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.
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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.
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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.
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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.
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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 INSTALLAn 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.
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The UNITE Manual can be viewed here. It is also accessible from within UNITE by hitting F1, or Help.
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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.
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Advantages
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UNITE let you search mulitple
mass-spectrometery search algorithms with a single
click.
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UNITE lets you use statistical validation
tools seamlessly.
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If you select more than one MS/MS search,
InterProphet is used to merge the
results!
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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.
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You can download your results into your
local PC for further analysis.
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What's new
APCF UNITE is now at Version Release
2.2
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2.3.0
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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.
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2.2.0
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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.
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2.1.0
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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.
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2.0.0
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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!
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1.9.2
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8th June 2011.
UNITE has the following features.
- A bug with X!!Tandem Uploads was fixed.
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1.9.1
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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.
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1.9.0
Stable Version |
7th December 2010
- UNITE Beta 1.9.15 becomes
"Release."
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UNITE Manual
The UNITE Manual can be viewed here. It is also accessible from within UNITE by hitting F1, or Help.
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Video Tutorials
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Known Issues
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| 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
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| 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
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