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Lyu J, Wang Y, Mao J, Yao Y, Wang S, Zheng Y, Ye M. Pseudotargeted MS Method for the Sensitive Analysis of Protein Phosphorylation in Protein Complexes. Anal Chem 2018; 90:6214-6221. [PMID: 29660285 DOI: 10.1021/acs.analchem.8b00749] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this study, we presented an enrichment-free approach for the sensitive analysis of protein phosphorylation in minute amounts of samples, such as purified protein complexes. This method takes advantage of the high sensitivity of parallel reaction monitoring (PRM). Specifically, low confident phosphopeptides identified from the data-dependent acquisition (DDA) data set were used to build a pseudotargeted list for PRM analysis to allow the identification of additional phosphopeptides with high confidence. The development of this targeted approach is very easy as the same sample and the same LC-system were used for the discovery and the targeted analysis phases. No sample fractionation or enrichment was required for the discovery phase which allowed this method to analyze minute amount of sample. We applied this pseudotargeted MS method to quantitatively examine phosphopeptides in affinity purified endogenous Shc1 protein complexes at four temporal stages of EGF signaling and identified 82 phospho-sites. To our knowledge, this is the highest number of phospho-sites identified from the protein complexes. This pseudotargeted MS method is highly sensitive in the identification of low abundance phosphopeptides and could be a powerful tool to study phosphorylation-regulated assembly of protein complex.
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Affiliation(s)
- Jiawen Lyu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center , Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center , Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Jiawei Mao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center , Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yating Yao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center , Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Shujuan Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yong Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics , Beijing 102206 , 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 (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
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Abstract
Proteomics and lipidomics are powerful tools to the large-scale study of proteins and lipids, respectively. Several methods can be employed with particular benefits and limitations in the study of human brain. This is a review of the rationale use of current techniques with particular attention to limitations and pitfalls inherent to each one of the techniques, and more importantly, to their use in the study of post-mortem brain tissue. These aspects are cardinal to avoid false interpretations, errors and unreal expectancies. Other points are also stressed as exemplified in the analysis of human neurodegenerative diseases which are manifested by disease-, region-, and stage-specific modifications commonly in the context of aging. Information about certain altered protein clusters and proteins oxidatively damaged is summarized for Alzheimer and Parkinson diseases.
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Affiliation(s)
- Isidro Ferrer
- Pathologic Anatomy Service, Institute of Neuropathology, Bellvitge University Hospital; Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona; and Network Center of Biomedical Research on Neurodegenerative Diseases, Institute Carlos III; Hospitalet de Llobregat, Llobregat, Spain.
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Sarbu M, Vukelić Ž, Clemmer DE, Zamfir AD. Ion mobility mass spectrometry provides novel insights into the expression and structure of gangliosides in the normal adult human hippocampus. Analyst 2018; 143:5234-5246. [DOI: 10.1039/c8an01118d] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
General work-flow for ganglioside analysis by IM-MS.
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Affiliation(s)
- Mirela Sarbu
- National Institute for Research and Development in Electrochemistry and Condensed Matter
- Timisoara
- Romania
| | - Željka Vukelić
- Department of Chemistry and Biochemistry
- University of Zagreb Medical School
- Zagreb
- Croatia
| | | | - Alina D. Zamfir
- National Institute for Research and Development in Electrochemistry and Condensed Matter
- Timisoara
- Romania
- “Aurel Vlaicu” University of Arad
- Arad
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Proteome-wide characterization of signalling interactions in the hippocampal CA4/DG subfield of patients with Alzheimer's disease. Sci Rep 2015; 5:11138. [PMID: 26059363 PMCID: PMC4462342 DOI: 10.1038/srep11138] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/27/2015] [Indexed: 12/02/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common form of dementia; however, mechanisms and biomarkers remain unclear. Here, we examined hippocampal CA4 and dentate gyrus subfields, which are less studied in the context of AD pathology, in post-mortem AD and control tissue to identify possible biomarkers. We performed mass spectrometry-based proteomic analysis combined with label-free quantification for identification of differentially expressed proteins. We identified 4,328 proteins, of which 113 showed more than 2-fold higher or lower expression in AD hippocampi than in control tissues. Five proteins were identified as putative AD biomarkers (MDH2, PCLO, TRRAP, YWHAZ, and MUC19 isoform 5) and were cross-validated by immunoblotting, selected reaction monitoring, and MALDI imaging. We also used a bioinformatics approach to examine upstream signalling interactions of the 113 regulated proteins. Five upstream signalling (IGF1, BDNF, ZAP70, MYC, and cyclosporin A) factors showed novel interactions in AD hippocampi. Taken together, these results demonstrate a novel platform that may provide new strategies for the early detection of AD and thus its diagnosis.
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New methods based on capillary electrophoresis for in vitro evaluation of protein tau phosphorylation by glycogen synthase kinase 3-β. Anal Bioanal Chem 2015; 407:2821-8. [PMID: 25711986 DOI: 10.1007/s00216-015-8495-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/11/2014] [Accepted: 01/14/2015] [Indexed: 10/23/2022]
Abstract
The hyperphosphorylation of tau protein is associated with the development of the neuronal pathology of Alzheimer's disease. As most conventional methods study only particular phosphorylation sites of tau, it is necessary to develop a simple and reliable assay to determine the phosphorylation of tau at multiple sites. Capillary electrophoresis (CE)-based enzymatic assays are not yet used to monitor tau phosphorylation. The present work aims to develop CE-based assays to evaluate tau phosphorylation by the glycogen synthase kinase 3-β (GSK3β). A novel pre-capillary CE assay was first developed. An in-capillary CE-based enzymatic assay was also used since this approach is known to be time- and cost- effective. The enzymatic reaction was monitored by quantifying the product adenosine 5'- diphosphate (ADP). The influence of two classes of glycosaminoglycan (GAG), namely heparin and heparan sulfate, on the phosphorylation reaction was also assessed. Results obtained by both CE approaches were comparable and in excellent agreement with those reported in the literature using conventional radiometric and immunoblotting methods. In fact, CE results confirmed the inductory effect of the sulfated sugars heparin and heparan sulfate on tau hyperphosphorylation, probably because of the exposition of new sites phosphorylatable by GSK3β. This study shows that simple (no-labeling), rapid (less than 30 min per assay), and eco-friendly (no-radioactivity) CE-based kinase assays can give insight into the abnormal phosphorylation of tau. They can be extended to screen different modulators of tau phosphorylation to highlight their function and to develop effective drugs for neurodegenerative disease treatments.
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