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                            {
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                                "name": "Huang H."
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                        "title": "Proteome of Caulobacter crescentus cell cycle publicly accessible on SWICZ server",
                        "abstract": "Here we present the Swiss-Czech Proteomics Server (SWICZ), which hosts the proteomic database summarizing information about the cell cycle of the aquatic bacterium Caulobacter crescentus. The database provides a searchable tool for easy access of global protein synthesis and protein stability data as examined during the C. crescentus cell cycle. Protein synthesis data collected from five different cell cycle stages were determined for each protein spot as a relative value of the total amount of [35S]methionine incorporation. Protein stability of pulse-labeled extracts were measured during a chase period equivalent to one cell cycle unit. Quantitative information for individual proteins together with descriptive data such as protein identities, apparent molecular masses and isoelectric points, were combined with information on protein function, genomic context, and the cell cycle stage, and were then assembled in a relational data-base with a world wide web interface (http://proteom.biomed.cas.cz), which allows the database records to be searched and displays the recovered information. A total of 1250 protein spots were reproducibly detected on two-dimensional gel electropherograms, 295 of which were identified by mass spectroscopy. The database is accessible either through clickable two-dimensional gel electrophoretic maps or by means of a set of dedicated search engines. Basic characterization of the experimental procedures, data processing, and a comprehensive description of the web site are presented. In its current state, the SWICZ proteome database provides a platform for the incorporation of new data emerging from extended functional studies on the C. crescentus proteome.",
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                            {
                                "name": "Vohradsky J."
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                            {
                                "name": "Janda I."
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                            {
                                "name": "Berndt P."
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                            {
                                "name": "Roder D."
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                        "title": "Systems level analysis of protein synthesis patterns associated with bacterial growth and metabolic transitions",
                        "abstract": "Gene expression databases, acquired by proteomics and transcriptomics, describe physiological and developmental programs at the systems level. Here we analyze proteosynthetic profiles in a bacterium undergoing defined metabolic changes. Streptomyces coelicolor cultured in a defined liquid medium displays four distinct patterns of gene expression associated with growth on glutamate, diauxic transition, and growth on maltose and ammonia that terminates by starvation for nitrogen and entry into stationary phase. Principal component and fuzzy duster analyses of the proteome database of 935 protein spot profiles revealed principal kinetic patterns. Online linkage of the proteome database (SWICZ) to a protein-function database (KEGG) revealed limited correlations between expression profiles and metabolic pathway activities. Proteins belonging to principal metabolic pathways defined characteristic kinetic profiles correlated with the physiological state of the culture. These analyses supported the concept that metabolic flux was regulated not by individual enzymes but rather by groups of enzymes whose synthesis responded to changes in nutritional conditions. Higher-level regulation is reflected by the distribution of all kinetic profiles into only nine groups. The observation that enzymes representing principal metabolic pathways displayed their own distinctive average kinetic profiles suggested that expression of a \"high-flux backbone\" may dominate regulation of metabolic flux. © 2006 Wiley-VCH Verlag GmbH & Co. KGaA.",
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                                "name": "Vohradsky J."
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                        "title": "PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface",
                        "abstract": "© 2015 American Chemical Society. Protein inference connects the peptide spectrum matches (PSMs) obtained from database search engines back to proteins, which are typically at the heart of most proteomics studies. Different search engines yield different PSMs and thus different protein lists. Analysis of results from one or multiple search engines is often hampered by different data exchange formats and lack of convenient and intuitive user interfaces. We present PIA, a flexible software suite for combining PSMs from different search engine runs and turning these into consistent results. PIA can be integrated into proteomics data analysis workflows in several ways. A user-friendly graphical user interface can be run either locally or (e.g., for larger core facilities) from a central server. For automated data processing, stand-alone tools are available. PIA implements several established protein inference algorithms and can combine results from different search engines seamlessly. On several benchmark data sets, we show that PIA can identify a larger number of proteins at the same protein FDR when compared to that using inference based on a single search engine. PIA supports the majority of established search engines and data in the mzIdentML standard format. It is implemented in Java and freely available at https://github.com/mpc-bioinformatics/pia.",
                        "citationCount": 23,
                        "authors": [
                            {
                                "name": "Uszkoreit J."
                            },
                            {
                                "name": "Maerkens A."
                            },
                            {
                                "name": "Perez-Riverol Y."
                            },
                            {
                                "name": "Meyer H.E."
                            },
                            {
                                "name": "Marcus K."
                            },
                            {
                                "name": "Stephan C."
                            },
                            {
                                "name": "Kohlbacher O."
                            },
                            {
                                "name": "Eisenacher M."
                            }
                        ],
                        "date": "2015-01-01T00:00:00Z",
                        "journal": "Journal of Proteome Research"
                    }
                }
            ],
            "homepage_status": 0,
            "credit": [
                {
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                        "Developer"
                    ],
                    "name": "Julian Uszkoreit",
                    "url": null,
                    "note": null,
                    "orcidid": "http://orcid.org/0000-0001-7522-4007",
                    "typeEntity": "Person",
                    "email": "julian.uszkoreit@rub.de"
                },
                {
                    "typeRole": [
                        "Provider"
                    ],
                    "name": "BioInfra.Prot",
                    "url": null,
                    "note": null,
                    "orcidid": null,
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                    "email": "bioinfoservice@rub.de"
                },
                {
                    "typeRole": [
                        "Primary contact"
                    ],
                    "name": "Julian Uszkoreit",
                    "url": null,
                    "note": null,
                    "orcidid": "http://orcid.org/0000-0001-7522-4007",
                    "typeEntity": "Person",
                    "email": "julian.uszkoreit@rub.de"
                },
                {
                    "typeRole": [
                        "Primary contact"
                    ],
                    "name": null,
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Person",
                    "email": "bioinfoservice@rub.de"
                }
            ],
            "biotoolsCURIE": "biotools:pia",
            "elixirPlatform": [],
            "elixirNode": [],
            "version": [
                "1.3.0"
            ],
            "elixir_badge": 0,
            "homepage": "https://mpc-bioinformatics.github.io/pia/",
            "function": [
                {
                    "note": "PIA allows you to inspect the results of common proteomics spectrum identification search engines, combine them seamlessly and conduct statistical analyses. The main focus of PIA lays on the integrated inference algorithms, i.e. concluding the proteins from a set of identified spectra. But it also allows you to inspect your peptide spectrum matches, calculate FDR values across different search engine results and visualize the correspondence between PSMs, peptides and proteins. Search engine results in several formats peptide spectrum matches (PSMs) and peptides Inferred Proteins",
                    "input": [
                        {
                            "data": {
                                "term": "Mass spectrometry spectra",
                                "uri": "http://edamontology.org/data_0943"
                            },
                            "format": [
                                {
                                    "term": "Mascot .dat file",
                                    "uri": "http://edamontology.org/format_3713"
                                },
                                {
                                    "term": "X!Tandem XML",
                                    "uri": "http://edamontology.org/format_3711"
                                },
                                {
                                    "term": "TSV",
                                    "uri": "http://edamontology.org/format_3475"
                                },
                                {
                                    "term": "PRIDE XML",
                                    "uri": "http://edamontology.org/format_3684"
                                },
                                {
                                    "term": "mzIdentML",
                                    "uri": "http://edamontology.org/format_3247"
                                },
                                {
                                    "term": "MSF",
                                    "uri": "http://edamontology.org/format_3702"
                                }
                            ]
                        }
                    ],
                    "operation": [
                        {
                            "term": "Analysis",
                            "uri": "http://edamontology.org/operation_2945"
                        }
                    ],
                    "cmd": null,
                    "output": [
                        {
                            "data": {
                                "term": "Peptide identification",
                                "uri": "http://edamontology.org/data_0945"
                            },
                            "format": [
                                {
                                    "term": "Sequence feature table format (text)",
                                    "uri": "http://edamontology.org/format_2206"
                                },
                                {
                                    "term": "KNIME datatable format",
                                    "uri": "http://edamontology.org/format_3765"
                                },
                                {
                                    "term": "idXML",
                                    "uri": "http://edamontology.org/format_3764"
                                },
                                {
                                    "term": "TSV",
                                    "uri": "http://edamontology.org/format_3475"
                                },
                                {
                                    "term": "mzTab",
                                    "uri": "http://edamontology.org/format_3681"
                                },
                                {
                                    "term": "mzIdentML",
                                    "uri": "http://edamontology.org/format_3247"
                                }
                            ]
                        },
                        {
                            "data": {
                                "term": "Protein identifier",
                                "uri": "http://edamontology.org/data_0989"
                            },
                            "format": [
                                {
                                    "term": "Sequence feature table format (text)",
                                    "uri": "http://edamontology.org/format_2206"
                                },
                                {
                                    "term": "KNIME datatable format",
                                    "uri": "http://edamontology.org/format_3765"
                                },
                                {
                                    "term": "idXML",
                                    "uri": "http://edamontology.org/format_3764"
                                },
                                {
                                    "term": "TSV",
                                    "uri": "http://edamontology.org/format_3475"
                                },
                                {
                                    "term": "mzTab",
                                    "uri": "http://edamontology.org/format_3681"
                                },
                                {
                                    "term": "mzIdentML",
                                    "uri": "http://edamontology.org/format_3247"
                                }
                            ]
                        }
                    ]
                }
            ],
            "lastUpdate": "2019-03-26T08:32:10Z",
            "otherID": [],
            "description": "The main focus lays on the integrated inference algorithms, concluding the proteins from a set of identified spectra. But it also allows you to inspect your peptide spectrum matches, calculate FDR values across different search engine results and visualize the correspondence between PSMs, peptides and proteins.",
            "toolType": [
                "Command-line tool",
                "Library",
                "Web application",
                "Desktop application"
            ],
            "editPermission": {
                "type": "group",
                "authors": [
                    "proteomics.bio.tools"
                ]
            },
            "language": [
                "Java"
            ],
            "link": [
                {
                    "url": "http://mpc-bioinformatics.github.io/pia/",
                    "note": null,
                    "type": "Repository"
                },
                {
                    "url": "http://www.mybiosoftware.com/pia-protein-inference-algorithms.html",
                    "note": null,
                    "type": "Registry"
                }
            ],
            "biotoolsID": "pia",
            "additionDate": "2016-07-12T10:54:05Z",
            "name": "PIA - Protein Inference Algorithms",
            "license": "BSD-3-Clause",
            "documentation": [
                {
                    "url": "https://github.com/mpc-bioinformatics/pia/wiki",
                    "note": null,
                    "type": "General"
                }
            ],
            "maturity": "Mature",
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ]
        },
        {
            "collectionID": [
                "KNIME",
                "de.NBI",
                "Proteomics",
                "OpenMS"
            ],
            "accessibility": [],
            "topic": [
                {
                    "term": "Proteomics experiment",
                    "uri": "http://edamontology.org/topic_3520"
                },
                {
                    "term": "Proteomics",
                    "uri": "http://edamontology.org/topic_0121"
                },
                {
                    "term": "Metabolomics",
                    "uri": "http://edamontology.org/topic_3172"
                }
            ],
            "owner": "jpfeuffer",
            "cost": "Free of charge",
            "download": [
                {
                    "url": "https://github.com/OpenMS/OpenMS",
                    "note": null,
                    "version": null,
                    "type": "Source code"
                },
                {
                    "url": "http://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-2.0/",
                    "note": null,
                    "version": null,
                    "type": "Binaries"
                },
                {
                    "url": "https://github.com/OpenMS/OpenMS",
                    "note": null,
                    "version": null,
                    "type": "Source code"
                }
            ],
            "validated": 0,
            "publication": [
                {
                    "doi": "10.1038/nmeth.3959",
                    "version": null,
                    "pmid": "27575624",
                    "type": "Primary",
                    "pmcid": null,
                    "metadata": {
                        "title": "OpenMS: A flexible open-source software platform for mass spectrometry data analysis",
                        "abstract": "© 2016 Nature America, Inc. All rights reserved.High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.",
                        "citationCount": 85,
                        "authors": [
                            {
                                "name": "Rost H.L."
                            },
                            {
                                "name": "Sachsenberg T."
                            },
                            {
                                "name": "Aiche S."
                            },
                            {
                                "name": "Bielow C."
                            },
                            {
                                "name": "Weisser H."
                            },
                            {
                                "name": "Aicheler F."
                            },
                            {
                                "name": "Andreotti S."
                            },
                            {
                                "name": "Ehrlich H.-C."
                            },
                            {
                                "name": "Gutenbrunner P."
                            },
                            {
                                "name": "Kenar E."
                            },
                            {
                                "name": "Liang X."
                            },
                            {
                                "name": "Nahnsen S."
                            },
                            {
                                "name": "Nilse L."
                            },
                            {
                                "name": "Pfeuffer J."
                            },
                            {
                                "name": "Rosenberger G."
                            },
                            {
                                "name": "Rurik M."
                            },
                            {
                                "name": "Schmitt U."
                            },
                            {
                                "name": "Veit J."
                            },
                            {
                                "name": "Walzer M."
                            },
                            {
                                "name": "Wojnar D."
                            },
                            {
                                "name": "Wolski W.E."
                            },
                            {
                                "name": "Schilling O."
                            },
                            {
                                "name": "Choudhary J.S."
                            },
                            {
                                "name": "Malmstrom L."
                            },
                            {
                                "name": "Aebersold R."
                            },
                            {
                                "name": "Reinert K."
                            },
                            {
                                "name": "Kohlbacher O."
                            }
                        ],
                        "date": "2016-08-30T00:00:00Z",
                        "journal": "Nature Methods"
                    }
                },
                {
                    "doi": "10.1007/978-1-60761-987-1_23",
                    "version": null,
                    "pmid": null,
                    "type": "Other",
                    "pmcid": null,
                    "metadata": null
                }
            ],
            "homepage_status": 0,
            "credit": [
                {
                    "typeRole": [
                        "Provider"
                    ],
                    "name": "ETH Zürich",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Institute",
                    "email": null
                },
                {
                    "typeRole": [
                        "Provider"
                    ],
                    "name": "Eberhard-Karls-Universität Tübingen",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Institute",
                    "email": null
                },
                {
                    "typeRole": [
                        "Provider"
                    ],
                    "name": "Freie Universität Berlin",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Institute",
                    "email": null
                },
                {
                    "typeRole": [],
                    "name": "Center for Integrative Bioinformatics (CiBi)",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Consortium",
                    "email": null
                },
                {
                    "typeRole": [
                        "Provider"
                    ],
                    "name": "cibi",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Institute",
                    "email": null
                },
                {
                    "typeRole": [
                        "Support"
                    ],
                    "name": "General Mailinglist",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": null,
                    "email": "open-ms-general@lists.sourceforge.net"
                },
                {
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                        "Primary contact"
                    ],
                    "name": "General Mailinglist",
                    "url": null,
                    "note": null,
                    "orcidid": null,
                    "typeEntity": "Person",
                    "email": "open-ms-general@lists.sourceforge.net"
                },
                {
                    "typeRole": [
                        "Contributor"
                    ],
                    "name": "Hannes Röst",
                    "url": null,
                    "note": null,
                    "orcidid": "http://orcid.org/0000-0003-0990-7488",
                    "typeEntity": "Person",
                    "email": null
                }
            ],
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            "elixirNode": [],
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            "elixir_badge": 0,
            "homepage": "http://www.openms.de",
            "function": [
                {
                    "note": null,
                    "input": [
                        {
                            "data": {
                                "term": "Mass spectrometry data",
                                "uri": "http://edamontology.org/data_2536"
                            },
                            "format": [
                                {
                                    "term": "pepXML",
                                    "uri": "http://edamontology.org/format_3655"
                                },
                                {
                                    "term": "mzQuantML",
                                    "uri": "http://edamontology.org/format_3248"
                                },
                                {
                                    "term": "dta",
                                    "uri": "http://edamontology.org/format_3652"
                                },
                                {
                                    "term": "FASTA",
                                    "uri": "http://edamontology.org/format_1929"
                                },
                                {
                                    "term": "protXML",
                                    "uri": "http://edamontology.org/format_3747"
                                },
                                {
                                    "term": "idXML",
                                    "uri": "http://edamontology.org/format_3764"
                                },
                                {
                                    "term": "OBO",
                                    "uri": "http://edamontology.org/format_2549"
                                },
                                {
                                    "term": "XML",
                                    "uri": "http://edamontology.org/format_2332"
                                },
                                {
                                    "term": "TraML",
                                    "uri": "http://edamontology.org/format_3246"
                                },
                                {
                                    "term": "mzML",
                                    "uri": "http://edamontology.org/format_3244"
                                },
                                {
                                    "term": "mzIdentML",
                                    "uri": "http://edamontology.org/format_3247"
                                },
                                {
                                    "term": "mzXML",
                                    "uri": "http://edamontology.org/format_3654"
                                },
                                {
                                    "term": "MGF",
                                    "uri": "http://edamontology.org/format_3651"
                                },
                                {
                                    "term": "qcML",
                                    "uri": "http://edamontology.org/format_3683"
                                }
                            ]
                        },
                        {
                            "data": {
                                "term": "Sequence record",
                                "uri": "http://edamontology.org/data_0849"
                            },
                            "format": [
                                {
                                    "term": "pepXML",
                                    "uri": "http://edamontology.org/format_3655"
                                },
                                {
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                                    "uri": "http://edamontology.org/format_3248"
                                },
                                {
                                    "term": "dta",
                                    "uri": "http://edamontology.org/format_3652"
                                },
                                {
                                    "term": "FASTA",
                                    "uri": "http://edamontology.org/format_1929"
                                },
                                {
                                    "term": "protXML",
                                    "uri": "http://edamontology.org/format_3747"
                                },
                                {
                                    "term": "idXML",
                                    "uri": "http://edamontology.org/format_3764"
                                },
                                {
                                    "term": "OBO",
                                    "uri": "http://edamontology.org/format_2549"
                                },
                                {
                                    "term": "XML",
                                    "uri": "http://edamontology.org/format_2332"
                                },
                                {
                                    "term": "TraML",
                                    "uri": "http://edamontology.org/format_3246"
                                },
                                {
                                    "term": "mzML",
                                    "uri": "http://edamontology.org/format_3244"
                                },
                                {
                                    "term": "mzIdentML",
                                    "uri": "http://edamontology.org/format_3247"
                                },
                                {
                                    "term": "mzXML",
                                    "uri": "http://edamontology.org/format_3654"
                                },
                                {
                                    "term": "MGF",
                                    "uri": "http://edamontology.org/format_3651"
                                },
                                {
                                    "term": "qcML",
                                    "uri": "http://edamontology.org/format_3683"
                                }
                            ]
                        },
                        {
                            "data": {
                                "term": "Peptide identification",
                                "uri": "http://edamontology.org/data_0945"
                            },
                            "format": [
                                {
                                    "term": "pepXML",
                                    "uri": "http://edamontology.org/format_3655"
                                },
                                {
                                    "term": "mzQuantML",
                                    "uri": "http://edamontology.org/format_3248"
                                },
                                {
                                    "term": "dta",
                                    "uri": "http://edamontology.org/format_3652"
                                },
                                {
                                    "term": "FASTA",
                                    "uri": "http://edamontology.org/format_1929"
                                },
                                {
                                    "term": "protXML",
                                    "uri": "http://edamontology.org/format_3747"
                                },
                                {
                                    "term": "idXML",
                                    "uri": "http://edamontology.org/format_3764"
                                },
                                {
                                    "term": "OBO",
                                    "uri": "http://edamontology.org/format_2549"
                                },
                                {
                                    "term": "XML",
                                    "uri": "http://edamontology.org/format_2332"
                                },
                                {
                                    "term": "TraML",
                                    "uri": "http://edamontology.org/format_3246"
                                },
                                {
                                    "term": "mzML",
                                    "uri": "http://edamontology.org/format_3244"
                                },
                                {
                                    "term": "mzIdentML",
                                    "uri": "http://edamontology.org/format_3247"
                                },
                                {
                                    "term": "mzXML",
                                    "uri": "http://edamontology.org/format_3654"
                                },
                                {
                                    "term": "MGF",
                                    "uri": "http://edamontology.org/format_3651"
                                },
                                {
                                    "term": "qcML",
                                    "uri": "http://edamontology.org/format_3683"
                                }
                            ]
                        }
                    ],
                    "operation": [
                        {
                            "term": "Protein identification",
                            "uri": "http://edamontology.org/operation_3767"
                        },
                        {
                            "term": "Parsing",
                            "uri": "http://edamontology.org/operation_1812"
                        },
                        {
                            "term": "Data handling",
                            "uri": "http://edamontology.org/operation_2409"
                        },
                        {
                            "term": "Chromatographic alignment",
                            "uri": "http://edamontology.org/operation_3628"
                        },
                        {
                            "term": "Mass spectra calibration",
                            "uri": "http://edamontology.org/operation_3627"
                        },
                        {
                            "term": "Formatting",
                            "uri": "http://edamontology.org/operation_0335"
                        },
                        {
                            "term": "Protein quantification",
                            "uri": "http://edamontology.org/operation_3630"
                        },
                        {
                            "term": "Retention time prediction",
                            "uri": "http://edamontology.org/operation_3633"
                        },
                        {
                            "term": "Annotation",
                            "uri": "http://edamontology.org/operation_0226"
                        },
                        {
                            "term": "Protein feature detection",
                            "uri": "http://edamontology.org/operation_3092"
                        },
                        {
                            "term": "Isotope-coded protein label",
                            "uri": "http://edamontology.org/operation_3705"
                        },
                        {
                            "term": "Label-free quantification",
                            "uri": "http://edamontology.org/operation_3634"
                        },
                        {
                            "term": "iTRAQ",
                            "uri": "http://edamontology.org/operation_3639"
                        },
                        {
                            "term": "Peptide identification",
                            "uri": "http://edamontology.org/operation_3631"
                        },
                        {
                            "term": "Peak detection",
                            "uri": "http://edamontology.org/operation_3215"
                        },
                        {
                            "term": "Mass spectrum visualisation",
                            "uri": "http://edamontology.org/operation_3694"
                        },
                        {
                            "term": "Labeled quantification",
                            "uri": "http://edamontology.org/operation_3635"
                        },
                        {
                            "term": "Splitting",
                            "uri": "http://edamontology.org/operation_3359"
                        },
                        {
                            "term": "Spectral analysis",
                            "uri": "http://edamontology.org/operation_3214"
                        },
                        {
                            "term": "Deisotoping",
                            "uri": "http://edamontology.org/operation_3629"
                        },
                        {
                            "term": "Target-Decoy",
                            "uri": "http://edamontology.org/operation_3649"
                        },
                        {
                            "term": "Prediction and recognition (protein)",
                            "uri": "http://edamontology.org/operation_3023"
                        },
                        {
                            "term": "Comparison",
                            "uri": "http://edamontology.org/operation_2424"
                        },
                        {
                            "term": "Standardisation and normalisation",
                            "uri": "http://edamontology.org/operation_3435"
                        }
                    ],
                    "cmd": null,
                    "output": [
                        {
                            "data": {
                                "term": "Peptide identification",
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                        "abstract": "© 2015 López-Fernández et al. Background: Mass spectrometry is one of the most important techniques in the field of proteomics. MALDI-TOF mass spectrometry has become popular during the last decade due to its high speed and sensitivity for detecting proteins and peptides. MALDI-TOF-MS can be also used in combination with Machine Learning techniques and statistical methods for knowledge discovery. Although there are many software libraries and tools that can be combined for these kind of analysis, there is still a need for all-in-one solutions with graphical user-friendly interfaces and avoiding the need of programming skills. Results: Mass-Up, an open software multiplatform application for MALDI-TOF-MS knowledge discovery is herein presented. Mass-Up software allows data preprocessing, as well as subsequent analysis including (i) biomarker discovery, (ii) clustering, (iii) biclustering, (iv) three-dimensional PCA visualization and (v) classification of large sets of spectra data. Conclusions: Mass-Up brings knowledge discovery within reach of MALDI-TOF-MS researchers. Mass-Up is distributed under license GPLv3 and it is open and free to all users at http://sing.ei.uvigo.es/mass-up.",
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                                "name": "Lopez-Fernandez H."
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                            {
                                "name": "Santos H.M."
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                            {
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                            {
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                        "title": "Laser ablation and inductively coupled plasma mass spectrometry focusing on bioimaging from elemental distribution using MatLab software: A practical guide",
                        "abstract": "© 2016 The Royal Society of Chemistry. The parameters influencing laser ablation inductively coupled plasma mass spectrometry as a tool for imaging elemental distribution in tissues are critically commented on in this work, and penile cancer tissue was used as a model. General aspects of LA-ICP-MS are discussed, and among them, issues regarding sample preparation and calibration. The optimization process of the following variables is described in detail in a step-by-step tutorial manner: laser intensity, laser frequency, laser resolution, ICP radiofrequency, nebulizer and auxiliary gas flow rates, and C isotopes as internal standards. Once the best condition is found for each variable, MATLAB software is used to generate two-dimensional images. Herein it is also explained how to use MATLAB software to generate tissue images using acquisition, exporting and data treatment parameters.",
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                                "name": "Pessoa G.D.S."
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