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APCF UNITE RELEASE 2.3 is now available. This is the final version of UNITE for the near future. This is functionally identical to 1.9.2, but exposes interfaces that allow users to point UNITE to other alternative APCF servers. This version replaces UNITE 1.8 and any version of UNITE 1.9 BETA. (BETA users should uninstall their version before installing this one.)

Users are recommended NOT to update to the most recent version of msconvert, as there are still issues with its peaklisting for some machine formats. In particular:

Waters format files are not peaklisted by any version of msconvert. Users should use other software to perform this task. UNITE will work correctly if you use a centroid-format mzML file.
WIFF files are also not peaklisted correctly in the most recent versions of msconvert. However the version that comes with UNITE will work correctly if you provide the appropriate vendor libraries. ABI do provide a beta test version of their own command line tool. Click here to get it. This is not supported in the UNITE pipeline yet. If you do use this tool, you must run it from the command line, and select the "-proteinpilot" option. As this tool has a bug in the mzML format it produces, you will need to download the latest msconvert to go mzML->mgf, as more recent versions work around the bug.

APCF UNITE 2.3 has the following features.

Some extra features have been added to the MassDownload tool. Users can select "ALL' jobs, as well as as search on exact or partial title names.

APCF UNITE 2.2 has the following features.

Mascot Search results now have two links, pointing to the new and old viewers for the Mascot results for Mascot Server 2.23.
A check is made when loading Mascot Parameter files to see if a Modification is present.

APCF UNITE 2+ has the following features.

Mascot MS/MS and PMF searches
X!!Tandem MS/MS searches
OMSSA MS/MS searches
Statistical validation of MS/MS research results can be done with peptideProphet and proteinProphet (from the Trans-Proteomic Pipeline (TPP)).
The results of two or more MS/MS searches can be merged with InterProphet (from the Trans-Proteomic Pipeline (TPP)).
The RAW file conversion routine msconvert (from ProteoWizard) is bundled with UNITE, with an automatic update facility to upload new versions.

The current version is UNITE Release 2.3.0. This is functionally identical to 1.9.2, and users need not update their versions. Users are recommended NOT to update to the most recent msconvert, as there are still issues with its peaklisting for some machine formats.

An APCF Username and Password is required to download APCF UNITE.

WINDOWS INSTALL

An APCF UNITE Windows Install program can be downloaded by clicking

Download UNITE 2.3 RELEASE INSTALL here. This is the preferred method, as it fully configures your PC to run UNITE.

The UNITE Manual can be viewed here. It is also accessible from within UNITE by hitting F1, or Help.

What is UNITE?

APCF UNITE is a unique Windows application, that allows users to access the software and hardware facilities of the APCF. Once you have installed UNITE on your desktop, you will be able to quickly and easily launch mass spectrometry searches on the APCF computer cluster. APCF UNITE allows single click-access to Mascot, X!!Tandem and OMSSA search algorithms. It can automate the conversion of your raw (machine) spectrum files, and simplifies the sharing of results within a group.

Advantages

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

UNITE Task Window

UNITE lets you use statistical validation tools seamlessly.

UNITE Task Window

If you select more than one MS/MS search, InterProphet is used to merge the results!

UNITE Task Window

UNITE automates the conversion of your raw mass-spectometery files. Proteowizard's msconvert comes bundles with UNITE, and a GUI helps you quickly build a command line. Note, you still may need propietary libaries for you particular machine.

UNITE Raw File Conversion

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

UNITE Mass Download Window

What's new

APCF UNITE is now at Version Release 2.2

2.3.0	14th November 2011. More features are added to the selection pane of the Mass Download tool. You can now select "ALL" tasks with one click.
2.2.0	6th September 2011. A sanity check is made, and warns users if they load a parameter file with a Mascot Modification that no longer exists.
2.1.0	5th September 2011. This is the last version of UNITE. It is functionally equivalent to 2.0. Due to an upgrade of Mascot Server to V2.3, UNITE now contains 2 web links to the Mascot results, for the old and new viewers. It does not support multiple database searches, and the "Databases" entry when viewing the results of a multiple database search will only display the first database searched. Other than that there should be no other impediment to using it.
2.0.0	29th June 2011. It is functionally equivalent to 1.9.2. It has this additional feature. The Advanced Settings tab in "Preferences" allows users to point UNITE to a different APCF server, should one exist. It is purely for potential future use, and users should not modify any settings, or things will NOT work!
1.9.2	8th June 2011. UNITE has the following features. A bug with X!!Tandem Uploads was fixed.
1.9.1	3rd June 2011. UNITE has the following features. uses mzML as the base format to support merging properly uses msconvert as the XML->mgf format improved error detection with msconvert Scaling to 1024*768 more robust saving code Fixed string error when appending to full text box Fixed bug with view-state Features not used by many people have been temporarily removed, i.e. i-tracker and TPP-resubmission. These features worked but were not tested to our level of satisfaction. They can be added in future releases if users request it.
1.9.0 Stable Version	7th December 2010 UNITE Beta 1.9.15 becomes "Release."

UNITE Manual

The UNITE Manual can be viewed here. It is also accessible from within UNITE by hitting F1, or Help.

Video Tutorials

The following tutorials need the Adobe Flash player installed on your system.

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.

Run an ISB Prophets job. This tutorial guides you through the steps needed to run a ISB Prophets job.

Known Issues

ISB Prophet tools take time.	ISB Prophet tools are single threaded and run on a single core of a CPU. We are working to distribute this amongst the APCF HPC environment .
Why do I need a mzXML file to run the ISB Prophet tools?	The noise-reduction algorithms in the ISB prophet tools are currently designed to work with a mzXML file that is generated directory from a RAW file. For this reason, UNITE currently supports either submitting a mzXML file or using msconvert to go: RAW-> mzXML-> mgf . The mgf file is sent to Mascot to be searched. The MzXML file is sent to the ISB tools. Future releases will use mzML format.
msconvert does not convert my RAW file.	For some RAW file types, msconvert needs appropriate manufacturer libraries. Please contact the APCF if you have any questions.
I have BioWorks but msconvert still does not work.	Copy the 4 critical DLL files directly into msconvert directory and it works like magic!!! ABSciex.DataAccess.WiffFileDataReader.dll Clearcore.dll ClearCore.Storage.dll rscoree.dll (courtesy Matt Chambers from Vanderbilt!) http://www.mail-archive.com/spctools-discuss@googlegroups.com/msg01793.html