TPP SEWW Demo2012

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1 Workflow at Institute for Systems Biology Setup and Demo

Workflow at Institute for Systems Biology Setup and Demo

setting up WISB

1. Download and install the TPP

To install on your Windows system as a localhost, please follow our TPP Windows Installation Guide, making sure that you select to download the latest version of TPP from our Sourceforge download site.

As a way to verify that the installation was successful, log into Petunia by double-clicking on the Trans-Proteomic Pipeline flower icon on your Desktop or through

the Start menu. Alternatively, you can open a browser window into the following URL: http://localhost/tpp-bin/tpp_gui.pl . You can use the credentials guest and guest as user name and password to log in.

Make sure that the WEBSERVER_ROOT environment variable is set. From the start menu check Control Panel.System.Advanced system settings.Environment Variables.... If you chose the default location for Petunia, WEBSERVER_ROOT should be c:/Inetpub/wwwroot

2. Install Jetty and WISB

To install on your Windows systems, please go to Sourceforge download site and select jetty-distribution-7.3.0.v20110203wWISB.zip for download into the directory you wish to install Jetty (c:\Jetty would be the standard directory). Right click on the zip file and select extract all. This will create the subdirectory jetty-distribution-7.3.0.v20110203. Now create the JETTY_HOME environment variable by going to Control Panel.System.Advanced system settings.Environment Variables... from the start menu. In the Systems variables field click on New ... and set Variable name: to 'JETTY_HOST' and Variable value: to the directory Jetty was installed to (c:\Jetty\jetty-distribution-7.3.0.v20110203 by default).

The Jetty distribution in sashimi has been updated to contain the necessary WISB related files.

3. Configure WISB

To configure your Windows systems, please go to Sourceforge download site and select wisb-svc-1.0.config.zip for download into some temporary directory. Right click on it and select Extract all into the temp directory. The following two files should be present:

createparamfile-1.0-SNAPSHOT.jar
initial-modules-workflows.config.xml

Move createparamfile-1.0-SNAPSHOT.jar into $WEBSERVER_ROOT$\tpp-bin.

Go to $JETTY_HOST$/ and double click on start.bat to start the Jetty server (double clinking on stop.bat will stop the service). Open Mozilla Firefox or Google Chrome and copy the following URL into the address window: [1]. Fill in a user name (no validation is done in this version) and click on the bootstrap button. This will take you to the WISB start page. Click the Load config(s) button and in the window select initial-modules-workflows.config.xml. From the start page click on the Templates and workflows button and you should see, as a template, Tandem To Protein Prophet Template.

WISB Demo

1. Download and install the test data and database

For this demo, we will be using a SILAC-labeled Yeast dataset, comprised of 2 runs on a high mass-accuracy Orbitrap instrument, along with a Yeast database appended with decoys. We also include a search parameters file. This is the same as for the Petunia demo.

download the mzML files (768Mb) and unzip.

Then, download the parameters and database files (2.1Mb)

and unzip.

Copy or move the yeast_orfs_all_REV.20060126.short.fasta file into the folder C:\Inetpub\wwwroot\ISB\data\dbase
Copy or move the two data files (OR20080317_S_SILAC-LH_1-1_01.mzML and OR20080317_S_SILAC-LH_1-1_11.mzML) as well as the tandem parameters file tandem.xml into the folder C:\Inetpub\wwwroot\ISB\data\demo2009\tandem. Create this last folder if necessary.

2. Setup the template

From the start page click on the Templates and workflows button.

Tandem To Protein Prophet Template is owned by public and is not editable. You should select it and do a Save as, choosing whatever name you would like and, for this demo, as a template. Selecting the template brings up the graphical representation of the workflow diagram. Notice that the ASAPratio module is included since these are SILAC based samples. Clicking on a component will bring up the parameter form for it, a right click will bring up a description.

As best practice, the template should have parameters set that do not vary for the particular MS/MS device that produced the files.

Explore the template

By clicking on the different nodes, you can see how the components are linked together. In all the components that represent the TPP executables there will be an input file that is linked to the previous component's output file and an output file that will be linked to by the next component's input file. Both these parameters are marked as value required by module since they always must be specified. The input value specifies what value it is linked to in the previous component. The ouput value has a check box to lock value. If this is checked for any parameter, then that parameter's value will not be able to be changed when the workflow is run.

The ASAP Ratio component has a few other parameters set to run XInteract as ASAP Ratio.

ASAP Ratio parameters

Click on the component and in the parameter form, chose the General Parameters tab
Click on the arrow at the bottom of the form to bring up the Advanced parameters
Notice that the field in the upper left is set to not run PeptideProphet
Click on Back to return to the workflow diagram

Click on the ASAP Parameters tab
Notice that in the upper left, the ASAP Options parameter is specified
Click on Back to return to the workflow diagram

We will come back to this form later to set more parameters.

Pepxml parameters

Click on Pepxml
Notice that The output file has a default
regex:|:{0}|:|PepXML Input File:|:(.+).tandem:|:$1.pep.xml by beginning with regex, this tells the workflow to use the PepXML Input File name and replace the extension of tandem with pep.xml
Since this is not marked as locked by the workflow, you can change this if you want.
Click on Back to return to the workflow diagram

Setup the initial input

Template Params File

This file defines the database search parameters that override the full set of default settings referenced in the file isb_default_input.

In this example, the mass tolerance is set to -2.1 Da to 4.1 Da in the template parameter file, and the residue modification mass is set to 57.021464@C. A wide mass tolerance is used to include all the spectra with precursor m/z off by one or more isotopic separations; the high accuracy achieved by the instrument is then modeled by PeptideProphet with the accurate mass model.

For more information, please go to TANDEM

Click on Template Params File
In the form, click on the Browse button
In the file browser, open the tandem folder and choose tandem.xml then click on the Select file button
Back in the form, click on 'Save' and then 'Back' to return to the workflow diagram page

Note that the form states that the value is required to run the workflow

Seq Database

This fasta file contains the Yeast protein sequences

Click on Seq Database
In the form, click on the Browse button
In the file browser, open the dbase folder and then the speclibs folder.
Choose yeast_orfs_all_REV.20060126.short.fasta then click on the Select file button
Back in the form, click on 'Save' and then 'Back' to return to the workflow diagram page

Runpath

Click on Runpath
Note that the form is grayed out and that the value is locked by the workflow.
Whatever runs are generated initiating from this template, a directory will be created for the run files. The initial files and the files generated by X!Tandem will go in this subdirectory.
Click on 'Back' to return to the workflow diagram page

MzXML File will not be set yet, this will be the final input before the workflow is run.

Setting Peptide Prophet parameters

There is one more set of parameters to be set based on the high accuracy of the MS/MS then the template can be saved as a workflow

Peptide Prophet parameters

Click on the Peptide Prophet module
Click on the Peptide Prophet tab
Find the PeptideProphet options parameter in the upper left
Check the specify options? check box
Since this template is being set up for high accuracy MS/MS, also check the lock value check box
Find the use accurate mass binning in PeptideProphet parameter in the third column
Check the specify options? check box
Also check the lock value check box
Click on 'Back' to return to the workflow diagram page

Saving as a workflow

Now save the template as a workflow. The template is now set up for high accuracy MS/MS. For this workflow we will setup the parameters for how the SILAC samples were prepared. If different isotopes are used for other SILAC runs, then the template can be saved as another workflow to capture that difference.

Choose Save as
Fill in MyWorkflow for the Name
Choose the Workflow button
Click the Save button

ASAP Ratio parameters

The sample specific parameters can now be set for ASAP Ratio

Click on the ASAP Ratio module
Click on the ASAP Parameters tab

change labeled residues parameter

Find the change labeled residues parameter at the top of the second column
Check the value needed? check box to let the workflow know this value will need to be set in order to run the workflow
Select K and R from the dropdown
leave lock value unchecked to allow this to be changed for a run if desired

range around precusor m/z to search for peak parameter

Find the range around precusor m/z to search for peak parameter in the middle of the first column
Check the value needed? check box
Select K and R from the dropdown

specified label masses parameter

Find the specified label masses (e.g. M74.325Y125.864), only relevant for static modification quantification parameter at the bottom of the third column
Check the value needed? check box
Set the following three amino acid values:
- Pick M from the Select one: dropdown and set a value of 147.035 and click Add choice
- Pick K from the Select one: dropdown and set a value of 136.10916 and click Add choice
- Pick R from the Select one: dropdown and set a value of 166.10941 and click Add choice
Click the Save button

Save as a compiled workflow

Now save the workflow as a compiled workflow. This will lock in the choices made and allow the compiled workflow to be run as many times as desired.

Click the 'Compile workflow' button
Name the workflow MyCompiledWorkflow
Click the Compile button

This will take you to the Compiled Workflows form and allow you to setup and run a workflow.

Run a workflow

Setup and run a workflow

HilightMy Compiled Workflow in the Compiled Workflows page
Click the Setup run button
In the Setup to run dialog, name the run MyFirstRun
Click the Setup button

Because the number of parameters that are required are drastically reduced at this point, the tabs reflect the components of the workflow.

ASAP Ratio

Click on the ASAP Ratio tab
Notice that we see the parameters that were required but not locked. These parameters can be changed
Click the arrow at the bottom of the form
Notice that this brings up the form that shows the values that are locked for this module.

MzXML File

Now click on the MzXML File tab to add the final paramter value to run the workflow
Click the Browse button
Open the tandem folder
Hilight OR20080317_S_SILAC-LH_1-1_01.mzML
Click the Select files button
Back on the parameter form clcik Save

Run the Workflow

Click the Run button

This brings up the workflow diagram which updates to show a graphical depiction of the workflow running. When it completes it will go to the output files form with a directory tree of where the output files ahve been saved.

Exploring the output

Place holder for now, a right click will be used to bring up the choices based on the file type

You can run the visualization and analysis tools in the output files form.

PeptideProphet results

Open the peptide_prophet directory
Click on interact.pep.shtml file
This will open a viewer. Sort the list in descending order based on Probabilities. The identifications at the top of the resulting list are most likely to be correct. Click on the hypertext link for any probability. This brings up a details page IMG:PlotModel which shows graphically how successful the modeling was. In the upper pane, it is desirable for the red curve (sensitivity) to hug the upper right corner, and for the green curve (error) to hug the lower left corner. The lower pane shows how well the data (black line) follows the PeptideProphet modeling for each charge state. The blue curve describes the modeling of the negative results, and the purple one, the positive results. If these two curves are well separated and fit the black line well, then the analysis for that charge state was successful.
Click the Close button

Click on the interact.pep.xml file
This will open the file using the PepXML viewer application.
Click on the Other Actions top-level tab, and then on the Generate Pep3D button. A new window will launch the Pep3D viewer.
Leave the default options (or change to taste) and click on the Generate Pep3D Image button.
After a few moments, you should see an image displayed on the page for per mzML input file. [http://tools.proteomecenter.org/wiki/index.php?title=Image:Pep3D.JPG

Inter Prophet results

Open the inter_prophet directory
Click on the interact.pep.shtml file to view and analyze the results. IMG:iprophet
Click the Close button

ASAP Ratio results

Open the asap_ratio directory
Click on the asap.pep.shtml file to view and analyze the results. The “asapratio” column contains quantitation results with a link to the ASAPRatio ion trace. The number listed in the “asapratio” column is the light to heavy ratio. IMG:ASAPRatioProfiles
Click the Close button

Protein Prophet results

Open the protein_prophet directory
Click on the asap.pep.shtml file to view and analyze the results. Protein groups are sorted in descending order by Probability so that the groups at the top of the page are the most confident identifications. The protein probabilities are the red numbers listed next to each protein group. IMG:Protxml
Click the Close button

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP_SEWW_Demo2012"

 === 1. Download and install the TPP ===
-To install on your Windows system as a localhost, please follow our TPP [[Windows Installation Guide]], making sure that you select to download the latest version of TPP from
+To install on your Windows system as a localhost, please follow our TPP [[Windows Installation Guide]], making sure that you select to download the latest version of TPP from our [http://sourceforge.net/projects/sashimi/files/ Sourceforge download site].
-our [http://sourceforge.net/projects/sashimi/files/ Sourceforge download site].
 As a way to verify that the installation was successful, log into ''Petunia'' by double-clicking on the '''Trans-Proteomic Pipeline''' flower icon on your Desktop or through
-the '''Start''' menu.  Alternatively, you can open a browser window into the following URL: http://localhost/tpp-bin/tpp_gui.pl . You can use the credentials ''guest'' and
+the '''Start''' menu.  Alternatively, you can open a browser window into the following URL: http://localhost/tpp-bin/tpp_gui.pl . You can use the credentials ''guest'' and ''guest'' as user name and password to log in.
-''guest'' as user name and password to log in.
+Make sure that the WEBSERVER_ROOT environment variable is set.  From the start menu check ''Control Panel.System.Advanced system settings.Environment Variables...''.  If you chose the default location for Petunia, WEBSERVER_ROOT should be ''c:/Inetpub/wwwroot''
-Make sure that the WEBSERVER_ROOT environment variable is set.  From the start menu check ''Control Panel.System.Advanced system settings.Environment Variables...''.  If you
-chose the default location for Petunia, WEBSERVER_ROOT should be ''c:/Inetpub/wwwroot''
 === 2. Install Jetty and WISB ===
-To install on your Windows systems, please go to [http://sourceforge.net/projects/sashimi/files/ Sourceforge download site] and select ''jetty-distribution-
+To install on your Windows systems, please go to [http://sourceforge.net/projects/sashimi/files/ Sourceforge download site] and select ''jetty-distribution-7.3.0.v20110203wWISB.zip'' for download into the directory you wish to install Jetty (''c:\Jetty'' would be the standard directory).  Right click on the zip file and select extract all.  This will create the subdirectory ''jetty-distribution-7.3.0.v20110203''.  Now create the '''JETTY_HOME''' environment variable by going to ''Control Panel.System.Advanced system settings.Environment Variables...'' from the start menu.  In the ''Systems variables'' field click on ''New ...'' and set ''Variable name:'' to 'JETTY_HOST' and ''Variable value:'' to the directory Jetty was installed to (''c:\Jetty\jetty-distribution-7.3.0.v20110203'' by default).
-.3.0.v20110203wWISB.zip'' for download into the directory you wish to install Jetty (''c:\Jetty'' would be the standard directory).  Right click on the zip file and select
+The Jetty distribution in sashimi has been updated to contain the necessary WISB related files.
-extract all.  This will create the subdirectory ''jetty-distribution-7.3.0.v20110203''.  Now create the '''JETTY_HOME''' environment variable by going to ''Control
-Panel.System.Advanced system settings.Environment Variables...'' from the start menu.  In the ''Systems variables'' field click on ''New ...'' and set ''Variable name:'' to
-'JETTY_HOST' and ''Variable value:'' to the directory Jetty was installed to (''c:\Jetty\jetty-distribution-7.3.0.v20110203'' by default).
-The Jetty distribution in sashimi has been updated to contain the necessary WISB related files
 === 3. Configure WISB ===
-To configure your Windows systems, please go to [http://sourceforge.net/projects/sashimi/files/ Sourceforge download site] and select ''wisb-svc-1.0.config.zip'' for download
+To configure your Windows systems, please go to [http://sourceforge.net/projects/sashimi/files/ Sourceforge download site] and select ''wisb-svc-1.0.config.zip'' for download into some temporary directory.  Right click on it and select ''Extract all'' into the temp directory.  The following two files should be present:
-into some temporary directory.  Right click on it and select ''Extract all'' into the temp directory.  The following two files should be present:
 * createparamfile-1.0-SNAPSHOT.jar
 * initial-modules-workflows.config.xml
-Move ''createparamfile-1.0-SNAPSHOT.jar'' into $WEBSERVER_ROOT$\tpp-bin
+Move ''createparamfile-1.0-SNAPSHOT.jar'' into ''$WEBSERVER_ROOT$\tpp-bin''.
-Go to $JETTY_HOST$/ and double click on start.bat to start the Jetty server (double clinking on stop.bat will stop the service).  Open Mozilla Firefox or Google Chrome and
+Go to $JETTY_HOST$/ and double click on start.bat to start the Jetty server (double clinking on stop.bat will stop the service).  Open Mozilla Firefox or Google Chrome and copy the following URL into the address window: [http://localhost:8888/wisb-svc-1.0-SNAPSHOT/html/bootstrap.html].  Fill in a user name (no validation is done in this version) and click on the ''bootstrap'' button.  This will take you to the WISB start page.  Click the ''Load config(s)'' button and in the window select ''initial-modules-workflows.config.xml''.  From the start page click on the ''Templates and workflows'' button and you should see, as a template, ''Tandem To Protein Prophet Template''.
-copy the following URL into the address window: [http://localhost:8888/wisb-svc-1.0-SNAPSHOT/html/bootstrap.html].  Fill in a user name (no validation is done in this
-version) and click on the ''bootstrap'' button.  This will take you to the WISB start page.  Click the ''Load config(s)'' button and in the window select ''initial-modules-
-workflows.config.xml''.  From the start page click on the ''Templates and workflows'' button and you should see, as a template, ''Tandem To Protein Prophet Template''.
 == WISB Demo ==
 === 1. Download and install the test data and database ===
-For this demo, we will be using a SILAC-labeled Yeast dataset, comprised of 2 runs on a high mass-accuracy Orbitrap instrument, along with a Yeast database appended with
+For this demo, we will be using a SILAC-labeled Yeast dataset, comprised of 2 runs on a high mass-accuracy Orbitrap instrument, along with a Yeast database appended with decoys.  We also include a search parameters file.  This is the same as for the Petunia demo.
-decoys.  We also include a search parameters file.  This is the same as for the Petunia demo.
 * [ftp://ftp:a@ftp.peptideatlas.org/pub/PeptideAtlas/Repository/TPP_Demo2009/TPP_Demo2009_mzML_data.zip download the mzML files] (768Mb) and unzip.
 * Copy or move the ''yeast_orfs_all_REV.20060126.short.fasta'' file into the folder ''C:\Inetpub\wwwroot\ISB\data\dbase''
-* Copy or move the two data files (''OR20080317_S_SILAC-LH_1-1_01.mzML'' and ''OR20080317_S_SILAC-LH_1-1_11.mzML'') as well as the tandem parameters file ''tandem.xml'' into
+* Copy or move the two data files (''OR20080317_S_SILAC-LH_1-1_01.mzML'' and ''OR20080317_S_SILAC-LH_1-1_11.mzML'') as well as the tandem parameters file ''tandem.xml'' into the folder ''C:\Inetpub\wwwroot\ISB\data\demo2009\tandem''. Create this last folder if necessary.
-the folder ''C:\Inetpub\wwwroot\ISB\data\demo2009\tandem''. Create this last folder if necessary.
 == 2. Setup the template ==
 From the start page click on the ''Templates and workflows'' button.
+''Tandem To Protein Prophet Template'' is owned by public and is not editable.  You should select it and do a ''Save as'', choosing whatever name you would like and, for this demo, as a template.  Selecting the template brings up the graphical representation of the workflow diagram.  Notice that the ASAPratio module is included since these are SILAC based samples.  Clicking on a component will bring up the parameter form for it, a right click will bring up a description.
-''Tandem To Protein Prophet Template'' is owned by public and is not editable.  You should select it and do a ''Save as'', choosing whatever name you would like and, for this
-demo, as a template.  Selecting the template brings up the graphical representation of the workflow diagram.  Notice that the ASAPratio module is included since these are
-SILAC based samples.  Clicking on a component will bring up the parameter form for it, a right click will bring up a description.
 As best practice, the template should have parameters set that do not vary for the particular MS/MS device that produced the files.
 * Click on the ''ASAP Parameters'' tab
-* Notice that in the upper left, the ''ASAP Options'' parameter is specified.
+* Notice that in the upper left, the ''ASAP Options'' parameter is specified
 * Click on ''Back'' to return to the workflow diagram
-We will come back to this form later to set more parameters
+We will come back to this form later to set more parameters.
 ''Pepxml'' parameters
 * Click on Pepxml
 * Notice that ''The output file'' has a default
-* ''regex:|:{0}|:|PepXML Input File:|:(.+).tandem:|:$1.pep.xml'' by beginning with regex, this tells the workflow to use the ''PepXML Input File'' name and replace the
+* ''regex:|:{0}|:|PepXML Input File:|:(.+).tandem:|:$1.pep.xml'' by beginning with regex, this tells the workflow to use the ''PepXML Input File'' name and replace the extension of ''tandem'' with ''pep.xml''
-extension of ''tandem'' with ''pep.xml''
 * Since this is not marked as locked by the workflow, you can change this if you want.
 * Click on ''Back'' to return to the workflow diagram
 ''Template Params File''
 :''This file defines the database search parameters that override the full set of default settings referenced in the file isb_default_input.''
-:''In this example, the mass tolerance is set to -2.1 Da to 4.1 Da in the template parameter file, and the residue modification mass is set to 57.021464@C. A wide mass
+:''In this example, the mass tolerance is set to -2.1 Da to 4.1 Da in the template parameter file, and the residue modification mass is set to 57.021464@C. A wide mass tolerance is used to include all the spectra with precursor m/z off by one or more isotopic separations; the high accuracy achieved by the instrument is then modeled by PeptideProphet with the accurate mass model.''
-tolerance is used to include all the spectra with precursor m/z off by one or more isotopic separations; the high accuracy achieved by the instrument is then modeled by
-PeptideProphet with the accurate mass model.''
 :''For more information, please go to [http://www.thegpm.org/TANDEM/api/ TANDEM]''
 * Click on ''Runpath''
 * Note that the form is grayed out and that the value is locked by the workflow.
-* Whatever runs are generated initiating from this template, a directory will be created for the run files.  The initial files and the files generated by X!Tandem will go in
+* Whatever runs are generated initiating from this template, a directory will be created for the run files.  The initial files and the files generated by X!Tandem will go in this subdirectory.
-this subdirectory.
 * Click on 'Back' to return to the workflow diagram page
-''Mz X M L File'' will not be set yet, this will be the final input before the workflow is run.
+''MzXML File'' will not be set yet, this will be the final input before the workflow is run.
 === Setting ''Peptide Prophet'' parameters ===
 === Saving as a workflow ===
-Now save the template as a workflow.  The template is now set up for high accuracy MS/MS.  For this workflow we will setup the parameters for how the SILAC samples were
+Now save the template as a workflow.  The template is now set up for high accuracy MS/MS.  For this workflow we will setup the parameters for how the SILAC samples were prepared.  If different isotopes are used for other SILAC runs, then the template can be saved as another workflow to capture that difference.
-prepared.  If different isotopes are used for other SILAC runs, then the template can be saved as another workflow to capture that difference.
 * Choose ''Save as''
 ** Pick ''K'' from the ''Select one:'' dropdown and set a value of '''136.10916''' and click ''Add choice''
 ** Pick ''R'' from the ''Select one:'' dropdown and set a value of '''166.10941''' and click ''Add choice''
 * Click the ''Save'' button
 ''ASAP Ratio''
 * Click on the ''ASAP Ratio'' tab
-* Notice that we see the parameters that were required but not locked.  Thes parameters can be changed
+* Notice that we see the parameters that were required but not locked.  These parameters can be changed
 * Click the arrow at the bottom of the form
 * Notice that this brings up the form that shows the values that are locked for this module.
 * Click the ''Run'' button
-This brings up the workflow diagram which updates to show a graphical depiction of the workflow running.  When it completes it will go to the output files form with a
+This brings up the workflow diagram which updates to show a graphical depiction of the workflow running.  When it completes it will go to the output files form with a directory tree of where the output files ahve been saved.
-directory tree of where the output files ahve been saved.
 === Exploring the output ===
-'''''Place holder for now'''''
+'''''Place holder for now, a right click will be used to bring up the choices based on the file type'''''
 You can run the visualization and analysis tools in the output files form.
 * Open the ''peptide_prophet'' directory
 * Click on ''interact.pep.shtml'' file
-* This will open a viewer.  Sort the list in descending order based on Probabilities.  The identifications at the top of the resulting list are most likely to be correct.
+* This will open a viewer.  Sort the list in descending order based on Probabilities.  The identifications at the top of the resulting list are most likely to be correct.  Click on the hypertext link for any probability.  This brings up a details page [http://tools.proteomecenter.org/wiki/index.php?title=Image:PlotModel.JPG IMG:PlotModel] which shows graphically how successful the modeling was. In the upper pane, it is desirable for the red curve (sensitivity) to hug the upper right corner, and for the green curve (error) to hug the lower left corner. The lower pane shows how well the data (black line) follows the PeptideProphet modeling for each charge state. The blue curve describes the modeling of the negative results, and the purple one, the positive results. If these two curves are well separated and fit the black line well, then the analysis for that charge state was successful.
-Click on the hypertext link for any probability.  This brings up a details page [http://tools.proteomecenter.org/wiki/index.php?title=Image:PlotModel.JPG IMG:PlotModel] which
-shows graphically how successful the modeling was. In the upper pane, it is desirable for the red curve (sensitivity) to hug the upper right corner, and for the green curve
-(error) to hug the lower left corner. The lower pane shows how well the data (black line) follows the PeptideProphet modeling for each charge state. The blue curve describes
-the modeling of the negative results, and the purple one, the positive results. If these two curves are well separated and fit the black line well, then the analysis for that
-charge state was successful.
 * Click the ''Close'' button