Notes on ChromQuest version 5.

0
March 12, 2008

This document contains last-minute information not contained in the help files or
in the manual. For more complete information, please refer to these sources.

New Features and Fixes in the 5.0 Version

Features
• New User Interface ChromQuest 5.0 has a new user interface from the 4.2 version.
• Support for Accela Drivers The Accela drivers have been included into the core
package.
• Support for Mixing Surveyor PDA Plus with SpectraSYSTEM The capability to
connect a Surveyor PDA Plus to SpectraSYSTEM units.
• Graphical Editing The software has some improvements to the graphical editing
and moving of the baselines
• Custom Parameters Per Peak There has been additional parameters added to the
peak definition capability.
• Improved Audit Trails User is capable of creating pre-defined reasons for changes
so you can select a specific reason.

Fixes
• Multi level bracketing calibrations is functioning as designed.

Seven-Day Demonstration Key

The software now ships with a key file that allows operation for seven days. It may only be
installed once on a computer. When the seven-day evaluation period is complete, the software
will revert to its normal demo mode. In its normal demo mode, only the demo data files may be
opened and no data may be collected. The installation procedure is the same as for a normal key
with the following exceptions. The .lkt file is located in the d:\ChrQuest directory (assuming that
d: is the CD drive). The serial number to use is: 01032200111. The enable code is: 8484 -
T2N3 - WPD2 - 6RFV - Y68Y - PSX3.

Important Operational Notes

Operational Differences between Surveyor and SpectraSYSTEM

• Pump shutdown methods for the Surveyor LC pump may not have any time lines.
Only the original conditions of the method will be downloaded.
• Sample preparation in Surveyor is accomplished by creating separate pretreatment
methods. Both the normal method and the pretreatment method must be included in
the sequence table. In SpectraSYSTEM, sample prep is part of the normal method.
• The pretreatment methods for Surveyor are free form. The allowable values for the
preparation step parameters will depend on the previous steps. Be sure to study the
rules in the manual, before creating a pretreatment method.
• After a pretreatment method has been saved, it should not be edited. Create new
methods from a blank template, not from other pretreatment methods. An edited
method may crash when it is run.
• When running samples using the sample prep feature of the AS3000, the samples
are placed in the vial position referenced by the sequence table and the injection
takes place from the last vial referenced by the prep method. When using the
pretreatment feature of the Surveyor autosampler, the injection will take place from
the vial referenced in the sequence table and the original sample should usually be
placed in another position.
• Method download for SpectraSYSTEM gives a message when the download is
successful. With Surveyor, only failure messages will be reported.
• The first time that a Surveyor instrument setup window is opened, it is best to resize
the graph portion of the window to view the entire setup interface. The new size
setting will be retained by the software.
• Systems using the Surveyor Autosamplers must be set up with external triggers.
Computer Notes
• This program was designed to run using English(United States) International settings
(Regional Options). There are a few issues in the SpectraSystem user interface with
some other International Settings. Also, decimal values in Advanced Reports
formulae must be represented by periods, regardless of the International Setting.
• As with all Windows NT applications, do not use any reserved characters in user-
named files. The more common characters that should be avoided are: *,?, ., /, \, |,
>, or < .
• When printing a screen with a colored background, Windows NT will automatically
change the background to white. The color of any information in the screen that is
white should be changed to another color before printing.
• Color printers are best used for producing presentation quality single reports.
However, they are poorly suited for routine analysis or batch printing. The printers
are relatively slow and spooling complex graphics can require most of the resources
in the computer.
• If your video card is an ATI RAGE PRO128 model, there may be a problem running
scanning detectors on the software with versions of the Windows NT video driver
earlier than 4.3.192. The latest driver should be obtained and installed in this case.
• ChromQuest does not support the use of large fonts or custom font scaling in the
Windows display settings for the video driver. The Windows display settings should
be set to "small fonts" if this option exists.
• When running time-critical programs such as ChromQuest data collection, it is best
not to use a screen saver. However, we have tested this version with the Windows
login screensaver and have not had any problems.
Software Operation Notes
• Care should be taken in the peak/groups table to ensure that the intended signal is
chosen in the analysis channel column.
• If a method that uses a scanning detector (Surveyor PDA, UV6000 or UV3000) is
changed from a scanning method to a non-scanning method, remember to delete
any multi chromatogram channels that have been setup in spectral options.
• When aborting a sample during sample prep, allow the prep to complete before
allowing the sequence to resume.
• Each line in the sequence table must have a method specified.
• When using copy/paste function to copy group information from one channel to
another, all group information except the group definitions are copied. This is a
known bug with no fix for the current spreadsheet format.
• The advanced reports spreadsheet has 5000 rows in it. Therefore, if you click the
corner of the spreadsheet to highlight all rows, then delete, this process can take
from 2 - 5 minutes. This procedure is not recommended.
• To create a shutdown method for a configuration containing an SS420, it is
necessary to deselect the analysis channel in the SS420 tab in Instrument Setup
before saving the method.
• If you are using dual tower, do not set up identical columns on the front and back,
inject similar samples and standards on the front and back, combine all injections in a
post run sequence, and perform a recalculation to get average results for the whole
sequence. Even though the front and back signals go into different data files, they go
in as different signals. One method cannot combine the results for both signals.
They will still be treated as two separate sets of data.
• The trend template that is included with the software is setup to work with the
LabTest data set and sequence. It can be modified for your analysis by adding or
subtracting peaks on the template. To add peaks highlight the last peak section on
the template and copy it below that section on the template. Change the peak
reference numbers in the formulae.
• Make sure that all modules are turned on before starting Baseline Check.
• In contrast to versions 3.0 and earlier of the software, the .dat extension is not added
to file names created in the single run dialog.
• In contrast to version 3.0, pressing the new sequence button does not open the
sequence wizard. The sequence wizard is accessible through the file/sequence
menu.
• Editing a running method in off-line mode will change that method for the next run in
the on-line mode.
• The units for noise in baseline check are μV and the units for drift are μV/hr. For
absorbance detectors these units would be μAU and μAU/hr respectively.
• It is best practice to close the view method custom report window when leaving the
window instead of switching to another window and leaving the view method custom
report window open.
• Methods should only be opened with the instrument type that they were created with.
If a Surveyor method is opened with a SpectraSystem instrument, the instrument
setup parameters will be reset to their default values. The default values will become
part of the method if saved.
• Sequences that are "read-only" will not run.

On-Line Manual
Before using the on-line manual it is necessary to install Adobe Acrobat® Reader. The
installation program is located in the Manual folder on the installation CD-ROM. The
complete path is Manual\Adobe Acrobat Reader\rs405eng.exe. Double click this icon
to run the program. Accept all defaults.

Installation

Computer Setup
• Ensure that Windows XP SP1 or Windows 2000 SP 3 is installed before installing
ChromQuest. If it is not installed you must install the appropriate service pack. They
are available for installation in the '\Updates\…' directories on the ChromQuest CD-
ROM.
• All users who login to a computer running ChromQuest must have the following user
rights: "act as part of the operating system", and " log on locally. In Windows 2000,
these rights are granted from the Control Panel/Administrative Tools/Security
Policy/Local Security Settings/User Rights Assignment.
• In a networked environment, if you which to use the domain security, make sure that
the Domain users that you wish to allow to run ChromQuest are assigned to the
Users group (or any appropriate group that you may have created) on the local
computer. After installing ChromQuest, go to Tools/Options, select Enterprise and
check "Enable instrument login..." and "domain controller". Click "Add Domain"
followed by "Refresh”, “Apply”, and OK. Finally, click on the System Administration
mode tool to select the first system administrator. This administrator can then assign
privileges to other users in the domain.

Other Setup Notes

• Rebooting after installing software is necessary. Skipping it will cause abnormal
behavior and/or crashes.
• Software key is needed for data collection.
• Uninstall all licenses before performing an upgrade from Versions 3.0 and 4.0.
• Back wiring SN4000-controlled instruments is required. Trigger must be performed
by the autosampler. The wiring harness that is supplied with SN4000-controlled
systems is designed to supply this trigger. Following diagram illustrates the
connection:

• For the best display the number of colors chosen in the display settings should be
greater than 256.
• It is necessary to configure "Event Configuration" to use the SS420 board or an
SS420x box in a system. If the hardware setup instructions are followed for the
SS420, the following settings should be used:
Name "Trigger"
Source "SS420"
Setup
Board # "as set on board"
Input "In1"
Triggered State "Closed"

Upgrading from PC1000

• The computer should be setup as a dual boot computer with Windows NT 4.0 with
service pack 5 as the other boot option.
• The firmware in the SN4000 should be changed to version 9.05. Remove both chips and
insert the new chip in U12.
• Transfer of data
Archive data files in PC1000, ideally using an 8.3 naming convention
If possible, transfer files to a FAT drive
If necessary, zip archived files and transfer to external (zip drive) (use WIN-OS/2 to
install and manage files)
Before compressing the archive files change the extension from .arc to .001.
Save drive with compressed archive files for transfer later to NT-readable drive.
• Removal of PC1000 and Warp
Boot the computer using the Warp installation diskettes.
After the third disk (disk2) has completed go to the command prompt.
At the A: prompt, enter fdisk.
Remove any HPFS formatted partitions, the partition with Warp and the boot
manager partition.
Set the partition with Windows NT to startable
Exit, remove the diskettes from the drive and reboot.
• Moving the ARC files to NT
Install the drive onto NT with NT drivers
Copy the .zip file to the target directory
Use WINZIP to extract the files
Rename the resulting .001 files by changing the extension back to .arc.
Delete the .zip file from the target directory

Instrument Support
ChromQuest 4.1 supports the following instrument ROM revisions.

System Controllers:
SN4000: 9.05
Pumps:
P1000: 4.01 or higher
P1500: 4.02 or higher
P2000: 4.03 or higher
P4000: 4.04 or higher
Surveyor LC pump 1.15 or higher (converter board), 1.00 or higher (main board)
Autosamplers:
AS1000: 3.31 or higher
AS3000: 3.31 or higher Note: Autoconfiguration works on versions 3.41
or higher
AS3500: 3.31 or higher
AS2000: 3.13 or higher
HS2000: 3.1a7 or higher
Surveyor AS 2.12 or higher
Surveyor AS Lite 2.13 or higher
Detectors
UV1000: 3.09 or higher
UV2000: 3.12 or higher
UV3000: all revs
FL2000: 3.11 or higher
FL3000: 3.11 or higher
UV6000: RAM 1.4
TRACE GC 2000: all revs
Surveyor UV-Vis 1.06 or higher (converter board), 3.12 or higher (main
board)
Surveyor PDA 1.17 or higher (converter board) 1.8 or higher (main board)

New Features and Fixes in the 4.2 Version

Features
• Support of Surveyor Plus Instruments Support has been added for the new
Surveyor LC Pump Plus, Autosampler Plus, Autosampler Plus Lite, PDA Plus
Detector, and UV/Vis Plus Detector.
• Windows XP SP2 Compatibility The software will be validated against Windows XP
Service Pack 2.
• Windows 2003 Server Compatibility The software will be validated against
Windows 2003 Server.
• Native Mode Active Directory Support The software will be modified as needed to
work with Windows 2000/XP native mode active directory domains.
• Post-Export User Program The software will have the ability to launch a user
program after acquisition, analysis printing and export have occurred.
• Enhancements to Mandatory Audit Trails Currently, the software includes an
option to force method or sequence audit trails on for an entire Enterprise. For this
version of the software, the System Administrator will be able to require audit trials on
a project-by-project basis. In addition, it will also be possible to specify the prompting
mode for audit trails when changes have been made.
• Default Project Lockout This version of the software will allow a System
Administrator to delete the default project, in order to prevent people from logging
into it.
• Peak Centroid Calculation A new peak result will be added to the values calculated,
annotated and exported by ChromQuest. The result will be called Peak Centroid and
is defined as the position in the peak at which 50% of the total peak area is reached.
• Single Login This version of the software will allow a System Administrator to
specify that users need only login once to the entire system and need not login to
each instrument individually. In addition, it will also be possible to automatically use
the credentials of the current Windows logged in user, eliminating any specific login
to ChromQuest.
• Separate Instrument Control Installation Currently, the majority of ChromQuest
instrument control drivers are installed automatically as part of the installation of
ChromQuest itself. For this version of the software, instrument control drivers will be
separated from the main ChromQuest installation and will be supplied on a separate
CD, where they can be installed on an as-needed basis.
• Group Range Annotation It is now possible to have the group range annotated on
the chromatogram. This is turned on in the Trace Annotation Properties dialog. When
this option is selected, the software will draw horizontal bars above the
chromatogram to indicate the extent of each region(s) over which an uncalibrated or
calibrated group is defined. This option will have no effect on Named Peak groups.
Group range annotations for an existing data file will not be displayed unless it is
analyzed.
• Single Label for Group Range When the Group Range Window is selected, this
version of the software will display a single label for each range block of the group, as
horizontal text above the range bar. The display of the group name is independent of
the peak/name annotation, and is instead coupled to the state of the Group Range
Window setting.
• Naming unnamed peaks in a group In previous versions, when one or more
unnamed peaks was found to be part of a group, ChromQuest would assign the
group name to each of the unnamed peaks in the group. In this version of the
software, the group name will continue to be used in conjunction with run report
tables and other places where the peak name is referenced, but it will NOT appear as
the peak name annotation for graphs.
• Graphical Group Range Adjustment When the Group Range Annotation is
displayed, the software will also support graphical updating of the Group Ranges.
This is done using a new graphical event, (Group Range Adjustment/Adj Group
Range button).
• Graphical Adjustment of expected RT Windows When the expected RT Windows
are displayed on the chromatogram, it is now possible to graphically change the
expected RT Window for a peak using a new graphical event (RT Window
Adjustment/ Adj RT Window button).

Fixes
• The Method Report in the Custom Report for the UV1000 and the UV2000 would
identify both lamps as deuterium lamps, the identification is now correct
• Surveyor UV/Vis would autozero even when autozero is turned off, now it does
not
• Now able to import spectral libraries from PC1000
• Fixed intermittent loss of packets of five data points from Surveyor UV/Vis
runs, resulting in added variance to retention times and peak areas
• Fixed issues with Surveyor methods requiring a longer pump run time than
detector run time.
• Improved security of Advanced Reports
• Fixed Advanced Report rounding problems
• Shows message when Surveyor Pump is turned off

New Features and Fixes in the 4.1 Version

Features
• Support of Surveyor Autosampler Lite Support has been added for the new, basic
version of the Surveyor Autosampler. Temperature control detection, a direct
command for temperature control upload and a direct command for a flush with the
injector in the fill position have been added.
• Centralized Administration Mode This mode will allow for all of the projects, data,
instruments and keys to be stored in a centralized, protected directory. The
Centralized Administration mode supports the Enhanced File Access Security below.
• Enhanced File Access Security Access to the contents of the Enterprise path will
be restricted so that unauthorized users cannot use Windows Explorer or other
programs to access files in the Enterprise Path. Inst.exe was modified so that it runs
in the context of a special service account that has full permissions in the Enterprise
Path. It will then intercept requests for all file access and validate them against the
credentials of the logged in user. No domain user accounts except this special
service account will have access permissions in the Enterprise Path.
• Multiple File Signature Tool Multiple files may be signed off at one time rather than
opening and signing each one individually.
• Prep-Only Sequence Sequences that run pretreatment without making injections are
now supported.
• Advanced Report Template Audit Trail An audit trail to log changes to Advanced
Report templates is now available. This audit trail has features that are similar to the
Method Audit trail.
• Log-Log Scaling for Calibration The software will support calibrations wherein
either a natural or common logarithmic scale may be selected for the X and/or Y
Axes.
• Analysis PC Identification Whenever a data file is analyzed, the name of the PC on
which the analysis occurred is stored with the results. A new entry, Analysis
Computer Name, was added to the insert field menu.
• New Baseline Integration Event A new integration event was added to the
software. This event will be available in the Integration Events spreadsheet, the
Manual Integration Fixes table and the Graphical Events toolbar. As with other
integration events, support is included for annotating data graphs, printing and audit
trailing of changes.
• Lowest Point Horizontal Baseline A new event called Lowest Point Horizontal
Baseline (Baseline Code: L) was added to the software. The Lowest Point Horizontal
Baseline is similar to the existing Horizontal Baseline, except that the lowest point in
the chromatogram determines the baseline. The parameter value associated with this
event represents the point (in minutes) of the chromatogram at which the search for
the lowest point will start. The spreadsheet will validate that the parameter value is
greater than the event start time.
• Improved File Checksum In previous versions the checksum embedded in data files
was calculated only on the actual data portions of the compound file. This version of
the software extends the calculation to cover all the information (method,
configuration, etc.) in the file.
• Mail Server Authentication On the e-mail configuration tab, controls have been
added to allow the administrator to optionally add login authentication for the SMTP
Mail Server.
• Identifying Electronically Signed Data Files
1. In File Open Dialog: In the File > Data > Open dialog box, when the
Description window is visible, if a data file has been electronically signed, an
entry will appear near the top of the description indicating this fact.
2. In Data Properties Dialog: A new tab was added to the dialog
displayed when the user selects the Data > Properties menu item. This tab
will contain static text describing the electronic signatures (if any) that have
been applied to the currently open data file. The text includes the same
information as is printed in the custom report (Date/Time, User, Reason, Role
and Comment).
• Changing Passwords of Data System Users
1. On the Enterprise tab of the dialog displayed when Tools > Options
menu item is selected, a button was added in Data System user mode to
allow an administrator to change the password of any user. Access to this
function will be limited to system administrators.
2. A menu item, called Change Password… was added to the Tools
menu. Selecting this menu item displays a dialog prompting for a user name,
old password and new password. This function will be accessible to all users.
• Batch Electronic Signature Support This version of the software supports the
ability to apply and revoke electronic signatures to multiple files at once, rather than
singly.
• System Activity Log A system activity log has been added to the main window of
the software. This activity log is similar to the instrument activity logs currently
available for each configured instrument, but tracks user administration level
activities.
• Sequence Audit Trail An audit trail to log changes made to sequences has been
added. The characteristics of the sequence audit trail feature are similar to the
method audit trail feature currently available in the software.
• Windows XP Support
• Administrative Mode Timeout This feature automatically will log out from system
administration mode after a user-specified period of inactivity. The user has the ability
to disable this feature as well as to specify the time of inactivity that triggers the
lockout.
• Electronic Data Signature Enhancements Fixed hierarchical roles and rules for
approval and revocation of signatures have been added. These roles are discrete
permissions that can be assigned to users and will control how electronic signatures
can be applied and revoked. When an electronic signature is applied to a data file,
the signer will be able to choose a reason from a fixed list specified by the system
administrator. When an electronic signature is applied to a data file, the signer will be
able to enter an optional, free form text comment. The inactivity timeout for closing
an in-process signature may now be configured in system options.
• Extract Configuration from Data File The ‘Open with Configuration’ option in the
File Open dialog has been replaced by an option in the initial instrument configuration
screen that enables the user to load instrument configuration settings from a stored
data file.
• New Integration Timed Events Two new integration events have been added to the
software. The two new events are Reset Baseline (Baseline Code: RB) and Reset
Baseline at Next Valley (Baseline Code: RN). In Reset Baseline, the baseline is
drawn to the chromatogram at the indicated time. This is functionally equivalent to
performing an Integration Off and Integration On event at the same time. Reset
Baseline at Next Valley, the baseline is drawn to the chromatogram at the next time
the chromatogram passes through a negative to positive slope transition. These
events are available in the Integration Events spreadsheet, the Manual Integration
Fixes table and the Graphical Events toolbar. As with other integration events,
support is included for annotating data graphs, printing and audit trailing of changes
• HTML Help The help file system for the software was converted to an HTML based
help system.
• Calibration enhancement The parameter for Scale has been updated. The choices
associated with Scale previously included: None, 1/x, 1/x^2, ln(x), 1/ln(x), sqrt(x),
x^2. The software was modified to allow the following choices. Note that “x” in the
previous scale choices is now displayed as “amount”. (None, 1/Amount, 1/ Amount
^2, ln(Amount), 1/ln(Amount), sqrt(Amount), Amount ^2, 1/Response, 1/ Response
^2, ln(Response), 1/ln(Response), sqrt(Response), Response ^2)
• Improved Method Security The user can no longer overwrite a method by using the
"save as" command. A user with the rights to do so must remove the original method
first.
• Legends for Surveyor UV-Vis Traces Now Contain Wavelengths
• Surveyor AS Loop Size Now in Configuration
• Instrument Logs Now Can Be Archived to and Read from a Delete Protected
Folder
• New Tool for Direct Creation of Multichromatogram Signals from Mixed View
Screen
• All Calculations Use Double Precision Some of the calculations in previous
versions used single precision variables. The results are now more precisely
calculated, but may vary in the sixth or seventh digit from prior results.

Fixes

• Correction of Spectral Confirm Problem: Previously the software would always

pass a spectral confirmation in cases where the reference spectrum was improperly
defined. The software will now fail these cases.
• Correction of Peak Purity Report Auto Scaling for Peaks from Discrete
Wavelengths: The x-axis auto scaling now works for these peaks.
• Issues with Surveyor AS Direct Commands with Microtitre Plate Configurations
Addressed: There was an addressing problem that caused problems with using
direct commands with these configurations. One consequence was that the move
needle command did not work. It is now fixed.
• P1000 Shutdown Methods Now Fixed
• Windows Domain Users Can Now Change Passwords Without Affecting Their
ChromQuest Rights: In the previous version, if a user changed their password,
they became a different user in ChromQuest.
• Wavelength Tables for Surveyor UV-Vis Now Printed in Method Contents
Reports
• Appearance Controls for Sample Data Trace in Spectrum Report Fixed
• Printing of Pretreatment Methods Fixed
• User Interface Problems in Surveyor LC Pump Setup and Direct Control Fixed
• Manual Spectral Library Search Reports Available

New Features and Fixes in the 4.0 Version

Features
• Support for Surveyor HPLC System
• Enhanced Regulatory Compliance Features
• New Login Lockout Feature: It is now possible for the system administrator
to enable a lockout of user after a specified number of attempts to log on.
The enterprise administrator can activate this function when login is enabled.
Failed login attempts can trigger an email notification.
• Instrument Activity Log Archive and Purge: It is now possible to purge
and archive the instrument activity log. These are now functions in the
File/Instrument Activity Log menu.
• Instrument Activity Log Administration: A function has been added to the
General Tab of the Tools menu to enable system administrator to allow
purge of instrument activity logs only after archive.
• Archived Log Viewer: A program has been added to allow users to open
and view instrument activity logs that have been archived.
• New User Rights: A new Purge Log user privilege has been added. This
right enables the user to purge the instrument activity log. New Advanced
Report user rights have been added.
• Method Audit Trail Modifications: The method creation date is not
imbedded in the method audit trail. When Method "Save As” command is
used to save a method with a new name the following now happens: The
audit trail of the existing method will not be copied over to the new method
and the first entry in the new method will be a line stating that this method
was saved from Method X with date and time.
• Data File Audit Trail: The creation date of the data file is now imbedded in
the data file audit trail as the first line.
• Data Save As 32-bit: The "Save As" command for data has been disabled
except when working with files of other formats, for example, a cdf file. If a
data file is saved using the "Save As 32-bit" command, a line is entered into
the Data audit trail stating that this data was saved from data X. Using the
Data Save As command for making copies of files using a new name must
now be implemented using Explorer.
• Logged in User Name No Longer Appears Automatically in Electronic
Signature Dialog: This change improves compliance with 21 CFR Part 11
regulations.
• Improved User Interface for Spectral Options Programming
• Improved User Interface for Control of Spectral Displays: A new tool bar on the
spectral windows provides direct access to commonly used commands.
• Improved Graphics for 3D Display
• New Similarity Pane Facilitates Comparisons of Spectra: The similarity between
all spectra shown in the spectrum pane is instantly calculated upon selection of a
reference spectrum.
• Addition and Subtraction of Spectra Now Possible: If spectra are overlaid in the
spectrum pane, there is an add and subtract operation available from the right-click
menu.
• Lambda Max Annotation Available in Spectrum Max Plot
• All Spectral Data Exportable to ASCII Files
• Background Correction Available for All Automatic Spectral Calculations
• Derivative Plots Now Default as Normalized for Easier Viewing
• New Scheduling of Single Runs and Sequences: Instrument runs may now be
scheduled for a user-determined time in the future. One application of this feature is
as an instrument warm-up method for the next morning.
• New Baseline Check Feature: It is now possible to automatically download the
initial conditions of a method and perform a baseline check until the noise and/or drift
meet user-determined conditions. This feature may be used in a sequence to
automatically start a run when the instrument is ready.
• New Multiplier and Dilutor Columns: There are now additional columns in the
sequence table. Multiplier 1, 2, and 3 and Dilutor 1, 2 and 3 are now available.
• Change to Single Run Acquisition Dialog: The single run dialog has been
changed to support the use of the new Multipliers and Dilutors.
• Print Toolbar Enhancement: A print icon has been added to the toolbar. The
selections will print as if the print command was used. The selections under the Print
icon are:
Print Configuration
Print Method
Print Sequence
Print Reports with the same sub menu as the "Report" "Print" menu item.
• New Clear Overlays Function: It is now possible to clear graph overlays with a
function available from the right mouse click menu.
• Time Program Annotations: Time programmed events from the data processing
and instrument method are available as annotation items on a chromatogram to show
when they were performed.
• Rolling Averages Now Calculated: It is now possible for the software to calculate a
rolling calibration average.
• Calibration Residual Value: The residual value calculation is now available. It is
located in the calibration view and reports and is available for reporting along with
other peak information.
• New Calibration Options Tab: A new tab has been added to Method Properties. It
contains response factor definition and number of replicates for rolling average.
• ASTM LOD (Limits of Detection) Calculation: A column has been added to the
peak table for calculation of the LOD value.
• ASTM LOQ (Limit of Quantitation) Calculation: A column has been added to the
peak table for calculation of the LOQ value.
• System Suitability Enhancements: The System Suitability Option now includes
peak-to-peak signal to noise calculations, Noise Calculations based on ASTM
method, and 6-Sigma rms Noise Method.
• List of Recent Methods, Data, and Sequences: It is now possible to see and open
the most recent method, data and sequences that have been opened in the current
instrument. The selections are found under the File Menu. The user can set the
number of recent files to be listed or clear them by using a dialog in View
Preferences. Up to 32 files of each type can be displayed.

Fixes

• Correction of "Manual Peak" Integration Event: Previously when this event was
used in conjunction with other events affecting the peak count (i.e. "Split Peak",
"Tangent Skim", etc.) it would not be applied correctly. Now Manual Peaks are
calculated before these other types of events. This will affect the number and
location of detected peaks.
• Correction of "Disable End-Peak Detection" Integration Event: Previously when
this event was used when valleys between the end points dropped below the
calculated baseline, the baseline could be drawn incorrectly. Now we draw the
baseline correctly, but the user should be warned that this might cause "baseline
penetration". A new integration code "D" was added to represent the case where
moving the baseline to adjust for penetration has been disabled.
• Fix for Front Tangent Skim Event: There has been a fix to the "front tangent skim"
integration event. Previously the baseline would be drawn from the start of the event
to the end of the solvent peak without regard for baseline penetration. This caused
the area for the solvent peak to be miscalculated. Now the baseline will start where
the baseline penetration would have occurred previously.
• Force Peak Stop Changes: A change has been made to the "Force Peak Stop"
integration event. Previously, the baseline could be drawn incorrectly if the event
occurred in any peak other than the first peak. This could cause baseline
penetration. In addition, the baselines for preceding peaks were affected, even if not
connected. This has been corrected. When a "Force Peak Stop" is encountered, the
current peaks' peak stop will be placed at that time and the peak start will be moved
forward to prevent baseline penetration.
• Events with Negative Delay Acquisition: The handling of integration events with
"negative delay" acquisition has changed. Previously, integration event start/stop
times were not adjusted correctly when negative delay was in effect. This caused a
shift in the application of the events with varying results. This has been corrected.
• Tangent Skim Integration Correction: Problems with the "tangent skim" integration
event have been corrected. Previously this event could result in baselines being
drawn without an endpoint. When this happened, peak areas were calculated
incorrectly. This happened when the solvent peaks start and stop times were lower
in amplitude than the following peaks in its group.
• Creation of New Sequences by Wizard During No Longer Allowed: Creation of
new sequences on a running system can lead to unpredictable results. In other
modes of sequence creation, this activity is not allowed. The fix prevents the wizard
from causing the same problem.
• Printed Sequences Show Vial and Volume Information: In version 3.0 this
information was not printed when a sequence was printed. A patch was made and
was brought forward into this version.
• Multiple SN4000-controlled Detectors Now Handled Correctly: Version 3.0 did
not handle the signals correctly in this situation. A patch was written and brought
forward into this release.
• Memory Leak in Printing of Advanced Reports Fixed: When an advanced report
is printed, a large block of memory is used temporarily. Before the patch, this
memory was only released when inst.exe closed. If a customer ran continuously and
the sequence used an advanced report that was printed, the system would eventually
hang-up due to lack of memory. A patch was created to fix this problem and was
brought forward into this release.
• Problem with Shutdown Methods Fixed: Shutdown methods that had more than
one timeline in the pump method and ended with a non-zero flow value would not
hold at the last value. The behavior is now correct.
• AS3000/AS1000 Now Accepts Download Method After A Shutdown Is Run:
After being shutdown the autosampler modules would not accept a method sent by
Download Method. It was necessary to run a sample to send a method to the
autosampler. This feature now works.
• Time Units for Spectral Plots Now Controlled By View/Preferences Choice:
Previously, they were all set to minutes.
• Peaks that Fail Spectral Confirm Now Reported By All Peaks Selection in Run
Report: In previous version these peaks were not reported.
• FL2000/3000 Display Scale Increased by a Factor of Ten: In previous versions
the fluorescence signals were displayed to a scale of 1000 Fluorescence Units = 1V.
In this version the scale is 100 Fluorescence Units = 1V. This change will make the
peak heights and peak areas match the values obtained with PC1000. Compared to
previous versions of ChromQuest, the heights and areas will be ten times greater.

New Features and Fixes in the 3.0 Version

Features
Implementation of Electronic Signatures
This version of ChromQuest contains an implementation of Electronic Signature. It is
possible for more than one person to put an electronic signature on a file. A password
and permission is required for Electronic Signatures. Once an electronic signature is
applied, that file can no longer be analyzed. Signatures also require a reason. Electronic
signatures can be revoked, which removes all electronic signatures from the file. A new
Electronic Signatures table can be inserted into the Custom Report that documents all
electronic signatures for the file. A bitmap indicating Results Approval may also be
included on the Method Custom Reports.
System/Method Wizard
Two new wizards are added to this release, the Instrument Wizard and the Method
Wizard.
New Advanced Reporting Feature
The Sequence/Summary report function has now been removed, as the Advanced
Reports feature replaces its functions.
New Extended Security Controls Project Folder Rights
Data File Checksum
HP 6890/7673 Instrument Control Option
Dual tower 7673a autosamplers supported in the following configurations:
Control via IEEE directly from ChromQuest, connected to an external autosampler
controller (Model G1512A).
Control via RS2332 directly from ChromQuest, connected to an external autosampler
controller (Model G1512A)
Multi-Line Pump Shutdown Methods Supported
Option for Automatically Enabling Method Audit Trail
Option for Saving All Results with Data Files
There has been a last minute improvement to the operation of this feature. This description
supersedes the manual and help files.
Versions 2.x data files: The labels "Original Results" and "Previous Last Results" will be
shown when opening files from these versions. Previous Last Results refers to the
results labeled "Last Results" by version 2.x. If the option is selected, all new results will
be labeled with the name of the analyst and a time stamp. If the option is not selected,
the first new results created with ChromQuest 3.0 and the most recent results will be
displayed with the analyst and time stamp label.
Version 3.0 data files: The labels "Original Results" and "Previous Last Results" will be
shown when opening files. Whether the option is chosen or not, the original result will be
displayed with an analyst and time stamp label. If the option is chosen, all further results
will also be displayed with this label. If the option is not shown, only the most recent
result will be displayed in the file open dialog.
Method now Saved with All Results
New Software License Key
The hardware license key is now obsolete. With this release, software license keys are
shipped on floppy disks (one to install the key, one to uninstall it if necessary). Users
upgrading from previous versions will no longer use the hardware keys. See the
Installation/Software License Key sections of the manual for additional details.
Scroll Feature Added
You can now scroll around on a chromatogram view. Hold the <CTRL><SHIFT> keys
down while the mouse cursor is inside the chromatogram graph area. As you move the
mouse, the cursor turns to a hand that lets you drag the chromatogram to a new location.
Hold the <CTRL><SHIFT> keys down while the mouse cursor is outside the graph, but
near an axis, and the cursor changes to an up/down or right/left arrow, allowing you to
scroll the graph up/down or right/left. See Basics of Operation/Chromatogram
Window/Scrolling the Chromatogram section of help or the manual.
Fill Down in Sequence Table Added
Data File Compression
Dual Tower Autosampler Control for GC
Addition of Current Response Factor Parameter
The existing parameter called "Response Factor" was renamed "Average RF."
Warning in Sequence Wizard when Calibration Vials Will Be Re-run as Unknowns
Reversing the Ordering of Calibration Replicates
In previous versions, calibration "rep <n>" was the most recent run and "rep 2" was the
first injection. This has been changed in ChromQuest 3.0 so that "rep 1" is the first injection and
"rep <n>" is the latest run. Existing methods will automatically be switched to this new
way of ordering replicates.
Addition of Sample Types to Method Custom Report
Modifications to Printing during a Sequence
A new Run Type called Print Additional Reports has been added to the run types of a
sequence run. The method contents report is printed by using this feature. The sequence
wizard can add the printing of the method contents report automatically to a sequence.
Allow Reference to Named Peaks for the Resolution Calculation
Creation of a Vial Summary Report
Enhancement in File Selection in Sequence Table
After the user selects a data file from the data file column ChromQuest now extracts the
Sample ID, Sample Amt., ISTD Amt., Multiplier, and Description from the data file and
displays it in the sequence spreadsheet on the selected line. Also if the data file path is the same
as that stored in the sequence properties the path is removed from the file and only the file
name is saved in the batch record.
Add Column Information to the Method
Added Performance Calculations
Simultaneous calculations for all performance calculation methods are now available.
Sequence Control of Standard Weight and Concentration
A new column has been added to the sequence table right after Level column. This
column is called Conc. and is active only for calibration runs. When this field is selected,
the Edit Concentration Overrides dialog is displayed. The dialog box contains check
boxes to select Peaks or Groups. The combo box contains all traces available in the
method. Selecting the trace displays Peak/Group names along with existing
concentration for the specified level. In the last column, a new concentration can be
entered. If this field is blank, the concentration specified in the peak table for this level is
used, otherwise this value is copied to the peak table and this event is changed logged if
change logging is on.
Change to the Sequence Wizard
A clear calibration check box has been added to the sequence wizard that will select the
Clear All Calibration run type for the first line of the sequence.
Simplify Specifying the Run Types in an Existing Sequence
Easier Scaling of X and Y Axes
Redesign of Trace Properties Dialog Box
Simplified Sequence Table Update
Pressing the F5 key will refresh the view, eliminate all blank rows, and move non-blank
rows up appropriately.
Change existing accelerator keys to eliminate conflict with reserved function keys
To eliminate conflict with some Microsoft Reserved behavior for some function keys, add
SHIFT + CTRL before all existing accelerator keys.
New SS420 Drivers
Report of Actual vs. Expected Retention Times
Add Tool Tips for Fields Containing Fully Qualified Filenames
Improvement in Graph Legend Options
Improved Print of Non-Solid Lines
The printer should be set to 300 dpi. for best results.
Instrument Abort Message in the Instrument Activity Log
Legend On/Off Conflicts Clarified
Legend settings have been confusing to a number of customers. The following statement
should help:
The Show Legends box in Axis Setup/General Options turns on or off the availability of
legends. The Legends box in the Trace Properties spreadsheet turns the legend on or
off for the selected trace, provided the Show Legends box in Axis Setup/General Options
is selected. If the Show Legends box in Axis Setup/General Options is not selected, the
Legends box for Trace Properties has no effect.
Addition of Trace Identifier to Sequence Reports
Relative Retention Time
Relative retention time was previously only reported for named peaks that have reference
peaks. It is now also calculated and reported for detected, unnamed peaks that are
members of uncalibrated or calibrated range groups that have a reference peak specified. The
reference peak specified in the group is used to calculate the Relative Retention Time
for the unnamed peaks using the same equation used for named peaks.

t 2 - ta
α=
t 1 - ta
Where
α= Relative retention.
t2 = The retention time measured from point of injection
ta = The retention time of an inert component not retained by the column,
taken from "Unretained Peak Time" in the Performance Options section of the method.
t1 = The retention time from point of injection for reference peak defined in
the peak table. If no reference peak is found, this value becomes zero.
Support for AIA Level 2 Import
Print Control in the Run Queue
Enhanced Data Audit Trail
Enhanced Demo Mode
All devices and analysis options can be configured in demo mode (no key
present).
Changes to File Open Dialog Search Criteria
Search terms for "last week" and "last month" have been changed to "last 7 day" and
"last 30 days". See Basics of Operation/Opening Files sections in the online help or
manual for details.
Sample ID Used for Analysis Saved with Results
Method Modified/Creation Dates Added to Method Custom Report and Method Contents Report
CIO/DIO Boards Now Supported
Note on installation of CIO/DIO boards: If multiple CIO/DIO boards are installed, and you
uninstall any board other than the last board installed, you must uninstall and reinstall all
boards in order for them to work properly.
Calculate Concentrations for Unnamed Peaks in Calibrated Range Groups
Seq. w/ Back-Calculate
Bracketed Sequences Now Report "Unknown" Results as "Original"
Method Custom Report and Sequence Report Printing Now Controlled from Run Dialogs
Programmable Pause between Calibration and Unknown Runs
Peak/Groups Table Usability Enhanced
Improvements in Reprocessing Performance
Support for the PE Nelson 941 and 960 Series (RS232) Interface Boxes

Fixes

Cubic Fit for Response Factors

Repair of Active Sequence Actions during Edits
Addition of Dates to Sequence Report
The sequence contents report now has the "Last Modified Date" and "Creation Date" of
the sequence displayed as part of the header.
Change in the Behavior of the Sequence Wizard
In previous versions, the Sequence Wizard put n-1 unknowns between samples when
"Run QC check standard every n unknowns" is selected. The Sequence Wizard was
changed such that the number of unknowns between QC check standards is n.
Change in Japanese Performance Parameter Calculation
The constant used in the equation has changed from 5.54 to 5.55. See the Equations
section of the online help or manual for details.
Crash in Graphical Threshold Event Programming with Offset Traces Fixed
Reprocessing Crash When Graph with Annotations Open Fixed
Crash While Analyzing with the "Define Single Peak" Dialog Open Fixed
Channel Selection for AIA Export now Functional
ISTD Concentration Displays Properly in AIA Export
Define Single Peak No Longer Allows Retention Time of Zero
Problems with Edits of Running Sequences Fixed
Clear All Calibrations with Multiple Repetitions in Sequence Line Now Functions Correctly
Integration Error when Manual Peak is overlaid onto a Fused Group is fixed
Intermittent Reporting Error in Area % Report for Named Peaks Group and No Detected Peaks
Fixed
Invalid Fit Results are Now Noted
EMG Calculation Changed to Use 10% Height
Improvement of Peak Apex Detection
The peak apex detection has been improved to correct errors that occurred for peaks
with gross overload or tailing. Peaks with these features may report a slightly different
retention time and peak height than was reported in previous versions. In very rare
cases, such as very under sampled peaks, the peak area may change slightly.
Crash of One SN4000 Server Does Not Crash Other Servers Connected to the Same Computer
Buffer size in Instrument Servers Increased to Improve Reliability
New Features and Fixes in the 2.51 Version
Features
Support of GC8000 Top
Support of HP5890 GC
Improved sequence wizard
Samples and standards named separately
New autonaming options for sample ID and data file
Option for system suitability on first data set only
Printed reports automatically indicate whether data are original or reprocessed
Method reports printed as sequence report
More significant figures for sample amount, multiplier and manual RF fields
Updated and improved manual

Fixes
Improvements to error handling and the ability to handle shutdown files
Improvements to communication to SN4000 and UV6000
Method audit trail can now be printed with the method report
Improved signal labeling along with other improvements in multiple signal handling
Improvements in software robustness, including a fix to a problem that affected very long runs
Fixes in data conversion
Many minor bugs fixed