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Analysis of Fatty Acid in Biological Samples Using Liquid Chromatography–Quadrupole-Orbitrap Mass Spectrometry Under parallel reaction monitoring Mode

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Journal of Analysis and Testing 2024年第2期8卷 210-217页

作者： Jingxuan Yang Wenjun Guo Xiaohang Xu Liang Zhao Yajuan Xu Yang Wang School of Pharmaceutical Sciences Changchun University of Chinese MedicineChangchun130117China Key Laboratory of Medicinal Materials Jilin Academy of Chinese Medicine SciencesChangchun130021China Jilin Ginseng Academy Changchun University of Chinese MedicineChangchun130117China

Fatty acids(FAs)are an important class of functional small molecules and participate in a variety of life biological processes.This experiment proposed a liquid chromatography–quadrupole-Qrbitrap mass spectrometry(LC–Q-Orbitrap MS)method to perform FA profiling under parallel reaction monitoring(PRM)acquisition mode.The FA was derivatized by 2-dimethylaminoethylamine(DMED)to increase the ionization e fficiency and provide the characterized fragment pattern.The mass spectra obtained from full scan,multiple ion monitoring(MIM),and PRM were compared.The results showed that the protonated ion of FA+DMED–H2O was detected and the neutral loss of 45.06 Da was observed in the tandem mass spectrum.The PRM method provided the highest selectivity and sensitivity for FA detection with the help of accurate mass weight and specific neutral loss-based fragments.The method validation was performed using the FA standards and pooled quality control serum sample,which showed that the established method had good repeatability,stability,and linearity.Finally,the developed method was successfully applied to analyze the rat serum and brain tissue samples for the drug e ffi-cacy evaluation of gross saponin of Tribulus terrestris L.fruit(GSTTF)against middle cerebral artery occlusion(MCAO)-induced ischemic stroke.This method has extensive practicability and great potential in the detection of FA,especially for the analysis of samples with complex matrices.

关键词： Fatty acid Derivatization LC-Q-Orbitrap MS parallel reaction monitoring Biological sample

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Quantitative analysis of therapeutic mAb glycoforms by hydrophilic interaction chromatography enrichment and parallel reaction monitoring

Quantitative analysis of therapeutic mAb glycoforms by hydro...

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中国化学会第30届学术年会-第二十三分会：复杂样品分离...

作者： Yuting Cong Lianghai Hu School of Life Sciences Jilin University

Monoclonal antibodies（mAbs）,are one of the most important protein drugs have attracted increasing attention.However,the pharmacokinetics of mAbs has not been fully investigated due to the complexity of protein drugs.Traditonal immuno-based approaches can not recognize the proteoforms of mAbs due to the long development cycles,prohibitive cost and interactions between different proteins.Therefore,reliable qualitative and quantitative analysis of the proteoforms of mAbs in biological samples is of crucial importance.Herein,a novel method was developed for absolute quantitation of mAbs and their glycoforms in complex biological samples such as serum and tissues.With the combination of HILIC enrichment and parallel reaction monitoring by high resolution mass spectrometry,most of the glycoforms can be accurately quantified at the fmol level through the use of the model mAb of bevacizumab.More importantly,the structural confirmation can be achieved simultaneously without the need for additional experiments.This strategy can be readily applied to the pharmacokinetic study of glycosylation modification and biomarker discovery for clinical applications.

关键词： Proteomics hydrophilic interaction chromatography therapeutic monoclonal antibody glycosylation parallel reaction monitoring

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Comprehensive Analysis of Acylcarnitine Species in db/db Mouse Using a Novel Method of High-Resolution parallel reaction monitoring Reveals Widespread Metabolic Dysfunction Induced by Diabetes

Comprehensive Analysis of Acylcarnitine Species in db/db Mou...

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2018年中国质谱学术大会（CMSC2018）

作者： Li Xiang Juntong Wei Zongwei Cai Yu Huang School of Biomedical Sciences and Institute of Vascular Medicine Chinese University of Hong Kong State Key Laboratory of Environmental and Biological Analysis Department of ChemistryHong Kong Baptist University

Acylcarnitines are exerting a variety of biological functions depending on the differences in lengths, saturation levels, and conjugation groups, which to a great extent contribute to the challenges of acylcarnitines quantifications due to various kinds of isomers. Here, we describe a novel method by using high-resolution parallel reaction monitoring(PRM) liquid chromatography-tandem mass spectrometry(LC-MS/MS). Both reversed phase and normal-phase column were used in order to get accurate, reliable, widespread quantification of acylcarnitines, and without tedious sample preparation procedure. The method provided the most comprehensive acylcarnitine profile with high-resolution MS and MS/MS confirmation to date. A total of 117 acylcarnitines were detected from plasma and urine samples. The application of targeted profiling of acylcarnitines in db/m+ control and db/db diabetic mice indicated incomplete amino acid and fatty acid oxidation on diabetic mice. Interestingly, the reduction of medium odd-numbered chain acylcarnitines in urine samples was first observed between db/m+ and db/db mice. The high-resolution PRM method makes it possible to monitor the widespread metabolic changes of the acylcarnitines in response to stimuli. Besides, the accurate MS and MS/MS spectra data of the 117 acylcarnitines could be used as mass spectrometric resources for the identification of acylcarnitines.

关键词： parallel reaction monitoring acylcarnitines db/db high resolution LC/MS

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Proteomics-based identification of proteins in tumor-derived exosomes as candidate biomarkers for colorectal cancer

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World Journal of Gastrointestinal Oncology 2023年第7期15卷 1227-1240页

作者： Ge-Yu-Jia Zhou Dong-Yan Zhao Teng-Fei Yin Qian-Qian Wang Yuan-Chen Zhou Shu-Kun Yao Department of Gastroenterology China-Japan Friendship Hospital(Institute of Clinical Medical Sciences)Beijing 100029China Graduate School Chinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100730China Graduate School Peking University China-Japan Friendship School of Clinical MedicineBeijing 100029China Department of Gastroenterology China-Japan Friendship HospitalBeijing 100029China

BACKGROUND Colorectal cancer(CRC)is the second leading cause of cancer-related death,with high morbidity worldwide.There is an urgent need to find reliable diagnostic biomarkers of CRC and explore the underlying molecular mechanisms.Exosomes are involved in intercellular communication and participate in multiple pathological processes,serving as an important part of the tumor microenvironment.AIM To investigate the proteomic characteristics of CRC tumor-derived exosomes and to identify candidate exosomal protein markers for CRC.METHODS In this study,10 patients over 50 years old who were diagnosed with moderately differentiated adenocarcinoma were recruited.We paired CRC tissues and adjacent normal intestinal tissues(>5 cm)to form the experimental and control groups.Purified exosomes were extracted separately from each tissue sample.Data-independent acquisition mass spectrometry was implemented in 8 matched samples of exosomes to explore the proteomic expression profiles,and differentially expressed proteins(DEPs)were screened by bioinformatics analysis.Promising exosomal proteins were verified using parallel reaction monitoring(PRM)analysis in 10 matched exosome samples.RESULTS A total of 1393 proteins were identified in the CRC tissue group,1304 proteins were identified in the adjacent tissue group,and 283 proteins were significantly differentially expressed between them.Enrichment analysis revealed that DEPs were involved in multiple biological processes related to cytoskeleton construction,cell movement and migration,immune response,tumor growth and telomere metabolism,as well as ECM-receptor interaction,focal adhesion and mTOR signaling pathways.Six differentially expressed exosomal proteins(NHP2,OLFM4,TOP1,SAMP,TAGL and TRIM28)were validated by PRM analysis and evaluated by receiver operating characteristic curve(ROC)analysis.The area under the ROC curve was 0.93,0.96,0.97,0.78,0.75,and 0.88(P<0.05)for NHP2,OLFM4,TOP1,SAMP,TAGL,and TRIM28,respectively,indicating their good ability to distinguish CRC tissues

关键词： Exosomes Colorectal cancer Data-independent acquisition parallel reaction monitoring Biomarker

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DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

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Genomics, Proteomics & Bioinformatics 2020年第2期18卷 104-119页

作者： Tiansheng Zhu Yi Zhu Yue Xuan Huanhuan Gao Xue Cai Sander R.Piersma Thang V.Pham Tim Schelfhorst Richard R.G.D.Haas Irene V.Bijnsdorp Rui Sun Liang Yue Guan Ruan Qiushi Zhang Mo Hu Yue Zhou Winan J.Van Houdt Tessa Y.S.Le Large Jacqueline Cloos Anna Wojtuszkiewicz Danijela Koppers-Lalic Franziska Bottger Chantal Scheepbouwer Ruud H.Brakenhoff Geert J.L.H.van Leenders Jan N.M.Ijzermans John W.M.Martens Renske D.M.Steenbergen Nicole C.Grieken Sathiyamoorthy Selvarajan Sangeeta Mantoo Sze S.Lee Serene J.Y.Yeow Syed M.F.Alkaff Nan Xiang Yaoting Sun Xiao Yi Shaozheng Dai Wei Liu Tian Lu Zhicheng Wu Xiao Liang Man Wang Yingkuan Shao Xi Zheng Kailun Xu Qin Yang Yifan Meng Cong Lu Jiang Zhu Jin'e Zheng Bo Wang Sai Lou Yibei Dai Chao Xu Chenhuan Yu Huazhong Ying Tony K.Lim Jianmin Wu Xiaofei Gao Zhongzhi Luan Xiaodong Teng Peng Wu Shi'ang Huang Zhihua Tao Narayanan G.Iyer Shuigeng Zhou Wenguang Shao Henry Lam Ding Ma Jiafu Ji Oi L.Kon Shu Zheng Ruedi Aebersold Connie R.Jimenez Tiannan Guo Zhejiang Provincial Laboratory of Life Sciences and Biomedicine Westlake UniversityHangzhou 310024China Key Laboratory of Structural Biology of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzhou 310024China School of Computer Science Shanghai Key Laboratory of Intelligent Information ProcessingFudan UniversityShanghai 200433China Thermo Fisher Scientific(BREMEN)GmbH Bremen 28195Germany OncoProteomics Laboratory Department of Medical OncologyVU University Medical CenterVU UniversityAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamUrologyCancer Center AmsterdamAmsterdam 1011The Netherlands Thermo Fisher Scientific Shanghai 201206China The Netherlands Cancer Institute Surgical OncologyAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamSurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPediatric Oncology/HematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamHematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamMedical OncologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamNeurosurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPathologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamOtolaryngology/Head and Neck SurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Erasmus MC University Medical Center PathologyRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center SurgeryRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center Medical OncologyRotterdam 1016LVThe Netherlands Department of Anatomical Pathology Singapore General HospitalSingapore 169608Singapore Division of Medical Scie

To address the increasing need for detecting and validating protein biomarkers in clinical specimens,mass spectrometry(MS)-based targeted proteomic techniques,including the selected reaction monitoring(SRM),parallel reaction monitoring(PRM),and massively parallel dataindependent acquisition(DIA),have been developed.For optimal performance,they require the fragment ion spectra of targeted peptides as prior knowledge.In this report,we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples.To build the spectral resource,we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker.We then applied the workflow to generate DPHL,a comprehensive DIA pan-human library,from 1096 data-dependent acquisition(DDA)MS raw files for 16 types of cancer samples.This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer(PCa)patients.Thereafter,PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated.As a second application,the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma(DLBCL)patients and 18 healthy control subjects.Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM.These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery.DPHL is freely accessible at https://***/page/project.html?id=IPX0001400000.

关键词： Data-independent acquisition parallel reaction monitoring Spectral library Prostate cancer Diffuse large B cell lymphoma

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