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Protein identification
Mass spectrometry OpenMS Peptide identification Protein Quantification MSstats Database search FDR
  1. 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
  2. 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
  3. 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
  4. Go to item
    Workflow
    Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT
    OpenMS Mass spectrometry Peptide identification
    +3
    ## Description OpenMS exam workflow for the analysis of isobaric data (e.g. TMT). A) Quantification via the IsobaricAnalzyer B) S…
    openms-team > Tutorial Workflows OpenMS 3.0 > Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT
    0
    openms-team
  5. 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 3.0 > basic_peptide_identification_with_inference
    0
    openms-team
  6. Go to item
    Workflow
    labelfree_with_protein_quantification
    OpenMS Mass spectrometry Peptide identification
    +2
    Identification with X!Tandem in the ID meta node, Protein Inference with Fido and protein quantification based on feature intensi…
    openms-team > Tutorial Workflows OpenMS 2.7 > labelfree_with_protein_quantification
    0
    openms-team
  7. 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 3.0 > Proteomics_LFQ
    0
    openms-team
  8. Go to item
    Workflow
    ProteomicsLFQ_tool_and_MSstats_postprocessing
    OpenMS Mass spectrometry Protein identification
    +2
    Uses the ProteomicsLFQ that contains the standard proteomics LFQ pipeline, after peptide and protein identification. Applies post…
    openms-team > Tutorial Workflows OpenMS 2.7 > ProteomicsLFQ_tool_and_MSstats_postprocessing
    0
    openms-team
  9. 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 3.0 > Phosphoproteomics_ID
    0
    openms-team
  10. Go to item
    Workflow
    labelfree_with_protein_quantification
    OpenMS Mass spectrometry Peptide identification
    +2
    Identification with X!Tandem in the ID meta node, Protein Inference with Fido and protein quantification based on feature intensi…
    openms-team > Getting Started with OpenMS > Labelfree with Protein Quantification
    0
    openms-team
  11. Go to item
    Workflow
    Identification_quantification_with_inference_isobaric
    OpenMS Mass spectrometry Peptide identification
    +3
    ## Description OpenMS exam workflow for the analysis of isobaric data (e.g. TMT). A) Quantification via the IsobaricAnalzyer B) S…
    openms-team > Tutorial Workflows OpenMS 2.7 > Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT
    0
    openms-team
  12. Go to item
    Workflow
    labelfree_with_protein_quantification
    OpenMS Mass spectrometry Peptide identification
    +2
    Identification with X!Tandem in the ID meta node, Protein Inference with Fido and protein quantification based on feature intensi…
    openms-team > Tutorial Workflows OpenMS 3.0 > labelfree_with_protein_quantification
    0
    openms-team

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