Proteogenomics 2: Database Search
8.0

Workflow Type: Galaxy

Associated Tutorial

This workflows is part of the tutorial Proteogenomics 2: Database Search, available in the GTN

Features

Thanks to...

Tutorial Author(s): Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Ray Sajulga, James Johnson, Praveen Kumar, Delphine Lariviere

Tutorial Contributor(s): Saskia Hiltemann, Subina Mehta, Nicola Soranzo, Björn Grüning, Helena Rasche, Melanie Föll

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Inputs

ID Name Description Type
MGF Collection MGF Collection n/a
  • File[]
Reference Protein Accessions Reference Protein Accessions n/a
  • File
Uniprot_cRAP_SAV_indel_translatedbed.FASTA Uniprot_cRAP_SAV_indel_translatedbed.FASTA n/a
  • File

Steps

ID Name Description
3 Identification Parameters toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/ident_params/4.0.41+galaxy1
4 Search GUI toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/4.0.41+galaxy1
5 Peptide Shaker toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.33+galaxy1
6 mz to sqlite toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.1.1+galaxy0
7 Removing reference proteins toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
8 Selecting sequence with length >6 and <30 toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
9 Peptides_for_BlastP_analysis toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1

Outputs

ID Name Description Type
Search GUI on input dataset(s) Search GUI on input dataset(s) n/a
  • File
output_certificate output_certificate n/a
  • File
mzidentML mzidentML n/a
  • File
output_psm output_psm n/a
  • File
Mz to sqlite Mz to sqlite n/a
  • File
Removing reference proteins Removing reference proteins n/a
  • File
Selecting sequence with length >6 and <30 Selecting sequence with length >6 and <30 n/a
  • File
Peptides_for_BlastP_analysis Peptides_for_BlastP_analysis n/a
  • File

Version History

8.0 (earliest) Created 2nd Jun 2025 at 10:52 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 10:52

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