SpecNote Instructional Manual

 

Kebing Yu

03/16/2009

1. Deploying source code

(Basic knowledge of Java programming and MySQL database is requried to compile SpecNote binaries)

There are three main versions of SpecNote you can build from source code:

1. SpecNote Applet -explore, validate and annotate MS/MS spectra in a web browser;
2. SpecNote PDF db -create a single PDF file for all MS/MS spectra stored in database;
3. SpecNote PDF disk -create a single PDF file for all MS/MS spectra stored on disk (distributed separately and no modification required); 

[Java] To deploy SpecNote source code in the Eclipse Environment, start a new java project and create project from existing source. Right click on the just created project and choose properties. Choose "Java Build Path" from left menu and choose the "Libraries" tab. Please make sure all libraries are sourced correctly: ....

To make one single Jar file that includes all libraries, fat jar eclipse plug-in has to be installed. Fat jar plug-in can be downloaded from http://fjep.sourceforge.net/ and follow its instruction to install it. Right click on the project and click on "build fat jar" to create a single binary executable.

You will need to change some parameters in the source code and recompile it to enable SpecNote applet function in your own system. To install SpecNote Applet, copy compiled vmsdb_applet.jar and vmsdb.asp to a folder and host them on a web server that supports ASP scripting language.

Java Runtime Environment 1.6 or higher needs to be installed in order to run SpecNote Applet or SpecNote PDF; 

[MySQL] MS/MS data are stored in MySQL tables and feed to SpecNote as the data source. In those tables, a numeric primary key 'fmcounter' is created as a unique idetifier for SpecNote to pull data out of MySQL database. Run mysql_table.sql to create those tables or change table names and field names in the SpecNote source code to adapt your own database system.

2. Modifying source code for your database

There is only one file you need to change if you are using tables created by mysql_table.sql. In file database.java, line 46:

change the database host, port, username and password according to your settings. Only the line with Mysql needs to be updated if you are using MySQL database.

Otherwise if you have your own table names and field names, update SQL queries in line 48, 68, 84, 108, 128, 154 of file database.java, SQL query (get DTA file content) in line 20 of file InternalAppletMZParser.java and SQL query (get OUT file content) in line 19 of file InternalAppletSOParser.java


3. Compiling binary exectuables

A configuration file is used to control which types of output file is generated. In Config.java, the following variables are set to switch work flows:

To build SpecNote Applet, set: APPLET_MODE=true; PDF_disk=false; DB_TYPE="mysql" (if you use postgresql, then set to pgsql). when building fatjar, choose 'vmsdb' as main class
To build SpecNote PDF db, set: APPLET_MODE=false; PDF_disk=false; DB_TYPE="mysql" (if you use postgresql, then set to pgsql). when building fatjar, choose 'vmsdb_pdf' as main class.
To build SpecNote PDF disk, set: APPLET_MODE=false; PDF_disk=true; DB_TYPE="disk". when building fatjar, choose 'vmsdb_pdf' as main class

4. Viewing and annotating your spectra - SpecNote Applet

SpecNote Applet allows you to maunally validate and annotate MS/MS spectra in a web browser. Data are read and write between Java interface and database back server. If your SpecNote Applet jar file is not 'vmsdb.jar', vmsdb.asp need to be modified (archive="{your_pack}.jar").  In any web browser, type http://your_webserver_url/vmsdb.asp?fmcounter=_spectra_identifier_required_&name=_protein_name_optional_. This will bring up the SpecNote Applet and display spectrum in window.

You can invoke the configuration panel in SpecNote Applet by press space button in the program window. Different ion types, such as b,y c, z, a, and x, as well as neutral loss of water, ammonia, and phosphate can be labeled. Also you may adjust the labeling threshold, the divisions of x-axis, and alter the sequence or modification site of the peptide.

By clicking on the modified amino acid and using the arrow key on the keyboard, to make a quick comparison of different repositioned post-translational modifications in both peak assignment and sequence coverage.


5. Creating PDF spectra from DTA/OUT in database - SpecNote PDF db

To make pdf spectra files from dta and out stored in database, SpecNote PDF db should be launched. First, a text file 'counters.txt' with a list of unique identifiers in database that point to DTA/OUT data is created in c:\. An example of the file format is illustrated here: (in general the format is identifier@protein_name, one line per spectrum)

Then in command window, run: java -Xms256M -Xmx1024M -jar "path_to_your_SpecNote_PDF_db_jar_file". All spectra are merged to a single pdf file which is located at {your_desktop}\output\*.pdf


6. Creating PDF spectra from DTA/OUT on disk - SpecNote PDF disk
[distributed separately]
To install SpecNote PDF disk, make sure Java Runtime Environment 6 or higher is installed in the system(www.java.com). Unzip software package to any folder.

In windows operating system, launch SpecNote PDF by double clicking the .bat file. In the resulting command terminal, input the folder name that contains .dta and .out files and in the following dialog input the folder name to save output files. The program automatically generates pdf files for all input dta/out pairs and then concatenates them into a single pdf file.
Note: .dta and .out should be in the same folder and ones with same filename (exclude extension) are paired together. Refer to 'Sample' folder as an example.

On a mac running OS X, simply run the mac create spetcra program and follow the on-screen instructions.

(a universal command to run SpecNote PDF disk is: java -Xms56M -Xmx512M -jar specnote_pdf_disk_obf.jar)