The Experts below are selected from a list of 27177 Experts worldwide ranked by ideXlab platform

Fernando Vargas - One of the best experts on this subject based on the ideXlab platform.

  • protocol for community created public ms ms reference spectra within the global natural products social molecular Networking Infrastructure
    Rapid Communications in Mass Spectrometry, 2020
    Co-Authors: Fernando Vargas, Kelly C Weldon, Nicole Sikora, Mingxun Wang, Zheng Zhang, Emily C Gentry, Morgan W Panitchpakdi, Andres Mauricio Caraballorodriguez
    Abstract:

    Rationale A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of tandem mass spectrometry (MS/MS) reference spectra in public databases. Currently, scientists purchase databases or use public databases such as Global Natural Products Social Molecular Networking (GNPS). The MSMS-Chooser workflow is an open-source protocol for the creation of MS/MS reference spectra directly in the GNPS Infrastructure. Methods An MSMS-Chooser Sample Template is provided and completed manually. The MSMS-Chooser Submission File and Sequence Table for data acquisition were programmatically generated. Standards from the Mass Spectrometry Metabolite Library (MSMLS) suspended in a methanol-water (1:1) solution were analyzed. Flow injection on an LC/MS/MS system was used to generate negative and positive mode data using data-dependent acquisition. The MS/MS spectra and Submission File were uploaded to MSMS-Chooser workflow in GNPS for automatic selection of MS/MS spectra. Results Data acquisition and processing required ~2 h and ~2 min, respectively, per 96-well plate using MSMS-Chooser. Analysis of the MSMLS, over 600 small molecules, using MSMS-Chooser added 889 spectra (including multiple adducts) to the public library in GNPS. Manual validation of one plate indicated accurate selection of MS/MS scans (true positive rate of 0.96 and a true negative rate of 0.99). The MSMS-Chooser output includes a table formatted for inclusion in the GNPS library as well as the ability to directly launch searches via MASST. Conclusions MSMS-Chooser enables rapid data acquisition, data analysis (selection of MS/MS spectra), and a formatted table for inspection and upload to GNPS. Open file-format data (.mzML or.mzXML) from most mass spectrometry platforms containing MS/MS spectra can be processed using MSMS-Chooser. MSMS-Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information.

  • protocol for community created public ms ms reference spectra within the global natural products social molecular Networking Infrastructure
    Rapid Communications in Mass Spectrometry, 2020
    Co-Authors: Fernando Vargas, Kelly C Weldon, Nicole Sikora, Mingxun Wang, Zheng Zhang, Emily C Gentry, Morgan W Panitchpakdi, Andres Mauricio Caraballorodriguez
    Abstract:

    RATIONALE: A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of tandem mass spectrometry (MS/MS) reference spectra in public databases. Currently, scientists purchase databases or use public databases such as Global Natural Products Social Molecular Networking (GNPS). The MSMS-Chooser workflow is an open-source protocol for the creation of MS/MS reference spectra directly in the GNPS Infrastructure. METHODS: An MSMS-Chooser Sample Template is provided and completed manually. The MSMS-Chooser Submission File and Sequence Table for data acquisition were programmatically generated. Standards from the Mass Spectrometry Metabolite Library (MSMLS) suspended in a methanol-water (1:1) solution were analyzed. Flow injection on an LC/MS/MS system was used to generate negative and positive mode data using data-dependent acquisition. The MS/MS spectra and Submission File were uploaded to MSMS-Chooser workflow in GNPS for automatic selection of MS/MS spectra. RESULTS: Data acquisition and processing required ~2 hours and ~2 min, respectively, per 96-well plate using MSMS-Chooser. Analysis of the MSMLS, over 600 small molecules, using MSMS-Chooser added 889 spectra (including multiple adducts) to the public library in GNPS. Manual validation of one plate indicated accurate selection of MS/MS scans (true positive rate of 0.96 and a true negative rate of 0.99). The MSMS-Chooser output includes a table formatted for inclusion in the GNPS library as well as the ability to directly launch searches via MASST. CONCLUSIONS: MSMS-Chooser enables rapid data acquisition, data analysis (selection of MS/MS spectra), and a formatted table for inspection and upload to GNPS. Open file-format data (.mzML or.mzXML) from most mass spectrometry platforms containing MS/MS can be processed using MSMS-Chooser. MSMS-Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information.

Andres Mauricio Caraballorodriguez - One of the best experts on this subject based on the ideXlab platform.

  • protocol for community created public ms ms reference spectra within the global natural products social molecular Networking Infrastructure
    Rapid Communications in Mass Spectrometry, 2020
    Co-Authors: Fernando Vargas, Kelly C Weldon, Nicole Sikora, Mingxun Wang, Zheng Zhang, Emily C Gentry, Morgan W Panitchpakdi, Andres Mauricio Caraballorodriguez
    Abstract:

    Rationale A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of tandem mass spectrometry (MS/MS) reference spectra in public databases. Currently, scientists purchase databases or use public databases such as Global Natural Products Social Molecular Networking (GNPS). The MSMS-Chooser workflow is an open-source protocol for the creation of MS/MS reference spectra directly in the GNPS Infrastructure. Methods An MSMS-Chooser Sample Template is provided and completed manually. The MSMS-Chooser Submission File and Sequence Table for data acquisition were programmatically generated. Standards from the Mass Spectrometry Metabolite Library (MSMLS) suspended in a methanol-water (1:1) solution were analyzed. Flow injection on an LC/MS/MS system was used to generate negative and positive mode data using data-dependent acquisition. The MS/MS spectra and Submission File were uploaded to MSMS-Chooser workflow in GNPS for automatic selection of MS/MS spectra. Results Data acquisition and processing required ~2 h and ~2 min, respectively, per 96-well plate using MSMS-Chooser. Analysis of the MSMLS, over 600 small molecules, using MSMS-Chooser added 889 spectra (including multiple adducts) to the public library in GNPS. Manual validation of one plate indicated accurate selection of MS/MS scans (true positive rate of 0.96 and a true negative rate of 0.99). The MSMS-Chooser output includes a table formatted for inclusion in the GNPS library as well as the ability to directly launch searches via MASST. Conclusions MSMS-Chooser enables rapid data acquisition, data analysis (selection of MS/MS spectra), and a formatted table for inspection and upload to GNPS. Open file-format data (.mzML or.mzXML) from most mass spectrometry platforms containing MS/MS spectra can be processed using MSMS-Chooser. MSMS-Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information.

  • protocol for community created public ms ms reference spectra within the global natural products social molecular Networking Infrastructure
    Rapid Communications in Mass Spectrometry, 2020
    Co-Authors: Fernando Vargas, Kelly C Weldon, Nicole Sikora, Mingxun Wang, Zheng Zhang, Emily C Gentry, Morgan W Panitchpakdi, Andres Mauricio Caraballorodriguez
    Abstract:

    RATIONALE: A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of tandem mass spectrometry (MS/MS) reference spectra in public databases. Currently, scientists purchase databases or use public databases such as Global Natural Products Social Molecular Networking (GNPS). The MSMS-Chooser workflow is an open-source protocol for the creation of MS/MS reference spectra directly in the GNPS Infrastructure. METHODS: An MSMS-Chooser Sample Template is provided and completed manually. The MSMS-Chooser Submission File and Sequence Table for data acquisition were programmatically generated. Standards from the Mass Spectrometry Metabolite Library (MSMLS) suspended in a methanol-water (1:1) solution were analyzed. Flow injection on an LC/MS/MS system was used to generate negative and positive mode data using data-dependent acquisition. The MS/MS spectra and Submission File were uploaded to MSMS-Chooser workflow in GNPS for automatic selection of MS/MS spectra. RESULTS: Data acquisition and processing required ~2 hours and ~2 min, respectively, per 96-well plate using MSMS-Chooser. Analysis of the MSMLS, over 600 small molecules, using MSMS-Chooser added 889 spectra (including multiple adducts) to the public library in GNPS. Manual validation of one plate indicated accurate selection of MS/MS scans (true positive rate of 0.96 and a true negative rate of 0.99). The MSMS-Chooser output includes a table formatted for inclusion in the GNPS library as well as the ability to directly launch searches via MASST. CONCLUSIONS: MSMS-Chooser enables rapid data acquisition, data analysis (selection of MS/MS spectra), and a formatted table for inspection and upload to GNPS. Open file-format data (.mzML or.mzXML) from most mass spectrometry platforms containing MS/MS can be processed using MSMS-Chooser. MSMS-Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information.

Kelly C Weldon - One of the best experts on this subject based on the ideXlab platform.

  • protocol for community created public ms ms reference spectra within the global natural products social molecular Networking Infrastructure
    Rapid Communications in Mass Spectrometry, 2020
    Co-Authors: Fernando Vargas, Kelly C Weldon, Nicole Sikora, Mingxun Wang, Zheng Zhang, Emily C Gentry, Morgan W Panitchpakdi, Andres Mauricio Caraballorodriguez
    Abstract:

    Rationale A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of tandem mass spectrometry (MS/MS) reference spectra in public databases. Currently, scientists purchase databases or use public databases such as Global Natural Products Social Molecular Networking (GNPS). The MSMS-Chooser workflow is an open-source protocol for the creation of MS/MS reference spectra directly in the GNPS Infrastructure. Methods An MSMS-Chooser Sample Template is provided and completed manually. The MSMS-Chooser Submission File and Sequence Table for data acquisition were programmatically generated. Standards from the Mass Spectrometry Metabolite Library (MSMLS) suspended in a methanol-water (1:1) solution were analyzed. Flow injection on an LC/MS/MS system was used to generate negative and positive mode data using data-dependent acquisition. The MS/MS spectra and Submission File were uploaded to MSMS-Chooser workflow in GNPS for automatic selection of MS/MS spectra. Results Data acquisition and processing required ~2 h and ~2 min, respectively, per 96-well plate using MSMS-Chooser. Analysis of the MSMLS, over 600 small molecules, using MSMS-Chooser added 889 spectra (including multiple adducts) to the public library in GNPS. Manual validation of one plate indicated accurate selection of MS/MS scans (true positive rate of 0.96 and a true negative rate of 0.99). The MSMS-Chooser output includes a table formatted for inclusion in the GNPS library as well as the ability to directly launch searches via MASST. Conclusions MSMS-Chooser enables rapid data acquisition, data analysis (selection of MS/MS spectra), and a formatted table for inspection and upload to GNPS. Open file-format data (.mzML or.mzXML) from most mass spectrometry platforms containing MS/MS spectra can be processed using MSMS-Chooser. MSMS-Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information.

  • protocol for community created public ms ms reference spectra within the global natural products social molecular Networking Infrastructure
    Rapid Communications in Mass Spectrometry, 2020
    Co-Authors: Fernando Vargas, Kelly C Weldon, Nicole Sikora, Mingxun Wang, Zheng Zhang, Emily C Gentry, Morgan W Panitchpakdi, Andres Mauricio Caraballorodriguez
    Abstract:

    RATIONALE: A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of tandem mass spectrometry (MS/MS) reference spectra in public databases. Currently, scientists purchase databases or use public databases such as Global Natural Products Social Molecular Networking (GNPS). The MSMS-Chooser workflow is an open-source protocol for the creation of MS/MS reference spectra directly in the GNPS Infrastructure. METHODS: An MSMS-Chooser Sample Template is provided and completed manually. The MSMS-Chooser Submission File and Sequence Table for data acquisition were programmatically generated. Standards from the Mass Spectrometry Metabolite Library (MSMLS) suspended in a methanol-water (1:1) solution were analyzed. Flow injection on an LC/MS/MS system was used to generate negative and positive mode data using data-dependent acquisition. The MS/MS spectra and Submission File were uploaded to MSMS-Chooser workflow in GNPS for automatic selection of MS/MS spectra. RESULTS: Data acquisition and processing required ~2 hours and ~2 min, respectively, per 96-well plate using MSMS-Chooser. Analysis of the MSMLS, over 600 small molecules, using MSMS-Chooser added 889 spectra (including multiple adducts) to the public library in GNPS. Manual validation of one plate indicated accurate selection of MS/MS scans (true positive rate of 0.96 and a true negative rate of 0.99). The MSMS-Chooser output includes a table formatted for inclusion in the GNPS library as well as the ability to directly launch searches via MASST. CONCLUSIONS: MSMS-Chooser enables rapid data acquisition, data analysis (selection of MS/MS spectra), and a formatted table for inspection and upload to GNPS. Open file-format data (.mzML or.mzXML) from most mass spectrometry platforms containing MS/MS can be processed using MSMS-Chooser. MSMS-Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information.

Shinji Sakamoto - One of the best experts on this subject based on the ideXlab platform.

  • a hybrid simulation system based on particle swarm optimization and distributed genetic algorithm for wmns performance evaluation considering normal and uniform distribution of mesh clients
    Network-Based Information Systems, 2018
    Co-Authors: Admir Barolli, Leonard Barolli, Shinji Sakamoto, Makoto Takizawa
    Abstract:

    The Wireless Mesh Networks (WMNs) are becoming an important Networking Infrastructure because they have many advantages such as low cost and increased high speed wireless Internet connectivity. In our previous work, we implemented a Particle Swarm Optimization (PSO) based simulation system, called WMN-PSO, and a simulation system based on Genetic Algorithm (GA), called WMN-GA, for solving node placement problem in WMNs. In this paper, we implement a hybrid simulation system based on PSO and distributed GA (DGA), called WMN-PSODGA. We analyze the performance of WMNs using WMN-PSODGA simulation system considering Normal and Uniform client distributions. Simulation results show that the WMN-PSODGA has good performance for Normal distribution compared with the case of Uniform distribution.

  • performance analysis of simulation system based on particle swarm optimization and distributed genetic algorithm for wmns considering different distributions of mesh clients
    Innovative Mobile and Internet Services in Ubiquitous Computing, 2018
    Co-Authors: Admir Barolli, Leonard Barolli, Shinji Sakamoto, Makoto Takizawa
    Abstract:

    The Wireless Mesh Networks (WMNs) are becoming an important Networking Infrastructure because they have many advantages such as low cost and increased high speed wireless Internet connectivity. In our previous work, we implemented a Particle Swarm Optimization (PSO) based simulation system, called WMN-PSO, and a simulation system based on Genetic Algorithm (GA), called WMN-GA, for solving node placement problem in WMNs. In this paper, we implement a hybrid simulation system based on PSO and distributed GA (DGA), called WMN-PSODGA. We analyze the performance of WMN-PSODGA by computer simulations considering different client distributions. Simulation results show that the WMN-PSODGA has good performance when the client distribution is Normal compared with the case of Exponential distribution.

  • design and implementation of a hybrid intelligent system based on particle swarm optimization hill climbing and distributed genetic algorithm for node placement problem in wmns a comparison study
    Advanced Information Networking and Applications, 2018
    Co-Authors: Shinji Sakamoto, Leonard Barolli, Admir Barolli, Makoto Takizawa
    Abstract:

    The Wireless Mesh Networks (WMNs) have low cost and high speed wireless Internet connectivity, therefore they are becoming an important Networking Infrastructure. In our previous work, we implemented a hybrid intelligent system based on Particle Swarm Optimization (PSO) and Hill Climbing (HC), called WMN-PSOHC, and a simulation system based on Genetic Algorithm (GA), called WMN-GA, for solving node placement problem in WMNs. In this paper, we implement a new hybrid simulation system based on PSOHC and distributed GA (DGA), called WMN-PSOHC-DGA. We evaluate WMN-PSOHC-DGA system by computer simulations. The simulation results show that the WMN-PSOHC-DGA system has a better performance compared with WMN-PSODGA.

  • implementation of intelligent hybrid systems for node placement problem in wmns considering particle swarm optimization hill climbing and simulated annealing
    Mobile Networks and Applications, 2018
    Co-Authors: Shinji Sakamoto, Makoto Ikeda, Kosuke Ozera, Leonard Barolli
    Abstract:

    Wireless Mesh Networks (WMNs) have many advantages such as low cost and increased high speed wireless Internet connectivity, therefore WMNs are becoming an important Networking Infrastructure. In our previous work, we implemented a Particle Swarm Optimization (PSO) based simulation system, called WMN-PSO. Also, we implemented a simulation system based on Hill Climbing (HC) and Simulated Annealing (SA) for solving node placement problem in WMNs, called WMN-HC and WMN-SA, respectively. In this paper, we implement two intelligent hybrid systems: PSO and HC based system called WMN-PSOHC and PSO and SA based system called WMN-PSOSA. Then we compare WMN-PSO with implemented intelligent hybrid systems by conducting simulations. Simulation results show that intelligent hybrid systems have better performance than WMN-PSO. Comparing intelligent hybrid systems, the WMN-PSOHC converges faster than WMN-PSOSA.

  • performance evaluation of intelligent hybrid systems for node placement in wireless mesh networks a comparison study of wmn psohc and wmn psosa
    Innovative Mobile and Internet Services in Ubiquitous Computing, 2017
    Co-Authors: Shinji Sakamoto, Tetsuya Oda, Makoto Ikeda, Kosuke Ozera, Leonard Barolli
    Abstract:

    Wireless Mesh Networks (WMNs) have many advantages such as low cost and increased high speed wireless Internet connectivity, therefore WMNs are becoming an important Networking Infrastructure. In our previous work, we implemented a Particle Swarm Optimization (PSO) based simulation system for node placement in WMNs, called WMN-PSO. Also, we implemented two intelligent hybrid systems for solving node placement problem in WMNs: PSO and Hill Climbing (HC) based system, called WMN-PSOHC, and PSO and Simulated Annealing (SA) based system, called WMN-PSOSA. In this paper, we evaluate two hybrid simulation systems WMN-PSOHC and WMN-PSOSA. We compare WMN-PSOHC with WMN-PSOSA by conducting computer simulations.

Leonard Barolli - One of the best experts on this subject based on the ideXlab platform.

  • a hybrid simulation system based on particle swarm optimization and distributed genetic algorithm for wmns performance evaluation considering normal and uniform distribution of mesh clients
    Network-Based Information Systems, 2018
    Co-Authors: Admir Barolli, Leonard Barolli, Shinji Sakamoto, Makoto Takizawa
    Abstract:

    The Wireless Mesh Networks (WMNs) are becoming an important Networking Infrastructure because they have many advantages such as low cost and increased high speed wireless Internet connectivity. In our previous work, we implemented a Particle Swarm Optimization (PSO) based simulation system, called WMN-PSO, and a simulation system based on Genetic Algorithm (GA), called WMN-GA, for solving node placement problem in WMNs. In this paper, we implement a hybrid simulation system based on PSO and distributed GA (DGA), called WMN-PSODGA. We analyze the performance of WMNs using WMN-PSODGA simulation system considering Normal and Uniform client distributions. Simulation results show that the WMN-PSODGA has good performance for Normal distribution compared with the case of Uniform distribution.

  • performance analysis of simulation system based on particle swarm optimization and distributed genetic algorithm for wmns considering different distributions of mesh clients
    Innovative Mobile and Internet Services in Ubiquitous Computing, 2018
    Co-Authors: Admir Barolli, Leonard Barolli, Shinji Sakamoto, Makoto Takizawa
    Abstract:

    The Wireless Mesh Networks (WMNs) are becoming an important Networking Infrastructure because they have many advantages such as low cost and increased high speed wireless Internet connectivity. In our previous work, we implemented a Particle Swarm Optimization (PSO) based simulation system, called WMN-PSO, and a simulation system based on Genetic Algorithm (GA), called WMN-GA, for solving node placement problem in WMNs. In this paper, we implement a hybrid simulation system based on PSO and distributed GA (DGA), called WMN-PSODGA. We analyze the performance of WMN-PSODGA by computer simulations considering different client distributions. Simulation results show that the WMN-PSODGA has good performance when the client distribution is Normal compared with the case of Exponential distribution.

  • design and implementation of a hybrid intelligent system based on particle swarm optimization hill climbing and distributed genetic algorithm for node placement problem in wmns a comparison study
    Advanced Information Networking and Applications, 2018
    Co-Authors: Shinji Sakamoto, Leonard Barolli, Admir Barolli, Makoto Takizawa
    Abstract:

    The Wireless Mesh Networks (WMNs) have low cost and high speed wireless Internet connectivity, therefore they are becoming an important Networking Infrastructure. In our previous work, we implemented a hybrid intelligent system based on Particle Swarm Optimization (PSO) and Hill Climbing (HC), called WMN-PSOHC, and a simulation system based on Genetic Algorithm (GA), called WMN-GA, for solving node placement problem in WMNs. In this paper, we implement a new hybrid simulation system based on PSOHC and distributed GA (DGA), called WMN-PSOHC-DGA. We evaluate WMN-PSOHC-DGA system by computer simulations. The simulation results show that the WMN-PSOHC-DGA system has a better performance compared with WMN-PSODGA.

  • implementation of intelligent hybrid systems for node placement problem in wmns considering particle swarm optimization hill climbing and simulated annealing
    Mobile Networks and Applications, 2018
    Co-Authors: Shinji Sakamoto, Makoto Ikeda, Kosuke Ozera, Leonard Barolli
    Abstract:

    Wireless Mesh Networks (WMNs) have many advantages such as low cost and increased high speed wireless Internet connectivity, therefore WMNs are becoming an important Networking Infrastructure. In our previous work, we implemented a Particle Swarm Optimization (PSO) based simulation system, called WMN-PSO. Also, we implemented a simulation system based on Hill Climbing (HC) and Simulated Annealing (SA) for solving node placement problem in WMNs, called WMN-HC and WMN-SA, respectively. In this paper, we implement two intelligent hybrid systems: PSO and HC based system called WMN-PSOHC and PSO and SA based system called WMN-PSOSA. Then we compare WMN-PSO with implemented intelligent hybrid systems by conducting simulations. Simulation results show that intelligent hybrid systems have better performance than WMN-PSO. Comparing intelligent hybrid systems, the WMN-PSOHC converges faster than WMN-PSOSA.

  • performance evaluation of intelligent hybrid systems for node placement in wireless mesh networks a comparison study of wmn psohc and wmn psosa
    Innovative Mobile and Internet Services in Ubiquitous Computing, 2017
    Co-Authors: Shinji Sakamoto, Tetsuya Oda, Makoto Ikeda, Kosuke Ozera, Leonard Barolli
    Abstract:

    Wireless Mesh Networks (WMNs) have many advantages such as low cost and increased high speed wireless Internet connectivity, therefore WMNs are becoming an important Networking Infrastructure. In our previous work, we implemented a Particle Swarm Optimization (PSO) based simulation system for node placement in WMNs, called WMN-PSO. Also, we implemented two intelligent hybrid systems for solving node placement problem in WMNs: PSO and Hill Climbing (HC) based system, called WMN-PSOHC, and PSO and Simulated Annealing (SA) based system, called WMN-PSOSA. In this paper, we evaluate two hybrid simulation systems WMN-PSOHC and WMN-PSOSA. We compare WMN-PSOHC with WMN-PSOSA by conducting computer simulations.