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stable isotope labeling of nanomaterials for biosafety evaluation and drug development

Chinese Chemical Letters 2022年第7期33卷 3303-3314页

作者： Xue-Ling Chang Lingyun Chen Boning Liu Sheng-Tao Yang Haifang Wang Aoneng Cao Chunying Chen CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety Institute of High Energy PhysicsChinese Academy of SciencesBeijing 100049China Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission School of Chemistry and EnvironmentSouthwest Minzu UniversityChengdu 610041China Institute of Nanochemistry and Nanobiology Shanghai UniversityShanghai 200444China CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology of Chinaand University of Chinese Academy of SciencesBeijing 100190China

Quantitative information,such as environmental migration,absorption,biodistribution,biotransformation,and elimination,is fundamental and essential for the nanosafety evaluations of *** to the complexity of biological and environmental systems,it is challenging to develop quantitative approaches and tools that could characterize intrinsic behaviors of nanomaterials in the *** isotopic tracers are ideal candidates to tune the physical properties of nanomaterials while preserving their chemical *** this review article,we summarized the stable isotope labeling methods of nanomaterials for evaluating their environmental and biological *** skeleton labeling protocols of carbon nanomaterials and metal/metal oxide nanoparticles were *** advantages and disadvantages of stable isotope labeling were discussed in comparison with other quantitative methods for *** quantitative information of nanomaterials in environmental and biological systems was summarized along with the biosafety *** benefits for drug development of nanomedicine were analyzed based on the targeting effects,persistent accumulation,and ***,the challenges and future perspectives of stable isotope labeling in nanoscience and nanotechnology were discussed.

关键词： stable isotope labeling Quantification Carbon nanomaterials Metal oxide nanoparticles Nanotoxicity Biomedical effects

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SILVER:A Software Tool for stable isotope labeling LC-MS data analysis in Quantitative Proteomics with Visual and Effective Function

SILVER:A Software Tool for Stable Isotope Labeling LC-MS dat...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Cheng Chang Jiyang Zhang Hanchang Sun Ping Xu Hongwei Xie Yunping Zhu State Key Laboratory of Proteomics Beijing Proteomc Research CenterBeijing Institute of Radiation Medicine Department of Automatic Control College of Mechatronies and AutomationNational University of Defense TechnologyChangshaHunan 410073China

Background:With the advance of experimental technologies,large-scale protein quantification is widely applied to sample analysis in *** stable isotope labeling methods have been developed for the comparison of different samples on the mass spectrometry(MS) *** software tools have been developed for single or multiple labeling ***,there are few software tools available that can support most of the widely used labeling techniques,and has easily accessible graph user interface (GUI) and fairish computation speed. Methods:Here,we present an effective tool for protein quantification based on the stable isotope labeling MS data,which introduces a compact Index MS raw data file(IdxRaw) to accelerate the quantitative information extraction,a least square fitting with nonlinear optimization algorithm for the universal quantitative calculation on single MS spectrum from different isotopic labeling techniques.S/N ratio and R-square of the linear fitting were calculated as filter criteria during the construction of extracted ion chromatogram(XIC).Then, linear regression normalization and Dixon’s Q-test are applied for combining the peptide ratio in reduplicate runs.A protein ratio was defined as a weighted average of unique peptide ratios. Results:In this tool,batch processing for the large scale data analysis and GUI for the manual inspection and validation are *** user can easily trace the details of protein quantification,including the extracted ion chromatogram(XIC) for each peptide,the paired isotopic peaks in the MS spectrum and several parameters for the result *** merits of SILVER were verified by applying it to datasets with different isotopic labeling. Conclusions:SILVER shows high accuracy and relative robustness on both the peptide level and the protein ***’s more,it also includes a user-friendly visualization platform, which permits users to validate the results.

关键词： Bioinformatics Quantitative Proteomics Protein quantification stable isotope labeling

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Transformation of 5-Carboxylcytosine to Cytosine Through C-C Bond Cleavage in Human Cells Constitutes a Novel Pathway for DNA Demethylation

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CCS Chemistry 2021年第4期3卷 994-1008页

作者： Yang Feng Neng-Bin Xie Wan-Bing Tao Jiang-Hui Ding Xue-Jiao You Cheng-Jie Ma Xiaoxue Zhang Chengqi Yi Xiang Zhou Bi-Feng Yuan Yu-Qi Feng Key Laboratory of Analytical Chemistry for Biology and Medicine(Ministry of Education) Sauvage Center for Molecular SciencesDepartment of ChemistryWuhan UniversityWuhan 430072 State Key Laboratory of Protein and Plant Gene Research School of Life SciencesPeking UniversityBeijing 100871 Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871 Department of Chemical Biology and Synthetic and Functional Biomolecules Center College of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871

Active demethylation of 5-methylcytosine(5mC)can be realized through ten-eleven translocation(TET)dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine(5hmC),5-formylcytosine(5fC),and 5-carboxylcytosine(5caC),followed by thymine DNA glycosylase(TDG)-initiated base excision repair(BER).The TDG-BER pathwaymay lead to the generation of DNA strand breaks,potentially compromising genome ***,direct decarboxylation of TET-produced 5caC is highly attractive because this mechanism allows for conversion of 5mC to cytosine without the formation of DNA strand ***,cleavage of the C–C bond in 5caC in human cells remains an open *** examined this reaction in cell extract and live cells using 5caC-carrying hairpin DNA *** incubation with whole-cell protein extract or transfection into human cells,we monitored the transformation of 5caC to cytosine through direct decarboxylation or BER using liquid chromatography–tandem mass spectrometry(LCMS/MS)analyses at both the mononucleotide and oligodeoxynucleotide *** results clearly showed the direct conversion of 5caC to cytosine in human cells,providing evidence to support a novel pathway for active DNA demethylation.

关键词： epigenetics DNA demethylation 5-carboxylcytosine decarboxylation mass spectrometry stable isotope labeling

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Application of quantitative PTM proteomics SILIA and AQUIP in plant hormone signaling

Application of quantitative PTM proteomics SILIA and AQUIP i...

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从植物科学到农业发展——2012全国植物生物学大会

作者： Guang Yu Guo,Yao Jun Li and Ning Li~* Division of Life Science,The Hong Kong University of Science and Technology,Clear water bay,Hong Kong SAR,China.

Hundreds of protein post-translational modifications(PTM) have been discovered over *** PTMs are known to play an important role in regulation of growth and development of an *** one of the most important PTMs,protein phosphorylation participates in regulating various cellular processes and biological *** spectrometry-based protein phosphosite identification has emerged as a high-throughput approach in discovery of phosphoproteins involved in regulation of cellular *** changes at these novel phosphosites can be accurately measured using a N-stable isotopic labeling in Arabidopsis(SILIA) quantitative proteomic *** unique characteristics of the SILIA-based quantitative phosphoproteomics approach are its versatile usages,simplicity in PTM peptide quantitation and the preservation of native PTM status on protein during peptide *** from SILIA is the absolute quantitation of isoforms of post-translationally modified proteins(AQUIP),which was developed by combining the advantages of AQUA and PSAQ with *** validation of phosphosite is performed using point-mutations at *** combined use of SILIA and AQUIP provides a novel strategy for investigation of in vivo biological functions of phosphoproteins at a large scale and ultimately for deciphering the combinatorial code and networks of PTM during plant growth and development.

关键词： SILIA AQUIP Arabidopsis quantitative proteomics stable isotope labeling post-translational modification networks.

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