LONI Trans-Proteomic Pipeline (TPP) Workflow

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LONI Trans-Proteomic Pipeline (TPP) Workflow

ISB TPP Pipeline Workflow

This page provides documentation on running the Trans-Proteomics Pipeline (TPP) tutorial using the BDDS Pipeline Environment. This diagram shows the various steps involved in the TPP pipeline

Pipeline GenomicsInformatics TPP F1.jpg

The TPP implements one specific protocol to identify and quantify peptides and proteins using mass spectrometry (MS) data. The following steps describe the core processes embedded in the TPP workflow:

1. Start with raw MS data (in mzML format): Converts proprietary raw data into a common mzML format.

2. Search the data

2.1 Using X!Tandem, an open-source search engine modified to include the K-Score scoring function.
2.2 Using with SpectraST, a search engine that compares acquired spectra against a library of pre-identified spectra to which peptide sequences have been assigned.

3. Validation of Peptide-Spectrum assignments:

3.1 Using PeptideProphet, which provides statistical validation of search engine results by assigning a probability to each peptide-spectrum match).
3.2 Using iProphet, a tool that provides statistical refinement of PeptidePropet results.

4. Visualize LC-MS/MS data using Pep3D, a tool for visualizing LC MS data, along with results from PeptideProphet.

5. Peptide Quantitation using ASAPRatio, a tool for measuring relative expression levels of peptides and proteins from isotopically-labeled samples (e.g. ICAT, SILAC, etc).

6. Result Inspection using reSpect, a tool that allows you to identify even more peptides from your existing spectra without collecting anymore data. It can help boost identification rates for low abundance ionic species in datasets containing chimeric spectra.


The steps below illustrate the complete protocol users can follow to start the Pipeline client, load the Pipeline graphical representation of the TPP workflow, as a network, execute the workflow and retrieve intermediate and final results:

Read the TPP Documentation

Pipeline GenomicsInformatics TPP F2.png

Run/Test the TPP Pipeline Workflow (via a web-browser)

Point your browser to the Pipeline TPP URL or http://bit.ly/1BROUxz.

The XML prescription of the TPP Pipeline workflow is available here.

You can also explore other end-to-end pipeline workflow solutions via the Pipeline Library Navigator.

Pipeline GenomicsInformatics TPP F3.png

Workflow Controls

Use the “View Source”, “Open”, “Download”, or “Run” options (bottom) to see, load, retrieve or start the TPP pipeline workflow (using guest-user credentials) on the LONI/INI/USC Pipeline Try-It-Now server.

  • Notes:
    • If you already have a user account on LONI and prefer to start your Pipeline client you can download the workflow and drag-and-drop it in the Pipeline canvas to display the TPP protocol as a pipeline workflow graph.
    • Another alternative is the load the TPP workflow from the LONI Cranium server library (see left hand-size), by double-clicking the TPP workflow under the ISB Suite.
    • TPP Pipeline Workflow (TPP_V2.pipe)
Pipeline GenomicsInformatics TPP F4.png


Click the Run button to initiate the execution of the workflow. Depending on the server utilization, the workflow may take up to 2 hours to complete. See the times for completing each of the steps (modules) in the image below. Different modules will take different amount of time to complete based on the complexity of the processing they represent.

Pipeline GenomicsInformatics TPP F5.png

Pipeline Interface

The Pipeline client user interface has three main components. The left hand panel contains a hierarchy of software tools and services already described within the environment. The main canvas displays the details of the pipeline workflow as a graph network showing the flow of data between nodes, which represent atomic or composite processing steps. The bottom horizontal panel contains the controls for starting (playing), stopping, and pausing a workflow execution, a server monitor, and sessions manager (important of multiple workflows are executed in parallel).

Pipeline GenomicsInformatics TPP F6.png

Inputs and Controls

The sample datasets used in the TPP tutorial are already available in in the pipeline server (or can be downloaded locally from the TPP web-site). These are represented by:

Pipeline GenomicsInformatics TPP F7.png

Workflow Status

After initiating the workflow execution (by pressing the Run button) you will see visual clues illustrating the status of the execution. Moving Blue circles indicate ongoing execution, Green circles indicate complete execution of a module, Orange circles for incomplete jobs, or Red circles show failing execution.

Pipeline GenomicsInformatics TPP F8.png

Inspect Results

To inspect intermediate, or final results of the workflow, right-click on a module and select “View Execution”. Then go to the Output Files and either Download or View the results.

Pipeline GenomicsInformatics TPP F9.png


Users can further share the pipeline workflow or its results with colleagues, as necessary.

Workflow Modification

Users can further modify the workflow by replacing specific processing steps with other software modules, generally modifying the protocol or expanding the workflow to include additional processing or analytic steps.

See also