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Gubbs, Inc.
265 Blue Spruce Circle
Alpharetta, GA 30005
P: 770-573-0169
F: 508-453-1338 gubbs@gubbsinc.com
www.gubbsinc.com
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Table of Contents
Section
1
Page 2 of 48
Page Number
INTRODUCTION ........................................................................................................................................................ 5
4
MANUAL HISTORY ................................................................................................................................................... 5
HIGH THROUGHPUT (HT) VS LOW THROUGHPUT (LT) ACQUISITION ................................................... 6
DEFINITIONS .............................................................................................................................................................. 6
5 INSTALLATION OVERVIEW .................................................................................................................................. 7
5.1
I NSPECT SYSTEM REQUIREMENTS AND PREREQUISITES ............................................................................................... 7
5.2
E XECUTE S ETUP .
EXE ................................................................................................................................................... 7
5.3
D ETERMINE THE PHYSICAL LOCATION OF THE GMSU DATABASE G UBBS _01.
MDB ( IF APPLICABLE ) .......................... 7
5.4
P REPARE W INDOWS
®
DIRECTORY SHARE AND DIRECTORY PERMISSIONS ( IF APPLICABLE ) ........................................ 7
5.5
C ONFIGURE DATABASE AND DSN ( IF NEEDED ) ........................................................................................................... 7
5.6
C ONFIGURE GMSU_ XX .
INI ......................................................................................................................................... 7
5.7
E XECUTE U PDATE GMSUD ATABASE .
XLS ( IF APPLICABLE ) ......................................................................................... 7
5.8
C ONFIGURE GMSU C ONFIGURATION D EFAULT P ARAMETERS ................................................................................... 7
6 SYSTEM REQUIREMENTS ...................................................................................................................................... 8
7 PRE-REQUISITES ...................................................................................................................................................... 8
7.1
S CIEX ENVIRONMENT .................................................................................................................................................. 8
7.2
T HERMO F INNIGAN ENVIRONMENT ............................................................................................................................. 9
8
9
SETUP EXECUTION .................................................................................................................................................. 9
8.1
D IRECTORY CREATION ................................................................................................................................................ 9
8.2
S YSTEM DSN ODBC FILE CREATION .......................................................................................................................... 9
8.3
GMSU_ XX .
INI FILE CREATION .................................................................................................................................. 10
8.4
G UBBS _01.
MDB FILE CREATION ................................................................................................................................ 10
PHYSICAL LOCATION OF GMSU DATABASE GUBBS_01.MDB .................................................................. 10
10 WINDOWS SHARE PERMISSIONS AND DIRECTORY PERMISSIONS ....................................................... 11
10.1
L OCAL D ATA D IRECTORY ......................................................................................................................................... 11
10.2
S HARED N ETWORK D ATA D IRECTORY ( IF APPLICABLE ) ........................................................................................... 12
10.3
S HARED L OCAL D ATA D IRECTORY ( IF APPLICABLE ) ................................................................................................. 13
11 DATABASE CONFIGURATION – MICROSOFT® ACCESS ............................................................................. 14
12 DSN CONFIGURATION – MICROSOFT® ACCESS .......................................................................................... 15
12.1
ODBC D ATA S OURCE A DMINISTRATOR ................................................................................................................... 15
12.2
C REATE N EW D ATASOURCE ..................................................................................................................................... 15
12.3
ODBC S ETUP ............................................................................................................................................................ 16
12.4
S ELECT DATABASE .................................................................................................................................................... 16
13 DATABASE CONFIGURATION – MICROSOFT® SQL SERVER ................................................................... 18
13.1
C REATE A SQL S ERVER DATABASE USING THE MS A CCESS U PSIZING W IZARD ....................................................... 18
13.2
C REATE A GMSU DATABASE ACCOUNT .................................................................................................................... 22
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Table of Contents
Section Page Number
13.3
R ECORD THE USER ACCOUNT AND PASSWORD INFORMATION ................................................................................... 22
13.4
L OCAL D ATA S OURCE N AME (DSN) G UBBS _100 ..................................................................................................... 22
14 DSN CONFIGURATION – MICROSOFT® SQL SERVER ................................................................................. 23
14.1
ODBC D ATA S OURCE A DMINISTRATOR ................................................................................................................... 23
14.2
C REATE NEW DATA SOURCE ...................................................................................................................................... 24
14.3
C REATE A NEW DATA SOURCE ................................................................................................................................... 25
14.4
E NTER CONNECTION PARAMETERS ............................................................................................................................ 26
14.5
A DDITIONAL PARAMETERS ........................................................................................................................................ 26
14.6
T EST CONNECTION .................................................................................................................................................... 27
15 GMSU_XX.INI ........................................................................................................................................................... 28
15.1
MS A CCESS GMSU_ XX .
INI CONFIGURATION ........................................................................................................... 28
15.2
SQL S ERVER GMSU_ XX .
INI CONFIGURATION .......................................................................................................... 29
16 GUBBS INC PASSWORD ENCRYPTION TOOL ................................................................................................. 29
17 GMSU DATABASE UPDATE .................................................................................................................................. 29
18 GMSU CONFIGURATION DEFAULT PARAMETERS ...................................................................................... 31
19 CONSOLE ................................................................................................................................................................... 31
20 CONFIGURATION UTILITY .................................................................................................................................. 32
20.1
C ACO G LOBAL ........................................................................................................................................................ 32
20.2
C ACO
– A NALYSIS T IME P OINTS ............................................................................................................................... 34
20.3
C ACO
– C HROMATOGRAPHY P EAK S ETS ................................................................................................................... 35
20.4
C ACO
– C ONSTANTS ................................................................................................................................................. 36
20.5
F LAGS ....................................................................................................................................................................... 37
20.6
G ENERIC V IEWER ...................................................................................................................................................... 38
20.7
G LOBAL .................................................................................................................................................................... 40
20.8
H EPATIC C LEARANCE C ALCULATOR ......................................................................................................................... 42
20.9
H EPATIC C LEARANCE C ALC .
E XPT .
C ONSTANTS
– E XISTING E XPERIMENTS T AB ..................................................... 43
20.10
H EPATIC C LEARANCE C ALC .
E XPT .
C ONSTANTS
– A DD S PECIES /T YPE T AB ............................................................. 44
20.11
H EPATIC C LEARANCE C ALC .
E XPT .
C ONSTANTS
– E XPERIMENT T IME P OINTS T AB ................................................. 45
20.12
M ODIFY M ETHOD ..................................................................................................................................................... 47
21 REFERENCES ........................................................................................................................................................... 48
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Table of Figures
Figure Page Number
F IGURE 1 N ETWORK BROWSE
F IGURE 2 MS A CCESS DNS D ATA S OURCE A DMINISTRATOR
F IGURE 3 MS A CCESS DNS C REATE A N EW D ATA S OURCE W IZARD
F IGURE 4 MS A CCESS DNS ODBC M ICROSOFT A CCESS S ETUP
F IGURE 5 MS A CCESS DNS S ELECT D ATABASE
F IGURE 6 MS A CCESS U PSIZING W IZARD
F IGURE 7 MS A CCESS U PSIZING W IZARD C HOOSE C REATE NEW DATABASE
F IGURE 8 MS A CCESS U PSIZING W IZARD C ONNECTION SETTINGS
F IGURE 9 MS A CCESS U PSIZING W IZARD E XPORT ALL TABLES
F IGURE 10 MS A CCESS U PSIZING W IZARD
– E XPORT ATTRIBUTES
F IGURE 11 MS A CCESS U PSIZING W IZARD
– N O APPLICATION CHANGES
F IGURE 12 MS A CCESS U PSIZING W IZARD F INISH
F IGURE 13 MS SQL S ERVER GMSU ACCOUNT ROLES
F IGURE 14 SQL S ERVER DNS D ATA S OURCE A DMINISTRATOR
F IGURE 15 SQL S ERVER DNS C REATE A N EW D ATA S OURCE W IZARD
F IGURE 16 SQL S ERVER DNS C REATE A NEW DATA SOURCE
F IGURE 17 SQL S ERVER DNS E NTER CONNECTION PARAMETERS
F IGURE 18 SQL S ERVER DNS E NTER ADDITIONAL PARAMETERS
F IGURE 19 SQL S ERVER DNS E NTER ADDITIONAL PARAMETERS
F IGURE 20 SQL S ERVER DNS T EST CONNECTION
F IGURE 21 SQL S ERVER DNS T EST CONNECTION
F IGURE 22 GMSU D ATABASE U PDATE U TILITY F IRST TIME USE SCREEN
F IGURE 23 GMSU D ATABASE U PDATE U TILITY
– A FTER E XECUTE
F IGURE 24 GMSU C ONSOLE
F IGURE 25 C ONFIGURATION U TILITY
– C ACO (P ERMEABILITY C ALCULATOR ) – G LOBAL
F IGURE 26 C ONFIGURATION U TILITY
– C ACO (P ERMEABILITY C ALCULATOR ) – A NALYSIS T IME P OINTS
F IGURE 27 C ONFIGURATION U TILITY
– C ACO (P ERMEABILITY C ALCULATOR ) – C HROMATOGRAPHY P EAK S ETS
F IGURE 28 C ONFIGURATION U TILITY
– C ACO (P ERMEABILITY C ALCULATOR ) – C ONSTANTS
F IGURE 29 C ONFIGURATION U TILITY F LAGS
F IGURE 30 C ONFIGURATION U TILITY
– G ENERIC V IEWER
F IGURE 31 C ONFIGURATION U TILITY G LOBAL
F IGURE 32 C ONFIGURATION U TILITY
– H EPATIC C LEARANCE C ALCULATOR
F IGURE 33 C ONFIGURATION U TILITY
– H EPATIC C LEARANCE C ALC .
E XPT .
C ONSTANTS
– E XISTING E XPERIMENTS
34
35
36
37
30
30
31
32
26
27
27
28
23
24
25
26
38
40
42
19
19
20
20
21
21
22
14
15
16
16
17
18
43
44
T AB
F IGURE 34 C ONFIGURATION U TILITY
– H EPATIC C LEARANCE C ALC .
E XPT .
C ONSTANTS
– A DD S PECIES /T YPE T AB
F IGURE 35 C ONFIGURATION U TILITY
– H EPATIC C LEARANCE C ALC .
E XPT .
C ONSTANTS
– E XPERIMENT T IME P OINTS
T AB I NITIAL
F IGURE 36 C ONFIGURATION U TILITY
– H EPATIC C LEARANCE C ALC .
E XPT .
C ONSTANTS
– E XPERIMENT T IME P OINTS
T AB E DIT
F IGURE 37 C ONFIGURATION U TILITY
– M ODIFY M ETHOD
45
46
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1
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Introduction
Gubbs Mass Spec Utilities (GMSU) is a suite of utilities that enhance the ability of scientists to perform high volume actions in mass spectrometer data acquisition systems. This is useful in laboratories engaged in high-throughput studies.
GMSU uses either Microsoft® (MS) Access or MS SQL Server as a datastore. MS Access may be used to quickly setup a GMSU instance for user testing or production use. MS SQL Server may be used if a more secure and possibly more efficient environment is desired. The MS Access database can be directly upgraded to SQL Server without loss of data.
GMSU may be used in a multi-user environment. There are several configuration possibilities for multi-
user environment which are described in more detail in Section 0. Briefly, the GMSU database and
acquired mass spectrometer raw data files may be stored in a common location accessible to others (either a shared network directory or a shared local directory). Multiple installations of GMSU may be configured to use the database and access the raw data files located in the common location. This allows users in the analytical department to use GMSU to generate and optimize chromatographic integration acquired data. Once the chromatographic integration data is approved, users in the pharmacokinetics department may be notified and can immediately generate pharmacokinetic data.
GMSU data are stored in a database. This data may be accessed or generated from multiple installations of GMSU.
2 Manual History
To view the changes between this version and the previous version of this manual, please do the following:

Open the MS Word version of the manual o The most recent versions of manuals are available at www.gubbsinc.com

Show the Reviewing toolbar in the Word document

In the Show button of the Reviewing toolbar, select Insertions and Deletions
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3 High Throughput (HT) vs Low Throughput (LT) Acquisition
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One of the salient features of GMSU is that it can process HT acquired data as well as LT acquired data.
Typically, mass spectrometry data acquisition systems require that compound(s) of interest occur once in a chromatographic analysis. Therefore, in order to analyze a 12-point assay, scientists had to acquire twelve separate ‘samples’ within a data file. This is referred to as LT acquisition in the GMSU system.
In HT acquisition, users open the data acquisition window for as long as needed and inject and acquire all assay time points in a single chromatographic run. The benefits of HT acquisition 1 - 4 include:

The ability to view all chromatographic peaks simultaneously to check for possible instrumental or sample handling problems and/or trends

When combined with multiple-column switching techniques, increases throughput by decreasing the time between sample injections and minimizes communication problems that can occur between instrument and data acquisition system.
NOTE: Currently HT acquisition data processing is supported on the Sciex platform in the Hepatic
Clearance and Permeability modules.
4 Definitions
Term
CDS
DSN
GMSU
HT
LT
Chromatography Data System
Data Source Name
Gubbs Mass Spec Utilities
High Throughput
Low Throughput
Definition
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5 Installation Overview
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GMSU Setup includes the following steps. Please refer to each referenced section for a detailed discussion of each step
Step Section
5.1
Inspect system requirements and prerequisites
Sections 6 - 7
Section 8
5.2
Execute Setup.exe
5.3
Determine the physical location of the GMSU database
Gubbs_01.mdb (if applicable)
5.4
Prepare Windows® directory share and directory permissions (if applicable)
Note: Does not need to be performed if upgrading an existing
GMSU installation

Thermo users please pay special attention to Section 10.3
5.5
Configure database and DSN (if needed)
Note: Does not need to be performed if upgrading an existing
GMSU installation

Microsoft Access

Microsoft SQL Sever
5.6
Configure GMSU_xx.ini
Notes: Does not need to be performed if upgrading an existing
GMSU installation
5.7
Execute UpdateGMSUDatabase.xls (if applicable)
To be performed with GMSU uprades
5.8
Configure GMSU Configuration Default Parameters
Admins must configure several default values for proper GMSU usage.
Notes: Does not need to be performed if upgrading an existing
GMSU installation
Section 9
Sections 10
Sections 11 - 12
Sections 13 - 14
Section 15
Section 17
Section 18
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6 System Requirements
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The following describes the environments on which GMSU was tested. The user is free to install GMSU on workstations of differing configuration with the understanding that GMSU should be tested before implementing.
OS
CPU (GHz)
RAM (MHz)
Sciex Analyst 1,4
Thermo Excalibur 2,4
Microsoft® Office 3
UpdateGMSUDatabase.xls
Client Workstations
MS Windows XP SP2
1.8
512
1.4.1, 1.4.2
2.0.5
Office 2003 SP2
MS Excel 2003 SP2
GubbsIncPswd_01.xls
1
MS Excel 2003 SP2
GMSU supports Sciex Analyst 1.3.x and Analyst 1.4.2
2 GMSU supports XCalibur 2.0.5 and previous versions
3 At a minimum, Word and Excel must be installed. GMSU is compatible with Office XP or later.
4
Not required for data reporting (see Section 7)
SQL Server
OS
CPU (GHz)
RAM (MHz)
1 If SQL Server is to be used
MS SQL Server Server 1
SQL Server 2000 SP4, SQL Server 2005
MS Windows Server 2003 SP1
1.3
1250
GMSU uses Microsoft Office to generate reports in Excel and Word.
7 Pre-Requisites
7.1
Sciex environment
7.1.1
Data Processing
In order to view chromatography and process PK data, Sciex Analyst must be installed on the workstation on which the GMSU client is being installed. GMSU uses several Sciex
Analyst Active X objects and .dll’s to ensure that information provided by GMSU is identical to information if it were to be generated on Sciex Analyst.
If Sciex Analyst is not installed on the workstation, GMSU will not allow the user to open data processing modules.
7.1.2
Data Reporting
Sciex Analyst is not required to be installed to report data. All data reporting modules are available.
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7.2
Thermo Finnigan environment
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7.2.1
Data Processing
The Thermo software development kit called ‘SDK Plus’ must be installed on the workstation on which the GMSU client is being installed. GMSU uses several XDK Plus
Active X objects and .dll’s.
If XDK Plus is not installed on the workstation, GMSU will not allow the user to open data processing modules.
7.2.2
Data Reporting
XDK Plus is not required to be installed to report data. All data reporting modules are available.
8 Setup Execution
Run the GMSU Setup.exe executable.
In addition to installing the GMSU software, Setup.exe will perform the following tasks:
8.1
Directory creation
Setup.exe will create a C:\GubbsInc\GMSU\ directory and several subdirectories related to
GMSU operation (see Section 10.1). If the directories already exist, then they will not be re-
created and existing files within these directories will not be deleted or modified.
8.2
System DSN ODBC file creation
Setup.exe will create a System DSN ODBC file used by GMSU to communicate with the GMSU database.
8.2.1
Original Installation
If the GMSU installation is an original installation on a workstation, Setup.exe will prompt the user to choose MS Access or MS SQL Server as the GMSU database.


If MS Access is chosen, no further DSN configuration is needed.
If MS SQL Server is chosen, then further database and DSN configuration is needed
as described in Section 13 and 14
NOTE: If for some reason Setup.exe cannot create the System DSN, Setup.exe will inform the user that DSN creation was unsuccessful. If this should happen,
then the DSN file will need to be created manually according Section 12 for
MS Access or Section 14 for MS SQL Server.
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8.2.2
Upgrade Installation
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If the GMSU installation is an upgrade, then the System DNS will not be created unless it does not exist for reason.
8.3
GMSU_xx.ini file creation
8.3.1
Original Installation
Setup.exe will create a GMSU_xx.ini file in C:\GubbsInc\GMSU\.
8.3.2
Upgrade Installation
If GMSU_xx.ini already exists in C:\GubbsInc\GMSU\. Setup.exe will not overwrite the file.
8.4
Gubbs_01.mdb file creation
8.4.1
Original Installation
Setup.exe will create a Gubbs_01.mdb file in C:\GubbsInc\GMSU\Database\.
8.4.2
Upgrade Installation
If Gubbs_01.mdb already exists in C:\GubbsInc\GMSU\Database\, Setup.exe will not overwrite the file.
9 Physical Location of GMSU database Gubbs_01.mdb
If MS SQL Server is to be used as the GMSU database, then this section may be ignored.
In order for GMSU to be used in a multi-user environment, the Gubbs_01.mdb file must be located in a shared directory to which all GMSU users have access. The preferable location for Gubbs_01.mdb is on a network directory, but it can also reside on a local directory that has been shared out to all GMSU users.
If a network directory will be used, it is at this point that the network directory should be defined for the
next installation step Section 10.
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10 Windows Share Permissions and Directory Permissions
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The person installing GMSU must be logged onto the workstation with an account that has administrative privileges to the local workstation.
10.1
Local Data Directory
The GMSU setup.exe will create the following GMSU directories.
C:\GubbsInc\GMSU\
C:\GubbsInc\GMSU\Database\ 1,2
C:\GubbsInc\GMSU\Export\ 3
C:\GubbsInc\GMSU\CompoundLists\ 3
C:\GubbsInc\GMSU\ChromatographyMethods\ 4
C:\GubbsInc\GMSU\Manuls\
The folder
The folder
…\Database\ is the location in which the GMSU database is originally stored 1,2 .
GMSU setup.exe places the GMSU database ‘Gubbs_01.mdb’ here.
…\Export\ is the location in which text file reports will be stored (for Sciex HT
The folder
Acquisition Tools).
…\CompoundLists\ is the location in which Automaton™ compound lists are
The folder stored (for Sciex HT Acquisition Tools).
…\ChromatographyMethods\ is the location in which Permeability Calculator
The folder chromatographic methods are stored (if chromatographic methods are generated by the user in an HT environment).
…\Manuals\ is the location in which GMSU Manuals are stored. GMSU setup.exe places current manuals in this directory.
1 If Microsoft Access is to be used as the backend database
2
If MS Access is to be used in a multi-user environment, see Section 10.2
3 Used in a Sciex environment only
4 Used only by the Permeability Calculator module
Notes:

If the GMSU database is to be shared by multiple instances of GMSU, it is HIGHLY
RECOMMENDED that all local installation GMSU directory structures are not modified once created by GMSU setup.exe. The database stores some local directory structure variables and assumes that all local installation directory structures are identical.
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10.2
Shared Network Data Directory (if applicable)
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If GMSU is to be configured such that multiple instances of GMSU will share the same database and access the same acquired data, a shared directory must be configured according to the following guidelines. This directory can be a directory on a network file server, or the appropriate local directories of a single data acquisition workstation can be shared. The following instructions assume that a network file server directory will be configured (Thermo users should see
Section 10.3).
Identify a location to which GMSU files will be stored. At this location, generate the following directories:
NOTE: The easiest way to perform this process is to simply copy a local \GubbsInc\... directory set to the network.
\\[network]\GubbsInc\GMSU\
\\[network]\GMSU\Database\ 1
\\[network]\GMSU\Export\ 2,3
\\[network]\GMSU\CompoundLists\ 2,3
\\[network]\GMSU\Data\ 2
\\[network]\GMSU\ChromatographyMethods\ 3,4
The folder
The folder
The folder
The folder
\\…\Database\ is the location in which the GMSU database is stored
\\…\Export\ is the location in which text file reports are stored.
1 .
\\…\CompoundLists\ is the location in which compound lists are stored.
\\…\Data\ is the location in which acquired .wiff files are copied. Note that if a network repository of acquired data already exists, that is acceptable. The acquired data directory location is configured as a variable within the GMSU
Configuration Module (for Sciex environment only).
The folder \\…\ChromatographyMethods\ is the location in which Permeability Calculator chromatographic methods is stored (if a chromatographic method is generated by the user).
1 If Microsoft Access is to be used as the backend database
2 Sciex environment only
3 Optional. If this information will be specific to an instrument, then local directories may be configured in GMSU Configuration (assumes local data directories are configured as
described in Section 10.1).
4 Used only by the Permeability Calculator module
10.2.1
Copy files
At a minimum, copy GMSU_01.mdb to \\[network]\GubbsInc\GMSU\Database\.
10.2.2
Share settings
Share the …\GMSU\ directory and configure GMSU users to have a minimum of
CHANGE share permissions.
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10.2.3
Directory permission settings
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Configure directory permissions at the …\GMSU\ and configure the subdirectories to inherit. At a minimum, users must be able to read and write to these directories
(MODIFY permissions).
Note: If the directory to which acquired data is stored is something other than a GMSU directory, users must be able to read and write to this directory (Psuedo HT acquisition chromatogram text files are written to this directory).
10.2.4
GubbsSciex_100 System DSN ODBC file
Remember that the network Gubbs_01.mdb will be used when configuring the MS
Access GubbsSciex_100 System DNS ODBC file described in Section 12.
10.3
Shared Local Data Directory (if applicable)
GMSU is especially useful when it is configured in a manner that all users have access to the raw chromatographic data (.wiff, .raw, .sld). This type of access is most easily attained when the raw data are stored on a centralized network server. However, it is recognized that the Thermo chromatographic raw data file structure mostly is not amenable to manual movement of data to a network directory. In addition, some Sciex administrators may not wish to include a manual raw data copy step in their data reporting process.
Therefore, if it is desired to use GMSU in a manner that all users have access to local chromatographic raw data, administrators must perform the following steps:
10.3.1
Share the raw data directory (e.g. C:\XCalibur\ or D:\Analyst Data\Projects\)
The raw data directory must be shared to GMSU users.
Give the share an intuitive name, such as ‘XCalibur’ or ‘Analyst’
Users must be granted a minimum of CHANGE share permissions.
10.3.2
Configure raw data directory security permissions
The directory security permissions of the raw data directory must be configured such that
GMSU users have a minimum of MODIFY permissions.
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10.3.3
GMSU Configuration Module – Generic Viewer
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Configure the appropriate Generic Viewer settings according to the table below.
NOTE: When configuring Default Data Directory, browse to the MICROSOFT
WINDOWS NETWORK to configure the share (see Figure 1).
Setting Value
Default Data Directory With the Browse button, browse to the NETWORK
share of the raw data directory (see Figure 1)
The result would be a UNC path configured as
Default Data Directory, e.g.:
\\gubbs03\XCalibur\ or \\gubbs03\Analyst\
Select Default CDS Environment Thermo(R) ‘for Thermo users’
Sciex(R) ‘for Analyst users’
Use UNC Path Yes
Figure 1 Network browse
11 Database Configuration – Microsoft® Access
If MS Access is to be used as the backend database, follow the instructions in this section.
Setup will place a copy of the Gubbs_01.mdb in the C:\GubbsInc\GMSU\Database\ directory.
Configure an appropriate DSN File according to Section 12.
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12 DSN Configuration – Microsoft® Access
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If Setup.exe could not create the GubbsSciex_100 System DSN ODBC file, then the administrator must manually create the DSN file according to this section.
GMSU communicates with the MS Access database via a system DSN named GubbsSciex_100. Create the DSN according to the following procedure:
12.1
ODBC Data Source Administrator
Open the Data Source Administrator and select the System DSN tab

Windows XP: via Control Panel – Administrative Tools – Data Sources
Figure 2 MS Access DNS - Data Source Administrator
12.2
Create New Datasource
Click on the Add… button to start the Create a New Data Source Wizard, select “Driver do
Microsoft Access (*.mdb), and click on Finish
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Figure 3 MS Access DNS - Create a New Data Source Wizard
12.3
ODBC Setup
At the ODBC Microsoft Access Setup window, enter the Data Source Name and Description as
shown in Figure 4. IMPORTANT: The Data Source Name must be entered exactly as shown.
Figure 4 MS Access DNS - ODBC Microsoft Access Setup
12.4
Select database
Click on the Select… button, navigate to the Gubbs_01.mdb, and click on OK
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Figure 5 MS Access DNS - Select Database
Click on the OK button to complete the DSN configuration process.
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13 Database Configuration – Microsoft® SQL Server
Page 18 of 48
If Microsoft SQL Server is to be used as the backend database, follow the instructions in this section.
13.1
Create a SQL Server database using the MS Access Upsizing Wizard
Setup will place a copy of the Gubbs_01.mdb in the [drive]:\Program Files\Gubbs Mass Spec
Utilities\ directory (or installation location configured by the user).
Open this file in MS Access and run the Upsizing Wizard
Figure 6 MS Access Upsizing Wizard
The following figures show the parameters to choose when performing the Upsize action
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Figure 7 MS Access Upsizing Wizard - Choose Create new database
Figure 8 MS Access Upsizing Wizard - Connection settings
Here, enter a login ID and password of an account with sufficient permissions to create a database
(e.g. sa). A GMSU user account will be generated at a later step. The database name can be of your choosing.
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Figure 9 MS Access Upsizing Wizard - Export all tables
Figure 10 MS Access Upsizing Wizard – Export attributes
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Figure 11 MS Access Upsizing Wizard – No application changes
Figure 12 MS Access Upsizing Wizard - Finish
At this point the Upsizing Wizard will generate a report which may be discarded.
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Create a GMSU database account
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In SQL Server, create a GMSU database account. The account name and password can be of your choosing.
Add the account to the GMSU database and assign the account the following roles:
Figure 13 MS SQL Server GMSU account roles
13.3
Record the user account and password information
Record the user account and password information on a sheet of paper. The user account and
password information is needed to update the GMSU_xx.ini file described in Section 15.
13.4
Local Data Source Name (DSN) Gubbs_100
GMSU communicates with the SQL Server database via a system DSN. Create the DSN
according to the procedure described in Section 14.
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14 DSN Configuration – Microsoft® SQL Server
Page 23 of 48
If MS SQL Server is to be used as the backend database, follow the instructions in this section.
If Setup.exe could not create the GubbsSciex_100 System DSN ODBC file, then the administrator must manually create the DSN file according to this entire section.
If Setup.exe was successful in creating the GubbsSciex_100 System DNS ODBC file, then the
administrator must complete the configuration starting with Step 14.3 of this section.
GMSU communicates with the SQL Server database via a system DSN named GubbsSciex_100. Create the DSN according to the following procedure:
14.1
ODBC Data Source Administrator
Open the Data Source Administrator and select the System DSN tab

Windows XP: via Control Panel – Administrative Tools – Data Sources
Figure 14 SQL Server DNS - Data Source Administrator
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Create new data source
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Click on the Add… button to start the Create a New Data Source Wizard, select “SQL Server”, and click on Finish
Figure 15 SQL Server DNS - Create a New Data Source Wizard
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Create a new data source
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At the Create a new data source window, enter ‘GubbsSciex_100’ as Name and Description as shown. Choose the server on which the GMSU SQL Server database was generated, then click
Next
IMPORTANT: The Data Source Name must be entered exactly as shown.
Figure 16 SQL Server DNS - Create a new data source
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Enter connection parameters
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Configure the next window as shown. Enter the userid and password combination created in
Section 13.2. Then click Next.
Figure 17 SQL Server DNS - Enter connection parameters
14.5
Additional parameters
Enter additional parameters as shown in the next two figures, then click Next and Finish:
NOTE: Ensure that the default database is the GMSU database.
Figure 18 SQL Server DNS - Enter additional parameters
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Figure 19 SQL Server DNS - Enter additional parameters
14.6
Test connection
Test the connection by clicking on the ‘Test Data Source’ button
Figure 20 SQL Server DNS - Test connection
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Figure 21 SQL Server DNS - Test connection
If the last line does note read “TESTS COMPLETED SUCCESSFULLY”, then contact your
GMSU administrator before proceeding.
Click on the OK button to complete the DSN configuration process.
15 GMSU_xx.ini
Setup will create an .ini file (named GMSU_xx where ‘xx’ is a number) located in the directory
C:\GubbsInc\GMSU\.
15.1
MS Access GMSU_xx.ini configuration
The default .ini content is for a MS Access installation. Please note that the UserID and Pswd entries of the .ini file may be ignored. Ensure that the .ini file has the following content: boolAccess boolSQLServer
True
False
UserID
Pswd
[USERID]
[PASSWORD]
Note: UserID is ignored
Pswd is ignored
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SQL Server GMSU_xx.ini configuration
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If SQL Server is to be used as database, ensure Ensure that the .ini file has the following content: boolAccess boolSQLServer
False
True
UserID
Pswd
[USERID]
[PASSWORD]
Note:
[USERID] is the SQL Server account generated in Section 13.2.
[PASSWORD] is the password of the SQL Server account generated in Section 13.2
IMPORTANT: The Gubbs Inc Password Encryption Tool described in Section 16 MUST be used
to encrypt the password. Copy the encrypted password form the Password Encryption Tool into the Pswd portion of the .ini file.
16 Gubbs Inc Password Encryption Tool
Setup will place a file named GubbsIncPswd_01.xls in the installation directory. Open this file to display the Gubbs Inc Password Encryption Tool. Copy the encrypted password to the .ini file if necessary.
17 GMSU Database Update
This utility should be run when GMSU is upgraded from a previous version. If GMSU database is a shared database or MS SQL Server database, the GMSU Database Update utility needs to executed only once. The utility does not need to be run when the system is initially installed and configured.
NOTE: Ensure that Excel Macro Security (Tools – Macro – Security) is set to Medium. If Macro Security is set to High, then the UpdateGMSUDatabase utility will not run.
Setup will create a file called UpdateGMSUDatabase.xls located in the installation directory. Open the file to display the GMSU Database Update Utility.
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Figure 22 GMSU Database Update Utility - First time use screen
At the displayed window, click on Execute Update.
Figure 23 GMSU Database Update Utility – After Execute
If the Notes report that the GMSU technical representative should be contacted, please contact Gubbs Inc.
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18 GMSU Configuration Default Parameters
Page 31 of 48
Please note that this section may be ignored if the GMSU installation is an upgrade to an existing GMSU installation.
Several GMSU configuration parameters must be configured in order that GMSU functions properly upon initial use. These parameters are defined in the following sections of the Administration Manual.
Note: If the GMSU Module will not be used, then the configuration section may be skipped.
GMSU Module Configuration Section
Caco (for Permeability Calculator Module)
Administration Manual
Reference
Section 20.1
Generic Viewer (for Generic Chromatographic Viewer Module)
Global
Hepatic Clearance
Section 20.6
Section 20.7
Section 20.8
19 Console
The GMSU Console is the module from which users navigate to other modules. The Console contents may differ slightly from what is shown.
Figure 24 GMSU Console
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Users click on the appropriate buttons either to open a utility or to navigate to an additional hierarchical level.
20 Configuration Utility
Administrators use the Configuration Utility to configure global variables and contents of module dropdown lists. Users choose the appropriate module to configure by choosing an item in the ‘Choose a
Category’ list.
The initial view of the Configuration Utility is a non-editable mode. In order to edit a value, the user must select the value, then click the Edit button. The user will be prompted to enter a new value, after which the user will click the Save button.
20.1
Caco - Global
The Caco – Global window contains default paths and values specific to the Permeability
Calculator. The parameters must be configured in order for proper GMSU operation follow the figure
Figure 25 Configuration Utility – Caco (Permeability Calculator) – Global
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20.1.1
Initial use parameter configuration
Page 33 of 48
The following are parameters that must be configured upon initial GMSU installation.
Note: If this module will not be used, then this section may be ignored.
20.1.1.1
Default Method Chromatography Path

This directory is where Permeability Chromatographic Method text files
(for HT Acquisition) are stored.

This directory is created by GMSU Setup.exe (see Section 10.1):
C:\GubbsInc\GMSU\ChromatographyMethods\
20.1.1.2
Default Data Directory

This directory is the root directory of where raw data is stored. This directory is shown initially when the Browse… button is clicked in the
Permeability Calculator module.
20.1.1.3
Show Low Throughput/High Throughput Option Window

Yes/No to view the LT/HT option window in the Permeability Calculator module.

If both LT and HT acquisition data (see Section 3 for a description of LT
and HT acquisition) will be viewed by users, then set this value to Yes.

If not, set this value to No
20.1.1.4
LT or HT Data Acquisition

Set value to LT if only LT acquisition data will be viewed.

Set value to HT if only HT acquisition data will be viewed.
 This value is ignored if ‘Show Low Throughput/High Throughput
Option Window’ is set to Yes
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Caco – Analysis Time Points
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The Analysis Time Points window is used to create Time Point Sets that will be assigned to analysis data files. ‘Time Points’ are defined as the assay time points in minutes.
Users click on the Edit button to configure a new Time Point Set. Users click on the Save button to actually create the Time Point Set. Once a Time Point Set has been created, it cannot be modified.
Figure 26 Configuration Utility – Caco (Permeability Calculator) – Analysis Time Points
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Caco – Chromatography Peak Sets
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The Chromatography Peak Sets window is used to create Chromatography Peak Sets that will be assigned to analysis data files. These sets provide identities of the chromatographic peaks of the acquired data.
Users click on the Edit button to edit an existing Chromatography Peak Set or configure a new
Chromatography Peak Set.
Peak identities are assigned by selecting the appropriate Peak Name in the Peak Name list, then double-clicking the appropriate row in the
Users click on the Create New Set button to configure a new Chromatography Peak Set. Users click on the Execute button to actually create the Chromatography Peak Set, then click the Save button to save the set.
Figure 27 Configuration Utility – Caco (Permeability Calculator) – Chromatography Peak Sets
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Caco – Constants
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The Constants window is used to create Constants Sets that will be assigned to analysis data files.
These sets include the various constants used in the calculation of Permeability Experiments.
Users click on the Edit button then Create New Set button to configure a new Constants Set.
Users click on the Save button to actually create the Constants Set. Once a Constants Set has been created, it cannot be modified.
Figure 28 Configuration Utility – Caco (Permeability Calculator) – Constants
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Flags
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The Flags window configures the contents of the ‘Chromatogr. Review’ dropdown box of the
Hepatic Clearance Calculator. ‘Results Flags’ are not configurable.
Figure 29 Configuration Utility - Flags
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Generic Viewer
Page 38 of 48
Figure 30 Configuration Utility – Generic Viewer
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The Generic Viewer window contains global parameters concerning default directory paths of system components.
20.6.1
Initial use parameter configuration
The following are parameters that must be configured upon initial GMSU installation.
Note: If this module will not be used, then this section may be ignored.
20.6.1.1
Default Data Directory

This directory is the root directory of where raw data is stored. This directory is shown initially when the Browse… button is clicked in the
Generic Chromatographic Viewer module.
20.6.1.2
Select Default CDS Environment
Used only if users will be viewing both Thermo and Sciex data. This setting governs the order in which ‘File Type Filter’ are displayed when the
Browse… button is clicked.
 If the setting is ‘Thermo(R)’, then the default choice is ‘.sld’.
 If the setting is ‘ABI(R)’, then the default choice is ‘.wiff’.
20.6.1.3
Use UNC Path
If it is desired that raw data be viewed directly from the data acquisition workstation, then this value must be set to Yes.
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Global
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The Global window contains global variables concerning default directory paths of system components.
Figure 31 Configuration Utility - Global
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The Global window contains global parameters concerning default directory paths of system components
20.7.1
Initial use parameter configuration
The following are parameters that must be configured upon initial GMSU installation.
20.7.1.1
Analyst Acquisition Data Path
Note: This parameter is related to Sciex HT Acquisition Tools. If these tools will not be used, then this section may be ignored.

This directory is the root directory of where Analyst raw data is stored.
20.7.1.2
Assay Request File Path
Note: This parameter is related to Sciex HT Acquisition Tools. If these tools will not be used, then this section may be ignored.

This directory is the root directory of where Assay Request Files (or may be referred to as Compound Lists) are stored. The Compound List is essentially the text file used by Automaton™.

This directory is generated by the GMSU Setup.exe (see Section 10.1):
C:\GubbsInc\GMSU\CompoundLists\
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Hepatic Clearance Calculator
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The Hepatic Clearance Calculator window contains default paths and values specific to the
Hepatic Clearance Calculator Utility. Such values include labels for the Species and Results sections.
Figure 32 Configuration Utility – Hepatic Clearance Calculator
20.8.1
Initial use parameter configuration
The following are parameters that must be configured upon initial GMSU installation.
Note: If this module will not be used, then this section may be ignored.
20.8.1.1
Default Data Directory

This directory is the root directory of where raw data is stored. This directory is shown initially when the Browse… button is clicked in the
Permeability Calculator module.
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Hepatic Clearance Calc. Expt. Constants – Existing Experiments Tab
Page 43 of 48
Administrators use this window to configure species- and experiment-specific constants that are used during Hepatic Clearance value calculations. The contents of the Species dropdown boxes in
the Hepatic Clearance Calculator are obtained from the Experiment list shown in Figure 33.
As an aid to administrators when configuring new Experiments, users may copy data from one experiment to another.
To add additional experiments, use the Add Species/Type tab (see Section 20.10).
Figure 33 Configuration Utility – Hepatic Clearance Calc. Expt. Constants – Existing Experiments
Tab
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Hepatic Clearance Calc. Expt. Constants – Add Species/Type Tab
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Here users add species and/or types. Once added, new experiments will be generated automatically.
Figure 34 Configuration Utility – Hepatic Clearance Calc. Expt. Constants – Add Species/Type Tab
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Hepatic Clearance Calc. Expt. Constants – Experiment Time Points Tab
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The Analysis Time Points window is used to create Time Point Sets that will be assigned to analysis data files. ‘Time Points’ are defined as each chromatographic peak (for HT acquisition) or each chromatographic injection (for LT acquisition).
Users click on the Edit button to configure a new Time Point Set. Users click on the Execute button to actually create the Time Point Set and the Save button to save the set. Once a Time
Point Set has been created, it cannot be modified.
In order to aid internal information technology (IT) department efforts to generate internal reports or transfer data to internal laboratory information management systems (LIMS), users may label peaks not used in actual regression analysis that are needed for additional internal process control information.
Figure 35 Configuration Utility – Hepatic Clearance Calc. Expt. Constants – Experiment Time Points
Tab - Initial
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Figure 36 Configuration Utility – Hepatic Clearance Calc. Expt. Constants – Experiment Time Points
Tab - Edit
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Modify Method
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The Modify Method window contains the contents of the LC Sync dropdown box of the Modify
Methods Utility. These contents are specific to Sciex instrumentation at this point in time.
Figure 37 Configuration Utility – Modify Method
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21 References
1 R. O. Cole. Quantitation of Biofluids with High Speed HPLC/MS/MS: Early Discovery Applications.
Invited Presentation, at “Early ADME and Toxicology in Drug Discovery: Techniques for accelerating and Optimizing Drug Candidate Selection”, Berkley, CA, October 1998.
2 Adam H. Brockman, Donna L. Hiller, and Roderic O. Cole. High Speed HPLC/MS/MS Analysis of
Biological Fluids in Support of ADME Screens: A Practical Review. Current Opinion in Drug Discovery,
4(3), (2000), 432.
3 Janiszewski JS, Rogers KJ, Whalen KM, Cole MJ, Liston TE, Duchoslav E, et al: A high capacity
LC/MS system for the bioanalysis of samples generated from plate-based metabolic screening. Anal
Chem 2001; 73:1495-1501.
4 Z. Yan, J. Wu, L.E. Elvebak, A. Brockman: Validation of a Totally Commercially Available High
Throughput -ADME System and Results for 60 Literature Compounds. Rapid Communications in Mass
Spectrometry, Rapid Commun. Mass Spectrom. 2005; 19: 1191–1199.
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