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Tumor-Specific CircRNA-Derived Antigen Peptide Identification for Hepatobiliary Tumors Article

Wenwen Wang, Lili Ma, Zheng Xing, Tinggan Yuan, Jinxia Bao, Yanjing Zhu, Xiaofang Zhao, Yan Zhao, Yali Zong, Yani Zhang, Siyun Shen, Xinyao Qiu, Shuai Yang, Hongyang Wang, Dong Gao, Peng Wang, Lei Chen

Engineering 2023, Volume 22, Issue 3,   Pages 159-170 doi: 10.1016/j.eng.2022.06.008

Abstract:

The application of tumor antigen-based immunotherapy is hindered by the rarity of validated immunogenicUsing RNA-sequencing (RNA-seq) with an algorithm-based score tool, 3950 translated tumor-specific circRNAspredicted antigen peptides were directly confirmed as HLA-A, -B, and -C (HLA-ABC) binding peptides with massspectrometry (MS)-based immunopeptidomics.

Keywords: Tumor antigen     Patient-derived hepatobiliary tumor organoid     Circular RNA     Mass-spectrometry-based immunopeptidomics    

considerations for semi-quantification of total naphthenic acids in oil sands process affected water by massspectrometry: A review

Kevin A. Kovalchik, Matthew S. MacLennan, Kerry M. Peru, John V. Headley, David D.Y. Chen

Frontiers of Chemical Science and Engineering 2017, Volume 11, Issue 3,   Pages 497-507 doi: 10.1007/s11705-017-1652-0

Abstract: informs the design of future standard methods for the semi-quantification of total naphthenic acids using massspectrometry.The design considerations are amenable to both time-of-flight and Orbitrap mass spectrometers.

Keywords: total naphthenic acids     environmental samples     oil sands process affected water     polar organics     mass spectrometry    

Peroxyacetyl nitrate measurements by thermal dissociation–chemical ionization mass spectrometry in an

Xinfeng Wang, Tao Wang, Likun Xue, Wei Nie, Zheng Xu, Steven C. N. Poon, Wenxing Wang

Frontiers of Environmental Science & Engineering 2017, Volume 11, Issue 4, doi: 10.1007/s11783-017-0925-7

Abstract: A rapid and highly selective technique of thermal dissociation–chemical ionization mass spectrometry

Keywords: TD-CIMS     Peroxyacetyl nitrate     Interference     Photochemical pollution     Formation efficiency    

Pyrolysis behaviors of oil sludge based on TG/FTIR and PY-GC/MS

Wei SONG, Jianguo LIU, Yongfeng NIE,

Frontiers of Environmental Science & Engineering 2010, Volume 4, Issue 1,   Pages 59-64 doi: 10.1007/s11783-009-0152-y

Abstract: Thermogravimetric Analysis-Fourier Transform Infrared Spectroscopy and Pyrolysis-Gas Chromatography/MassSpectrometry were employed to investigate the pyrolysis process and products of oil sludge.

Keywords: Thermogravimetric Analysis-Fourier Transform Infrared Spectroscopy (TG-FTIR)     Pyrolysis-Gas Chromatography/MassSpectrometry (PY-GC/MS)    

Metabolomics in human type 2 diabetes research

Jingyi Lu, Guoxiang Xie, Weiping Jia, Wei Jia

Frontiers of Medicine 2013, Volume 7, Issue 1,   Pages 4-13 doi: 10.1007/s11684-013-0248-4

Abstract:

The high prevalence of diabetes and diabetic complications has caused a huge burden on the modern society. Although scientific advances have led to effective strategies for preventing and treating diabetes over the past several decades, little progress has been made toward curing the disease or even getting it under control, from a public health and overall societal standpoint. There is still a lack of reliable biomarkers indicative of metabolic alterations associated with diabetes and different drug responses, highlighting the need for the development of early diagnostic and prognostic markers for diabetes and diabetic complications. The emergence of metabolomics has allowed researchers to systemically measure the small molecule metabolites, which are sensitive to the changes of both environmental and genetic factors and therefore, could be regarded as the link between genotypes and phenotypes. During the last decade, the progression made in metabolomics has provided insightful information on disease development and disease onset prediction. Recent studies using metabolomics approach coupled with statistical tools to predict incident diabetes revealed a number of metabolites that are significantly altered, including branched-chain and aromatic amino acids, such as isoleucine, leucine, valine, tyrosine and phenylalanine, as diagnostic or highly-significant predictors of future diabetes. This review summarizes the current findings of metabolomic studies in human investigations with the most common form of diabetes, type 2 diabetes.

Keywords: metabolomics     type 2 diabetes     metabolic pathway     mass spectrometry     nuclear magnetic resonance (NMR)    

five taste and odor compounds in surface water using solid-phase extraction and gas chromatography-massspectrometry

Wenfeng SUN, Ruibao JIA, Baoyu GAO

Frontiers of Environmental Science & Engineering 2012, Volume 6, Issue 1,   Pages 66-74 doi: 10.1007/s11783-010-0257-3

Abstract: In this paper, a method using solid-phase extraction (SPE) and gas chromatography-mass spectrometry (The mass spectrometry was operated in selective ion monitoring (SIM) mode.

Keywords: solid-phase extraction (SPE)     gas chromatography-mass spectrometry (GC-MS)     taste and odor compounds     surface    

several classes of antibiotics in water, sediments, and fish muscles by liquid chromatography–tandem massspectrometry

WEI Yimei,ZHANG Yuan,XU Jian,GUO Changsheng,LI Lei,FAN Wenhong

Frontiers of Environmental Science & Engineering 2014, Volume 8, Issue 3,   Pages 357-371 doi: 10.1007/s11783-013-0580-6

Abstract: Liquid chromatography–tandem mass spectrometry (LC-MS/MS) with multiple reaction monitoring (MRM) detection

Keywords: antibiotics     liquid chromatography–tandem mass spectrometry (LC-MS/MS)     water     sediment     fish muscle    

Application of proteomics in environmental science

Xiaona CHU, Jiangyong HU, Say Leong ONG,

Frontiers of Environmental Science & Engineering 2009, Volume 3, Issue 4,   Pages 393-403 doi: 10.1007/s11783-009-0145-x

Abstract: article provides a review on the development of the main proteomic technologies, including both the gel basedand non-gel based technologies, and their applications in environmental science.

Keywords: proteomics     environmental stress     two dimensional (2D) gel electrophoresis     mass spectrometry    

of persistent organic pollutants by gas chromatography/laser multiphoton ionization/time-of-flight massspectrometry

Osamu SHITAMICHI, Taiki MATSUI, Yamei HUI, Weiwei CHEN, Totaro IMASAKA

Frontiers of Environmental Science & Engineering 2012, Volume 6, Issue 1,   Pages 26-31 doi: 10.1007/s11783-011-0374-7

Abstract: capillary column, since the retention time was reduced and the amount of analytes introduced into the massAs demonstrated, a technique involving laser multiphoton ionization/time-of-flight mass spectrometry

Keywords: biphenyls (PCBs)     polycyclic aromatic hydrocarbons (PAHs)     laser multiphoton ionization/time-of-flight massspectrometry (MPI/TOF-MS)    

Detecting

Chengkun WANG, Xiaojian ZHANG, Jun WANG, Chao CHEN

Frontiers of Environmental Science & Engineering 2012, Volume 6, Issue 6,   Pages 770-777 doi: 10.1007/s11783-012-0412-0

Abstract: An ultra-performance liquid chromatography-tandem mass spectrometry method with solid phase extraction

Keywords: nitrosamines     water treatment plant     distribution system     ultra-performance liquid chromatography-tandem massspectrometry    

using liquid-liquid microextraction coupled with gas chromatography—positive chemical ionization-tandem massspectrometry

Jian LU,Paul S. WILLS,P. CHRIS WILSON

Frontiers of Environmental Science & Engineering 2016, Volume 10, Issue 3,   Pages 477-481 doi: 10.1007/s11783-015-0820-z

Abstract: off-flavor/odor compounds in fresh and salt water using gas chromatography with chemical ionization-tandem massspectrometry.

Keywords: off-flavor/odor compounds     liquid-liquid microextraction     gas chromatography-tandem mass spectrometry    

Characteristics and removal mechanism of the precursors of N-chloro-2,2-dichloroacetamide in a drinking water treatment process at Taihu Lake

Frontiers of Environmental Science & Engineering 2021, Volume 15, Issue 5, doi: 10.1007/s11783-020-1338-6

Abstract:

• N-Cl-DCAM, an emerging N-DBP in drinking water was investigated.

Keywords: N-chloro-2     2-dichloroacetamide     Liquid chromatography with tandem mass spectrometry     Precursors     Removal    

Etiology of invasive candidosis agents in Russia: a multicenter epidemiological survey

N.V. Vasilyeva, E.R. Raush, M.V. Rudneva, T.S. Bogomolova, A.E. Taraskina, Yong Fang, Fengmin Zhang, N.N. Klimko

Frontiers of Medicine 2018, Volume 12, Issue 1,   Pages 84-91 doi: 10.1007/s11684-017-0612-x

Abstract: The species were identified by DNA sequencing and MALDI-TOF mass-spectrometry.

Keywords: prevalence     &Scy     andida species     invasive candidosis     nosocomial     etiology     MALDI-TOF mass-spectrometry    

water using automated online solid-phase extraction with large-volume injection/gas chromatography/massspectrometry

Yongtao LI, Christina L. MCCARTY, Ed J. GEORGE

Frontiers of Environmental Science & Engineering 2011, Volume 5, Issue 3,   Pages 417-425 doi: 10.1007/s11783-011-0310-x

Abstract: technique coupled with programmed-temperature vaporization large-volume injection gas chromatography/massspectrometry.The water samples were extracted by using a fully automated mobile rack system based on x-y-z robotic

Keywords: solid-phase extraction     programmed-temperature vaporization     large-volume injection     gas chromatography/massspectrometry     semi-volatile organic compounds     water analysis    

Metabonomic study of the biochemical profiles of heterozygous myostatin knockout swine

Jianxiang XU,Dengke PAN,Jie ZHAO,Jianwu WANG,Xiaohong HE,Yuehui MA,Ning LI

Frontiers of Agricultural Science and Engineering 2015, Volume 2, Issue 1,   Pages 90-99 doi: 10.15302/J-FASE-2015045

Abstract: We applied chromatography and mass spectrometry based metabonomics to assess system-wide metabolic response

Keywords: myostatin     transforming growth factor-β family     skeletal muscle     metabolic disorders     chromatography     massspectrometry     metabonomics    

Title Author Date Type Operation

Tumor-Specific CircRNA-Derived Antigen Peptide Identification for Hepatobiliary Tumors

Wenwen Wang, Lili Ma, Zheng Xing, Tinggan Yuan, Jinxia Bao, Yanjing Zhu, Xiaofang Zhao, Yan Zhao, Yali Zong, Yani Zhang, Siyun Shen, Xinyao Qiu, Shuai Yang, Hongyang Wang, Dong Gao, Peng Wang, Lei Chen

Journal Article

considerations for semi-quantification of total naphthenic acids in oil sands process affected water by massspectrometry: A review

Kevin A. Kovalchik, Matthew S. MacLennan, Kerry M. Peru, John V. Headley, David D.Y. Chen

Journal Article

Peroxyacetyl nitrate measurements by thermal dissociation–chemical ionization mass spectrometry in an

Xinfeng Wang, Tao Wang, Likun Xue, Wei Nie, Zheng Xu, Steven C. N. Poon, Wenxing Wang

Journal Article

Pyrolysis behaviors of oil sludge based on TG/FTIR and PY-GC/MS

Wei SONG, Jianguo LIU, Yongfeng NIE,

Journal Article

Metabolomics in human type 2 diabetes research

Jingyi Lu, Guoxiang Xie, Weiping Jia, Wei Jia

Journal Article

five taste and odor compounds in surface water using solid-phase extraction and gas chromatography-massspectrometry

Wenfeng SUN, Ruibao JIA, Baoyu GAO

Journal Article

several classes of antibiotics in water, sediments, and fish muscles by liquid chromatography–tandem massspectrometry

WEI Yimei,ZHANG Yuan,XU Jian,GUO Changsheng,LI Lei,FAN Wenhong

Journal Article

Application of proteomics in environmental science

Xiaona CHU, Jiangyong HU, Say Leong ONG,

Journal Article

of persistent organic pollutants by gas chromatography/laser multiphoton ionization/time-of-flight massspectrometry

Osamu SHITAMICHI, Taiki MATSUI, Yamei HUI, Weiwei CHEN, Totaro IMASAKA

Journal Article

Detecting

Chengkun WANG, Xiaojian ZHANG, Jun WANG, Chao CHEN

Journal Article

using liquid-liquid microextraction coupled with gas chromatography—positive chemical ionization-tandem massspectrometry

Jian LU,Paul S. WILLS,P. CHRIS WILSON

Journal Article

Characteristics and removal mechanism of the precursors of N-chloro-2,2-dichloroacetamide in a drinking water treatment process at Taihu Lake

Journal Article

Etiology of invasive candidosis agents in Russia: a multicenter epidemiological survey

N.V. Vasilyeva, E.R. Raush, M.V. Rudneva, T.S. Bogomolova, A.E. Taraskina, Yong Fang, Fengmin Zhang, N.N. Klimko

Journal Article

water using automated online solid-phase extraction with large-volume injection/gas chromatography/massspectrometry

Yongtao LI, Christina L. MCCARTY, Ed J. GEORGE

Journal Article

Metabonomic study of the biochemical profiles of heterozygous myostatin knockout swine

Jianxiang XU,Dengke PAN,Jie ZHAO,Jianwu WANG,Xiaohong HE,Yuehui MA,Ning LI

Journal Article