TTPish workflow for MASSyPup64 with text search

Created: 2015-12-10 00:20:48

This proteomics workflow performs a comet search and subsequently a validation of the results with PeptideProphet/Protein Prophet. Results are exported in various formats, to facilitate the downstream evaluation in other programs and the sharing of data (EXCEL, csv, mzIdentML).

Contrary to a standard Trans-Proteomic-Pipeline (TPP) installation, the workflow can be to mass spectrometry data in whatever localization (i.e. the files do not have to be uploaded/ copied to a special directory).

The workflow was described in the article: Winkler R. An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64. PeerJ. 2015 (https://peerj.com/articles/1401/).

Since all dependencies (comet, TPP, ..) are installed on MASSyPup64, this m64 workflow should run without any further configuration.

Additionally to my previously uploaded protein identifcation workflow, the validated results are searched for a text pattern (e.g. protein name containing "xxx") and matching results are written into a separate csv file.

Information Preview

Information Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/4786/download?version=1
[ More InfoExpand ]


Information Workflow Components

Information Authors (0)
Information Titles (0)
Information Descriptions (0)
Information Dependencies (0)
Inputs (2)
Processors (8)
Beanshells (0)
Outputs (8)
Datalinks (17)
Coordinations (7)

Information Workflow Type

Taverna 2

Information Uploader

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (0)

None

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

 

Citations (0)

None


Version History

In chronological order:



Reviews Reviews (0)

No reviews yet

Be the first to review!



Comments Comments (0)

No comments yet

Log in to make a comment




Workflow Other workflows that use similar services (0)

There are no workflows in myExperiment that use similar services to this Workflow.