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OpenMS
Mass spectrometry Peptide identification Protein identification Protein quantification Metabolomics MSstats QC Introduction Community Nodes Utilities
+7
  1. Go to item
    Workflow
    MSstatsTMT
    OpenMS Mass spectrometry MSstats
    +1
    Post processing workflow for MSstatsTMT. Requires output from MSstatsConverter output. As an example input, an intermediate resul…
    openms-team > Tutorial Workflows OpenMS 2.7 > MSstatsTMT
    1
    openms-team
  2. Go to item
    Workflow
    Liquid chromatography-coupled mass-spectrometry introduction
    Mass spectrometry OpenMS Visualization
    +1
    Load mass spectra, process (e.g. filter) them "in-file", then convert them to tables, and visualize them.
    jpfeuffer > Share > LCMS Introduction
    1
    jpfeuffer
  3. Go to item
    Workflow
    Liquid chromatography-coupled mass-spectrometry introduction
    Mass spectrometry OpenMS Visualization
    +1
    Load mass spectra, process (e.g. filter) them "in-file", then convert them to tables, and visualize them.
    pe_bodet > Public > LCMS Introduction
    1
    pe_bodet
  4. Go to item
    Workflow
    Liquid chromatography-coupled mass-spectrometry introduction
    Mass spectrometry OpenMS Visualization
    +1
    Load mass spectra, process (e.g. filter) them "in-file", then convert them to tables, and visualize them.
    openms-team > Blog workflows > LCMS Introduction
    1
    openms-team
  5. Go to item
    Workflow
    Liquid chromatography-coupled mass-spectrometry introduction
    Mass spectrometry OpenMS Visualization
    +1
    Updated version for KNIME 4.7 and OpenMS 3.0 (nightly). Load mass spectra as tables, filter them and visualize them in different …
    jpfeuffer > Share > Massspec_Bokeh_Server
    1
    jpfeuffer
  6. Go to item
    Node / Manipulator
    AccurateMassSearch
    Community Nodes OpenMS Utilities
    Match MS signals to molecules from a database by mass. Web Documentation for AccurateMassSearch
    1
    openms-team
  7. Go to item
    Node / Manipulator
    FeatureTextReader
    Community Nodes OpenMS Conversion
    This node can be used to read the output of the TextExporter tool into a KNIME table. The TextExporter, when applied to a feature…
    1
    openms-team
  8. Go to item
    Node / Manipulator
    TextExporter
    Community Nodes OpenMS File Handling
    Exports various XML formats to a text file. Web Documentation for TextExporter
    1
    openms-team
  9. Go to item
    Workflow
    MSstats_statPostProcessing_iPRG2015
    OpenMS Mass Spectrometry MSstats
    +1
    Uses MSstatsConverter to make tables that are processed in short R code scripts in various nodes. A consensusXML file from an LFQ…
    openms-team > Tutorial Workflows OpenMS 2.7 > MSstats_statPostProcessing_iPRG2015.knwf
    0
    openms-team
  10. Go to item
    Workflow
    basic_peptide_identification_with_inference
    OpenMS Mass spectrometry Peptide identification
    +4
    This workflow performs a basic peptide identification search, infers proteins and computes abundances using spectral counting. Th…
    openms-team > Tutorial Workflows OpenMS 2.7 > basic_peptide_identification_with_inference
    0
    openms-team
  11. Go to item
    Workflow
    DIAMetAlyzer_2.0
    OpenMS Mass spectrometry Metabolomics
    +3
    Uses Decoy generation from DDA data, targeted DIA analysis using OpenSWATH and pyprophet for statistical validation. Example inpu…
    openms-team > Tutorial Workflows OpenMS 2.7 > DIAMetAlyzer_2.0
    0
    openms-team
  12. Go to item
    Workflow
    Proteomics_LFQ
    OpenMS Mass spectrometry Peptide identification
    +2
    Combines peptide identifications from X!Tandem and Comet. Uses normalized feature intensities for peptide quantification. No smar…
    openms-team > Tutorial Workflows OpenMS 2.7 > Proteomics_LFQ
    0
    openms-team
  13. Go to item
    Workflow
    Metabolite_Adduct_Grouping
    OpenMS Mass spectrometry Metabolomics
    Uses accurate mass based on multiple adduct grouping steps (adducts, neutral losses). Example input data: To download the data fr…
    openms-team > Tutorial Workflows OpenMS 2.7 > Metabolite_Adduct_Grouping
    0
    openms-team
  14. Go to item
    Workflow
    OpenSwath
    OpenMS Mass spectrometry OpenSWATH
    +2
    Directly uses the OpenSWATHWorkflow node with inputs and outputs. Requires an existing Assay Library as input. Example input data…
    openms-team > Tutorial Workflows OpenMS 2.7 > OpenSwath
    0
    openms-team
  15. Go to item
    Workflow
    Phosphoproteomics_ID
    OpenMS Mass spectrometry Peptide identification
    +1
    Uses MSGFPlus and Percolator for peptide identification, Luciphor to identify phosphorylation sites on peptide sequences and then…
    openms-team > Tutorial Workflows OpenMS 2.7 > Phosphoproteomics_ID.knwf
    0
    openms-team
  16. Go to item
    Workflow
    Metabolite_ID
    OpenMS Mass spectrometry Metabolomics
    Quantification and identification via accurate mass search with downstream processing and visualisation. Example input data: To d…
    openms-team > Tutorial Workflows OpenMS 2.7 > Metabolite_ID
    0
    openms-team
  17. Go to item
    Workflow
    MSstats_statPostProcessing_iPRG2015
    OpenMS Mass Spectrometry MSstats
    +1
    Uses MSstatsConverter to make tables that are processed in short R code scripts in various nodes. A consensusXML file from an LFQ…
    openms-team > Tutorial Workflows OpenMS 3.0 > MSstats_statPostProcessing_iPRG2015
    0
    openms-team
  18. Go to item
    Workflow
    Metabolite_ID
    OpenMS Mass spectrometry Metabolomics
    Quantification and identification via accurate mass search with downstream processing and visualisation. Example input data: To d…
    openms-team > Tutorial Workflows OpenMS 3.0 > Metabolite_ID
    0
    openms-team
  19. Go to item
    Workflow
    QC_with_OpenMS
    OpenMS Mass spectrometry QC
    Uses X!Tandem to identify peptides and then uses various Meta Nodes for QC metrics. Requires mzML spectrum files as input, and a …
    openms-team > Tutorial Workflows OpenMS 3.0 > QC_with_OpenMS
    0
    openms-team
  20. Go to item
    Workflow
    Metabolite_DeNovoID
    OpenMS Mass spectrometry Metabolomics
    Uses adduct grouping and de-novo identification with SIRIUS/CSI:FingerID. Example input data: To download the data from the archi…
    openms-team > Tutorial Workflows OpenMS 2.7 > Metabolite_DeNovoID
    0
    openms-team

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