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Product: MassHunter Acquistion for TOF and QTOF Rev. B.02.00 Patch 3
P/N:      
Date:     19 - February - 2009

__________________________________________________________________________________________________

Patch 3 has been created to fix several serious or critical defects. 

It is a cummulative patch and contains the fixes from Patch 1, Patch 2 and 
the new defect fixes in Patch 3.


*******************************************************************************
Patch 3 defect fixes included in this patch:

Team Track ID # 13498:  Erroneous optics parameters from context change with fast polarity switching.

Team Track ID # 13575:  Wrong polarity switching on 1 GHz TOF 

Team Track ID # 13576:  Setpoint Rounding Error on Horizontal Quad, Slits, Etc.

Team Track ID # 13583:  HPLC Chip Method User Interface, Inner Valve field incorrect after loading a chip
 
Team Track ID # 13603:  Missing reference mass ions error message not captured by logbook

Team Track ID # 13645:  Time Segment Based Polarity Switching Not Available After B.02.00 Upgrade


*******************************************************************************
Patch 2 defect fixes included in this patch:

Team Track ID # 13204: Wrong polarity set points causes loss of ions in negative ion

Team Track ID # 13206: VCap read back is wrong in the tune report

Team Track ID # 13207: Mid Mirror needs 1 decimal point accuracy

Team Track ID # 13208: Add acquisition rate and acquisition time to the tune report

Team Track ID # 13209:
Maximum mass is not accurate in the tune reports
TOF vacuum readback is absent in TOF reports
Format of vacuum readbacks is not consistent, fixed formatting
Rename calibration coefficients labels in tune report to reflect the software terminology
Output calibration coefficients in microseconds
Format Calibration coefficients and all numbers in the TTI Spectrum to match the B.01.03 report
Add units to calibration coefficients

Team Track ID # 13345: CE TOF Specific Firmware Is Not Loaded With the B.02.00 
Firmware Update Tool. Firmware update tool is now revision 1.39. The firmware
files themselves have not changed.


*******************************************************************************
Patch 1 defect fixes included in this patch:

1) The Calibration Script is available as a pre/post-run script.  The script now successfully 
calibrates positive and negative polarities (regardless of Fast Polarity Switching status). 
This is required for Easy Access B.02.00.

2) Updated Help file.

3) Acquisition Rate is set to 1Hz for all Initial TOF Autotunes, including Fast Polarity 
Switching.  All non-Initial Autotunes will just use whatever the user has entered in the UI. 
This does not mean that the instrument mode is set to 1 GHz for 4 GHz based systems. It refers 
only to the acquisition rate used to tune the instrument. Any 4 GHz based instrument must still 
be tuned in 2 GHz acquisition mode.

4) A 1 nanosecond shift is observed on 4 GHz based TOF systems. This can be seen while in the 
tune context in 1 GHz mode. Changing any parameter causes a 1 nanosecond shift which appears 
as a 0.2 amu shift on the 2721 ion.

5) Delta Collision Energy in AutoMSMS and TargetedMSMS method tabs which is no longer used is 
hidden.

6) Actuals display fixed to display decimal digits correctly.

7) Sheath Gas Temp in Tune context has been changed to 325C to improve 
stability of Agilent Jet Stream autotunes.


*******************************************************************************
Files replaced with this patch:

1) Directory: C:\Program Files\MassHunter\Workstation\Acq\Bin\release

agtpiccube.ocx				  422 KB	02/05/2009 1:45 PM
agtqtof_acqmain.ocx			1,841 KB	02/04/2009 3:09 PM
agtqtof_tune.ocx			1,433 KB	02/04/2009 3:10 PM
agtqtofautotune.exe		  	  713 KB	11/17/2008 1:00 PM
agtqtofdrv.dll				  612 KB	02/04/2009 3:08 PM
AgtQTOFTuneSpecCtl.ocx		   	   81 KB	02/04/2009 3:09 PM
agtmsspimo.dll				  196 KB	02/04/2009 3:07 PM
AgtMSConfiguration.exe			  116 KB	02/04/2009 3:07 PM


2) Directory: C:\Program Files\MassHunter\Workstation\Acq\Bin\QTOF

qtof_MSActualDefs_Example.xml		21 KB		11/17/2008 12:56 PM



3) Directory: C:\Program Files\MassHunter\Workstation\Acq\Bin\TOF

tof_MSActualDefs_Example.xml		15 KB		11/17/2008 12.56 PM



4) Directory: C:\Program Files\MassHunter\Workstation\Acq\help

acq.chm					1,354 KB	 10/28/2008 1:17 PM


5) Directory: D:\MassHunter\scripts\Acq

agtqtofacqscriptplugin.dll		32 KB		 11/17/2008 1:06 PM
Interop.AGTINSTMANAGERLib.dll		36 KB		 11/17/2008 1:06 PM
Interop.agtmsspimoifclib.dll		19 KB		 11/17/2008 1:06 PM
Interop.AGTPICAPPPLUGINIFCLib.dll	13 KB		 11/17/2008 1:06 PM
Interop.AGTPICENGINELib.dll		 8 KB		 11/17/2008 1:06 PM
Interop.AGTPICLAUNCHERLib.dll		 5 KB		 11/17/2008 1:06 PM
Interop.agtpiclogbookdata.dll		 4 KB		 11/17/2008 1:06 PM
Interop.agtpiclogbooklib.dll		 5 KB		 11/17/2008 1:06 PM
Interop.agtpicmtlib.dll			24 KB		 11/17/2008 1:06 PM
Interop.agtpicreginfo.dll		 3 KB		 11/17/2008 1:06 PM
Interop.AGTPICSYSSERVICESLib.dll	 9 KB		 11/17/2008 1:06 PM
Interop.agtqtofautotune.dll		28 KB		 11/17/2008 1:06 PM
Interop.AGTQTOFDRVLib.dll		36 KB		 11/17/2008 1:06 PM
Interop.AUTOIFACETYPELIBLib.dll		60 KB		 11/17/2008 1:06 PM
Interop.HpChemIfc.dll			17 KB		 11/17/2008 1:06 PM
Interop.INSTIFACETYPELIBLib.dll		11 KB		 11/17/2008 1:06 PM
Interop.RTCSpecificationsLib.dll	13 KB		 11/17/2008 1:06 PM
Interop.SIGNALBUFFERSERVICELib.dll	28 KB		 11/17/2008 1:06 PM


6) Directory: D:\MassHunter\Configuration\Instruments\LCMS

agtmsconfiguration.xml			279 KB		02/06/2009 11:02 AM


7) Directory: D:\MassHunter\Tune\QTOF

qtofTuneParams.xml			35 KB		10/31/2008 10:21 AM


8) Directory: D:\MassHunter\Tune\TOF

qtofTuneParams.xml			35 KB		10/31/2008 10:21 AM

__________________________________________________________________________________________________


*******************************************************************************
The software patch is a self-extracting executable file which will extract the 
software files and install them in the appropriate directories.

*******************************************************************************

This patch should only be applied to 6200 Series TOF and 6500 Series Q-TOF systems. 
It is not intended for QQQ systems.

NOTE: All MassHunter processes must be stopped before applying the patch. 

DO NOT use the REMOVE MASSHUNTER PROCESSES tool to stop the MassHunter Acquisition software.

Please exit the MassHunter Acquisition software and then use the Acq System Launcher tool
to stop the MassHunter Engines. 

Finally, please use the Remove Processes tool to ensure a complete shutdown the MassHunter 
Acquisition software.



*******************************************************************************

Installing the Software Patch

1) Close all MassHunter software applications and engines.

2) Browse to the directory, CD, or USB drive where the patch file is located.

3) Find and double-click on the file named TOF-QTOF Acquisition B.02.00 Patch 03.exe.

When the file is double-clicked, a window will appear with 
information regarding the installation of the patch. You will not be able to
make any changes unless the software was not installed in the default 
locations. 

IMPORTANT NOTE: If the patch executable stops with a Visual Basic Scripting error,
simply click OK to accept the error. Then double-click on the executable again
to restart the patch process.

Once you click OK, a process cleaner will run ensuring that the MassHunter Acquisition
software is completely shutdown. The patch will then be applied.

4) Next, the firmware update tool will be launched during the patch process. 

IMPORTANT NOTE: If the firmware update tool detects that the firmware installed on the
TOF or Q-TOF matches the update version, the firmware update tool process can be
safely aborted. There is no need to reflash the firmware.

FOR 6200 SERIES TOF SYSTEMS:
The firmware update tool will now install the CE-TOF specific firmware when
the user selects the option. By default, the CE-TOF specific firmware is NOT
installed.

The firmware update tool also prompts the user to enter the serial number
of the instrument. The serial number must be entered using numbers only.
For example, the instrument serial number is US12345678, it must be entered
as 12345678. If the serial number is not entered, it will not appear on the 
tune report which is critical to customers in compliant laboratories.

FOR 6500 SERIES Q-TOF SYSTEMS:
There are no changes to the firmware. However, the firmware can be reflashed without
issue.

5) After the firmware has been updated and the patch has been installed, allow the
TOF or Q-TOF to completely reboot (approximately 60 seconds), restart the MassHunter 
Acquisition software.

6) Go into the Tune Context and recalibrate the system.

The patch is now complete.

After applying this patch, the MassHunter Acquisition revision number located in 
the Help => About panel will be MassHunter Acquisition for TOF and QTOF B.02.00
Build 1128.5 with Patches 1,2,3.


*******************************************************************************

After applying the patch, test the tune file to see if it is corrupted. Use
these steps for testing the tune file:

1) Create and save a method in negative ion mode.
2) Exit MassHunter Acquisition and stop the engines.
3) Restart MassHunter Acquisition. This should load the negative ion method 
that was just used.
4) Change to Tune Context. It will start in Positive Ion mode.
5) Change to Negative Polarity. A fault will occur and report to the user that
the Hex DC is at the wrong value for the range. Subsequently, all other 
Optics 2 elements will report the wrong value. A final message will appear that
some values for the tune file appear to be wrong and that the tune file should
be reloaded. This is the defect.

If an error occurs, the tune file must be deleted.

Shutdown the MassHunter Acquisition software and stop the engines. Delete the
Autotune.tun file. 

For TOF, the directory path is:

D:\MassHunter\tune\TOF

For Q-TOF, the directory path is:

D:\MassHunter\tune\QTOF

The instrument will then need to be retuned from initial values in both 
polarities, Quad Tunes for Q-TOF, and Polarity Switching Mode for TOF.