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Article ; Online: BoxCar data-dependent acquisition improves the MS/MS coverage in liquid chromatography-mass spectrometry-based metabolomics analysis

Yang Wang / Shuying Liu

Arabian Journal of Chemistry, Vol 16, Iss 12, Pp 105325- (2023)

2023

Abstract: Tandem mass spectrometry (MS2) information is always applied for compound identification or annotation in liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics study. Due to the complex chemical composition of the biological ... ...

Abstract	Tandem mass spectrometry (MS2) information is always applied for compound identification or annotation in liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics study. Due to the complex chemical composition of the biological sample, acquiring MS2 spectra that cover all components is still challenging. Data-dependent acquisition (DDA) is commonly applied to obtain the MS2 data, but intensity-based trigger criteria restrict low abundance ions for fragmentation. BoxCar DDA was introduced on an LC- quadrupole time of flight (Q-TOF) MS in this study to improve the MS2 coverage of conventional DDA. BoxCar DDA with sub-mass ranges of 50, 25, and 10 was applied to perform sample analysis, respectively. The performance of multi-parallel collision-induced dissociation MS (MSe), DDA, and BoxCar DDA was compared. The results showed BoxCar DDA significantly increased the MS2 coverage and improved the signal quality. The MS2 coverage increased with the reduction of the sub-mass range. BoxCar (10) DDA exhibited the highest coverage of MS2 information. The signal quality acquired from DDA is better than that obtained under MSe, and the BoxCar (10) also showed superior for ions with low intensity. The plant material of gross saponin of Tribulus Terrestris L. fruit (GSTTF) was detected using the established BoxCar DDA, and the informative MS2 data was used to perform compound identification. The newly developed BoxCar DDA method could provide comprehensive MS2 data of analyte, which will not only be helpful to increase the confidence of compound identification in untargeted metabolomics but also facilitate ion pair detection in pseudotargeted analysis.
Keywords	Mass spectrometry ; Data dependent acquisition ; BoxCar DDA ; Metabolomics ; MS2 coverage ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Remote Sensing Classification based on Improved Ant Colony Rules Mining Algorithm

Shuying Liu

Journal of Multimedia, Vol 9, Iss 9, Pp 1105-

2014 Volume 1112

Abstract: Data mining can uncover previously undetected relationships among data items using automated data analysis techniques. In data mining, association rule mining is a prevalent and well researched method for discovering useful relations between variables in ...

Abstract	Data mining can uncover previously undetected relationships among data items using automated data analysis techniques. In data mining, association rule mining is a prevalent and well researched method for discovering useful relations between variables in large databases. This paper investigates the principle of traditional rule mining, which will produce more non-essential candidate sets when it reads data into candidate items. Particularly when it deals with massive data, if the minimum support and minimum confidence are relatively small, combinatorial explosion of frequent item sets will occur and computing power and storage space required are likely to exceed the limits of machine. A new ant colony algorithm based on conventional Ant-Miner algorithm is proposed and is used in rules mining. Measurement formula of effectiveness of the rules is improved and pheromone concentration update strategy is also carried out. The experiment results show that execution time of proposed algorithm is lower than traditional algorithm and has better execution time and accuracy
Keywords	Ant Colony ; Association Rule ; Remote Sensing ; Electronic computers. Computer science ; QA75.5-76.95 ; Instruments and machines ; QA71-90 ; Mathematics ; QA1-939 ; Science ; Q
Subject code	006
Language	English
Publishing date	2014-09-01T00:00:00Z
Publisher	Academy Publisher
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Quantitative Analysis and Differential Evaluation of Radix Bupleuri Cultivated in Different Regions Based on HPLC-MS and GC-MS Combined with Multivariate Statistical Analysis

Zhenhuan Wang / Huanxi Zhao / Lu Tian / Mengya Zhao / Yusheng Xiao / Shuying Liu / Yang Xiu

Molecules, Vol 27, Iss 15, p

2022 Volume 4830

Abstract: The quality of Radix Bupleuri is greatly affected by its growing environment. In this study, Radix Bupleuri samples that were harvested from seven different regions across northwest China were examined by high-performance liquid chromatography (HPLC) and ...

Abstract	The quality of Radix Bupleuri is greatly affected by its growing environment. In this study, Radix Bupleuri samples that were harvested from seven different regions across northwest China were examined by high-performance liquid chromatography (HPLC) and gas chromatography (GC) coupled with mass spectrometry (MS) to reveal significant differences in quality contributed by the cultivation region. An HPLC-MS method was firstly established and used in the multiple reaction monitoring mode for the quantitative analysis of five saikosaponins in Radix Bupleuri so as to evaluate the difference in the absolute content of saikosaponins attributable to the cultivation region. The effect on the components of Radix Bupleuri was further investigated based on the profiles of the representative saponins and volatile compounds, which were extracted from the Radix Bupleuri samples and analyzed by HPLC-MS and GC-MS. Multivariate statistical analysis was employed to differentiate the Radix Bupleuri samples cultivated in different regions and to discover the differential compositions. The developed quantitative method was validated to be accurate, stable, sensitive, and repeatable for the determination of five saikosaponins. Further statistical tests revealed that the collected Radix Bupleuri samples were distinctly different from each other in terms of both saponins and volatile compounds, based on the provinces where they were grown. In addition, twenty-eight saponins and fifty-eight volatile compounds were identified as the differentially accumulated compositions that contributed to the discrimination of the Radix Bupleuri samples. The Radix Bupleuri samples grown in Shouyang county showed the highest content of saikosaponins. All of the results indicated that the cultivation region significantly affected the accumulation and diversity of the main chemical components of Radix Bupleuri. The findings of this research provide insights into the effect of the cultivation region on the quality of Radix Bupleuri and the differentiation ...
Keywords	Radix Bupleuri ; HPLC-MS ; GC-MS ; multivariate statistical analysis ; saikosaponins ; volatile compounds ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2022-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Isolation and functional diversification of dihydroflavonol 4-Reductase gene HvDFR from Hosta ventricosa indicate its role in driving anthocyanin accumulation

Shijie Qin / Yitong Liu / Baiqi Cui / Jianlin Cheng / Shuying Liu / Hongzhang Liu

Plant Signaling & Behavior, Vol 17, Iss

2022 Volume 1

Abstract: Anthocyanins are natural colorants are synthesized in a branch of the flavonoid pathway. Dihydroflavonol-4reductase (DFR) catalyzes dihydroflavonoids into anthocyanins biosynthesis, which is a key regulatory enzyme of anthocyanin biosynthesis in plants. ... ...

Abstract	Anthocyanins are natural colorants are synthesized in a branch of the flavonoid pathway. Dihydroflavonol-4reductase (DFR) catalyzes dihydroflavonoids into anthocyanins biosynthesis, which is a key regulatory enzyme of anthocyanin biosynthesis in plants. Hosta ventricosa is an ornamental plant with elegant flowers and rich colorful leaves. How the function of HvDFR contributes to the anthocyanins biosynthesis is still unknown. In this study, the DFR homolog was identified from H. ventricosa and sequence analysis showed that HvDFR possessed the conserved NADPH binding and catalytic domains. A phylogenetic analysis showed that HvDFR was close to the clade formed with MaDFR and HoDFR in Asparagaceae. Gene expression analysis revealed that HvDFR was constitutive expressed in all tissues and expressed highly in flower as well as was positively correlated with anthocyanin content. In addition, the subcellular location of HvDFR showed that is in the nucleus and cell membrane. Overexpression of HvDFR in transgenic tobacco lines enhanced the anthocyanins accumulation along with the key genes upregulated, such as F3H, F3ʹH, ANS, and UFGT. Our results indicated a functional activity of the HvDFR, which provide an insight into the regulation of anthocyanins content in H. ventricosa.
Keywords	anthocyanins ; dihydroflavonol 4-reduetase (dfr) ; h. ventricosa ; ectopic expression ; Plant ecology ; QK900-989 ; Biology (General) ; QH301-705.5
Subject code	580
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	Taylor & Francis Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Bioinformatic Analysis of PTTG Family and Prognosis and Immune Cell Infiltration in Gastric Cancer

Xiao Li / Yanghao Tai / Shuying Liu / Yating Gao / Kaining Zhang / Jierong Yin / Huijuan Zhang / Xia Wang / Xiaofei Li / Dongfeng Zhang

Stem Cells International, Vol

2023 Volume 2023

Abstract: Gastric cancer is the sixth highest incidence rate in the world. Although treatment has made progress, the prospect of gastric cancer patients is bleak. Difficulties and future prospects of immunotherapy in cancer treatment. Adaptive cell therapy, cancer ...

Abstract	Gastric cancer is the sixth highest incidence rate in the world. Although treatment has made progress, the prospect of gastric cancer patients is bleak. Difficulties and future prospects of immunotherapy in cancer treatment. Adaptive cell therapy, cancer vaccines, gene therapy, and monoclonal antibody therapy have all been used in gastric cancer with some initial success. PTTGs (pituitary tumor-transforming genes) have been proven to be closely related to the prognosis of many malignant tumors. However, the prognosis and immune cell infiltration of gastric adenocarcinoma (STAD) remain unclear. We retrieved multiple databases to understand the possible activity of PTTGs and their expression in gastric cancer, as well as their relationship with clinical data, overall survival rate, first progression, and survival rate after progression. PTTGs are overexpressed in STAD tumor tissues. Many clinical variables are closely related to PTTGs. In addition, PTTG was associated with overall survival independent of disease. In addition, the expression of PTTG1/2 was positively correlated with the molecular status of the immune checkpoint and negatively correlated with the infiltration of various immune cells. Data research shows that PTTG and STAD are closely related. This paved the way for future research, revealed the complex pathophysiology of gastric cancer, and introduced an effective new treatment.
Keywords	Internal medicine ; RC31-1245
Subject code	616
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Heterogeneous Transformation of Ginsenoside Rb1 with Ethanol Using Heteropolyacid-Loaded Mesoporous Silica and Identification by HPLC-MS

Mengya Zhao / Lu Tian / Yusheng Xiao / Yanyan Chang / Yujiang Zhou / Shuying Liu / Huanxi Zhao / Yang Xiu

ACS Omega, Vol 8, Iss 45, Pp 43285-

2023 Volume 43294

Keywords	Chemistry ; QD1-999
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	American Chemical Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effect of Phosphorus, Iron, Zinc, and Their Combined Deficiencies on Photosynthetic Characteristics of Rice ( Oryza sativa L.) Seedlings

Dapeng Gao / Cheng Ran / Kun Dang / Xiaolei Wang / Yunhe Zhang / Yanqiu Geng / Shuying Liu / Zhengwen Guan / Liying Guo / Xiwen Shao

Agronomy, Vol 13, Iss 1657, p

2023 Volume 1657

Abstract: Combined elemental deficiencies are more complex and insidious physiological metabolic responses than single elemental stresses. To determine the effects of phosphorus (P), iron (Fe), zinc (Zn), and their deficient combinations on photosynthetic ... ...

Abstract	Combined elemental deficiencies are more complex and insidious physiological metabolic responses than single elemental stresses. To determine the effects of phosphorus (P), iron (Fe), zinc (Zn), and their deficient combinations on photosynthetic characteristics of rice seedlings, we investigated their effects on dry weight, chlorophyll (Chl) content, rapid photosynthetic carbon assimilation CO 2 responses, and Chl fluorescence in four-week-old rice (CB9 and BJ1 cultivars) seedlings. The results showed that the dry matter, maximum carboxylation efficiency ( V c,max ), and maximum electron transfer efficiency ( J max ) of seedlings were all reduced to different degrees under the element deficiency treatments. JIP-test analysis showed that the decrease in the concentration of active PSII reaction centers (RC/ABS) under -Zn treatment was the main reason for the inhibition of performance index PI ABS . The -P treatment reduced RC/ABS and inhibited electron transfer ( ψ Eo ). Primary photochemical reactions ( φ Po ) of -P-Zn treated seedlings were also inhibited compared to the -P treatment. The -Fe and -Fe-Zn treatments inhibited photosynthesis most severely, which not only reduced RC/ABS but also severely inhibited φ Po and ψ Eo . Notably, the -P-Fe and -P-Fe-Zn treatments of the CB9 improved the RC/ABS, alleviating the limitation of Fe deficiency. These results help enhance the understanding of the complex relationship between nutrient balance and photosynthesis, especially for P, Fe, Zn, and their combined deficiency.
Keywords	phosphate iron and zinc ; rice ; photosynthetic characteristic ; Chl a fluorescence ; JIP-test ; Agriculture ; S
Subject code	290
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Functional characterization of chalcone isomerase gene HvCHI revealing its role in anthocyanin accumulation in Hosta ventricosa

Shijie, Qin / Xue, Zhao / Baiqi, Cui / Jianlin, Cheng / Shuying, Liu / Hongzhang, Liu

Revista brasileira de botânica. 2022 June, v. 45, no. 2

2022

Abstract: Anthocyanins are natural colorants are synthesized in a branch of the flavonoid pathway. chalcone isomerase gene HvCHI catalyzes the conversion of chalcones to flavanones which is a key regulatory enzyme of anthocyanin biosynthesis in plants. Hosta ... ...

Abstract	Anthocyanins are natural colorants are synthesized in a branch of the flavonoid pathway. chalcone isomerase gene HvCHI catalyzes the conversion of chalcones to flavanones which is a key regulatory enzyme of anthocyanin biosynthesis in plants. Hosta ventricosa is an ornamental plant with elegant flowers and rich colorful leaves. How the function of HvCHI contributes to the anthocyanins biosynthesis is still unknown. In this study, the CHI homolog was identified from H. ventricosa and sequence analysis showed that HvCHI possessed the conserved substrate binding and catalytic domains. A phylogenetic analysis showed HvCHI had a strong sister relationship with Dracaena cambodiana CHI. Gene expression analysis revealed that HvCHI was constitutive expressed in all tissues and expressed highly in flower as well as was positively correlated with anthocyanin content. In addition, the subcellular location of HvCHI showed that is in cytoplasm. Overexpression of HvCHI in transgenic tobacco lines enhanced the anthocyanins accumulation along with the key genes upregulated, such as NtF3H, NtF3′H, NtF3′5′H, NtDFR, NtUFGT, and NtANS. Our results indicated a functional activity of the HvCHI, which provide an insight into the regulation of anthocyanins content in H. ventricosa.
Keywords	Dracaena ; Hosta ventricosa ; anthocyanins ; biosynthesis ; chalcone isomerase ; chalcones ; cytoplasm ; flavanones ; flowers ; genes ; ornamental plants ; phylogeny ; sequence analysis ; tobacco
Language	English
Dates of publication	2022-06
Size	p. 635-643.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	2686406-X
ISSN	1806-9959 ; 0100-8404
ISSN (online)	1806-9959
ISSN	0100-8404
DOI	10.1007/s40415-022-00805-4
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Compressed Sensing Image Reconstruction Based on Convolutional Neural Network

Yuhong Liu / Shuying Liu / Cuiran Li / Danfeng Yang

International Journal of Computational Intelligence Systems, Vol 12, Iss

2019 Volume 2

Abstract: Compressed sensing theory is widely used in image and video signal processing because of its low coding complexity, resource saving, and strong anti-interference ability. Although the compression sensing theory solves the problems brought by the ... ...

Abstract	Compressed sensing theory is widely used in image and video signal processing because of its low coding complexity, resource saving, and strong anti-interference ability. Although the compression sensing theory solves the problems brought by the traditional signal processing methods to a certain extent, it also encounters some new problems: the reconstruction time is long and the algorithm complexity is high. In order to solve these problems and further improve the quality of image processing, a new convolutional neural network structure CombNet is proposed, which uses the measured value of compression sensing as the input of the convolutional neural network, and connects a complete connection layer to get the final Output. Experiments show that CombNet has lower complexity and better recovery performance. At the same sampling rate, the peak signal-to-noise ratio (PSNR) is 12.79%–52.67% higher than Tval3 PSNR, 16.31%–158.37% higher than D-AMP, 1.00%–3.79% higher than DR2-Net, and 0.06%–2.60% higher than FCMN. It still has good visual appeal when the sampling rate is very low (0.01).
Keywords	Image reconstruction ; Compressed sensing ; CNN ; Reconstruction accuracy ; PSNR ; Electronic computers. Computer science ; QA75.5-76.95
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Springer
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Chemical Differentiation and Quantitative Analysis of Different Types of Panax Genus Stem-Leaf Based on a UPLC-Q-Exactive Orbitrap/MS Combined with Multivariate Statistical Analysis Approach

Lele Li / Yang Wang / Yang Xiu / Shuying Liu

Journal of Analytical Methods in Chemistry, Vol

2018 Volume 2018

Abstract: Two quantitative methods (−ESI full scan and −ESI PRM MS) were developed to analyze ginsenosides in ginseng stem-leaf by using UPLC-Q-Exactive Orbitrap/MS. By means of −ESI PRM MS method, the contents of eighteen ginsenosides in Asian ginseng stem-leaf ( ... ...

Abstract	Two quantitative methods (−ESI full scan and −ESI PRM MS) were developed to analyze ginsenosides in ginseng stem-leaf by using UPLC-Q-Exactive Orbitrap/MS. By means of −ESI PRM MS method, the contents of eighteen ginsenosides in Asian ginseng stem-leaf (ASGSL) and American ginseng stem-leaf (AMGSL) were analyzed. The principal component analysis (PCA) model was built to discriminate Asian ginseng stem-leaf (ASGSL) from American ginseng stem-leaf (AMGSL) based on −ESI PRM MS data, and six ginsenosides (F11, Rf, R2, F1, Rb1, and Rb3) were obtained as the markers. To further explore the differences between cultivated ginseng stem-leaf and forest ginseng stem-leaf, the partial least squares-discriminant analysis (PLS-DA) model was built based on −ESI full scan data. And twenty-six markers were selected to discriminate cultivated ginseng stem-leaf (CGSL) from forest ginseng stem-leaf (FGSL). This study provides reliable and effective methods to quantify and discriminate among different types of ginseng stem-leaf in the commercial market.
Keywords	Analytical chemistry ; QD71-142
Subject code	571
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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