Introduction

M2Lite is a lightweight, easily pluggable, and extremely fast conversion software tool. M2Lite converts msf files to the proteomics community standard mzIdentML file format

Configuration

SYSTEM REQUIREMENT

• Java 6 or above. You may download the latest version from http://www.java.com/en/download/index.jsp
• R 2.15.2 or above. You may download the latest version from http://www.r-project.org/
• 2GB RAM available memory for program to run

NB: These represent minimum requirement of the system on which M2Lite was built and well tested. Also note, M2Lite was built and well tested in the Windows operating system environment

HOW TO INSTALL

• Download the program folder
• Unzip M2Lite3.0.XXXX.XX.XX.zip folder
• Install CRAN R program
• Install R package "RSQLite"
• Set "Rscript" program file as a path enviroment variable
• Place M2Lite3.0.XXXX.XX.XX folder in directory of choice

RUNNING THE PROGRAM

• Navigate to Program directory/folder
• Modify the "M2Lite.config" SearchDBPath option accordingly. This is the RefSeq protein database file full path.
• Run the command

    java -Xmx2G -cp ./M2Lite.jar msfparser.M2Lite [FILE|DIRECTORY] [mzid|pepXML|text]

** NOTES ON GENERATING TPP (Trans Proteomics Pipeline) COMPATIBLE pepXMLs. This simply requires modifying the 'M2Lite.config' file option TPPCompatibleOutput=TRUE. If you intend to use the generated pep.xml files in TPP, we recommend that you convert the MSF files in a TPP "inetpub/wwwroot/ISB/data" subdirectory (because it appears TPP will not permit you to run analysis on files outside its "inetpub/wwwroot/ISB/data" subdirectory tree. Also, for spectra information, TPP requires mzXML or mzML files of corresponding pep.xml files generated. Therefore, place the Proteome Discoverer searched mzML file(s) in the same TPP inetpub/wwwroot/data subdirectory in which your MSF(s) were converted.

The M2Lite.config

The ".config" file contains the program associated default and user-modifiable options. The currently implemented options include;

• RDBQueryFilesLibrary - indicates the directory in which the R-program component library scripts are placed. Defaults to ./lib/rLib

• SearchDatabaseType - indicates the database type of the searched database. It currently defaults to an NCBI RefSeq database REFSEQ. Other alternate option is IPIv387 i.e the deprecated International Protein Index protein sequence database. Theoretically, any other database type should still run.

• SearchDBPath - The full file path to the searched database, e.g /Users/home/full-path-to-database

• IncludeiTRAQ4plexValues - indicates whether to include iTRAQ values in the MSF file. This option is only useful when the user requested output is the tab-delimited output type. Option defaults to FALSE.
• includeProteinsInTextOutput - A logical, applicable to text conversion only. It specifies whether proteins to which peptide spectrum matches are found should be included in the text output.
• FileChooserOption - Options indicates whether to initiate a file chooser window to select MSF files to convert. In which case the [FILE|DIRECTORY] path is expected to be a directory. It defaults to FALSE.
• TPPCompatibleOutput - A logical, applicable to pepXML conversion only. It specifies whether the derived pepXML(.pep.xml) should be compatible with the Trans-Proteomics Pipeline (TPP)