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Home modified by Giese, Sven

Giese, Sven — Thu, 17 Oct 2013 11:24:03 -0000

--- v4
+++ v5
@@ -2,7 +2,7 @@

-1) How to use apmsWAPP in a integrated workflow? [LINK](https://sourceforge.net/p/apmswapp/wiki/KNIME/)
+1) How to use apmsWAPP in an integrated workflow? [Tutorial](https://sourceforge.net/p/apmswapp/wiki/KNIME/)

 The wiki uses [Markdown](/p/apmswapp/wiki/markdown_syntax/) syntax.

Home modified by Giese, Sven

Giese, Sven — Thu, 17 Oct 2013 11:23:41 -0000

--- v3
+++ v4
@@ -2,7 +2,7 @@

-How to use apmsWAPP in a integrated workflow?
+1) How to use apmsWAPP in a integrated workflow? [LINK](https://sourceforge.net/p/apmswapp/wiki/KNIME/)

 The wiki uses [Markdown](/p/apmswapp/wiki/markdown_syntax/) syntax.

Home modified by Giese, Sven

Giese, Sven — Thu, 17 Oct 2013 11:22:30 -0000

--- v2
+++ v3
@@ -1,49 +1,9 @@
 Welcome to the apmsWAPP wiki!

-Find below a short introduction how to use the apmsWAPP implementation in a complete proteomics workflow. The workflow contains the following steps: decoy database creation, spectra converting, spectra identification and the reliable quantification via apmsWAPP. The workflow is realized making use of the OpenMS framework integrated to KNIME. 

-Dependencies
-------------------
-- KNIME
-- OpenMS
-- R
-- OpenMS (Knime plugin)
-- R Scripting (Knime Plugin)

-Most dependencies are straight forward to install. To ensure that the R Scripting plugin works correctly you should carefully read the instructions at https://github.com/knime-mpicbg/knime-scripting/wiki. To start the RServer follow the instructions given here https://github.com/knime-mpicbg/knime-scripting/wiki/R-server-for-knime . If  R is installed and the RServer is working you will probably need to configure the R path in KNIME, as well as the connection details for the communication between KNIME and R. In KNIME: File->Preferences->KNIME->R Scripting – just fill in the field near “Location of R…” and check if the “localhost” value is equal to the one described in the RServer installation instructions.
+How to use apmsWAPP in a integrated workflow?

-Preparing the workflow
-------------------
-- start knime and import the workflow via: File -> Import Knime-workflow
-- Before executing any nodes it is strictly necessary to split your Bait and Control files into 2 separate folders.
-- Select the node named “FASTA Reference” and choose your FASTA reference, as well as the “Decoy Reference” node and create an output fasta file. 
-Execute the 3 nodes in “(0) Prepare Database Searching” by selecting them and hitting “F7”.
-- Most MS/MS identification tools require the input to be in blast database format. To convert the fasta file to this format you need to run the following command on a commandline: makeblastdb -in my.fasta -dbtype prot -parse_seqids
-- The “Choose Files” nodes expect files present in mzml format. If the spectra files does not have this format you need to run the three converter nodes. Conifgure these three nodes to match your desired in- and output files and the fileformat. OpenMS provides also the commandline tool “FileConverter” to convert the files. Assuming the spectra is in mgf format the syntax would be:  
-FileConverter –in file1.mgf  –out file1.mzml 
-
-Executing the workflow
-------------------
-- Select the “Choose Control Files” node and point it to the directory where your control files are located (the same procedure needs to be repeated for the bait files in the lower node)
-- Configure the nodes in the “(4) Write (Intermediate) Results” window if you wish to have a look at these files.
-- Configure the nodes in the “(5) Plotting” window if you wish to save some basic plots
-- After initializing all nodes with their respective outputfile (and successful converting / preparation of the databases) the workflow can be executed.
-
-Customizing the workflow
-------------------
-Most MS/MS identifications differ in their settings based on instrument resolution and preparation protocols. To adjust the workflow to your specific wishses go to the respective node and change the settings the way you prefer. For that matter the OpenMS nodes are of primary interest. OpenMS nodes are:
-
-- DecoyDatabase – settings for the creation of the decoy database
-- OMSSAAdapter – adapter to run he popular OMSSA search engine. This node can be replaced by any other *Adapter. Modifications, mass tolerances etc. is set here.
-- PeptideIndexer – annotation of decoy and reference hits, as well as sequence coverage support.
-- FalseDiscoveryRate – select FDR computation modes (i.e. FDR, qvalue)
-- IDFilter – Filter results based on constraings (FDR, qvalue, shared peptides, modifications)
-
-Each of these nodes occurs twice (in the bait analysis and the control analysis). It is sufficient to adjust one set of nodes and copy these to the other metanode (ATTENTION(!) only the OpenMS nodes can be interchanged without destroying the workflow)
-
-Links:
-[OpenMS](http://open-ms.sourceforge.net/)
-[KNIME](http://www.knime.org/)

 The wiki uses [Markdown](/p/apmswapp/wiki/markdown_syntax/) syntax.

Home modified by Giese, Sven

Giese, Sven — Thu, 17 Oct 2013 08:38:20 -0000

--- v1
+++ v2
@@ -1,6 +1,49 @@
-Welcome to your wiki!
+Welcome to the apmsWAPP wiki!

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
+Find below a short introduction how to use the apmsWAPP implementation in a complete proteomics workflow. The workflow contains the following steps: decoy database creation, spectra converting, spectra identification and the reliable quantification via apmsWAPP. The workflow is realized making use of the OpenMS framework integrated to KNIME. 
+
+Dependencies
+------------------
+- KNIME
+- OpenMS
+- R
+- OpenMS (Knime plugin)
+- R Scripting (Knime Plugin)
+
+Most dependencies are straight forward to install. To ensure that the R Scripting plugin works correctly you should carefully read the instructions at https://github.com/knime-mpicbg/knime-scripting/wiki. To start the RServer follow the instructions given here https://github.com/knime-mpicbg/knime-scripting/wiki/R-server-for-knime . If  R is installed and the RServer is working you will probably need to configure the R path in KNIME, as well as the connection details for the communication between KNIME and R. In KNIME: File->Preferences->KNIME->R Scripting – just fill in the field near “Location of R…” and check if the “localhost” value is equal to the one described in the RServer installation instructions.
+
+Preparing the workflow
+------------------
+- start knime and import the workflow via: File -> Import Knime-workflow
+- Before executing any nodes it is strictly necessary to split your Bait and Control files into 2 separate folders.
+- Select the node named “FASTA Reference” and choose your FASTA reference, as well as the “Decoy Reference” node and create an output fasta file. 
+Execute the 3 nodes in “(0) Prepare Database Searching” by selecting them and hitting “F7”.
+- Most MS/MS identification tools require the input to be in blast database format. To convert the fasta file to this format you need to run the following command on a commandline: makeblastdb -in my.fasta -dbtype prot -parse_seqids
+- The “Choose Files” nodes expect files present in mzml format. If the spectra files does not have this format you need to run the three converter nodes. Conifgure these three nodes to match your desired in- and output files and the fileformat. OpenMS provides also the commandline tool “FileConverter” to convert the files. Assuming the spectra is in mgf format the syntax would be:  
+FileConverter –in file1.mgf  –out file1.mzml 
+
+Executing the workflow
+------------------
+- Select the “Choose Control Files” node and point it to the directory where your control files are located (the same procedure needs to be repeated for the bait files in the lower node)
+- Configure the nodes in the “(4) Write (Intermediate) Results” window if you wish to have a look at these files.
+- Configure the nodes in the “(5) Plotting” window if you wish to save some basic plots
+- After initializing all nodes with their respective outputfile (and successful converting / preparation of the databases) the workflow can be executed.
+
+Customizing the workflow
+------------------
+Most MS/MS identifications differ in their settings based on instrument resolution and preparation protocols. To adjust the workflow to your specific wishses go to the respective node and change the settings the way you prefer. For that matter the OpenMS nodes are of primary interest. OpenMS nodes are:
+
+- DecoyDatabase – settings for the creation of the decoy database
+- OMSSAAdapter – adapter to run he popular OMSSA search engine. This node can be replaced by any other *Adapter. Modifications, mass tolerances etc. is set here.
+- PeptideIndexer – annotation of decoy and reference hits, as well as sequence coverage support.
+- FalseDiscoveryRate – select FDR computation modes (i.e. FDR, qvalue)
+- IDFilter – Filter results based on constraings (FDR, qvalue, shared peptides, modifications)
+
+Each of these nodes occurs twice (in the bait analysis and the control analysis). It is sufficient to adjust one set of nodes and copy these to the other metanode (ATTENTION(!) only the OpenMS nodes can be interchanged without destroying the workflow)
+
+Links:
+[OpenMS](http://open-ms.sourceforge.net/)
+[KNIME](http://www.knime.org/)

 The wiki uses [Markdown](/p/apmswapp/wiki/markdown_syntax/) syntax.

Home modified by Giese, Sven

Giese, Sven — Wed, 09 Oct 2013 16:07:57 -0000

Welcome to your wiki!

This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

The wiki uses Markdown syntax.

Project Members:

Giese, Sven (admin)