The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Ruedi Aebersold - One of the best experts on this subject based on the ideXlab platform.
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REPORT A uniform proteomics MS/MS analysis platform
2016Co-Authors: Andrew Keller, Ning Zhang, Jimmy Eng, Ruedi AebersoldAbstract:The analysis of tandem mass (MS/MS) data to identify and quantify proteins is hampered by the heterogeneity of File formats at the raw spectral data, peptide identification, and protein identification levels. Different mass spectrometers output their raw spectral data in a variety of proprietary formats, and alternative methods that assign peptides to MS/MS spectra and infer protein identifications from those peptide assignments each write their results in different formats. Here we describe an MS/MS analysis platform, the Trans-Proteomic Pipeline, which makes use of open Xml File formats for storage of data at the raw spectral data, peptide, and protein levels. This platform enables uniform analysis and exchange ofMS/MS data generated from a variety of different instruments, and assigned peptides using a variety of different database search programs. We demonstrate this by applying the pipeline to data sets generated by ThermoFinnigan LCQ, ABI 4700 MALDI-TOF/TOF, andWaters Q-TOF instruments, and searched in turn using SEQUEST,Mascot, and COMET
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A uniform proteomics MS/MS analysis platform utilizing open Xml File formats.
Molecular systems biology, 2005Co-Authors: Andrew Keller, Jimmy K. Eng, Ning Zhang, Ruedi AebersoldAbstract:The analysis of tandem mass (MS/MS) data to identify and quantify proteins is hampered by the heterogeneity of File formats at the raw spectral data, peptide identification, and protein identification levels. Different mass spectrometers output their raw spectral data in a variety of proprietary formats, and alternative methods that assign peptides to MS/MS spectra and infer protein identifications from those peptide assignments each write their results in different formats. Here we describe an MS/MS analysis platform, the Trans-Proteomic Pipeline, which makes use of open Xml File formats for storage of data at the raw spectral data, peptide, and protein levels. This platform enables uniform analysis and exchange of MS/MS data generated from a variety of different instruments, and assigned peptides using a variety of different database search programs. We demonstrate this by applying the pipeline to data sets generated by ThermoFinnigan LCQ, ABI 4700 MALDI-TOF/TOF, and Waters Q-TOF instruments, and searched in turn using SEQUEST, Mascot, and COMET.
Andrew Keller - One of the best experts on this subject based on the ideXlab platform.
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REPORT A uniform proteomics MS/MS analysis platform
2016Co-Authors: Andrew Keller, Ning Zhang, Jimmy Eng, Ruedi AebersoldAbstract:The analysis of tandem mass (MS/MS) data to identify and quantify proteins is hampered by the heterogeneity of File formats at the raw spectral data, peptide identification, and protein identification levels. Different mass spectrometers output their raw spectral data in a variety of proprietary formats, and alternative methods that assign peptides to MS/MS spectra and infer protein identifications from those peptide assignments each write their results in different formats. Here we describe an MS/MS analysis platform, the Trans-Proteomic Pipeline, which makes use of open Xml File formats for storage of data at the raw spectral data, peptide, and protein levels. This platform enables uniform analysis and exchange ofMS/MS data generated from a variety of different instruments, and assigned peptides using a variety of different database search programs. We demonstrate this by applying the pipeline to data sets generated by ThermoFinnigan LCQ, ABI 4700 MALDI-TOF/TOF, andWaters Q-TOF instruments, and searched in turn using SEQUEST,Mascot, and COMET
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A uniform proteomics MS/MS analysis platform utilizing open Xml File formats.
Molecular systems biology, 2005Co-Authors: Andrew Keller, Jimmy K. Eng, Ning Zhang, Ruedi AebersoldAbstract:The analysis of tandem mass (MS/MS) data to identify and quantify proteins is hampered by the heterogeneity of File formats at the raw spectral data, peptide identification, and protein identification levels. Different mass spectrometers output their raw spectral data in a variety of proprietary formats, and alternative methods that assign peptides to MS/MS spectra and infer protein identifications from those peptide assignments each write their results in different formats. Here we describe an MS/MS analysis platform, the Trans-Proteomic Pipeline, which makes use of open Xml File formats for storage of data at the raw spectral data, peptide, and protein levels. This platform enables uniform analysis and exchange of MS/MS data generated from a variety of different instruments, and assigned peptides using a variety of different database search programs. We demonstrate this by applying the pipeline to data sets generated by ThermoFinnigan LCQ, ABI 4700 MALDI-TOF/TOF, and Waters Q-TOF instruments, and searched in turn using SEQUEST, Mascot, and COMET.
Ning Zhang - One of the best experts on this subject based on the ideXlab platform.
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REPORT A uniform proteomics MS/MS analysis platform
2016Co-Authors: Andrew Keller, Ning Zhang, Jimmy Eng, Ruedi AebersoldAbstract:The analysis of tandem mass (MS/MS) data to identify and quantify proteins is hampered by the heterogeneity of File formats at the raw spectral data, peptide identification, and protein identification levels. Different mass spectrometers output their raw spectral data in a variety of proprietary formats, and alternative methods that assign peptides to MS/MS spectra and infer protein identifications from those peptide assignments each write their results in different formats. Here we describe an MS/MS analysis platform, the Trans-Proteomic Pipeline, which makes use of open Xml File formats for storage of data at the raw spectral data, peptide, and protein levels. This platform enables uniform analysis and exchange ofMS/MS data generated from a variety of different instruments, and assigned peptides using a variety of different database search programs. We demonstrate this by applying the pipeline to data sets generated by ThermoFinnigan LCQ, ABI 4700 MALDI-TOF/TOF, andWaters Q-TOF instruments, and searched in turn using SEQUEST,Mascot, and COMET
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A uniform proteomics MS/MS analysis platform utilizing open Xml File formats.
Molecular systems biology, 2005Co-Authors: Andrew Keller, Jimmy K. Eng, Ning Zhang, Ruedi AebersoldAbstract:The analysis of tandem mass (MS/MS) data to identify and quantify proteins is hampered by the heterogeneity of File formats at the raw spectral data, peptide identification, and protein identification levels. Different mass spectrometers output their raw spectral data in a variety of proprietary formats, and alternative methods that assign peptides to MS/MS spectra and infer protein identifications from those peptide assignments each write their results in different formats. Here we describe an MS/MS analysis platform, the Trans-Proteomic Pipeline, which makes use of open Xml File formats for storage of data at the raw spectral data, peptide, and protein levels. This platform enables uniform analysis and exchange of MS/MS data generated from a variety of different instruments, and assigned peptides using a variety of different database search programs. We demonstrate this by applying the pipeline to data sets generated by ThermoFinnigan LCQ, ABI 4700 MALDI-TOF/TOF, and Waters Q-TOF instruments, and searched in turn using SEQUEST, Mascot, and COMET.
Jimmy K. Eng - One of the best experts on this subject based on the ideXlab platform.
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A uniform proteomics MS/MS analysis platform utilizing open Xml File formats.
Molecular systems biology, 2005Co-Authors: Andrew Keller, Jimmy K. Eng, Ning Zhang, Ruedi AebersoldAbstract:The analysis of tandem mass (MS/MS) data to identify and quantify proteins is hampered by the heterogeneity of File formats at the raw spectral data, peptide identification, and protein identification levels. Different mass spectrometers output their raw spectral data in a variety of proprietary formats, and alternative methods that assign peptides to MS/MS spectra and infer protein identifications from those peptide assignments each write their results in different formats. Here we describe an MS/MS analysis platform, the Trans-Proteomic Pipeline, which makes use of open Xml File formats for storage of data at the raw spectral data, peptide, and protein levels. This platform enables uniform analysis and exchange of MS/MS data generated from a variety of different instruments, and assigned peptides using a variety of different database search programs. We demonstrate this by applying the pipeline to data sets generated by ThermoFinnigan LCQ, ABI 4700 MALDI-TOF/TOF, and Waters Q-TOF instruments, and searched in turn using SEQUEST, Mascot, and COMET.
Markus Stoeckli - One of the best experts on this subject based on the ideXlab platform.
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imzml a common data format for the flexible exchange and processing of mass spectrometry imaging data
Journal of Proteomics, 2012Co-Authors: Thorsten Schramm, Alfons Hester, Ivo Klinkert, Jeanpierre Both, Ron M A Heeren, Alain Brunelle, Olivier Laprevote, Nicolas Desbenoit, Mariefrance Robbe, Markus StoeckliAbstract:The application of mass spectrometry imaging (MS imaging) is rapidly growing with a constantly increasing number of different instrumental systems and software tools. The data format imzML was developed to allow the flexible and efficient exchange of MS imaging data between different instruments and data analysis software. imzML data is divided in two Files which are linked by a universally unique identifier (UUID). Experimental details are stored in an Xml File which is based on the HUPO-PSI format mzML. Information is provided in the form of a 'controlled vocabulary' (CV) in order to unequivocally describe the parameters and to avoid redundancy in nomenclature. Mass spectral data are stored in a binary File in order to allow efficient storage. imzML is supported by a growing number of software tools. Users will be no longer limited to proprietary software, but are able to use the processing software best suited for a specific question or application. MS imaging data from different instruments can be converted to imzML and displayed with identical parameters in one software package for easier comparison. All technical details necessary to implement imzML and additional background information is available at www.imzml.org.
