Peptide And Protein ID Tutorial 4.0
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Associated Tutorial
This workflows is part of the tutorial Peptide and Protein ID using SearchGUI and PeptideShaker, available in the GTN
Thanks to...
Tutorial Author(s): Florian Christoph Sigloch, Björn Grüning
Tutorial Contributor(s): Saskia Hiltemann, Nicola Soranzo, Björn Grüning, Melanie Föll, Bérénice Batut, William Durand, Clemens Blank, Florian Christoph Sigloch, Subina Mehta, Niall Beard, Helena Rasche, Martin Čech, Armin Dadras
Funder(s): ELIXIR Europe, de.NBI, University of Freiburg
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input: Protein Database | Input: Protein Database | n/a |
|
| Input: mzML file | Input: mzML file | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | PeakPickerHiRes | PeakPickerHiRes |
| 3 | FileConverter | FileConverter |
| 4 | Search GUI | toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/2.9.0 |
| 5 | Peptide Shaker | toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.11.0 |
| 6 | Select | Output: all identified contaminants. Grep1 |
| 7 | Select | Output: all identified proteins without common contaminants. CAVE: some proteins may be both! Grep1 |
| 8 | Select | Output: only those non-contaminant proteins not evaluated to be "Doubtful". Grep1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_3 | _anonymous_output_3 | n/a |
|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
|
| _anonymous_output_5 | _anonymous_output_5 | n/a |
|
| _anonymous_output_6 | _anonymous_output_6 | n/a |
|
| _anonymous_output_7 | _anonymous_output_7 | n/a |
|
| _anonymous_output_8 | _anonymous_output_8 | n/a |
|
| _anonymous_output_9 | _anonymous_output_9 | n/a |
|
| _anonymous_output_10 | _anonymous_output_10 | n/a |
|
Version History
master
Creators and Submitter
Views: 1239 Downloads: 169 Runs: 0
Created: 2nd Jun 2025 at 10:51
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