Workflow Type: Galaxy

Automated inference of stable isotope incorporation rates in proteins for functional metaproteomics

Inputs

ID Name Description Type
Centroided LC-MS datasets Centroided LC-MS datasets mgf, ms2, mzml or mzxml datasets
  • File[]
Fasta Database Fasta Database A protein sequence database in FASTA format
  • File
Fixed modifications Fixed modifications used for the MSGF+ search
  • string
Labeled element Labeled element Used for MetaProSIP (single letter code)
  • string
Precursor monoisotopic mass tolerance (ppm) Precursor monoisotopic mass tolerance (ppm) passed to - MSGF+ -precursor_mass_tolerance - MetaProSIP -mz_tolerance_ppm
  • float
Variable modifications Variable modifications used for the MSGF+ search
  • string

Steps

ID Name Description
6 Sort collection __SORTLIST__
7 DecoyDatabase toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/3.1+galaxy0
8 FeatureFinderMultiplex toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/3.1+galaxy0
9 MSGFPlusAdapter toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/3.1+galaxy0
10 PeptideIndexer toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/3.1+galaxy0
11 FalseDiscoveryRate toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/3.1+galaxy0
12 IDMapper toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/3.1+galaxy0
13 MetaProSIP toolshed.g2.bx.psu.edu/repos/galaxyp/openms_metaprosip/MetaProSIP/3.1+galaxy0

Outputs

ID Name Description Type
Feature fitting result Feature fitting result n/a
  • File
Peptide centric result Peptide centric result n/a
  • File

Version History

v0.2 (latest) Created 22nd Jun 2024 at 03:01 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 b4e7999

v0.1 (earliest) Created 20th Oct 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 798090c
help Creators and Submitter
Creator
  • Matthias Bernt
Submitter
License
Activity

Views: 1852   Downloads: 114

Created: 20th Oct 2023 at 03:01

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