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 r...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://www.iprox.org/page/project.html?id=IPX0001400000.展开更多
We present a theoretical study of the magnetic properties of the lanthanum copper manganate double perovskite La2CuMnO6 ceramic,using Monte Carlo simulations.We analyze and discuss the ground state phase diagrams in d...We present a theoretical study of the magnetic properties of the lanthanum copper manganate double perovskite La2CuMnO6 ceramic,using Monte Carlo simulations.We analyze and discuss the ground state phase diagrams in different planes to show the effect of every physical parameter.Based on the Monte Carlo simulations,which combine Metropolis algorithm and Ising model,we explore the thermal behavior of the total magnetization and susceptibility.We also present and discuss the influence of physical parameters such as the external magnetic field,the exchange coupling interactions between magnetic atoms,and the exchange magnetic field on the magnetization of the system.Moreover,the critical temperature of the system is about Tc=70 K,in agreement with the experimental value.Finally,the hysteresis loops of La2CuMnO6 are discussed.展开更多
We study the magnetic properties of the double perovskite ruthenate compound Sr2YRuO6 using Monte Carlo simulations(MCS).We elaborate the ground state phase diagrams for all possible and stable configurations.The magn...We study the magnetic properties of the double perovskite ruthenate compound Sr2YRuO6 using Monte Carlo simulations(MCS).We elaborate the ground state phase diagrams for all possible and stable configurations.The magnetizations and the susceptibilities as a function of temperature for the studied system are also reported.The effects of the exchange coupling interactions and the crystal field are examined and discussed.On the other hand, since the compound Sr2YRuO6 exhibits an antiferromagnetic behavior, we find its Néel temperature, TN≈ 31 K, which is in good agreement with the experimental results in the literature.To complete this study, the hysteresis loops and the coercive field as a function of the external magnetic field are also obtained for fixed values of the physical parameters.展开更多
基金supported by the National Natural Science Foundation of China(Grant No.81972492)National Science Fund for Young Scholars(Grant No.21904107)+7 种基金Zhejiang Provincial Natural Science Foundation for Distinguished Young Scholars(Grant No.LR19C050001)Hangzhou Agriculture and Society Advancement Program(Grant No.20190101A04)Westlake Startup Grantresearch funds from the National Cancer Centre Singapore and Singapore General Hospital,Singaporethe National Key R&D Program of China(Grant No.2016YFC0901704)Zhejiang Innovation Discipline Project of Laboratory Animal Genetic Engineering(Grant No.201510)the Netherlands Cancer Society(Grant No.NKI 2014-6651)The Netherlands Organization for Scientific Research(NWO)-Middelgroot(Grant No.91116017)
文摘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://www.iprox.org/page/project.html?id=IPX0001400000.
文摘We present a theoretical study of the magnetic properties of the lanthanum copper manganate double perovskite La2CuMnO6 ceramic,using Monte Carlo simulations.We analyze and discuss the ground state phase diagrams in different planes to show the effect of every physical parameter.Based on the Monte Carlo simulations,which combine Metropolis algorithm and Ising model,we explore the thermal behavior of the total magnetization and susceptibility.We also present and discuss the influence of physical parameters such as the external magnetic field,the exchange coupling interactions between magnetic atoms,and the exchange magnetic field on the magnetization of the system.Moreover,the critical temperature of the system is about Tc=70 K,in agreement with the experimental value.Finally,the hysteresis loops of La2CuMnO6 are discussed.
文摘We study the magnetic properties of the double perovskite ruthenate compound Sr2YRuO6 using Monte Carlo simulations(MCS).We elaborate the ground state phase diagrams for all possible and stable configurations.The magnetizations and the susceptibilities as a function of temperature for the studied system are also reported.The effects of the exchange coupling interactions and the crystal field are examined and discussed.On the other hand, since the compound Sr2YRuO6 exhibits an antiferromagnetic behavior, we find its Néel temperature, TN≈ 31 K, which is in good agreement with the experimental results in the literature.To complete this study, the hysteresis loops and the coercive field as a function of the external magnetic field are also obtained for fixed values of the physical parameters.
