APCF UNITE DOWNLOAD

APCF UNITE can be downloaded by clicking Download UNITE here.

What is UNITE?

Advantages

UNITE let you search mulitple mass-spectrometery search algorithms with a single click.

UNITE automates the conversion of your raw mass-spectometery files.

You can download your results into your local PC for further analysis.

What's new

APCF UNITE is now at Version Release 1.8.6

• UNITE Version Release 1.8.x has the following features:
  • Version Release 1.8.6 has more stable recovery from poor Internet connections. It will not produce errors when veiwing TPP Prophet jobs submitted from UNITE Beta 1.9 (Earlier versions of UNITE will)
  • Version Release 1.8.5 fixes a potential problem with resizing the job submission window.
  • Version Release 1.8.4 fixes a problem with logging into Mascot via Proxy Servers. A button to test Mascot logins is now present in "Preferences" window.
  • Version Release 1.8.3 fixes an error caused by entering the Status Tab before all the data has downloaded.
  • Version Release 1.8.2 fixes a memory bug caused by concatenating large files in the input option. It also has a more precise link to the APCF DTA Generator download page.
  • The mass export of Mascot Files to pepXML and other formats is supported. This is identical to what can be done when viewing the job results from the Mascot Web Page. However this can now be automated across any number of result files. (Note, pepXML files can be very large, and take a long time to generate). This can be accessed from the Mass Download window.
  • UNITE supports raw file conversion using DTA Generator from Josh Coon's Laboratory. A command-line version of DTA Generator can be downloaded from the APCF Wiki
  • Raw file conversion converts Raw files to mgf format (The dta format can have problems due to CR/LF issues)
  • UNITE automatically saves Mascot Daemon ".par" files, and can import them too. This is useful when performing post-processing, or interacting with Mascot Daemon.
  • UNITE now treats .txt files as a mgf format (ABI machines export files as .txt).
  • Status Viewing has been completely rewritten to be considerably faster.
  • Internet connectivity has been made more robust, and UNITE contains internal test facilities for you to test the connection.
  • If users choose to merge input files, then UNITE gives you the option to keep or delete the merged file.
• UNITE Version Release 1.7 has the following features:
  • Compression has been improved by using Win32 GNU executables (which are installed with UNITE). For those not using Windows, users can select to use the .NET native libraries via an option in the Preferences window. A bug in compressing large files has been fixed.
  • Mascot Queuing has been improved. Users can no longer block other users with very large jobs.
• UNITE Version 1.6 has the following features:
  • During Raw File Conversion, users can now specify if they want to keep or delete temproary files. Temporary files are moved into the working directory, automatically overwritting any files of the same name that might be there. Temporary files currently consist of DTA files (extractMSM) or mzXML files (all other programs).
  • A bug was fixed. During Raw File Conversion it was possible for a file to be moved onto itself during the disk cleanup after the file conversion.
• UNITE Verions 1.5 beta has the following features:
  • A Clone button allows users to clone tasks from the Status window. Users select an task or job that has already been run, and then they hit the "Clone" button. This takes them to the Task Editor window with all the search parameter files and spectrum files already loaded. This is useful if users want to run several searches on the same spectrum file with slightly different parameters. Only jobs submitted from UNITE Beta 1.5 onwards contain the full clone information. Earlier jobs can only be partially cloned.
  • The File Conversion Executables window has been re-designed to be clearer. Users can download public-domain tools from this page.
• UNITE Verions 1.4 beta has many improvements
  • UNITE now supports the latest versions of the file-conversion tools from the Seattle Proteome Centre and ProteoWizard. As some command line options have changed, please check your options by hitting the "Command Line Options" button when you do your raw file conversion, and hit "OK" to save your options.
  • UNITE allows you to use different versions of the raw file conversion tools, by allowing you to enter your own command line.
  • UNITE now supports the use of multiple WIFF files embedded in one single WIFF file. These files are treated as separate entities. If you wish to merge them into a single entitiy, please hit "Merge MS/mS files into a single search" checkbox in the Task Editor window.
  • Temporary files in the raw file conversion are now deleted. (i.e. all the individual dta or mzXML files). The output file (i.e. the mgf or merged-dta file) of the raw file conversion is placed in your current working directory. This is to reduce the clutter and size of files in your system.
• APCF UNITE Version 1.3 Beta now correctly displays OMSSA taxonomies. Due to the variations in FASTA formats used in protein databases, OMSSA taxonomies can only be supported on several databases. Please contact the APCF if you have a particular requirement.
• APCF UNITE Version 1.2 Beta now uses Microsoft .NET Framework 3.5. This will be installed automatically from the install script below. The move to this framework will mean that your computer has the most recent .NET Framework, and also means that the single install script works for both 32 bit and 64 bit Microsoft Operating Systems.
• UNITE uploads to Mascot are now compressed, so there should be an order-of-magnitude improvement in file submission times. (Previously only X!!Tandem and Omssa uploads were compressed).
• There is a 'ping' facility from the Preferences window, to enable easier detection of network problems.
• Mass Download no longer breaks when encountering a file that does not exist yet - it continues onto the next file.

Instructions For Download

1. APCF UNITE can be downloaded by clicking ( Download UNITE here. (APCF username/password required.) Download this ZIP file, and extract it.
2. Install APCF UNITE by running setup.exe.
3. UNITE needs the Microsoft .NET Framework V3.5 to run. This should be present on newer Windows machines. If not present, it will install itself on your machine automatically. If you want UNITE to run on an older version of .NET, or inside MONO for other operating systems, please contact the APCF.
4. If setup.exe installs Microsoft .NET Framework V3.5, your computer may require a reboot. In this case, you may need to rerun setup.exe to finish the install.

If you have any difficulties, please contact the APCF by emailing apcf@ludwig.edu.au.

Known Issues

• Does your PC have a Firewall? If so, you may need to make an exception for APCF UNITE. UNITE uses secure sockets to communicate with the APCF server.
• OMSSA taxonomies are still being worked on. Please contact APCF if you wish to use taxonomies with OMSSA.

Video Tutorials

Installation. This tutorial guides you through the steps needed to download and install UNITE.

Configuration. This tutorial guides you through the steps needed to run UNITE for the first time and how to configure it.

Performing mass spectrometry searches. This tutorial shows you how to run searches with UNITE.

Raw file conversion. This tutorial shows you how to perform the automatic conversion of raw instrument files with UNITE.

Viewing the results of your searches. This tutorial shows you how to view the results of your searches.

Mass download of result files. This tutorial shows you how to view the MEDIC mass download tool inside UNITE.

Mass Export of Mascot result files. This tutorial shows you how to view the MEDIC mass download export tool, which can be used to export Mascot result files into other formats, such as pepXML.