count: 2505
list:
- accessibility: Open access
  additionDate: '2020-06-05T08:52:25Z'
  biotoolsCURIE: biotools:calibracurve
  biotoolsID: calibracurve
  collectionID:
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  - CUBiMed.RUB
  confidence_flag: null
  cost: Free of charge
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  - email: martin.eisenacher@rub.de
    fundrefid: null
    gridid: null
    name: PD Dr. Martin Eisenacher
    note: If contacting use "SPARROW" in subject line to avoid mail deluge.
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: de.NBI
    note: Service provision and maintenance funded by de.NBI.
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    - Maintainer
    - Support
    url: https://www.denbi.de/
  - email: michael.kohl@rub.de
    fundrefid: null
    gridid: null
    name: Dr. Michael Kohl
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  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.
  documentation:
  - note: null
    type:
    - Installation instructions
    - Citation instructions
    - General
    - User manual
    - Training material
    - Terms of use
    url: https://github.com/mpc-bioinformatics/CalibraCurve
  download:
  - note: null
    type: Downloads page
    url: https://github.com/mpc-bioinformatics/CalibraCurve
    version: '2.0'
  editPermission:
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    - karin
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  - Proteomics
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  - Germany
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  - Tools
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  function:
  - cmd: null
    input:
    - data:
        term: Text data
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      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Analysis
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    - data:
        term: Image
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    - data:
        term: Text data
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  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://github.com/mpc-bioinformatics/CalibraCurve
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-06-04T08:07:22.002962Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/mpc-bioinformatics/CalibraCurve
  maturity: Mature
  name: CalibraCurve
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  - Linux
  - Windows
  - Mac
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  owner: BioInfra.Prot
  publication:
  - doi: 10.1002/pmic.201900143
    metadata:
      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.
      authors:
      - name: Kohl M.
      - name: Stepath M.
      - name: Bracht T.
      - name: Megger D.A.
      - name: Sitek B.
      - name: Marcus K.
      - name: Eisenacher M.
      citationCount: 4
      date: '2020-06-01T00:00:00Z'
      journal: Proteomics
      title: 'CalibraCurve: A Tool for Calibration of Targeted MS-Based Measurements'
    note: null
    pmcid: null
    pmid: '32086983'
    type:
    - Primary
    version: '2.0'
  relation: []
  toolType:
  - Workflow
  - Script
  - Desktop application
  - Plug-in
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Experimental design and studies
    uri: http://edamontology.org/topic_3678
  validated: 1
  version:
  - '2.0'
- accessibility: Open access
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  biotoolsCURIE: biotools:mpa-cloud
  biotoolsID: mpa-cloud
  collectionID: []
  confidence_flag: null
  cost: Free of charge
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  - email: null
    fundrefid: null
    gridid: null
    name: Kay Schallert
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
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    name: Daniel Kautzner
    note: null
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    typeEntity: null
    typeRole: []
    url: null
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    gridid: null
    name: Benjamin J. Saalfeld
    note: null
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    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Prof. Dr.-Ing. Robert Heyer
    note: null
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    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ludwig Knoche
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Malte Böttcher
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  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.
  documentation:
  - note: null
    type:
    - User manual
    url: https://mdoa-tools.bi.denbi.de/mpacloud/documentation
  download: []
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  function: []
  homepage: https://mdoa-tools.bi.denbi.de/mpacloud/
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  language:
  - Java
  - TypeScript
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  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.com/mdoa-group/mpa-website
  - note: null
    type:
    - Repository
    url: https://gitlab.com/mdoa-group/mpa-cloud-server
  maturity: Mature
  name: MetaProteomeAnalyzer-Cloud
  operatingSystem: []
  otherID: []
  owner: benjamin4
  publication:
  - doi: 10.1038/s41596-020-0368-7
    metadata: null
    note: null
    pmcid: null
    pmid: '32859984'
    type: []
    version: null
  - doi: 10.3389/fmicb.2019.01883
    metadata: null
    note: null
    pmcid: PMC6707425
    pmid: '31474963'
    type: []
    version: null
  - doi: 10.1021/acs.analchem.7b03544
    metadata: null
    note: null
    pmcid: PMC5757220
    pmid: '29215871'
    type: []
    version: null
  - doi: 10.1021/pr501246w
    metadata: null
    note: null
    pmcid: null
    pmid: '25660940'
    type: []
    version: null
  relation:
  - biotoolsID: metaproteomeanalyzer
    type: isNewVersionOf
  - biotoolsID: mpa_portable
    type: isNewVersionOf
  toolType:
  - Web service
  topic:
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Metaproteomics
    uri: http://edamontology.org/topic_4060
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2019-11-14T19:27:27Z'
  biotoolsCURIE: biotools:PolySTest
  biotoolsID: PolySTest
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  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.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
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  elixirNode:
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  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
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        term: Expression data
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      format:
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        uri: http://edamontology.org/format_3751
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Statistical modelling
      uri: http://edamontology.org/operation_3664
    - term: Differential protein expression profiling
      uri: http://edamontology.org/operation_3741
    output:
    - data:
        term: Q-value
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      format:
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        uri: http://edamontology.org/format_3752
    - data:
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        uri: http://edamontology.org/format_3752
    - data:
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    - data:
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      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Gene expression profile
        uri: http://edamontology.org/data_0928
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: http://computproteomics.bmb.sdu.dk/app_direct/PolySTest
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-05-21T08:49:15.617162Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
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  name: PolySTest
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: veitveit11
  publication:
  - doi: 10.1074/mcp.RA119.001777
    metadata:
      abstract: ''
      authors: []
      citationCount: 26
      date: '2020-08-01T00:00:00Z'
      journal: Molecular and Cellular Proteomics
      title: 'PolySTest: Robust statistical testing of proteomics data with missing
        values improves detection of biologically relevant features'
    note: null
    pmcid: PMC8015005
    pmid: '32424025'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  validated: 1
  version: []
- accessibility: null
  additionDate: '2026-05-09T05:54:48.710729Z'
  biotoolsCURIE: biotools:digestedproteindb
  biotoolsID: digestedproteindb
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  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.
  documentation: []
  download: []
  editPermission:
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  elixir_badge: 0
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  homepage: https://digestedproteindb.pbf.hr
  homepage_status: 0
  language: []
  lastUpdate: '2026-05-15T09:15:20.517959Z'
  license: null
  link: []
  maturity: null
  name: DigestedProteinDB
  operatingSystem: []
  otherID: []
  owner: janko
  publication: []
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-05-01T11:24:48.399204Z'
  biotoolsCURIE: biotools:pyprophet
  biotoolsID: pyprophet
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: PyProphet is a tool for semi-supervised learning and scoring of OpenSWATH
    results in mass-spectrometry based proteomics.
  documentation:
  - note: null
    type:
    - API documentation
    - User manual
    url: https://pyprophet.readthedocs.io/
  download: []
  editPermission:
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  function:
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    note: null
    operation:
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    metadata: null
    note: null
    pmcid: null
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    type:
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  - doi: 10.1038/nmeth.4398
    metadata: null
    note: null
    pmcid: PMC5581544
    pmid: '28825704'
    type:
    - Method
    version: null
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  toolType:
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  - term: Bioinformatics
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  version:
  - 3.0.14
- accessibility: Open access
  additionDate: '2026-04-20T14:52:49.621012Z'
  biotoolsCURIE: biotools:proteopy
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  - proteomics
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  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Isabell Bludau
    note: Junior Group Leader at the Department of Neuropathology, University Hospital
      Heidelberg
    orcidid: https://orcid.org/0000-0002-2601-238X
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: IanDirk.Fichtner@med.uni-heidelberg.de
    fundrefid: null
    gridid: null
    name: Ian Dirk Fichtner
    note: PhD student at the Department of Neuropathology, University Hospital Heidelberg
      and Division of Artificial Intelligence in Oncology, German Cancer Research
      Center (DKFZ)
    orcidid: https://orcid.org/0009-0002-3000-2907
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: ProteoPy is a lightweight Python library for protein- and peptide-level
    quantitative proteomics analysis, built around the AnnData class as its core data
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  - note: null
    type:
    - General
    url: https://proteopy.readthedocs.io/en/latest/
  download:
  - note: null
    type: Source code
    url: https://github.com/UKHD-NP/proteopy/archive/refs/heads/main.zip
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  link:
  - note: null
    type:
    - Repository
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  - note: null
    type:
    - Discussion forum
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  - note: null
    type:
    - Issue tracker
    url: https://github.com/UKHD-NP/proteopy/issues
  - note: Documentation
    type:
    - Other
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  - Mac
  - Linux
  otherID: []
  owner: ifichtner
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  - doi: 10.64898/2026.03.31.715273
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
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  - biotoolsID: anndata
    type: uses
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  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  validated: 0
  version:
  - 0.1.1
- accessibility: null
  additionDate: '2026-03-27T22:54:37.826608Z'
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  - Transcriptomics
  - metabolomic platform
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  cost: Commercial
  credit: []
  description: "Omics Studio is a bioinformatics platform designed to support the\
    \ exploration, contextualization, interpretation, and presentation of omics data.\
    \ It provides guided workflows, visualization, annotation, database search, and\
    \ analysis tools that help researchers work more efficiently with complex biological\
    \ datasets. \n\nOmics Studio is intended for use in applications such as biomarker\
    \ discovery, systems biology, and precision medicine."
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  - note: null
    type:
    - Quick start guide
    url: https://help.omicsstudio.com/
  download: []
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  function:
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  - cmd: null
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    note: null
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  homepage_status: 0
  language:
  - Other
  lastUpdate: '2026-03-27T22:54:48.583664Z'
  license: Proprietary
  link:
  - note: If you already have an account, or would like to sign up, please use this
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    type:
    - Service
    url: https://platform.omicsstudio.com
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  name: Omics Studio
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  - Linux
  - Windows
  otherID: []
  owner: OmicsStudio
  publication: []
  relation: []
  toolType:
  - Web application
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    uri: http://edamontology.org/topic_0091
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Transcriptomics
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  - term: Multiomics
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- accessibility: null
  additionDate: '2017-01-17T14:50:59Z'
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  - Proteomics
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  - email: robert.winkler@ira.cinvestav.mx
    fundrefid: null
    gridid: null
    name: Robert Winkler
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
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    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
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  description: Charge state determination and molecular weight calculation for low
    resolution electrospray ionization data.
  documentation:
  - note: null
    type:
    - General
    url: http://www.lababi.bioprocess.org/index.php/lababi-software/84-esiprot
  download:
  - note: null
    type: Source code
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    version: null
  - note: null
    type: Source code
    url: http://www.bioprocess.org/esiprot/esiprot.zip
    version: null
  editPermission:
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    - kilpejen
    type: group
  elixirCommunity: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
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    note: null
    operation:
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  homepage: https://nube-gran.de/esiprot
  homepage_status: 0
  language:
  - Python
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  license: GPL-3.0
  link:
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    type:
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    metadata:
      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.
        The program code was released under the open-source GPLv3 license to support
        future developments of mass spectrometry software. © 2010 John Wiley & Sons,
        Ltd.
      authors:
      - name: Winkler R.
      citationCount: 75
      date: '2010-01-01T00:00:00Z'
      journal: Rapid Communications in Mass Spectrometry
      title: 'ESIprot: A universal tool for charge state determination and molecular
        weight calculation of proteins from electrospray ionization mass spectrometry
        data'
    note: null
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  description: Pyxis is a vendor-neutral desktop application for ion mobility spectrometry
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  description: ProTransDeconv is an R package designed for deconvolving cell-type-specific
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  description: MMSA is an interactive web-based tool that improves the interpretability
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  description: IHMValidation is a pipeline for assessing integrative hybrid structure
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  description: Protrec2 is a probabilistic framework for missing protein recovery
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  description: ReX is an R package that infers residue-level hydrogen deuterium exchange
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