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Specific functions for different cyclic nucleotide phosphodiesterases (PDEs) have not yet been identified in most cell types. Conventional approaches to study PDE function typically rely on measurements of global cAMP, general increases in cAMP-dependent protein kinase (PKA), or the activity of exchange protein activated by cAMP (EPAC). Although newer approaches using subcellularly targeted FRET reporter sensors have helped define more compartmentalized regulation of cAMP, PKA, and EPAC, they have limited ability to link this regulation to downstream effector molecules and biological functions. To address this problem, we have begun to use an unbiased mass spectrometry-based approach coupled with treatment using PDE isozyme-selective inhibitors to characterize the phosphoproteomes of the functional pools of cAMP/PKA/EPAC that are regulated by specific cAMP-PDEs (the PDE-regulated phosphoproteomes). In Jurkat cells we find multiple, distinct PDE-regulated phosphoproteomes that can be defined by their responses to different PDE inhibitors. We also find that little phosphorylation occurs unless at least two different PDEs are concurrently inhibited in these cells. Moreover, bioinformatics analyses of these phosphoproteomes provide insight into the unique functional roles, mechanisms of action, and synergistic relationships among the different PDEs that coordinate cAMP-signaling cascades in these cells. The data strongly suggest that the phosphorylation of many different substrates contributes to cAMP-dependent regulation of these cells. The findings further suggest that the approach of using selective, inhibitor-dependent phosphoproteome analysis can provide a generalized methodology for understanding the roles of different PDEs in the regulation of cyclic nucleotide signaling.
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Sahu PK, Ramisetti NR, Cecchi T, Swain S, Patro CS, Panda J. An overview of experimental designs in HPLC method development and validation. J Pharm Biomed Anal 2017; 147:590-611. [PMID: 28579052 DOI: 10.1016/j.jpba.2017.05.006] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/01/2017] [Accepted: 05/04/2017] [Indexed: 01/25/2023]
Abstract
Chemometric approaches have been increasingly viewed as precious complements to high performance liquid chromatographic practices, since a large number of variables can be simultaneously controlled to achieve the desired separations. Moreover, their applications may efficiently identify and optimize the significant factors to accomplish competent results through limited experimental trials. The present manuscript discusses usefulness of various chemometric approaches in high and ultra performance liquid chromatography for (i) methods development from dissolution studies and sample preparation to detection, considering the progressive substitution of traditional detectors with tandem mass spectrometry instruments and the importance of stability indicating assays (ii) method validation through screening and optimization designs. Choice of appropriate types of experimental designs so as to either screen the most influential factors or optimize the selected factors' combination and the mathematical models in chemometry have been briefly recalled and the advantages of chemometric approaches have been emphasized. The evolution of the design of experiments to the Quality by Design paradigm for method development has been reviewed and the Six Sigma practice as a quality indicator in chromatography has been explained. Chemometric applications and various strategies in chromatographic separations have been described.
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Affiliation(s)
- Prafulla Kumar Sahu
- Department of Pharmaceutical Analysis and Quality Assurance, Raghu College of Pharmacy, Dakamarri, Bheemunipatnam Mandal, Visakhapatnam, 531162, Andhra Pradesh, India
| | - Nageswara Rao Ramisetti
- Analytical Chemistry Division, CSIR-Indian Institute of Chemical Technology (IICT), Tarnaka, Hyderabad, 500007, Telangana, India.
| | - Teresa Cecchi
- Chemistry Department, ITT MONTANI, Via Montani 7, 63900, Fermo, FM, Italy.
| | - Suryakanta Swain
- Department of Pharmaceutics, SIMS College of Pharmacy, Mangaladas Nagar, Vijayawada Road, Guntur, 522 001, Andhra Pradesh, India
| | - Chandra Sekhar Patro
- Department of Pharmaceutical Analysis and Quality Assurance, Raghu College of Pharmacy, Dakamarri, Bheemunipatnam Mandal, Visakhapatnam, 531162, Andhra Pradesh, India
| | - Jagadeesh Panda
- Department of Pharmaceutical Analysis and Quality Assurance, Raghu College of Pharmacy, Dakamarri, Bheemunipatnam Mandal, Visakhapatnam, 531162, Andhra Pradesh, India
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The analysis of heterotaxy patients reveals new loss-of-function variants of GRK5. Sci Rep 2016; 6:33231. [PMID: 27618959 PMCID: PMC5020398 DOI: 10.1038/srep33231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/19/2016] [Indexed: 11/08/2022] Open
Abstract
G protein-coupled receptor kinase 5 (GRK5) is a regulator of cardiac performance and a potential therapeutic target in heart failure in the adult. Additionally, we have previously classified GRK5 as a determinant of left-right asymmetry and proper heart development using zebrafish. We thus aimed to identify GRK5 variants of functional significance by analysing 187 individuals with laterality defects (heterotaxy) that were associated with a congenital heart defect (CHD). Using Sanger sequencing we identified two moderately frequent variants in GRK5 with minor allele frequencies <10%, and seven very rare polymorphisms with minor allele frequencies <1%, two of which are novel variants. Given their evolutionarily conserved position in zebrafish, in-depth functional characterisation of four variants (p.Q41L, p.G298S, p.R304C and p.T425M) was performed. We tested the effects of these variants on normal subcellular localisation and the ability to desensitise receptor signalling as well as their ability to correct the left-right asymmetry defect upon Grk5l knockdown in zebrafish. While p.Q41L, p.R304C and p.T425M responded normally in the first two aspects, neither p.Q41L nor p.R304C were capable of rescuing the lateralisation phenotype. The fourth variant, p.G298S was identified as a complete loss-of-function variant in all assays and provides insight into the functions of GRK5.
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Smith LC, Ralston-Hooper KJ, Ferguson PL, Sabo-Attwood T. The G Protein-Coupled Estrogen Receptor Agonist G-1 Inhibits Nuclear Estrogen Receptor Activity and Stimulates Novel Phosphoproteomic Signatures. Toxicol Sci 2016; 151:434-46. [PMID: 27026707 DOI: 10.1093/toxsci/kfw057] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Estrogen exerts cellular effects through both nuclear (ESR1 and ESR2) and membrane-bound estrogen receptors (G-protein coupled estrogen receptor, GPER); however, it is unclear if they act independently or engage in crosstalk to influence hormonal responses. To investigate each receptor's role in proliferation, transcriptional activation, and protein phosphorylation in breast cancer cells (MCF-7), we employed selective agonists for ESR1 propyl-pyrazole-triol (PPT), ESR2 diarylpropionitrile (DPN), and GPER (G-1) and also determined the impact of xenoestrogens bisphenol-A (BPA) and genistein on these effects. As anticipated, 17β-estradiol (E2), PPT, DPN, BPA, and genistein each enhanced proliferation and activation of an ERE-driven reporter gene whereas G-1 had no significant impact. However, G-1 significantly reduced E2-, PPT-, DPN-, BPA-, and genistein-induced proliferation and ERE activation at doses greater than 500 nM indicating that G-1 mediated inhibition is not ESR isotype specific. As membrane receptors initiate cascades of phosphorylation events, we performed a global phosphoproteomic analysis on cells exposed to E2 or G-1 to identify potential targets of receptor crosstalk via downstream protein phosphorylation targets. Of the 211 phosphorylated proteins identified, 40 and 13 phosphoproteins were specifically modified by E2 and G-1, respectively. Subnetwork enrichment analysis revealed several processes related to cell cycle were specifically enriched by G-1 compared with E2. Further there existed a number of newly identified proteins that were specifically phosphorylated by G-1. These phosphorylation networks highlight specific proteins that may modulate the inhibitory effects of G-1 and suggest a novel role for interference with nuclear receptor activity driven by E2 and xenoestrogens.
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Affiliation(s)
- L Cody Smith
- *Department of Physiological Sciences, Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida 32611
| | - Kimberly J Ralston-Hooper
- Department of Civil and Environmental Engineering, Nicholas School of the Environment, Duke University, Durham, North Carolina 27708
| | - P Lee Ferguson
- Department of Civil and Environmental Engineering, Nicholas School of the Environment, Duke University, Durham, North Carolina 27708
| | - Tara Sabo-Attwood
- Department of Environmental and Global Health, Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida 32611;
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Kwon OK, Kim SJ, Lee YM, Lee YH, Bae YS, Kim JY, Peng X, Cheng Z, Zhao Y, Lee S. Global analysis of phosphoproteome dynamics in embryonic development of zebrafish (Danio rerio). Proteomics 2015; 16:136-49. [DOI: 10.1002/pmic.201500017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 09/04/2015] [Accepted: 10/01/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Oh Kwang Kwon
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
| | - Sun Ju Kim
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
| | - You-Mie Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
| | - Young-Hoon Lee
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program); Kyungpook National University; Daegu Korea
| | - Young-Seuk Bae
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program); Kyungpook National University; Daegu Korea
| | - Jin Young Kim
- Mass Spectrometry Research Center; Korea Basic Science Institute; Ochang Chungbuk Republic of Korea
| | - Xiaojun Peng
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd; Hangzhou P. R. China
| | - Zhongyi Cheng
- Advanced Institute of Translational Medicine; Tongji University; Shanghai P. R. China
| | - Yingming Zhao
- Ben May Department for Cancer Research; University of Chicago; Chicago IL USA
| | - Sangkyu Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
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Figueiredo-Freitas C, Dulce RA, Foster MW, Liang J, Yamashita AMS, Lima-Rosa FL, Thompson JW, Moseley MA, Hare JM, Nogueira L, Sorenson MM, Pinto JR. S-Nitrosylation of Sarcomeric Proteins Depresses Myofilament Ca2+)Sensitivity in Intact Cardiomyocytes. Antioxid Redox Signal 2015; 23:1017-34. [PMID: 26421519 PMCID: PMC4649751 DOI: 10.1089/ars.2015.6275] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
AIMS The heart responds to physiological and pathophysiological stress factors by increasing its production of nitric oxide (NO), which reacts with intracellular glutathione to form S-nitrosoglutathione (GSNO), a protein S-nitrosylating agent. Although S-nitrosylation protects some cardiac proteins against oxidative stress, direct effects on myofilament performance are unknown. We hypothesize that S-nitrosylation of sarcomeric proteins will modulate the performance of cardiac myofilaments. RESULTS Incubation of intact mouse cardiomyocytes with S-nitrosocysteine (CysNO, a cell-permeable low-molecular-weight nitrosothiol) significantly decreased myofilament Ca(2+) sensitivity. In demembranated (skinned) fibers, S-nitrosylation with 1 μM GSNO also decreased Ca(2+) sensitivity of contraction and 10 μM reduced maximal isometric force, while inhibition of relaxation and myofibrillar ATPase required higher concentrations (≥ 100 μM). Reducing S-nitrosylation with ascorbate partially reversed the effects on Ca(2+) sensitivity and ATPase activity. In live cardiomyocytes treated with CysNO, resin-assisted capture of S-nitrosylated protein thiols was combined with label-free liquid chromatography-tandem mass spectrometry to quantify S-nitrosylation and determine the susceptible cysteine sites on myosin, actin, myosin-binding protein C, troponin C and I, tropomyosin, and titin. The ability of sarcomere proteins to form S-NO from 10-500 μM CysNO in intact cardiomyocytes was further determined by immunoblot, with actin, myosin, myosin-binding protein C, and troponin C being the more susceptible sarcomeric proteins. INNOVATION AND CONCLUSIONS Thus, specific physiological effects are associated with S-nitrosylation of a limited number of cysteine residues in sarcomeric proteins, which also offer potential targets for interventions in pathophysiological situations.
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Affiliation(s)
- Cícero Figueiredo-Freitas
- 1 Department of Biomedical Sciences, College of Medicine, Florida State University , Tallahassee, Florida.,2 Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro , Rio de Janeiro, Brazil .,3 Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami , Miami, Florida
| | - Raul A Dulce
- 4 Interdisciplinary Stem Cell Institute, University of Miami , Miami, Florida
| | - Matthew W Foster
- 5 Pulmonary, Allergy and Critical Care Medicine, Duke University Medical Center , Durham, North Carolina.,6 Proteomics and Metabolomics Shared Resource, Duke University Medical Center , Durham, North Carolina
| | - Jingsheng Liang
- 3 Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami , Miami, Florida
| | - Aline M S Yamashita
- 2 Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro , Rio de Janeiro, Brazil
| | - Frederico L Lima-Rosa
- 2 Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro , Rio de Janeiro, Brazil
| | - J Will Thompson
- 6 Proteomics and Metabolomics Shared Resource, Duke University Medical Center , Durham, North Carolina
| | - M Arthur Moseley
- 6 Proteomics and Metabolomics Shared Resource, Duke University Medical Center , Durham, North Carolina
| | - Joshua M Hare
- 4 Interdisciplinary Stem Cell Institute, University of Miami , Miami, Florida
| | - Leonardo Nogueira
- 2 Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro , Rio de Janeiro, Brazil
| | - Martha M Sorenson
- 2 Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro , Rio de Janeiro, Brazil
| | - José Renato Pinto
- 1 Department of Biomedical Sciences, College of Medicine, Florida State University , Tallahassee, Florida.,3 Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami , Miami, Florida
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14
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Piersma SR, Knol JC, de Reus I, Labots M, Sampadi BK, Pham TV, Ishihama Y, Verheul HM, Jimenez CR. Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines. J Proteomics 2015; 127:247-58. [DOI: 10.1016/j.jprot.2015.03.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/13/2015] [Accepted: 03/05/2015] [Indexed: 02/03/2023]
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15
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Kauko O, Laajala TD, Jumppanen M, Hintsanen P, Suni V, Haapaniemi P, Corthals G, Aittokallio T, Westermarck J, Imanishi SY. Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling. Sci Rep 2015; 5:13099. [PMID: 26278961 PMCID: PMC4642524 DOI: 10.1038/srep13099] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/06/2015] [Indexed: 11/11/2022] Open
Abstract
Hyperactivated RAS drives progression of many human malignancies. However, oncogenic activity of RAS is dependent on simultaneous inactivation of protein phosphatase 2A (PP2A) activity. Although PP2A is known to regulate some of the RAS effector pathways, it has not been systematically assessed how these proteins functionally interact. Here we have analyzed phosphoproteomes regulated by either RAS or PP2A, by phosphopeptide enrichment followed by mass-spectrometry-based label-free quantification. To allow data normalization in situations where depletion of RAS or PP2A inhibitor CIP2A causes a large uni-directional change in the phosphopeptide abundance, we developed a novel normalization strategy, named pairwise normalization. This normalization is based on adjusting phosphopeptide abundances measured before and after the enrichment. The superior performance of the pairwise normalization was verified by various independent methods. Additionally, we demonstrate how the selected normalization method influences the downstream analyses and interpretation of pathway activities. Consequently, bioinformatics analysis of RAS and CIP2A regulated phosphoproteomes revealed a significant overlap in their functional pathways. This is most likely biologically meaningful as we observed a synergistic survival effect between CIP2A and RAS expression as well as KRAS activating mutations in TCGA pan-cancer data set, and synergistic relationship between CIP2A and KRAS depletion in colony growth assays.
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Affiliation(s)
- Otto Kauko
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Department of Pathology, University of Turku, FI-20520 Turku, Finland [3] Turku Doctoral Program of Biomedical Sciences (TuBS), Turku, Finland
| | - Teemu Daniel Laajala
- 1] Department of Mathematics and Statistics, University of Turku, FI-20014 Turku, Finland [2] Drug Research Doctoral Programme (DRDP), Turku, Finland
| | - Mikael Jumppanen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland
| | - Petteri Hintsanen
- Institute for Molecular Medicine Finland, Tukholmankatu 8, FI-00290 Helsinki, Finland
| | - Veronika Suni
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Turku Centre for Computer Science, FI-20520 Turku, Finland
| | - Pekka Haapaniemi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland
| | - Garry Corthals
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, Tukholmankatu 8, FI-00290 Helsinki, Finland
| | - Jukka Westermarck
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Department of Pathology, University of Turku, FI-20520 Turku, Finland
| | - Susumu Y Imanishi
- 1] Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistokatu 6, FI-20520 Turku, Finland [2] Faculty of Pharmacy, Meijo University, Yagotoyama 150, Tempaku, Nagoya 468-8503, Japan
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16
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Giansanti P, Aye T, van den Toorn H, Peng M, van Breukelen B, Heck A. An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas. Cell Rep 2015; 11:1834-43. [DOI: 10.1016/j.celrep.2015.05.029] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/27/2015] [Accepted: 05/17/2015] [Indexed: 11/29/2022] Open
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17
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Slade WO, Werth EG, McConnell EW, Alvarez S, Hicks LM. Quantifying reversible oxidation of protein thiols in photosynthetic organisms. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:631-640. [PMID: 25698223 DOI: 10.1007/s13361-014-1073-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 12/18/2014] [Accepted: 12/18/2014] [Indexed: 06/04/2023]
Abstract
Photosynthetic organisms use dynamic post-translational modifications to survive and adapt, which include reversible oxidative modifications of protein thiols that regulate protein structure, function, and activity. Efforts to quantify thiol modifications on a global scale have relied upon peptide derivatization, typically using isobaric tags such as TMT, ICAT, or iTRAQ that are more expensive, less accurate, and provide less proteome coverage than label-free approaches--suggesting the need for improved experimental designs for studies requiring maximal coverage and precision. Herein, we present the coverage and precision of resin-assisted thiol enrichment coupled to label-free quantitation for the characterization of reversible oxidative modifications on protein thiols. Using C. reinhardtii and Arabidopsis as model systems for algae and plants, we quantified 3662 and 1641 unique cysteinyl peptides, respectively, with median coefficient of variation (CV) of 13% and 16%. Further, our method is extendable for the detection of protein abundance changes and stoichiometries of cysteine oxidation. Finally, we demonstrate proof-of-principle for our method, and reveal that exogenous hydrogen peroxide treatment regulates the C. reinhardtii redox proteome by increasing or decreasing the level of oxidation of 501 or 67 peptides, respectively. As protein activity and function is controlled by oxidative modifications on protein thiols, resin-assisted thiol enrichment coupled to label-free quantitation can reveal how intracellular and environmental stimuli affect plant survival and fitness through oxidative stress.
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Affiliation(s)
- William O Slade
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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18
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Rinalducci S, Longo V, Ceci LR, Zolla L. Targeted quantitative phosphoproteomic analysis of erythrocyte membranes during blood bank storage. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:326-335. [PMID: 25800014 DOI: 10.1002/jms.3531] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 09/29/2014] [Accepted: 10/15/2014] [Indexed: 06/04/2023]
Abstract
One of the hallmarks of blood bank stored red blood cells (RBCs) is the irreversible transition from a discoid to a spherocyte-like morphology with membrane perturbation and cytoskeleton disorders. Therefore, identification of the storage-associated modifications in the protein-protein interactions between the cytoskeleton and the lipid bilayer may contribute to enlighten the molecular mechanisms involved in the alterations of mechanical properties of stored RBCs. Here we report the results obtained analyzing RBCs after 0, 21 and 35 days of storage under standard blood banking conditions by label free mass spectrometry (MS)-based experiments. We could quantitatively measure changes in the phosphorylation level of crucial phosphopeptides belonging to β-spectrin, ankyrin-1, α-adducin, dematin, glycophorin A and glycophorin C proteins. Data have been validated by both western blotting and pseudo-Multiple Reaction Monitoring (MRM). Although each phosphopeptide showed a distinctive trend, a sharp increase in the phosphorylation level during the storage duration was observed. Phosphopeptide mapping and structural modeling analysis indicated that the phosphorylated residues localize in protein functional domains fundamental for the maintenance of membrane structural integrity. Along with previous morphological evidence acquired by electron microscopy, our results seem to indicate that 21-day storage may represent a key point for the molecular processes leading to the erythrocyte deformability reduction observed during blood storage. These findings could therefore be helpful in understanding and preventing the morphology-linked mechanisms responsible for the post-transfusion survival of preserved RBCs.
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Affiliation(s)
- Sara Rinalducci
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
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19
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Schechter MA, Hsieh MKH, Njoroge LW, Thompson JW, Soderblom EJ, Feger BJ, Troupes CD, Hershberger KA, Ilkayeva OR, Nagel WL, Landinez GP, Shah KM, Burns VA, Santacruz L, Hirschey MD, Foster MW, Milano CA, Moseley MA, Piacentino V, Bowles DE. Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure. PLoS One 2014; 9:e104157. [PMID: 25117565 PMCID: PMC4130503 DOI: 10.1371/journal.pone.0104157] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/06/2014] [Indexed: 12/31/2022] Open
Abstract
The molecular differences between ischemic (IF) and non-ischemic (NIF) heart failure are poorly defined. A better understanding of the molecular differences between these two heart failure etiologies may lead to the development of more effective heart failure therapeutics. In this study extensive proteomic and phosphoproteomic profiles of myocardial tissue from patients diagnosed with IF or NIF were assembled and compared. Proteins extracted from left ventricular sections were proteolyzed and phosphopeptides were enriched using titanium dioxide resin. Gel- and label-free nanoscale capillary liquid chromatography coupled to high resolution accuracy mass tandem mass spectrometry allowed for the quantification of 4,436 peptides (corresponding to 450 proteins) and 823 phosphopeptides (corresponding to 400 proteins) from the unenriched and phospho-enriched fractions, respectively. Protein abundance did not distinguish NIF from IF. In contrast, 37 peptides (corresponding to 26 proteins) exhibited a ≥ 2-fold alteration in phosphorylation state (p<0.05) when comparing IF and NIF. The degree of protein phosphorylation at these 37 sites was specifically dependent upon the heart failure etiology examined. Proteins exhibiting phosphorylation alterations were grouped into functional categories: transcriptional activation/RNA processing; cytoskeleton structure/function; molecular chaperones; cell adhesion/signaling; apoptosis; and energetic/metabolism. Phosphoproteomic analysis demonstrated profound post-translational differences in proteins that are involved in multiple cellular processes between different heart failure phenotypes. Understanding the roles these phosphorylation alterations play in the development of NIF and IF has the potential to generate etiology-specific heart failure therapeutics, which could be more effective than current therapeutics in addressing the growing concern of heart failure.
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Affiliation(s)
- Matthew A. Schechter
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael K. H. Hsieh
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Linda W. Njoroge
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - J. Will Thompson
- Duke Proteomics Core, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Erik J. Soderblom
- Duke Proteomics Core, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Bryan J. Feger
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Constantine D. Troupes
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kathleen A. Hershberger
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Olga R. Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Whitney L. Nagel
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Gina P. Landinez
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kishan M. Shah
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Virginia A. Burns
- Duke Translational Research Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Lucia Santacruz
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Matthew D. Hirschey
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Matthew W. Foster
- Division of Pulmonary, Allergy and Critical Care, Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Carmelo A. Milano
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - M. Arthur Moseley
- Duke Proteomics Core, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Valentino Piacentino
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Dawn E. Bowles
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
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20
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Wang Y, Li Z, Liu D, Xu J, Wei X, Yan L, Yang C, Lou Z, Shui W. Assessment of BAK1 activity in different plant receptor-like kinase complexes by quantitative profiling of phosphorylation patterns. J Proteomics 2014; 108:484-93. [PMID: 24953020 DOI: 10.1016/j.jprot.2014.06.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 05/17/2014] [Accepted: 06/02/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED Plant receptor-like kinases (RLKs) constitute a large family of receptors coordinating developmental programs with adaptation to environmental stresses including immune defenses. BRI1-ASSOCIATED KINASE 1 (BAK1), a member of the plant RLK family, forms receptor complexes with multiple RLK proteins including BRI1, FLS2, EFR and BIK1 to regulate responses to growth hormones or PAMPs. RLK activation and signal initiation involve protein complex formation and phosphorylation/dephosphorylation between BAK1 and its interacting partners. To gain new insight into how phosphorylation contributes to BAK1-mediated signaling specificity, we first mapped the phosphorylation patterns of BAK1 associated with different RLK partners (BRI1, FLS2, EFR and BIK1). Quantitative phospho-pattern profiling by label-free mass spectrometry revealed that differential phosphorylation patterns of RLK partners resulted from altered BAK1 phosphorylation status. More interestingly, the study of two BAK1 mutants (T450A and C408Y) both showing severe defect in immune defense yet normal growth phenotype suggested that varied phosphorylation patterns of RLK partners by BAK1 could be the molecular basis for selective regulation of multiple BAK1-dependent pathways. Taken together, this phospho-pattern profiling strategy allowed for explicit assessment of BAK1 kinase activity in different RLK complexes, which would facilitate elucidation of BAK1 diverse functions in plant development, defense, and adaptation. BIOLOGICAL SIGNIFICANCE BAK1 is a functionally important co-receptor known to interact with different receptor-like kinases (RLKs) to coordinate plant development and immune defenses. Our study first mapped the phosphorylation patterns of BAK1 associated with four RLK partners (BRI1, FLS2, EFR and BIK1), and further revealed that differential phosphorylation patterns of multiple RLK partners resulted from altered BAK1 phosphorylation status. More interestingly, the study of two BAK1 mutants suggested that varied phosphorylation patterns of RLK partners by BAK1 could be the basis for selective regulation of signaling pathways. Taken together, this phospho-pattern profiling strategy allowed for explicit assessment of BAK1 kinase activity in different RLK complexes, which would facilitate elucidation of BAK1 diverse functions in plant development, defense, and adaptation.
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Affiliation(s)
- Yilin Wang
- College of Life Sciences, Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin 300071, China; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Zhucui Li
- College of Life Sciences, Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin 300071, China; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Dan Liu
- College of Life Sciences, Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin 300071, China; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Jinhua Xu
- College of Life Sciences, Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin 300071, China; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Xiaochao Wei
- College of Life Sciences, Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin 300071, China; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Liming Yan
- Laboratory of Structural Biology and MOE Laboratory of Protein Science, School of Medicine and Life Sciences, Tsinghua University, Beijing 100084, China
| | - Cheng Yang
- High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Zhiyong Lou
- Laboratory of Structural Biology and MOE Laboratory of Protein Science, School of Medicine and Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenqing Shui
- College of Life Sciences, Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin 300071, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
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21
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de Graaf EL, Giansanti P, Altelaar AFM, Heck AJR. Single-step enrichment by Ti4+-IMAC and label-free quantitation enables in-depth monitoring of phosphorylation dynamics with high reproducibility and temporal resolution. Mol Cell Proteomics 2014; 13:2426-34. [PMID: 24850871 DOI: 10.1074/mcp.o113.036608] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Quantitative phosphoproteomics workflows traditionally involve additional sample labeling and fractionation steps for accurate and in-depth analysis. Here we report a high-throughput, straightforward, and comprehensive label-free phosphoproteomics approach using the highly selective, reproducible, and sensitive Ti(4+)-IMAC phosphopeptide enrichment method. We demonstrate the applicability of this approach by monitoring the phosphoproteome dynamics of Jurkat T cells stimulated by prostaglandin E2 (PGE2) over six different time points, measuring in total 108 snapshots of the phosphoproteome. In total, we quantitatively monitored 12,799 unique phosphosites over all time points with very high quantitative reproducibility (average r > 0.9 over 100 measurements and a median cv < 0.2). PGE2 is known to increase cellular cAMP levels, thereby activating PKA. The in-depth analysis revealed temporal regulation of a wide variety of phosphosites associated not only with PKA, but also with a variety of other classes of kinases. Following PGE2 stimulation, several pathways became only transiently activated, revealing that in-depth dynamic profiling requires techniques with high temporal resolution. Moreover, the large publicly available dataset provides a valuable resource for downstream PGE2 signaling dynamics in T cells, and cAMP-mediated signaling in particular. More generally, our method enables in-depth, quantitative, high-throughput phosphoproteome screening on any system, requiring very little sample, sample preparation, and analysis time.
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Affiliation(s)
- Erik L de Graaf
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Piero Giansanti
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - A F Maarten Altelaar
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
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22
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Longo V, Marrocco C, Zolla L, Rinalducci S. Label-free quantitation of phosphopeptide changes in erythrocyte membranes: towards molecular mechanisms underlying deformability alterations in stored red blood cells. Haematologica 2014; 99:e122-5. [PMID: 24705185 DOI: 10.3324/haematol.2013.103333] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Valentina Longo
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Cristina Marrocco
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Lello Zolla
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Sara Rinalducci
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
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23
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Sun Z, Hamilton KL, Reardon KF. Evaluation of quantitative performance of sequential immobilized metal affinity chromatographic enrichment for phosphopeptides. Anal Biochem 2013; 445:30-7. [PMID: 24096195 DOI: 10.1016/j.ab.2013.09.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/28/2013] [Accepted: 09/24/2013] [Indexed: 11/30/2022]
Abstract
We evaluated a sequential elution protocol from immobilized metal affinity chromatography (SIMAC) employing gallium-based immobilized metal affinity chromatography (IMAC) in conjunction with titanium dioxide-based metal oxide affinity chromatography (MOAC). The quantitative performance of this SIMAC enrichment approach, assessed in terms of repeatability, dynamic range, and linearity, was evaluated using a mixture composed of tryptic peptides from caseins, bovine serum albumin, and phosphopeptide standards. Although our data demonstrate the overall consistent performance of the SIMAC approach under various loading conditions, the results also revealed that the method had limited repeatability and linearity for most phosphopeptides tested, and different phosphopeptides were found to have different linear ranges. These data suggest that, unless additional strategies are used, SIMAC should be regarded as a semiquantitative method when used in large-scale phosphoproteomics studies in complex backgrounds.
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Affiliation(s)
- Zeyu Sun
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
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24
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Richardson BM, Soderblom EJ, Thompson JW, Moseley MA. Automated, reproducible, titania-based phosphopeptide enrichment strategy for label-free quantitative phosphoproteomics. J Biomol Tech 2013; 24:8-16. [PMID: 23542237 DOI: 10.7171/jbt.13-2401-002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An automated phosphopeptide enrichment strategy is described using titanium dioxide (TiO2)-packed, fused silica capillaries for use with liquid chromatography (LC)-mass spectrometry (MS)/MS-based, label-free proteomics workflows. To correlate an optimum peptide:TiO2 loading ratio between different particle types, the ratio of phenyl phosphate-binding capacities was used. The optimum loading for the column was then verified through replicate enrichments of a range of quantities of digested rat brain tissue cell lysate. Fractions were taken during sample loading, multiple wash steps, and the elution steps and analyzed by LC-MS/MS to gauge the efficiency and reproducibility of the enrichment. Greater than 96% of the total phosphopeptides were detected in the elution fractions, indicating efficient trapping of the phosphopeptides on the first pass of enrichment. The quantitative reproducibility of the automated setup was also improved greatly with phosphopeptide intensities from replicate enrichments exhibiting a median coefficient of variation (CV) of 5.8%, and 80% of the identified phosphopeptides had CVs below 11.1%, while maintaining >85% specificity. By providing this high degree of analytical reproducibility, this method allows for label-free phosphoproteomics over large sample sets with complex experimental designs (multiple biological conditions, multiple biological replicates, multiple time-points, etc.), including large-scale clinical cohorts.
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Affiliation(s)
- Brenna McJury Richardson
- Duke Proteomics Core Facility, Institute for Genome Sciences & Policy, Duke University School of Medicine, Durham, NC 27708, USA
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25
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Hoos MD, Richardson BM, Foster MW, Everhart A, Thompson JW, Moseley MA, Colton CA. Longitudinal study of differential protein expression in an Alzheimer's mouse model lacking inducible nitric oxide synthase. J Proteome Res 2013; 12:4462-77. [PMID: 24006891 DOI: 10.1021/pr4005103] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative process that involves altered brain immune, neuronal and metabolic functions. Understanding the underlying mechanisms has relied on mouse models that mimic components of AD pathology. We used gel-free, label-free LC-MS/MS to quantify protein and phosphopeptide levels in brains of APPSwDI/NOS2-/- (CVN-AD) mice. CVN-AD mice show a full spectrum of AD-like pathology, including amyloid deposition, hyperphosphorylated and aggregated tau, and neuronal loss that worsens with age. Tryptic digests, with or without phosphopeptide enrichment on an automated titanium dioxide LC system, were separated by online two-dimensional LC and analyzed on a Waters Synapt G2 HDMS, yielding relative expression for >950 proteins and >1100 phosphopeptides. Among differentially expressed proteins were known markers found in humans with AD, including GFAP and C1Q. Phosphorylation of connexin 43, not previously described in AD, was increased at 42 weeks, consistent with dysregulation of gap junctions and activation of astrocytes. Additional alterations in phosphoproteins suggests dysregulation of mitochondria, synaptic transmission, vesicle trafficking, and innate immune pathways. These data validate the CVN-AD mouse model of AD, identify novel disease and age-related changes in the brain during disease progression, and demonstrate the utility of integrating unbiased and phosphoproteomics for understanding disease processes in AD.
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Affiliation(s)
- Michael D Hoos
- Department of Medicine/Neurology, ‡Institute for Genome Sciences & Policy, School of Medicine, and §Division of Pulmonary, Allergy and Critical Care Medicine, Duke University Medical Center, Duke University , Durham, North Carolina 27710, United States
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26
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Xu J, Wei X, Yan L, Liu D, Ma Y, Guo Y, Peng C, Zhou H, Yang C, Lou Z, Shui W. Identification and functional analysis of phosphorylation residues of the Arabidopsis BOTRYTIS-INDUCED KINASE1. Protein Cell 2013; 4:771-81. [PMID: 24104392 DOI: 10.1007/s13238-013-3053-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 07/26/2013] [Indexed: 11/30/2022] Open
Abstract
Arabidopsis BOTRYTIS-INDUCED KINASE1 (BIK1) is a receptor-like cytoplasmic kinase acting early in multiple signaling pathways important for plant growth and innate immunity. It is known to form a signaling complex with a cell-surface receptor FLS2 and a co-receptor kinase BAK1 to transduce signals upon perception of pathogen-associated molecular patterns (PAMPs). Although site-specific phosphorylation is speculated to mediate the activation and function of BIK1, few studies have been devoted to complete profiling of BIK1 phosphorylation residues. Here, we identified nineteen in vitro autophosphorylation sites of BIK1 including three phosphotyrosine sites, thereby proving BIK1 is a dual-specificity kinase for the first time. The kinase activity of BIK1 substitution mutants were explicitly assessed using quantitative mass spectrometry (MS). Thr-237, Thr-242 and Tyr-250 were found to most significantly affect BIK1 activity in autophosphorylation and phosphorylation of BAK1 in vitro. A structural model of BIK1 was built to further illustrate the molecular functions of specific phosphorylation residues. We also mapped new sites of FLS2 phosphorylation by BIK1, which are different from those by BAK1. These in vitro results could provide new hypotheses for more in-depth in vivo studies leading to deeper understanding of how phosphorylation contributes to BIK1 activation and mediates downstream signaling specificity.
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Affiliation(s)
- Jinhua Xu
- College of Life Sciences and Tianjin State Laboratory of Protein Science, Nankai University, Tianjin, 300071, China
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27
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Foster MW, Thompson JW, Que LG, Yang IV, Schwartz DA, Moseley MA, Marshall HE. Proteomic analysis of human bronchoalveolar lavage fluid after subsgemental exposure. J Proteome Res 2013; 12:2194-205. [PMID: 23550723 DOI: 10.1021/pr400066g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The analysis of airway fluid, as sampled by bronchoalveolar lavage (BAL), provides a minimally invasive route to interrogate lung biology in health and disease. Here, we used immunodepletion, coupled with gel- and label-free LC-MS/MS, for quantitation of the BAL fluid (BALF) proteome in samples recovered from human subjects following bronchoscopic instillation of saline, lipopolysaccharide (LPS) or house dust mite antigen into three distinct lung subsegments. Among more than 200 unique proteins quantified across nine samples, neutrophil granule-derived and acute phase proteins were most highly enriched in the LPS-exposed lobes. Of these, peptidoglycan response protein 1 was validated and confirmed as a novel marker of neutrophilic inflammation. Compared to a prior transcriptomic analysis of airway cells in this same cohort, the BALF proteome revealed a novel set of response factors. Independent of exposure, the enrichment of tracheal-expressed proteins in right lower lung lobes suggests a potential for constitutive intralobar variability in the BALF proteome; sampling of multiple lung subsegments also appears to aid in the identification of protein signatures that differentiate individuals at baseline. Collectively, this proof-of-concept study validates a robust workflow for BALF proteomics and demonstrates the complementary nature of proteomic and genomic techniques for investigating airway (patho)physiology.
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Affiliation(s)
- Matthew W Foster
- Division of Pulmonary, Allergy and Critical Care Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA.
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28
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Zhang P, Yang Y, Candiello J, Thorn TL, Gray N, Halfter WM, Hu H. Biochemical and biophysical changes underlie the mechanisms of basement membrane disruptions in a mouse model of dystroglycanopathy. Matrix Biol 2013; 32:196-207. [PMID: 23454088 DOI: 10.1016/j.matbio.2013.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 01/24/2013] [Accepted: 02/11/2013] [Indexed: 01/11/2023]
Abstract
Mutations in glycosyltransferases, such as protein O-mannose N-acetylglucosaminyltransferase 1 (POMGnT1), causes disruptions of basement membranes (BMs) that results in neuronal ectopias and muscular dystrophy. While the mutations diminish dystroglycan-mediated cell-ECM interactions, the cause and mechanism of BM disruptions remain unclear. In this study, we established an in vitro model to measure BM assembly on the surface of neural stem cells. Compared to control cells, the rate of BM assembly on POMGnT1 knockout neural stem cells was significantly reduced. Further, immunofluorescence staining and quantitative proteomic analysis of the inner limiting membrane (ILM), a BM of the retina, revealed that laminin-111 and nidogen-1 were reduced in POMGnT1 knockout mice. Finally, atomic force microscopy showed that the ILM from POMGnT1 knockout mice was thinner with an altered surface topography. The results combined demonstrate that reduced levels of key BM components cause physical changes that weaken the BM in POMGnT1 knockout mice. These changes are caused by a reduced rate of BM assembly during the developmental expansion of the neural tissue.
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Affiliation(s)
- Peng Zhang
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, USA
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29
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QIU FANGHUA, HUANG DEHONG, XIAO HONGGUANG, QIU FANGYING, LU LIMING, NIE JING. Detection of tyrosine-phosphorylated proteins in hepatocellular carcinoma tissues using a combination of GST-Nck1-SH2 pull-down and two-dimensional electrophoresis. Mol Med Rep 2013; 7:1209-14. [DOI: 10.3892/mmr.2013.1324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 01/22/2013] [Indexed: 11/05/2022] Open
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30
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Circadian acetylome reveals regulation of mitochondrial metabolic pathways. Proc Natl Acad Sci U S A 2013; 110:3339-44. [PMID: 23341599 DOI: 10.1073/pnas.1217632110] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The circadian clock is constituted by a complex molecular network that integrates a number of regulatory cues needed to maintain organismal homeostasis. To this effect, posttranslational modifications of clock proteins modulate circadian rhythms and are thought to convert physiological signals into changes in protein regulatory function. To explore reversible lysine acetylation that is dependent on the clock, we have characterized the circadian acetylome in WT and Clock-deficient (Clock(-/-)) mouse liver by quantitative mass spectrometry. Our analysis revealed that a number of mitochondrial proteins involved in metabolic pathways are heavily influenced by clock-driven acetylation. Pathways such as glycolysis/gluconeogenesis, citric acid cycle, amino acid metabolism, and fatty acid metabolism were found to be highly enriched hits. The significant number of metabolic pathways whose protein acetylation profile is altered in Clock(-/-) mice prompted us to link the acetylome to the circadian metabolome previously characterized in our laboratory. Changes in enzyme acetylation over the circadian cycle and the link to metabolite levels are discussed, revealing biological implications connecting the circadian clock to cellular metabolic state.
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31
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Soderblom EJ, Thompson JW, Schwartz EA, Chiou E, Dubois LG, Moseley MA, Zennadi R. Proteomic analysis of ERK1/2-mediated human sickle red blood cell membrane protein phosphorylation. Clin Proteomics 2013; 10:1. [PMID: 23286773 PMCID: PMC3558407 DOI: 10.1186/1559-0275-10-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 12/19/2012] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED BACKGROUND In sickle cell disease (SCD), the mitogen-activated protein kinase (MAPK) ERK1/2 is constitutively active and can be inducible by agonist-stimulation only in sickle but not in normal human red blood cells (RBCs). ERK1/2 is involved in activation of ICAM-4-mediated sickle RBC adhesion to the endothelium. However, other effects of the ERK1/2 activation in sickle RBCs leading to the complex SCD pathophysiology, such as alteration of RBC hemorheology are unknown. RESULTS To further characterize global ERK1/2-induced changes in membrane protein phosphorylation within human RBCs, a label-free quantitative phosphoproteomic analysis was applied to sickle and normal RBC membrane ghosts pre-treated with U0126, a specific inhibitor of MEK1/2, the upstream kinase of ERK1/2, in the presence or absence of recombinant active ERK2. Across eight unique treatment groups, 375 phosphopeptides from 155 phosphoproteins were quantified with an average technical coefficient of variation in peak intensity of 19.8%. Sickle RBC treatment with U0126 decreased thirty-six phosphopeptides from twenty-one phosphoproteins involved in regulation of not only RBC shape, flexibility, cell morphology maintenance and adhesion, but also glucose and glutamate transport, cAMP production, degradation of misfolded proteins and receptor ubiquitination. Glycophorin A was the most affected protein in sickle RBCs by this ERK1/2 pathway, which contained 12 unique phosphorylated peptides, suggesting that in addition to its effect on sickle RBC adhesion, increased glycophorin A phosphorylation via the ERK1/2 pathway may also affect glycophorin A interactions with band 3, which could result in decreases in both anion transport by band 3 and band 3 trafficking. The abundance of twelve of the thirty-six phosphopeptides were subsequently increased in normal RBCs co-incubated with recombinant ERK2 and therefore represent specific MEK1/2 phospho-inhibitory targets mediated via ERK2. CONCLUSIONS These findings expand upon the current model for the involvement of ERK1/2 signaling in RBCs. These findings also identify additional protein targets of this pathway other than the RBC adhesion molecule ICAM-4 and enhance the understanding of the mechanism of small molecule inhibitors of MEK/1/2/ERK1/2, which could be effective in ameliorating RBC hemorheology and adhesion, the hallmarks of SCD.
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Affiliation(s)
- Erik J Soderblom
- Division of Hematology and Duke Comprehensive Sickle Cell Center, Department of Medicine, Duke University Medical Center, Durham, NC, USA.
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Thompson JW, Robeson A, Andersen JL. Identification of deacetylase substrates with the biotin switch approach. Methods Mol Biol 2013; 1077:133-148. [PMID: 24014404 DOI: 10.1007/978-1-62703-637-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The identification of lysine-acetylated proteins and deacetylase substrates has primarily relied on protein immune-affinity techniques with antibodies that recognize acetylated lysine residues (Kac antibodies). While these antibody-based techniques are continuously improving, they can be limited by the narrow and many times unknown epitope specificity of Kac antibodies. An alternative approach is the biotin switch capture of deacetylated proteins. Similar in part to other biotin switch methodologies, this technique relies on the blocking of native lysine residues and removal of the modification of interest in vitro, after which the newly deacetylated proteins can be captured and identified by mass spectrometry (MS). In this chapter, we cover the essential steps of the procedure, highlight key points in the assay to reduce false positive protein identification, and discuss the quantitative MS methods useful for identifying the captured deacetylase substrates. We also discuss potential strategies and future improvements to overcome current limitations of the assay.
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Affiliation(s)
- J Will Thompson
- Duke Proteomics Core Facility, Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, NC, USA
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Solid-phase capture for the detection and relative quantification of S-nitrosoproteins by mass spectrometry. Methods 2012; 62:130-7. [PMID: 23064468 DOI: 10.1016/j.ymeth.2012.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 04/04/2012] [Accepted: 10/02/2012] [Indexed: 01/18/2023] Open
Abstract
The proteomic analysis of S-nitrosylated protein (SNO-proteins) has long depended on the biotin switch technique (BST), which requires blocking of free thiols, ascorbate-based denitrosylation of SNO-Cys, biotinylation of nascent thiol and avidin-based affinity isolation. A more recent development is resin assisted-capture of SNO-proteins (SNO-RAC), which substitutes thiopropyl Sepharose (TPS) for biotin-avidin, thus reducing the number of steps required for enrichment of S-nitrosylated proteins. In addition, SNO-RAC facilitates on-resin proteolytic digestion following SNO-protein capture, greatly simplifying the purification of peptides containing sites of S-nitrosylation ("SNO-sites"). This resin-based approach has also now been applied to detection of alternative Cys-based modifications, including S-palmitoylation (Acyl-RAC) and S-oxidation (Ox-RAC). Here, we review the important steps to minimize false-positive identification of SNO-proteins, give detailed methods for processing of protein-bound TPS for mass spectrometry (MS) based analysis, and discuss the various quantitative MS methods that are compatible with SNO-RAC. We also discuss strategies to overcome the current limitations surrounding MS-based SNO-site localization in peptides containing more than one potential target Cys residue. This article therefore serves as a starting point and guide for the MS-focused exploration of SNO-proteomes by SNO-RAC.
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Catterall JB, Hsueh MF, Stabler TV, McCudden CR, Bolognesi M, Zura R, Jordan JM, Renner JB, Feng S, Kraus VB. Protein modification by deamidation indicates variations in joint extracellular matrix turnover. J Biol Chem 2012; 287:4640-51. [PMID: 22179616 PMCID: PMC3281605 DOI: 10.1074/jbc.m111.249649] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 11/25/2011] [Indexed: 11/06/2022] Open
Abstract
As extracellular proteins age, they undergo and accumulate nonenzymatic post-translational modifications that cannot be repaired. We hypothesized that these could be used to systemically monitor loss of extracellular matrix due to chronic arthritic diseases such as osteoarthritis (OA). To test this, we predicted sites of deamidation in cartilage oligomeric matrix protein (COMP) and confirmed, by mass spectroscopy, the presence of deamidated (Asp(64)) and native (Asn(64)) COMP epitopes (mean 0.95% deamidated COMP (D-COMP) relative to native COMP) in cartilage. An Asp(64), D-COMP-specific ELISA was developed using a newly created monoclonal antibody 6-1A12. In a joint replacement study, serum D-COMP (p = 0.017), but not total COMP (p = 0.5), declined significantly after replacement demonstrating a joint tissue source for D-COMP. In analyses of 450 participants from the Johnston County Osteoarthritis Project controlled for age, gender, and race, D-COMP was associated with radiographic hip (p < 0.0001) but not knee (p = 0.95) OA severity. In contrast, total COMP was associated with radiographic knee (p < 0.0001) but not hip (p = 0.47) OA severity. D-COMP was higher in soluble proteins extracted from hip cartilage proximal to OA lesions compared with remote from lesions (p = 0.007) or lesional and remote OA knee (p < 0.01) cartilage. Total COMP in cartilage did not vary by joint site or proximity to the lesion. This study demonstrates the presence of D-COMP in articular cartilage and the systemic circulation, and to our knowledge, it is the first biomarker to show specificity for a particular joint site. We believe that enrichment of deamidated epitope in hip OA cartilage indicates a lesser repair response of hip OA compared with knee OA cartilage.
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MESH Headings
- Aged
- Aged, 80 and over
- Antibodies, Monoclonal, Murine-Derived/chemistry
- Arthroplasty, Replacement, Hip
- Arthroplasty, Replacement, Knee
- Asparagine/metabolism
- Aspartic Acid/metabolism
- Cartilage/metabolism
- Cartilage/pathology
- Cartilage/surgery
- Cartilage Oligomeric Matrix Protein
- Cohort Studies
- Enzyme-Linked Immunosorbent Assay
- Extracellular Matrix Proteins/metabolism
- Female
- Glycoproteins/metabolism
- Humans
- Male
- Mass Spectrometry
- Matrilin Proteins
- Middle Aged
- Osteoarthritis, Hip/metabolism
- Osteoarthritis, Hip/pathology
- Osteoarthritis, Hip/surgery
- Osteoarthritis, Knee/metabolism
- Osteoarthritis, Knee/pathology
- Osteoarthritis, Knee/surgery
- Protein Processing, Post-Translational
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Affiliation(s)
| | | | | | | | | | | | - Joanne M. Jordan
- the Thurston Arthritis Research Center and
- Departments of Medicine
- Orthopaedics, and
| | - Jordan B. Renner
- the Thurston Arthritis Research Center and
- Radiology, University of North Carolina, Chapel Hill, North Carolina 27514
| | - Sheng Feng
- Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27710 and
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Heintz D, Gallien S, Compagnon V, Berna A, Suzuki M, Yoshida S, Muranaka T, Van Dorsselaer A, Schaeffer C, Bach TJ, Schaller H. Phosphoproteome exploration reveals a reformatting of cellular processes in response to low sterol biosynthetic capacity in Arabidopsis. J Proteome Res 2012; 11:1228-39. [PMID: 22182420 DOI: 10.1021/pr201127u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Sterols are membrane-bound isoprenoid lipids that are required for cell viability and growth. In plants, it is generally assumed that 3-hydroxy-3-methylglutaryl-CoA-reductase (HMGR) is a key element of their biosynthesis, but the molecular regulation of that pathway is largely unknown. In an attempt to identify regulators of the biosynthetic flux from acyl-CoA toward phytosterols, we compared the membrane phosphoproteome of wild-type Arabidopsis thaliana and of a mutant being deficient in HMGR1. We performed a N-terminal labeling of microsomal peptides with a trimethoxyphenyl phosphonium (TMPP) derivative, followed by a quantitative assessment of phosphopeptides with a spectral counting method. TMPP derivatization of peptides resulted in an improved LC-MS/MS detection due to increased hydrophobicity in chromatography and ionization efficiency in electrospray. The phosphoproteome coverage was 40% higher with this methodology. We further found that 31 proteins were in a different phosphorylation state in the hmgr1-1 mutant as compared with the wild-type. One-third of these proteins were identified based on novel phosphopeptides. This approach revealed that phosphorylation changes in the Arabidopsis membrane proteome targets major cellular processes such as transports, calcium homeostasis, photomorphogenesis, and carbohydrate synthesis. A reformatting of these processes appears to be a response of a genetically reduced sterol biosynthesis.
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Affiliation(s)
- Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique-Unité Propre de Recherche 2357, Université de Strasbourg , 28 rue Goethe, 67083 Strasbourg, France
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36
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Stasyk T, Huber LA. Mapping in vivo signal transduction defects by phosphoproteomics. Trends Mol Med 2012; 18:43-51. [DOI: 10.1016/j.molmed.2011.11.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 11/03/2011] [Accepted: 11/03/2011] [Indexed: 01/02/2023]
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37
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Chen CJ, Chen WY, Tseng MC, Chen YR. Tunnel frit: a nonmetallic in-capillary frit for nanoflow ultra high-performance liquid chromatography-mass spectrometryapplications. Anal Chem 2011; 84:297-303. [PMID: 22097963 DOI: 10.1021/ac202549y] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In this study, an easy method to fabricate a durable in-capillary frit was developed for use in nanoflow liquid chromatography (nanoLC). A small orifice was tunneled into the sol-gel frit during the polymerization process resulting in the simple fabrication of a tunnel frit. A short packing tunnel frit column (2 cm, C(18) particles) was able to sustain over 10,000 psi continuous liquid flow for 10 days without observation of particle loss, and back pressure variation was less than 5%. The tunnel frit was successfully applied to the fabrication of nanoflow ultra high-performance liquid chromatography (nano-UHPLC) trap and analytical columns. In the analysis of tryptic peptides, the tunnel frit trap and analytical columns were demonstrated to have high separation efficiency and sensitivity. In analysis of phosphopeptides, the use of the nonmetallic tunnel frit column showed better sensitivity than the metallic frit column. This design can facilitate the preparation of nano-HPLC and nano-UHPLC columns and the packing material can easily be refilled when the column is severely contaminated or clogged.
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Affiliation(s)
- Chao-Jung Chen
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 404, Taiwan
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38
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Affiliation(s)
- Carol L Nilsson
- Department of Pharmacology & Toxicology, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas 77555-0617, United States.
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39
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Wang F, Song C, Cheng K, Jiang X, Ye M, Zou H. Perspectives of Comprehensive Phosphoproteome Analysis Using Shotgun Strategy. Anal Chem 2011; 83:8078-85. [DOI: 10.1021/ac201833j] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chunxia Song
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kai Cheng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xinning Jiang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hanfa Zou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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40
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Sarwal MM, Sigdel TK, Salomon DR. Functional proteogenomics—Embracing complexity. Semin Immunol 2011; 23:235-51. [DOI: 10.1016/j.smim.2011.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 08/05/2011] [Indexed: 01/30/2023]
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