ACQUITY UPLC Systems June 2011 Driver Pack and Firmware Updates

R E L E A S E N O T E S ACQUITY UPLC Systems June 2011 Driver Pack and Firmware Updates What s new in this release... 3 Reasons for installing this software release... 3 Installation Notes... 3 Recommended firmware... 4 New Features and enhancements... 4 ACQUITY UPLC Console... 4 Column Managers... 4 Solvent Managers... 5 Leak testing... 5 Pressure limits... 5 Miscellaneous changes... 5 Sample Managers... 6 Detectors... 6 Photodiode Array (PDA) Detector... 6 Optics temperature stabilization feature... 7 Enhancement to the lamp and flow-cell resident memory... 7 Failing result on the wavelength verification test... 7 Re-creating the method... 7 Sample Organizer... 7 Ensuring the correct configuring of vial caps and shelf locations... 8 Analyst Software... 8 ACQUITY, ACQUITY UPLC, Connections INSIGHT, nanoacquity UPLC, Synapt, Waters, and Xevo are registered trademarks and Auto Blend, ecord, Empower, LAC/E 32, MassLynx, Q-Tof, and THE SCIENCE OF WHAT S POSSIBLE. are trademarks of Waters Corporation. All other trademarks are the sole property of their respective owners. Copyright 2011-2012 Waters Corporation *716003340* *Rev.B* Page 1 of 28

MassLynx software... 8 Empower 3 software... 8 Clinical/IVD ACQUITY UPLC Systems... 8 Connections INSIGHT... 9 Waters Pump Control for MassLynx software... 9 Waters Columns Calculator... 9 Contents of ACQUITY UPLC Systems June 2011 Driver Pack DVD... 9 Hardware and Software Requirements... 14 Supported Waters hardware:... 14 Supported Waters and third-party software... 14 Backward Compatibility... 15 Supported operating systems... 15 ACQUITY UPLC minimum hardware requirements and maximum detector data rates... 16 Installing the ACQUITY UPLC Systems June 2011 Driver Pack Release... 16 Installation method... 17 Using the repair function... 18 Installing the Updated Firmware Release... 18 Installing this Release in an Empower Enterprise Environment... 19 Installing Empower ICS on a Citrix server... 20 Troubleshooting and Uninstalling... 20 ICS Companion... 21 Overview... 21 Technical information... 22 Installation validation... 22 Workaround... 22 Disabling the service... 22 Restoring an SQ and TQ Empower 2 project for use with IntelliStart... 23 Defects addressed by this release... 24 Known defects in this release... 26 ACQUITY UPLC System Qualification... 27 Requalification Guidelines... 27 Contacting the Waters Technical Service Organization... 27 Page 2 of 28

What s new in this release The following items are new to revision B of the ACQUITY UPLC June 2011 Driver Pack: Revised release notes Additional firmware updates for the ACQUITY UPLC sample managers, the ACQUITY UPLC Sample Organizer, and the ACQUITY UPLC Column Manager with Active Preheater. See also: ACQUITY UPLC Sample Managers Firmware Version 1.51 Release Notes Waters ACQUITY UPLC Systems June 2011 Driver Pack Addendum Release Notes Reasons for installing this software release You must install this software release to perform the following tasks: Operate ACQUITY UPLC I-Class systems (all configurations). Operate an ACQUITY UPLC System with 2D Technology. (For details, refer to the ACQUITY UPLC Systems with 2D Technology Release Notes.) To benefit from improvements to the Waters Column Calculator. To enable remedies and enhancements for existing products (such as ACQUITY UPLC H-Class Systems). Important: Revision B of the ACQUITY UPLC June 2011 Driver Pack media includes both the firmware from the original release of the June 2011 driver pack and additional firmware updates specific to revision B. The additional firmware updates, specific to revision B, are available separately on the media and must be installed manually after you complete the installation of the driver pack. For details, refer to the installation instructions on page 16. See page 4 to determine whether or not a firmware upgrade is required for your system. Note: The ACQUITY UPLC 2011 Driver Pack is only compatible with firmware installed by the driver pack. Follow the driver pack instllation instructions on page 16 to ensure that the correct firmware is installed on your instruments. A list of problems addressed in this release appears later in this document. See also: Your system s user documentation CD for information about system modules. Installation Notes On an Empower Enterprise (client/server) system, install the driver/firmware according to the instructions on page 16. You must do so on all clients, LAC/E 32 modules, and Citrix application servers in the system. You need not, however, install the driver/firmware on the database server unless the server s client software interacts with an instrument or device. Customers with Empower Enterprise systems who use both ACQUITY UPLC and ACQUITY UPLC H-Class systems must update all ACQUITY instrument control software (ICS) implementations in their environment to the June 2011 Driver Pack. The ACQUITY UPLC Systems June 2011 Driver Pack does not support mixed use of ACQUITY UPLC ICS versions. Important: Revision B of the ACQUITY UPLC June 2011 Driver Pack media includes both the firmware from the original release of the June 2011 driver pack and additional firmware updates specific to revision Page 3 of 28

B. The additional firmware updates, specific to revision B, are available separately on the media and must be installed manually after you complete the installation of the driver pack. For details, refer to the installation instructions on page 16. See page 4 to determine whether or not a firmware upgrade is required for your system. Recommended firmware Waters recommends installing the ACQUITY UPLC Sample Managers Firmware, version 1.51. The firmware is available separately on this media, or may already be installed on new systems. Users should upgrade the firmware for their sample manager or sample organizer to version 1.51 in the following systems: Notes: ACQUITY UPLC, ACQUITY UPLC H-Class, or ACQUITY UPLC I-Class systems that run the ACQUITY UPLC Systems June 2011 Driver Pack and ACQUITY UPLC Sample Managers firmware, version 1.50. ACQUITY UPLC systems that include a sample organizer that displays the error message "Transfer Shuttle homing error". Do not install the ACQUITY UPLC Sample Managers firmware, version 1.51 upgrade on any ACQUITY UPLC, ACQUITY UPLC H-Class, or ACQUITY UPLC I-Class systems supported by a driver pack version earlier than the ACQUITY UPLC Systems June 2011 Driver Pack. The ACQUITY UPLC Sample Manager driver is the same for both the ACQUITY UPLC Sample Manager and the ACQUITY UPLC Sample Manager FL. Waters recommends installing the ACQUITY UPLC Column Manager with Active Preheater Firmware, version 1.51. The firmware is available separately on this disk. For some new systems, it is already installed. New Features and enhancements This section details new features and enhancements to the ACQUITY UPLC systems and components. ACQUITY UPLC Console The ACQUITY UPLC Console s About box now includes build dates. Column Managers In MassLynx software, column managers are now configured as detectors. The column manager firmware installed by the ACQUITY UPLC Systems June 2011 Driver Pack installer is version 1.50. Nevertheless, a newer version of the firmware, version 1.51, is included on the June 2011 Driver Pack media. After installing the June 2011 Driver Pack, you must manually install the version 1.51 column manager firmware. For details, refer to the installation instructions on page 16. Requirement: In the case of ACQUITY UPLC systems that include column managers, you must re-create preexisting MassLynx methods. New, advanced-mode features of the column manager with active preheater (CM-A) include the ability to directly control two, internal, 6-port, 2-position valves in the CM-A through the inlet method editor. Page 4 of 28

Use advanced mode features only with the CM-A. Do not use them with older column managers (CM). You can use as many as three external valves with the CM-A. External valve Part number 10-port, 2-position, Titanium 417000138 7-port, 6-position, PEEK 417000139 11-port, 10-position, stainless steel 417000150 Solvent Managers Leak testing The static leak test is no longer available. Instead, the binary solvent manager offers a dynamic leak test, which you can perform on an individual pump or system. The test can compresses fluids to the test pressure condition. It can accommodate both highly compressible fluids and the additional fluid volume compressed during a system test. You can specify a short time interval, to prime system components, before running the dynamic leak test. The criterion for passing an individual pump test is a leak rate of less than 200 nl/min. For a passing system test, it is a leak rate of less than 600 nl/min. Note: It is possible to pass the new dynamic leak test with a negative result. In some instances, the accumulator check valve can leak back into the primary actuator at a very low rate, causing a negative result. The test parameters allow negative results to -50 nl/min. Pressure limits In ACQUITY UPLC I-Class systems, the maximum pressure limit you can specify in the method editor is 18,000 psi. If your system includes a pump that cannot accommodate that pressure, an error message stating so appears on-screen when the maximum pressure limit is reached. In ACQUITY UPLC H-Class systems, however, the maximum pressure limit that you can specify in the method editor is 15,000 psi. The maximum pressure limit of a method persists after it runs. To change the limit, you must load a new method that specifies a different maximum pressure limit. Miscellaneous changes This update to the ACQUITY UPLC Systems June 2011 Driver Pack includes these additional changes: You can now access the Waters Columns Calculator from the method editor. The binary solvent manager now offers a Gradient Start feature, similar to that of the quaternary solvent manager. Use this feature to start the gradient function before an injection, for a specified period. You can also delay the start of the gradient after the injection, for a specified period. The method editor now graphically displays gradient conditions. You can now graphically display gradient conditions when you select Auto Blend mode for the ACQUITY UPLC Quaternary Solvent Manager. You can expand the gradient table so that it displays additional rows. Page 5 of 28

Sample Managers The sample manager firmware released as part of the ACQUITY UPLC Systems June 2011 Driver Pack is version 1.50. Nevertheless, a newer version of the firmware, version 1.51, is included on the June 2011 Driver Pack media. After installing the June 2011 Driver Pack, you must manually install the version 1.51 sample manager firmware. For details, refer to the installation instructions on page 16. These are the sample manager changes associated with the ACQUITY UPLC Systems June 2011 Driver Pack: For the sample manager and sample manager-fl, to help reduce persistent carryover, you can now select a timed event, Cycle inject valve. Cycling the injection valve for one or more cycles (at the end of a gradient run, for example) can help reduce carryover. Caution: To avoid reducing valve life, necessitating relatively frequent valve replacements, do not cycle the valve more than is necessary to minimize carryover. For the sample manager, sample manager-ftn, and sample manager-fl, to prevent carryover resulting from contact of the puncture needle with sample in plates whose wells are shallow, the pierce depth of the puncture needle is now 5 mm on all plates less than 15 mm high. Note, however, that pierce depth of all 384-well plates is 5 mm, regardless of plate height. For the sample manager and sample manager-fl, you now specify options in the Advanced window. For the sample manager, sample manager-ftn, and sample manager-fl, a No Injection option is now available in the Advanced section of the Method editor. For the sample manager and sample manager-fl, when using Empower 3 software, the injection volume is now limited to the available sample loop volume. For the sample manager-ftn, in Empower 3 software, the injection volume is now limited to the extension loop volume when the configured loop volume is greater than zero. Otherwise, the maximum injection volume equals the configured needle volume less 5 µl. For the sample manager, sample manager-ftn, and sample manager-fl, an R-calibration procedure is available to ensure correct needle and vial (or well) positioning. This calibration is necessary only when using 384-well plates. The sample manager-ftn Console plots are updated to include the Inject Mark feature. Detectors Photodiode Array (PDA) Detector For the photodiode array (PDA) detector, on the general tab of the instrument method editor, you can now specify a negative absorbance margin to accommodate increases in optical transmission during a gradient run (HILIC chromatography, for example). The default value is -0.07 AU. You typically need a greater negative absorbance margin when the absorbance baseline saturates or exhibits a flat, noiseless trace within the chromatogram. Note, however, that a greater negative absorbance margin can decrease the positive end of the linear dynamic range. Page 6 of 28

Optics temperature stabilization feature For thermally enhanced detectors the photodiode array (PDA), eλ PDA, and tunable UV (TUV) an optics temperature stabilization feature helps reduce the sensitivity of the absorbance signal to environmental fluctuations (temperature and humidity, for example). This feature is available only for thermally enhanced detectors. This table specifies settings and instrument environments. Setting Normal temperature (default) Elevated temperature Maximum cooling Instrument environment Suitable for most air-conditioned environments. Recommended for environments where the sustained average temperature exceeds 30 C. (These are typically environments that are not air conditioned.) Recommended for any environment where the lowest possible temperature for the flowcell or lamp is desired. Optimum baseline stability is typically not achieved on this setting. You can access this feature by clicking Configure > Preferences > Optics Temperature Stabilization. Enhancement to the lamp and flow-cell resident memory For thermally enhanced detectors the photodiode array (PDA), eλ PDA, and tunable UV (TUV) an enhancement to the lamp and flow-cell resident memory automatically includes, at your option, lamp history and flow-cell characteristics in comprehensive status reports. The feature thus associates chromatographic results with the condition of the lamp and the type of flow cell you used. By default, this feature is inactive. You can activate it by clicking Configure > Preferences > Component Identification Requirement. Failing result on the wavelength verification test For the PDA detector, if the wavelength verification test indicates a failing result during initialization, an error (previously a warning) occurs. To correct the error, establish flow through the instrument and cycle power to the detector. If the error persists, run the erbium calibration diagnostic. Re-creating the method For the PDA detector, when you create a method, the analog output capabilities of the instrument included in the system are associated with the method (two analog outputs, for example). To accurately reflect the analog output capabilities of a different PDA detector (one analog output, for example), you must re-create the method when that instrument is connected to the system. Sample Organizer The sample organizer firmware released as part of the ACQUITY UPLC Systems June 2011 Driver Pack installer is version 1.50. Nevertheless, a newer version of the firmware, version 1.51, is included on the June 2011 Driver Pack media. After installing the June 2011 Driver Pack, you must manually install the version 1.51 sample organizer firmware. For details, refer to the installation instructions on page 16. Page 7 of 28

The following options are available for sample organizers compatible with sample managers fitted with a rotary tray: Option Plate Transfer (From the Troubleshoot menu) Plate Sensor On/Off (From the Troubleshoot menu) Disable Motors (From the Control menu) Interactive Display Description Transfers all plates into and out of the sample manager a specified number of times. Turns the plate sensors on or off. Disables the z axis motor for maintenance operations. Allows direct control of sample organizer features. Ensuring the correct configuring of vial caps and shelf locations For sample organizers used with sample managers without a rotary tray, you can now select a Disable shelf check option from the Configure menu. When you do so, the option prevents the sample organizer from configuring vial caps as shelves and also the subsequent change warning resulting from the incorrect configuration. Shelf locations are correctly configured during the Scan and store shelf layout procedure and remain unchanged during a Reset or Verify command. Requirement: You must remove reflective caps before using the Scan and store shelf layout command. Analyst Software With Analyst Software, use only the Horizontal Discontinuous mode to configure the order of injections. MassLynx software This table shows software change notes (SCN) and the model of mass spectrometer they support in this release: SCN Mass spectrometer supported 733 quadrupoles SQD and TQD 781 Synapt G2 series 802 Xevo G2 Q-Tof /Tof 805 quadrupoles SQD and TQD 810 Xevo TQ and TQ-S 855 Xevo TQD and SQD2 Empower 3 software The Sys Startup function replaces the Sys Prep function. Clinical/IVD ACQUITY UPLC Systems This driver pack release should not be used for ACQUITY UPLC IVD marked systems. Page 8 of 28

Connections INSIGHT These changes apply: Connections INSIGHT, included with this driver pack, is installed by default. You can now disable instrument status monitoring within Connections INSIGHT for a specific time period. Additional diagnostic information is now uploaded to Connections INSIGHT during an ihelp request. Connections INSIGHT is now fully supported on client server networks. Waters Pump Control for MassLynx software This driver pack release includes Waters Pump Control. Pump Control now supports using as many as three model 515 pumps (P/N WAT207000) to accommodate ACQUITY UPLC Systems with 2D Technology. Waters Columns Calculator These changes apply: The calculator now supports using 75-mm columns. When you launch the calculator from a method editor window, you cannot change your unit preferences from the calculator s menu. The calculator uses the same unit preferences as those displayed in the Console software. When you launch the calculator independently (that is, not from a method editor window), and the Console software is also running, you can select unit preferences in either software application. When you change an aspect of one software application, the other reflects the change. Tip: You must click the software window to see the preference update. The calculator now correctly formats data for printing. The calculator now displays, in the main window, the column volumes for both the input and output columns. The calculator can now resolve time entries in the gradient table to 0.001 minutes. Example: The software can distinguish between 2.27 and 2.28 minutes. Commands of Copy and Paste between the QSM or BSM method editors and the calculator window now function correctly. The calculator s high-pressure limit is now 20,000 psi. Contents of ACQUITY UPLC Systems June 2011 Driver Pack DVD Recommendation: Install this driver pack update on all ACQUITY UPLC Systems, to ensure features and capabilities are current. See Reasons for installing this software release on page 3. Page 9 of 28

Requirement: Customers with Empower Enterprise systems who have both ACQUITY UPLC H-Class and ACQUITY UPLC systems must update all ACQUITY Instrument Control Software (ICS) implementations in their environment to the June 2011 Driver Pack. Mixing of ACQUITY UPLC ICS versions is not supported with the ACQUITY UPLC Systems June 2011 Driver Pack. The DVD includes these items: All current instrument drivers for ACQUITY UPLC I-Class System, ACQUITY UPLC H-Class, ACQUITY UPLC H-Class Bio, and ACQUITY UPLC instrument modules and detectors. See also: Your system s user documentation CD for information on instrument modules. Additional firmware files in the folder --- Firmware Updates --- ACQUITY UPLC Columns Calculator (for methods transfer) Connections Insight Waters Pump Control Deployment Manager ACQUITY UPLC Console The systems and modules currently supported appear in the following tables. Important: The ACQUITY UPLC Systems June 2011 Driver Pack installer does not install the newest version of the firmware, even though it is included on the media (version 1.50 instead of 1.51, for example). After installing the June 2011 Driver Pack, you must manually install the newest version. For details, refer to the installation instructions on page 16. ACQUITY UPLC I-Class System Modules Part Number Software Version ACQUITY UPLC I- Class BSM ACQUITY UPLC I- Class SM-FTN ACQUITY UPLC I- Class SM-FTN ACQUITY UPLC I- Class SM-FL ACQUITY UPLC I- Class SM-FL ACQUITY UPLC I- Class CH-A ACQUITY UPLC I- Class CM-A ACQUITY UPLC I- Class CM-A Firmware Version 186015000 1.50 1.50 Firmware Checksum 0x3ACBD4A5 186015046 1.50 1.50 (newer 0x3E83519D version available) 186015046 1.50 1.51 0x377AE410 186015060 1.50 1.50 (newer 0x66BA7F79 version available) 186015060 1.50 1.51 0x39374BCC 186015042 N/A N/A 186015043 1.50 1.50 (newer 0x19B6E386 version available) 186015043 1.50 1.51 0x19B50B4D N/A Page 10 of 28

ACQUITY UPLC H-Class/H-Class Bio Systems Modules Part Number Software Version ACQUITY UPLC H- 186015018 Class QSM/ Bio QSM 186015041 ACQUITY UPLC H- Class SM-FTN / Bio SM-FTN ACQUITY UPLC H- Class SM-FTN / Bio SM-FTN ACQUITY UPLC H- Class CH-A/H- Class Bio CH-A ACQUITY UPLC H- Class CM-A / H- Class Bio CM-A ACQUITY UPLC H- Class CM-A / H- Class Bio CM-A ACQUITY UPLC H- Class CM-Aux / H- Class Bio CM-Aux 186015017 186015040 186015017 186015040 Firmware Version 1.50 1.50 1.50 1.50 (newer version available) 186015042 N/A N/A Firmware Checksum 0xAE400516 0x3E83519D 1.50 1.51 0x377AE410 186015043 1.50 1.50 (newer version available) 186015043 1.50 1.51 N/A 0x19B6E386 0x19B50B4D 186015049 N/A N/A N/A ACQUITY UPLC System Modules Part Number Software Firmware Version Version ACQUITY UPLC BSM 186015001 1.50 1.50 ACQUITY UPLC SM ACQUITY UPLC SM ACQUITY UPLC HTCH ACQUITY UPLC Column Heater ACQUITY UPLC CM (Right Inlet) ACQUITY UPLC CM (Left Inlet) ACQUITY UPLC Column Heater/Cooler 186015005, 186015006 186015005, 186015006 1.50 1.50 (newer version available) Firmware Checksum 0x3ACBD4A5 0x66BA7F79 1.50 1.51 0x62CDAE6E 186015010 N/A N/A N/A N/A N/A 186015007 1.50 1.40 186015009 1.50 1.40 N/A N/A 0x8F9312BD 0x8F9312BD 186015008 1.50 N/A N/A Page 11 of 28

Detectors Modules ACQUITY UPLC TUV ACQUITY UPLC TUV Thermally Enhanced ACQUITY UPLC PDA ACQUITY UPLC PDA Thermally Enhanced ACQUITY UPLC eλ PDA ACQUITY UPLC eλ PDA Thermally Enhanced ACQUITY UPLC FLR ACQUITY UPLC ELSD Waters 2420 ELS Detector Waters 2424 ELS Detector Waters 2998 PDA Detector Compatible Systems Part Number Software Version Firmware Version All UPLC systems 186015028 1.50 1.50 All UPLC systems 186015031 1.50 1.50 All UPLC systems 186015026 1.50 1.51 All UPLC systems 186015032 1.50 1.51 All UPLC systems 186015030 1.50 1.51 All UPLC systems 186015033 1.50 1.51 All UPLC systems 186015029 1.40 1.40 All UPLC systems 186015027 1.40 1.40 Waters HPLC Systems Waters HPLC Systems Waters HPLC Systems 186002420 1.40 1.30 186002424 1.40 1.30 186002998 1.30 1.40 (download from Waters.com) Firmware Checksum 0xC09B9CB2 0xDBA6242F 0xF1B095E6 0xE6BBA016 0xF1B095E6 0xE6BBA016 0xDFF5C6F9 0x216F9370 0x21A5BED0 0x21A5B8D0 0x1AA04214 Waters 2489 UV/Visible Detector Waters HPLC Systems 186002487 1.31 1.40 (download from Waters.com) 0xE447C04B SQ Detector All UPLC systems 176000872 Empowercontrolled N/A N/A systems: 1.40.1435 TQ Detector All UPLC systems 176001263 Empowercontrolled N/A N/A systems: 1.40.2335 Note: Version 1.40 of the firmware for the Waters 2998 PDA detector and version 1.40 of the firmware for the Waters 2489 UV/Visible detector are not included with this driver pack. Download these firmware versions from Waters.com. Page 12 of 28

Accessories Modules Sample Organizer Sample Organizer Compatible Systems ACQUITY UPLC Systems only ACQUITY UPLC Systems only Sample Organizer ACQUITY UPLC I- Class / ACQUITY UPLC H-Class and H-Class Bio Systems Sample Organizer ACQUITY UPLC I- Class / ACQUITY UPLC H-Class and H-Class Bio Systems ACQUITY UPLC 30-cm Column Heater/Cooler ACQUITY UPLC CH- 30A Column Manager Auxiliary Units Local Console Controller Part Number 186015020 186015021 186015020 186015021 Software Version N/A N/A Firmware Version 1.50 (newer version available) 1.51 186015014 N/A 1.50 (newer version available) Firmware Checksum 0x98B4D459 0x98ADABF7 0x98B4D459 186015014 N/A 1.51 0x98ADABF7 All UPLC Systems 186015011 N/A N/A N/A ACQUITY UPLC I- Class / ACQUITY UPLC H-Class and H-Class Bio Systems 186015045 N/A N/A N/A ACQUITY UPLC H- 186015049 N/A N/A N/A Class and H-Class Bio Systems All UPLC systems 725000464 1.51 N/A N/A Additional Software Software Compatible Systems Software Version Connections INSIGHT All UPLC systems 3.1 ACQUITY UPLC Columns Calculator All UPLC systems 1.50 Deployment Manager All UPLC systems 3.0 Waters Pump Control Software All UPLC systems 2.20 ACQUITY UPLC Console All UPLC systems 1.51 Microsoft.NET Framework All UPLC systems 3.5 Note: The 3100 Mass Detector is supported with ACQUITY UPLC H-Class systems, but its software is not included on this DVD. Refer to the 3100 Mass Detector installation media for details. Page 13 of 28

See also: ACQUITY UPLC, ACQUITY UPLC H-Class, and ACQUITY UPLC H-Class Bio System Documentation Set CDs ACQUITY UPLC Console Online Help ACQUITY UPLC Systems January 2010 Release Notes ACQUITY UPLC Systems June 2010 Release Notes ACQUITY UPLC Systems June 2010 Supplemental Driver Pack II Release Notes Controlling Contamination in Ultra Performance LC/MS and HPLC/MS Systems Limitations This release does not apply to nanoacquity UPLC systems. The ACQUITY UPLC H-Class and H-Class Bio systems are supported for use with the SQ and TQ mass spectrometers. The ACQUITY UPLC H-Class system is also supported for use with the Waters 3100 mass spectrometer. Hardware and Software Requirements Supported Waters hardware: ACQUITY UPLC System ACQUITY UPLC H-Class System ACQUITY UPLC H-Class Bio System ACQUITY UPLC I-Class System ACQUITY UPLC Systems with 2D Technology (For details, refer to the ACQUITY UPLC Systems with 2D Technology Release Notes.) Supported Waters and third-party software System Empower 1154: ACQUITY Service Pack to SP M (English and Japanese) ACQUITY UPLC System ACQUITY UPLC H-Class System Empower 2: base release to SP H (English, Chinese, Japanese, and Korean) Empower 3 MassLynx (see list of SCNs, below) Yes Yes Yes Yes Yes Standalone ACQUITY Console Yes Yes Yes Yes Yes No Analyst Versions 1.4.2, 1.5.0, and 1.5.1 Page 14 of 28

System Empower 1154: ACQUITY Service Pack to SP M (English and Japanese) ACQUITY UPLC H-Class Bio System ACQUITY UPLC I-Class System Empower 2: base release to SP H (English, Chinese, Japanese, and Korean) Empower 3 MassLynx (see list of SCNs, below) Standalone ACQUITY Console No Yes Yes Yes Yes No No Yes Yes Yes Yes Refer to the following sources: Compatibility information about third-party control software, as published by the software developer. Page 8 for a list of MassLynx software change notes compatible with this release. Analyst Versions 1.4.2, 1.5.0, and 1.5.1 Requirement: If an SQ, TQ, or 3100 mass spectrometer is part of the system, you must install, at a minimum, Empower 2 Feature Release 4. Note that the Empower 2 System Suitability option is required. Backward Compatibility Existing ACQUITY UPLC methods are compatible with the new I-Class System. This software does not support existing MassLynx methods for ACQUITY UPLC systems that include column managers. Because column managers are now configured as detectors in MassLynx, you must re-create your methods. When using Empower 1154 or Empower 2 on a system containing CM-A and CM-Aux modules, you cannot select positions 5 and 6 from the column selection field of the sample queue. Instead, create an instrument method for a specific column position (5 or 6, for example) and save it with a unique name. From within your sample queue, select the appropriate method set (that includes the instrument method you created) to specify the column position. Supported operating systems Refer to the following sources: The Waters web site, for software release notes that include details on test configurations, operating systems, service packs, and hotfixes. Empower and MassLynx Release Notes, for additional information on supported operating systems for servers in workgroup or enterprise environments Empower Service Packs and Feature Releases MassLynx Service Packs and software change notes Recommendation: Upgrade your Instrument LAN network card drivers to the most recent version when running this software on a supported Empower workstation. Consult the network card's manufacturer for the most up-to-date network card drivers. Page 15 of 28

Notes: For this release, a standalone or acquisition client workstation is supported only with a single MSbased system. Waters publishes incremental information on operating system and hotfix support to the Services and Support area of its web site. ACQUITY UPLC minimum hardware requirements and maximum detector data rates For Intel Pentium IV 2.8 GHz Processor, with 800 MHz FSB and 1 GB of RAM, one of the following sets of specifications can apply: 2 PDA detectors at 80 Hz, 210-400 nm, 4.8 nm, normal (0.05 sec), 2-Absorbance or Fluorescence 2D channels, 2-MBF 2D channels, 30 minutes run time; Empower's Run and Report Mode. 2 PDA detectors at 40 Hz, 210-400 nm, 1.2 nm, normal (0.10 sec), 2-Absorbance or Fluorescence 2D channels, 2-MBF 2D channels, 30 minutes run time, Empower's Run and Report Mode. Important: These specifications fit Waters Configuration 10, 11, and 12 LAC/E 32 Acquisition Servers. Configuration 10 systems require a memory upgrade. For Intel Pentium IV 1.7 GHz Processor with 400 MHz FSB and 1 GB of RAM, one of the following sets of specifications can apply. 2 PDA detectors at 20 Hz, 210-400 nm, 1.2 nm, normal (0.20 sec), 2-Abs 2D channels, 2-MBF 2D channels, 30 minutes run time, Empower's Run and Report Mode. 4 TUV detectors at 80 Hz, MBF enabled, 60 minutes run time, Empower's Run and Report Mode. Important: These specifications fit Waters Configuration 8, 9, 10, 11, and 12 LAC/E 32 Acquisition Servers. Configuration 8, 9, and 10 systems require a memory upgrade. Installing the ACQUITY UPLC Systems June 2011 Driver Pack Release Caution: To avoid damaging the needle, when upgrading from ICS version 1.45, recalibrate the seal and z axis of the SM-FTN after installing this release. Important: If you are using real-time virus scanning, after installation, exclude all Empower-related folders and their sub-directories from the scans. Some real-time virus scanners mistake normal Empower functionality for virus activity and can therefore interfere with data buffering. Requirement: Customers with Empower Enterprise systems who have both ACQUITY UPLC and ACQUITY UPLC H-Class systems must update all ACQUITY Instrument Control Software (ICS) implementations in their environment to the June 2011 Driver Pack. Mixing of ACQUITY UPLC ICS versions is not supported with the ACQUITY UPLC Systems June 2011 Driver Pack. Page 16 of 28

Installation method You can install this software release according to one of these methods: The DVD provided with this document. Downloading from the Waters Web site. To do so, visit http://www.waters.com/waters/home.htm, and click Services & Support > Support > Software Downloads (support plan required). Recommendation: Remove the Internet information system (IIS) for the local console controller when upgrading from firmware version 1.00 to this release (the default Web site has been disabled). Note: Push installation is now supported using PsExec for all ACQUITY (non MS) modules. To install or upgrade the ACQUITY UPLC Systems June 2011 Driver Pack: 1. Exit all applications, and restart the computer. 2. Run Setup.exe on the DVD. 3. On the Welcome page of the setup wizard, click Next, and then select Install / Upgrade. 4. Accept release notes message and software license. Result: The Deployment Manager Instrument Component Software page for your system appears. Tip: For a MassLynx-controlled ACQUITY UPLC system, the SQ and TQ detectors do not appear in the deployment manager. Instead, select the instruments during MassLynx installation. 5. Select the drivers for the instruments that you want to install, and then click Next. 6. Click Install, and then wait for the process to finish. 7. Click Finish. Note: If prompted, select Yes to restart the computer. Result: The Waters Autoloader, which selects the instruments or devices that require firmware upgrades, is automatically launched. Tips: To see versions and checksums, scroll to the right. To see the location where the firmware is installed on a hard drive, hover the pointer over the instrument or device name. If the firmware version installed on an instrument appears as Unknown in the Autoloader, no firmware files for that instrument are present on the host PC. 8. Click Load Firmware, to start the autoloader loading all selected firmware. Tip: The Waters Autoloader simplifies installing the release software. It automatically detects the presence of compatible software and installs the appropriate support for your ACQUITY configuration. By default, the installer appears in the language of your workstation settings. For Empower installations, ACQUITY instrument support is installed in C:\Empower\Instruments. For all other installations, ACQUITY instrument support is installed in C:\Program Files\Waters Instruments. Result: When the status is Cycle Power, the firmware is installed. Page 17 of 28

Caution: To avoid corrupting the firmware, do not cycle power to any system module until firmware for all modules is installed. Tip: If the Autoloader application does not begin to load the firmware, or if it fails to successfully complete the process, re-run autoloader.exe from one of the following locations: A PC running Empower: C:\Empower\Instruments\Firmware A PC running MassLynx (or other data system): C:\Program Files\Waters Instruments\Firmware 9. When the status of all system modules is Cycle Power, restart each module. 10. When the status of all system modules is Load Complete, click OK, and then restart the computer. Using the repair function If an earlier ACQUITY UPLC CD or DVD (or a non-acquity CD or DVD) is used to install an instrument driver, use the ACQUITY UPLC Systems June 2011 Driver Pack media Repair feature in the Deployment Manager (DM) to reconcile any incompatibility you might have introduced. Caution: To avoid introducing incompatible versions of drivers, install older drivers before newer drivers. If you encounter a compatibility problem, use the Repair feature in the ACQUITY UPLC June 2011 Driver Pack Deployment Manager (DM). If any ICS from ACQUITY UPLC June 2011 Driver Pack is installed, the Repair feature will be enabled on the system. If an incompatibility is found, restart the computer. If no ICS from the ACQUITY UPLC June 2011 Driver Pack is installed, you can run the Repair function from the DM: 1. Exit all applications. 2. Run Setup.exe on the DVD. 3. Click Next. 4. Click Repair, and then click Repair again. 5. Restart the system. Installing the Updated Firmware Release Since the original release of the ACQUITY UPLC June 2011 Driver Pack, the firmware for the ACQUITY UPLC sample managers, the ACQUITY UPLC Sample Organizer, and the ACQUITY UPLC Column Manager with Active Preheater has been updated. To install this newer firmware, follow the instructions, below. See also: For more information about the updated firmware, please consult the firmware release notes contained in the --- Firmware Updates --- folder on the ACQUITY UPLC June 2011 Driver Pack (Revision B) media. To install the updated firmware release: 1. Reboot the sample manager, sample organizer, and column manager. Tip: If installing sample organizer firmware, deconfigure the sample organizer from the sample manager before loading firmware. Page 18 of 28

2. Run ACQUITY Sample Managers v1.51.exe or ACQUITY Column Manager II v1.51.exe from the --- Firmware Updates --- folder (Windows 7 users must right-click the file and select "Run as administrator"), and unzip the files to one of the following locations, depending on whether the operating software is Empower or MassLynx: For Empower: C:\Empower\Instruments\Firmware For MassLynx on Windows XP: C:\Program Files\Waters Instruments\Firmware For MassLynx on Windows 7: C:\Program Files (x86)\waters Instruments\Firmware 3. When asked to overwrite files, select Yes. 4. Navigate to the location you selected in step 2, and run Loader.exe. 5. On the Welcome page, select Scan for instruments. 6. Select the instrument you are updating, and then click OK. Result: The Select the File to Load window opens. 7. In the Select the File to Load window, click Browse, to find and select the appropriate.sft file from the location you selected in step 4: For an ACQUITY UPLC Sample Manager, select ACQUITY Sample Manager.sft. For an ACQUITY UPLC Sample Manager - FL, select ACQUITY Sample Manager FL.sft. For an ACQUITY UPLC Sample Manager - FTN, select ACQUITY Sample Manager FTN.sft. For an ACQUITY UPLC Sample Organizer, select ACQUITY Sample Organizer.sft. For an ACQUITY UPLC Column Manager-A, select ACQUITY Column Manager II.sft. 8. Click Next to begin loading the firmware. When firmware loading is 100% complete, click Finish, and then reboot the instrument. Installing this Release in an Empower Enterprise Environment Requirement: Customers with Empower Enterprise systems who use both ACQUITY UPLC and ACQUITY UPLC H-Class systems must update all ACQUITY instrument control software (ICS) implementations in their environment to the June 2011 Driver Pack. The ACQUITY UPLC Systems June 2011 Driver Pack does not support mixed use of ACQUITY UPLC ICS versions. For consistency, install the driver/firmware on all clients, LAC/E 32 modules, and Citrix application servers. You need not install the driver/firmware on the database server unless Client software is loaded on the server to interact with the instrument or device. On an Empower Enterprise (Client/Server) system, install the driver/firmware according to the preceding instructions. You must do so on every computer (LAC/E 32 module, client, and Citrix application server) that interacts with the instrument or device. In workgroup and enterprise environments, MS acquisition is supported via acquisition clients only. 32 LAC/E acquisitions are not supported. For information on Empower Enterprise server systems or Citrix server systems, refer to the Waters Empower 2 Feature Release 5 Release Notes, Waters Empower 2 Service Pack D Release Notes, or Empower 2 Feature Release 4 Release Notes. Page 19 of 28

Installing Empower ICS on a Citrix server Requirement: Customers with Empower Enterprise systems who use both ACQUITY UPLC and ACQUITY UPLC H-Class systems must update all ACQUITY instrument control software (ICS) implementations in their environment to the June 2011 Driver Pack. The ACQUITY UPLC Systems June 2011 Driver Pack does not support mixed use of ACQUITY UPLC ICS versions. You can install the Empower ICS on a Citrix server in one of two ways: via the command line or by adding or removing software. To install Empower ICS on a Citrix Server using the command line: 1. Change user/install. 2. Install software via the setup.exe on the June 2011 Driver Pack DVD. 3. Change user/execute. To install Empower ICS on a Citrix Server by adding or removing software: 1. Insert the ICS disk into the media drive. 2. Open the computer s control panel, and double-click Add/Remove Programs. 3. Click Add New Programs. 4. In the Run Installation Program dialog box, click Browse. 5. Browse to the location where the media is installed. 6. Select the setup.exe file, and then click Open. Tip: It can be necessary to select All Files from the Files of type list. 7. Follow all prompts, to finish the installation. Tip: It is necessary to ensure the Local Windows Administrator level privilege is used on the Citrix server for access to directories and registry keys to be successful. 8. To verify a successful installation, the C:\Windows\Empower.log file must contain this entry below after the Deployment Manager has run: "The ICS configuration completed successfully..." 9. In some cases, the following DOS command line can be executed on the Citrix server if the ICSCompanionService has not installed correctly. From the path where the ICSCompanionSetup.exe is located, type the following string: ICSCompanionSetup.exe /v"skip=true ALLUSERS=1". Troubleshooting and Uninstalling If the installation fails, uninstall previous versions. To uninstall previous versions of the software: 1. Exit all applications and restart the computer. 2. Run Setup.exe, on the DVD. 3. Select Remove, to remove the previously installed instruments, and then click Next. Page 20 of 28

4. Select all of the instruments and devices you want to remove, and then click Next. 5. Click Finish. 6. Restart the computer. 7. Repeat the installation procedure. ICS Companion Overview The ICS Companion service monitors and manages the deployment of Waters-developed drivers and related utilities. The service resolves various problems associated with installing older drivers, which, if not installed in a particular order, can sometimes compromise the functionality of newer drivers. The operation of some older drivers and utilities differs regarding the manner in which they deploy shared components and configurations. The ICS Companion ensures that shared components are compatible with respect to different driver releases, regardless of their order of installation. Delivered with newer drivers by the deployment manager, the ICS Companion continuously monitors subsequent legacy installations for potential incompatibilities, which, on encountering, it resolves. A minor defect (D-25201) in the current version of the ICS Companion affects the header of Empower software's Verify Files report. The service fails to list some previously installed drivers and utilities, such as the Waters HCO v2.0. Significantly, the defect's effect extends only to the missing header section of the Verify Files report. The actual driver software loads correctly and becomes fully operational. In no case does the ICS companion uninstall another driver or other software component. The following figure illustrates how the defect affects the header of the Verify Files report: a new instrument driver (Agilent LC) was installed, and the header is incomplete: Before new install After new install Present before the Agilent LC install but Missing the 2420, 2424, CCAD, and HCO in new header Installed Agilent LC Page 21 of 28

The following example shows that only the header is affected and the detail content displays correctly. No change in actual content Technical information The ICS Companion scans the registry keys under HKLM\SOFTWARE\Waters\Instruments\Setup and validates the installation. If an installation is not found, the value for "Installed" will be set to "0". Installation validation The ICS companion reads the value of "LocaleName" under HKLM\SOFTWARE\Waters\Instruments\Setup\ICS and if the LocaleName value name does not exist, the companion uses the ICS (registry key) as the product name and validates it with the installed products under HKCR\Installer\Products\ProductName. Workaround Add a string value named "LocaleName" under HKLM\SOFTWARE\Waters\Instruments\Setup\ICS and assign the product name for its value. ICS - Instrument name, example Waters CCAD or Waters HCO v2.0 Disabling the service The ICS Companion service can be safely disabled with no impact other than the loss of protection of potential incompatibilities with legacy drivers that are installed later. Disabling the ICS Companion service should be executed by an administrator using the following three steps from the Windows command line. 1. 2. 3. sc stop WatersICSCompanionSvc sc config WatersICSCompanionSvc start= disabled sc config WatersICSCompanionSvc start= disabled Page 22 of 28

Restoring an SQ and TQ Empower 2 project for use with IntelliStart During installation of the instrument driver, a template project is installed to this subdirectory: <Drive Letter>\Empower\Instruments\Projects. The installer creates a new Projects subdirectory under the file path <Drive Letter>\Empower\Instruments. It then copies the supplied project to the subdirectory. To use the IntelliStart functionality, you must restore the supplied project for your detector in Empower 2, which contains the appropriate methods for a detector to run IntelliStart. You must use the supplied project to clone all future projects. The supplied instrument methods are based on a chromatographic system consisting of the TQ or SQ detector, along with the ACQUITY UPLC Quaternary Solvent Manager and the ACQUITY UPLC Sample Manager Flow Through Needle. If your configuration differs, modify the instrument method to include all modules configured in the current chromatographic system. Add additional system hardware to the instrument method using the Add Instrument option. Refer to the Empower online Help for information on adding instruments to a method. Once a project is restored, right-click it, and select Project Properties. From the Project Properties dialog box, clear the Dissolution, GPC, GPCV, and Chemical Structures check boxes. Leave all other properties at their default values. See also: Empower or Empower 2 online Help, for further details about restoring projects, cloning projects, and user privileges. Empower 2 Installation and Configuration Guide, for details about workstation and server setup. Page 23 of 28

Defects addressed by this release The following table contains a list of the software problems corrected in this release. The PCS (product change system) numbers identify software issues that Waters personnel monitor within a system change request tracking tool. Module PCS Number Description Analyst 19238 While running a sample queue, the system no longer stops functioning properly when you abort a sample. Analyst 19689 Analyst software retains the ACQUITY login information of a user that is logged off. Analyst 19846 You cannot disable and then enable the hardware profile within Analyst without losing the ability to run a method. Analyst 20346 Analyst does not function normally when the system s mass spectrometer is in Standby mode. Analyst 21314 After you click Stop Flow in the ACQUITY Console, you cannot restart a sample run in Analyst. ACQUITY Console ACQUITY Console 21337 When Empower software is running, the System Startup pages are occasionally blank. 21670 In MassLynx, if you ignite the lamp via the ACQUITY Console at the top level, the lamp icon changes to green, while the Inlet editor s icon remains red; the lamp control button also suggests that the lamp did not ignite. BSM 19329 BSM Console plots (Japanese language only) do not display a unit of time. CM-A 21737 The column manager occasionally becomes unresponsive, resulting in a communications failure. CM-A 22671 The column manager does not properly transition between changes in column and selection pump flow rates. CM-A 24536 Column manager methods created with the ACQUITY UPLC Systems June 2010 Driver Pack and June 2010 Supplemental Driver Pack (versions 1.45 and 1.46) are not compatible with the June 2011 Driver Pack (version 1.50). CM-A 24540 If the column manager is set to Bypass when running under Empower control, a Sample Set failure error message appears. PDA 18612 The shutter does not close when the Read Energy diagnostic completes. PDA 19317 The Reference Compensation Channel is not reported correctly in Empower Reports. PDA 21021 You cannot use a comma as a decimal separator, if supported by your regional settings. PDA, TUV 20939 The installation date is not automatically updated upon installation of a new lamp. PDA, TUV 18868, 21146 If the lamp is extinguished when a new sample queue was started, the system occasionally initiates the injection before the lamp is ignited and stable. SM 18735 The wash needle function fails if the total wash volume is programmed over 2500 µl and generates a "Not enough volume left in Wash Syringe" message during operation. Page 24 of 28

Module PCS Number Description SM 25234 The sample manager fails to function correctly when a high-temperature column heater and a 30-cm column heater/cooler are both connected to the instrument using a Y-cable. SM 25254 The sample manager moves the needle and continues with injections when the sample compartment door is open. SM 25394 When using load-ahead mode, a sample manager communications failure occasionally occurs. Workaround: Installing the ACQUITY UPLC Sample Managers Firmware, version 1.51. SM-FL, SM-FTN SM-FL, SM-FTN SM-FL, SM-FTN SM-FL, SM-FTN SM-FL, SM-FTN 25449 The rotary tray occasionally moves when the door is open and the plate tray is extended. 24669 The sample manager's firmware can stop working and require rebooting when the following three conditions are met simultaneously: 1. The sample manager s rotary tray is in motion, to cool the tray. 2. A plate is moving between the sample manager and sample organizer. 3. An alarm is triggered, or a user aborts a process. 24859 The sample manager firmware triggers a column-temperature alarm when a shorted circuit affects the sample compartment's heat-sink temperature sensor. 25436 When the sample manager is idle, the needle moves between the inject and load positions every 30 minutes. 24285 The R-Axis Calibration service diagnostic, added in ACQUITY UPLC Systems June 2011 Driver Pack, allows robust support for the 384/100 µl wellplates and proper needle positioning for ACQUITY UPLC I-Class SM-FTN and SM- FL injectors. SM-FL 25161 After a running sample set is aborted, the sample manager needle stops working. To regain function, power-off and then power-on the device. SM-FTN 22042 SM-FTN firmware includes a modification that addresses an increase in the minimum temperature of the sample chamber heat sink, from -0.5 C to 0 C. The increase in temperature eliminates the potential icing of the heat sink. SM-FTN 19943 The standalone Console software can now accept column temperature settings above 65 C for a compatible column heater. SM-FTN 20645 The SM-FTN stops the injection in error if a vial specified by auto addition is missing. This action avoids wasting sample from the other vials which are present. SM-FTN 21632 Repeatedly opening and closing the sample compartment door could result in an incorrect temperature setting. SM-FTN 21732 An incorrect SM-FTN extension loop size appears in the Post Run Report. SM-FTN 22715 Auxiliary vials do not honor the Skip Missing Vial configuration feature on the SM-FTN. SM-FTN 22924 Detection of tray loss-of-sync has been rendered less sensitive to avoid errors from insignificant misalignment. Page 25 of 28