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{ "count": 2505, "next": "?page=2", "previous": null, "list": [ { "name": "CalibraCurve", "description": "A highly useful and flexible tool for calibration of targeted MS‐based measurements. CalibraCurve enables an automated batch-mode determination of dynamic linear ranges and quantification limits for both targeted proteomics and similar assays. The software uses a variety of measures to assess the accuracy of the calibration and provides intuitive visualizations.", "homepage": "https://github.com/mpc-bioinformatics/CalibraCurve", "biotoolsID": "calibracurve", "biotoolsCURIE": "biotools:calibracurve", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3591", "term": "tiff" } ] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow", "Script", "Desktop application", "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3678", "term": "Experimental design and studies" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "BSD-3-Clause", "collectionID": [ "BioInfra.Prot", "de.NBI", "CUBiMed.RUB" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [ "Proteomics" ], "link": [ { "url": "https://github.com/mpc-bioinformatics/CalibraCurve", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/mpc-bioinformatics/CalibraCurve", "type": "Downloads page", "note": null, "version": "2.0" } ], "documentation": [ { "url": "https://github.com/mpc-bioinformatics/CalibraCurve", "type": [ "Installation instructions", "Citation instructions", "General", "User manual", "Training material", "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1002/pmic.201900143", "pmid": "32086983", "pmcid": null, "type": [ "Primary" ], "version": "2.0", "note": null, "metadata": { "title": "CalibraCurve: A Tool for Calibration of Targeted MS-Based Measurements", "abstract": "Targeted proteomics techniques allow accurate quantitative measurements of analytes in complex matrices with dynamic linear ranges that span up to 4–5 orders of magnitude. Hence, targeted methods are promising for the development of robust protein assays in several sensitive areas, for example, in health care. However, exploiting the full method potential requires reliable determination of the dynamic range along with related quantification limits for each analyte. Here, a software named CalibraCurve that enables an automated batch-mode determination of dynamic linear ranges and quantification limits for both targeted proteomics and similar assays is presented. The software uses a variety of measures to assess the accuracy of the calibration, namely precision and trueness. Two different kinds of customizable graphs are created (calibration curves and response factor plots). The accuracy measures and the graphs offer an intuitive, detailed, and reliable opportunity to assess the quality of the model fit. Thus, CalibraCurve is deemed a highly useful and flexible tool to facilitate the development and control of reliable SRM/MRM-MS-based proteomics assays.", "date": "2020-06-01T00:00:00Z", "citationCount": 4, "authors": [ { "name": "Kohl M." }, { "name": "Stepath M." }, { "name": "Bracht T." }, { "name": "Megger D.A." }, { "name": "Sitek B." }, { "name": "Marcus K." }, { "name": "Eisenacher M." } ], "journal": "Proteomics" } } ], "credit": [ { "name": "PD Dr. Martin Eisenacher", "email": "martin.eisenacher@rub.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider", "Primary contact" ], "note": "If contacting use \"SPARROW\" in subject line to avoid mail deluge." }, { "name": "de.NBI", "email": null, "url": "https://www.denbi.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider", "Maintainer", "Support" ], "note": "Service provision and maintenance funded by de.NBI." }, { "name": "Dr. Michael Kohl", "email": "michael.kohl@rub.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "BioInfra.Prot", "additionDate": "2020-06-05T08:52:25Z", "lastUpdate": "2026-06-04T08:07:22.002962Z", "editPermission": { "type": "group", "authors": [ "karin" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MetaProteomeAnalyzer-Cloud", "description": "The MetaProteomeAnalyzer Cloud (MPA Cloud) is an intuitive, open-source tool for metaproteomics data analysis and interpretation, designed to analyse comprehensive metaproteomics data from tandem mass spectrometry experiments through a web interface.", "homepage": "https://mdoa-tools.bi.denbi.de/mpacloud/", "biotoolsID": "mpa-cloud", "biotoolsCURIE": "biotools:mpa-cloud", "version": [], "otherID": [], "relation": [ { "biotoolsID": "metaproteomeanalyzer", "type": "isNewVersionOf" }, { "biotoolsID": "mpa_portable", "type": "isNewVersionOf" } ], "function": [], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_4060", "term": "Metaproteomics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [], "language": [ "Java", "TypeScript" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://gitlab.com/mdoa-group/mpa-website", "type": [ "Repository" ], "note": null }, { "url": "https://gitlab.com/mdoa-group/mpa-cloud-server", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://mdoa-tools.bi.denbi.de/mpacloud/documentation", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1038/s41596-020-0368-7", "pmid": "32859984", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.3389/fmicb.2019.01883", "pmid": "31474963", "pmcid": "PMC6707425", "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1021/acs.analchem.7b03544", "pmid": "29215871", "pmcid": "PMC5757220", "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1021/pr501246w", "pmid": "25660940", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Kay Schallert", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Daniel Kautzner", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Benjamin J. 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Robert Heyer", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Ludwig Knoche", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Malte Böttcher", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "benjamin4", "additionDate": "2026-06-03T08:48:08.426169Z", "lastUpdate": "2026-06-03T11:12:01.769057Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PolySTest", "description": "Robust statistical testing of quantitative proteomics data. The tool comprises and combines different tests and includes a new method for combined statistics of quantitative and missing values.", "homepage": "http://computproteomics.bmb.sdu.dk/app_direct/PolySTest", "biotoolsID": "PolySTest", "biotoolsCURIE": "biotools:PolySTest", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3664", "term": "Statistical modelling" }, { "uri": "http://edamontology.org/operation_3741", "term": "Differential protein expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3932", "term": "Q-value" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1669", "term": "P-value" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1636", "term": "Heat map" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_3905", "term": "Histogram" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_0928", "term": "Gene expression profile" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Denmark" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/computproteomics/PolySTest", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1074/mcp.RA119.001777", "pmid": "32424025", "pmcid": "PMC8015005", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PolySTest: Robust statistical testing of proteomics data with missing values improves detection of biologically relevant features", "abstract": "", "date": "2020-08-01T00:00:00Z", "citationCount": 26, "authors": [], "journal": "Molecular and Cellular Proteomics" } } ], "credit": [], "owner": "veitveit11", "additionDate": "2019-11-14T19:27:27Z", "lastUpdate": "2026-05-21T08:49:15.617162Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "DigestedProteinDB", "description": "DigestedProteinDB provides a scalable computational infrastructure for indexing and querying peptide cleavage data. Designed for seamless integration into high-throughput mass spectrometry pipelines, it enables low-latency searches and advanced filtering of digested protein datasets to accelerate experimental spectra cross-referencing.", "homepage": "https://digestedproteindb.pbf.hr", "biotoolsID": "digestedproteindb", "biotoolsCURIE": "biotools:digestedproteindb", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "janko", "additionDate": "2026-05-09T05:54:48.710729Z", "lastUpdate": "2026-05-15T09:15:20.517959Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PyProphet", "description": "PyProphet is a tool for semi-supervised learning and scoring of OpenSWATH results in mass-spectrometry based proteomics.", "homepage": "https://github.com/PyProphet/pyprophet", "biotoolsID": "pyprophet", "biotoolsCURIE": "biotools:pyprophet", "version": [ "3.0.14" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3631", "term": "Peptide identification" }, { "uri": "http://edamontology.org/operation_3630", "term": "Protein quantification" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://pyprophet.readthedocs.io/", "type": [ "API documentation", "User manual" ], "note": null } ], "publication": [ { "doi": "10.1038/nmeth.1584", "pmid": "21423193", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1038/nmeth.4398", "pmid": "28825704", "pmcid": "PMC5581544", "type": [ "Method" ], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "n.m.palmblad@lumc.nl", "additionDate": "2026-05-01T11:24:48.399204Z", "lastUpdate": "2026-05-01T11:24:48.401288Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ProteoPy", "description": "ProteoPy is a lightweight Python library for protein- and peptide-level quantitative proteomics analysis, built around the AnnData class as its core data structure. 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If you do not yet have access, contact support@omicsstudio.com." } ], "download": [], "documentation": [ { "url": "https://help.omicsstudio.com/", "type": [ "Quick start guide" ], "note": null } ], "publication": [], "credit": [], "owner": "OmicsStudio", "additionDate": "2026-03-27T22:54:37.826608Z", "lastUpdate": "2026-03-27T22:54:48.583664Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ESIprot", "description": "Charge state determination and molecular weight calculation for low resolution electrospray ionization data.", "homepage": "https://nube-gran.de/esiprot", "biotoolsID": "esiprot", "biotoolsCURIE": "biotools:esiprot", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0398", "term": "Protein molecular weight calculation" }, { "uri": "http://edamontology.org/operation_2929", "term": "Protein fragment weight comparison" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0944", "term": "Peptide mass fingerprint" }, "format": [ { "uri": "http://edamontology.org/format_3245", "term": "Mass spectrometry data format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0944", "term": "Peptide mass fingerprint" }, "format": [ { "uri": "http://edamontology.org/format_3245", "term": "Mass spectrometry data format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.bioprocess.org/esiprot/esiprot_form.php", "type": [ "Mirror" ], "note": null }, { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://www.bioprocess.org/esiprot/esiprot.zip", "type": "Source code", "note": null, "version": null }, { "url": "http://www.bioprocess.org/esiprot/esiprot.zip", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://www.lababi.bioprocess.org/index.php/lababi-software/84-esiprot", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/rcm.4384", "pmid": "20049890", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "ESIprot: A universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data", "abstract": "Electrospray ionization (ESI) ion trap mass spectrometers with relatively low resolution are frequently used for the analysis of natural products and peptides. Although ESI spectra of multiply charged protein molecules also can be measured on this type of devices, only average spectra are produced for the majority of naturally occurring proteins. Evaluating such ESI protein spectra would provide valuable information about the native state of investigated proteins. However, no suitable and freely available software could be found which allows the charge state determination and molecular weight calculation of single proteins from average ESI-MS data. Therefore, an algorithm based on standard deviation optimization (scatter minimization) was implemented for the analysis of protein ESI-MS data. The resulting software ESIprot was tested with ESI-MS data of six intact reference proteins between 12.4 and 66.7kDa. In all cases, the correct charge states could be determined. The obtained absolute mass errors were in a range between -0.2 and 1.2Da, the relative errors below 30ppm. The possible mass accuracy allows for valid conclusions about the actual condition of proteins. Moreover, the ESIprot algorithm demonstrates an extraordinary robustness and allows spectral interpretation from as little as two peaks, given sufficient quality of the provided m/z data, without the necessity for peak intensity data. ESIprot is independent from the raw data format and the computer platform, making it a versatile tool for mass spectrometrists. 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