OpenMS Installers#

Workflows#

Workflow

Description

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ProteomicsLFQ_tool_and_MSstats_postprocessing

Label-free identification and quantification using the comet search engine, the ProteomicsLFQ tool and statistical down-stream processing using MSstats. Compared to the other proteomics LFQ workflows, it is less complex as it combines quantification and inference steps in a single ProtemicLFQ tool.

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DIAMetAlyzer

Metabolomics assay library construction with decoy generation from DDA data and targeted DIA analysis using OpenSWATH and pyprophet for statistical validation.

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Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT

Identification and quantification for isobaric experiments using MSGFPlus as search engine, epifany for inference and MSstatsTMT for statistical down-stream analysis.

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labelfree_with_protein_quantification

Label-free with protein quantification steps implemented using individual OpenMS tools

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Metabolite_Adduct_Grouping

Quantification and identification via accurate mass based on multiple adduct grouping steps (adducts, neutral losses).

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Metabolite_DeNovoID

Quantification and identification via adduct grouping and de-novo identification using SIRIUS/CSI:FingerID.

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Metabolite_ID

Quantification and identification via accurate mass based with downstream processing and visualisation.

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Metabolite_SpectralID

Identification via spectral library search for small molecules.

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MSstats_statPostProcessing_iPRG2015

Post processing workflow for using MSstats based on “Example_OneTool_ProteomicsLFQ_MSstats.knwf”

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MSstatsTMT

Post processing workflow for using MSstatsTMT based on “Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT”.

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OpenSWATH

Targeted extraction and scoring of transitions in DIA data based on an (iRT) assay library.

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Phosphoproteomics_ID

Identification of Phosphorilation sites.

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Other Resources#

Name

Description

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Schemas

Documented schemas of the OpenMS formats

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iPRG2016 data

Dataset mxMLs, Fasta database, Identification file (idXML), Big Data (idXML)

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