Installation and configuration instructions for the MassSpec software (see Barbarini et al. Bioinformatics 2009). The MassSpec software can be downloaded freely for non-profit institutions from http://aimed11.unipv.it/MassSpec. Executable files for Windows and LINUX platforms are available. The program requires the user to install the MATLAB runtime libraries, that are distributed together with the MassSpec files. The installation steps are here detailed. MassSpec distribution. ----------------------- The following files can be downloaded from the MassSpec web site: - README (this file) that contains installation instructions and a tutorial to follow for analyzing the provided test data. - MassSpec1.1-WIN.zip that contains all files necessary for installation of MassSpec software on Windows platforms. - MassSpec1.1-MCRInstaller7.6-WIN.zip that contains all files necessary for installation of MassSpec software on Windows platforms, and the version 7.6 of MCRInstaller which is necessary if the same version of the MATLAB library files are not already installed. - MassSpec1.1-LINUXx86_64.zip that contains all files necessary for installation of MassSpec software on Linux 64bits platforms. - MassSpec1.1-MCRInstaller7.4-LINUXx86_64.zip that contains all files necessary for installation of MassSpec software on LINUX 64bits platforms, and the version 7.4 of MCRInstaller which is necessary if the same version of the MATLAB library files are not already installed. - TestData.zip that contains an example mass spectrum (initial resolution power = 8000) in mzXML format ("Example.mzXML") and a directory, called "DatasetTXT", with 20 txt files which constitute a data set of 20 replicates (initial resolution power = 8000) to evaluate MassSpec. How to install MassSpec. ------------------------- 1) Download the distribution file for the desired platform. 2) Extract all files from MassSpecX.X zip file on a temporary directory. 3) Install the MATLAB libraries trough the MCRInstaller (if the same version of the MATLAB library files are not already installed) in the following way: - for Windows machines a) run the MCRInstaller.exe. The setup wizard starts. b) add the following directory to your system path (on Windows XP, this directory is automatically added to your path) \ver\runtime\win32 - for Unix machines a) copy the MCRInstaller.zip in the installation directory and unzip the MCRInstaller.zip file. b) update your dynamic library path as follows: *Linux x86 32bit* export LD_LIBRARY_PATH="//bin/glnx86://runtime/glnx86://sys/os/glnx86://sys/java/jre/glnx86/jre1.5.0/lib/i386/native_threads://sys/java/jre/glnx86/jre1.5.0/lib/i386/client://sys/java/jre/glnx86/jre1.5.0/lib/i386:" export XAPPLRESDIR="//X11/app-defaults" unset LANG *Linux x86-64 64bit. export LD_LIBRARY_PATH="//runtime/glnxa64: //sys/os/glnxa64://sys/java/jre/glnxa64/jre1.5.0/lib/amd64/native_threads://sys/java/jre/glnxa64/jre1.5.0/lib/amd64/client://sys/java/jre/glnxa64/jre1.5.0/lib/amd64/server://sys/java/jre/glnxa64/jre1.5.0/lib/amd64:" export XAPPLRESDIR="//X11/app-defaults" Note. If you have already installed MATLAB on your machine there is a limitation regarding directories on your path: this tool requires that mcr_root directory is first on the path, MATLAB requires that the matlabroot directory is first on the path. 4) Copy the MassSpec executable file in your application root directory 5) Run for the first time the MassSpec executable file and close the application clicking on the exit button on the left top of the screen. In this step the MassSpec_mcr directory and its subdirectories are created. 6) Extract all files from TestData.zip file. 7) Run again the MassSpec executable file and try the two examples presented here. Tutorial: two examples. ------------------------ A- Single spectrum (mzXML format) 1) Select the radiobutton "Create new project" on the left in the first tabbed panel "Load Data" 2) Select the radiobutton "Select a raw file:" on the top and then select "Example.mzXML" file in the TestData directory by "Browse" button 3) To change the name of the project directory which will be created, click on "Change" button. 4) Click in "Create project" button to create the new project and wait till the spectrum appears on the bottom. The project directory will appear on the top on the screen. 5) Use plot/image radiobutton to change the type of visualization. Select a region of the spectrum keeping the button pressed to zoom on such a region. Click on the button on the right top of the spectrum to come back to the original zoom. 6) Pass to the "Preprocessing" tabbed panel, select the preprocessing operation (e.g. Standard=double baseline adjust) by the pop-up menu to apply on the current data shown on the top. 7) Click on "Apply" button to apply the preprocessing operation selected and wait till the resulting spectrum appears on the bottom. 8) Click on the "Save prepr.data as current data" to save preprocessed spectrum as current spectrum. 9) Pass to the "Peak list extraction" tabbed panel, insert initial resolution power of the loaded data (in this case is about 8000). 10) Select by pop-up menu the maximal ionization charge of the loaded data (in this case z=1). 11) Select by pop-up menu the method to apply for calculating the intensity threshold for peak selection (e.g. "Data dependent"). When "Constant" method is selected, insert also the number of highest peaks to consider for peak list (isotopic distributions) extraction. 12) At last check one or more reference amino acid to use for theoretical isotopic distribution generation (e.g. "AverageUpdated"). 13) Click on "Peak list extraction" button to perform all the operations needed fot peak list generation and wait till the spectrum appears on the bottom. 14) To explore the results you can zoom on the spectrum on the bottom or click on a row of the preview of peak list to visualized in the spectrum on the top the single isoopic distribution. 15) Click on "Export peak list" button to export the peak list in a txt file as visulatized in the preview with or without header line. You can add or remove columns by check box and select by which coluns sort the list by "Order by" pop-up menu. 16) Click on exit button on the right top to close the application and to load this project: - run again the MassSpec executable file; - select the radiobutton "Create new project" on the left in the first tabbed panel "Load Data"; - select the project directory by "Browse" button; - select which type of data to load as current data; - then click on "Load project" button. PS: In project directory the result of each perfomed operation is stored; when such a operation is already required the result is simply reloaded and not recalculated. B- Dataset of replicates spectra (TXT-ASCII) 1) Select the radiobutton "Create new project" on the left in the first tabbed panel "Load Data" 2) Select the radiobutton "Select folder containing raw files:" on the top and then select "DatasetTXT" directory in the TestData directory by "Browse" button 3) Follow the steps described for example A from 3 to 12. In this case 20 replicates spectra are plotted. Use the same parameter of example A: resolution power 8000 and ionization charge z=1. 4) To use optional functionalities (Spectra alignment and management of overlapping isotopic distributions), check on the flag under "Peak list extraction" button. 5) Click on "Peak list extraction" button to perform all the operations needed fot peak list generation and wait till the spectrum appears on the bottom. 6) To explore and export the results, and then to reload the project, follow the steps described for example A from 13 to 16.