MassLynx TM 4.1 SCN 916 Release Notes

Transcription

1 MassLynx TM 4.1 SCN 916 Release Notes Page 1 of _1 Waters is a registered trademark, Waters the Science of What s Possible and MassLynx are trademark of Waters Corporation All other trademarks are the sole property of their respective owners Copyright 2013 Waters Corporation

2 MASSLYNX 4.1 SCN 916 SYNAPT G2-S/G2-SI MS/HDMS... 3 INTRODUCTION:... 3 SUPPORTED PRODUCTS/CONFIGURATIONS:... 3 OPERATING SYSTEMS:... 4 SECURITY:... 4 SCN 916 INSTALLATION PROCEDURE:... 5 UN-INSTALLATION:... 8 MS... ERROR! BOOKMARK NOT DEFINED. ENHANCEMENTS:... 9 CONCESSIONS: INFORMATIONAL: INLETS CONCESSIONS: INFORMATIONAL: APPLICATIONS: SUPPORTED COMPUTERS, OPERATING SYSTEMS, HOT FIXES AND ANTI-VIRUS SOFTWARE: ANTIVIRUS WINDOWS UPDATES Page 2 of 19 Document No: 46154_1

3 MassLynx 4.1 SCN 916 SYNAPT G2-S/G2- Si MS/HDMS Introduction: Software Change Note #916 is based on MassLynx v4.1 It supersedes SCN902 and SCN883. SCN 916 supports dual installation for either Synapt G2-S or Synapt G2-Si. SYNAPT G2-S/G2-Si provides resolution in three dimensions. Chromatography. Mobility. Mass. SYNAPT G2-S/G2-Si delivers a third dimension to your analysis, proven to transform your analytical perspective whatever the application. SYNAPT G2-S/G2-Si combines T-Wave ion mobility with new innovative data acquisition routines and informatics capabilities to transform your targeted and untargeted analyses. Supported Products/Configurations: MassLynx 4.1 SCN 916 supports the following configurations: MS SYNAPT G2-S/G2-Si MS SYNAPT G2-S/G2-Si HDMS MALDI SYNAPT G2-S/G2-Si MS MALDI SYNAPT G2-S/G2-Si HDMS LC / Inlets (ICS Supported with SCN 916) ACQUITY Binary Solvent Manager ACQUITY Sample Manager (ICS version ) ACQUITY PDA Detector (ICS version ) ACQUITY TUV Detector (ICS version ) ACQUITY Column Manager (ICS version ) Waters A7890 Software (ICS Version ) ACQUITY UPLC H-Class Systems Sample Manager Flow Through Needle (SM- FTN) (ICS version ) Quaternary Solvent Manager (QSM) (ICS version ) nanoacquity Systems nanoacquity Binary Solvent Manager (ICS version ) nanoacquity Sample Manager (ICS version ) ACQUITY Auxillary Solvent Manager (ICS version ) ACQUITY UPLC I-Class Systems Binary Solvent Manager (BSM) Sample Manager (SM) Page 3 of 19 Document No: 46154_1

4 MS LC / Inlets (ICS Supported with SCN 916) Agilent 7890 GC system (ICS version ) PTV, COC, Split/Splitless, Purged Packed Volatile Interface and Multimode inlets. Agilent 7683B Autosampler Agilent 7693A Autosampler GC PAL and Combi PAL Autosampler Agilent 7890GC Dean Switch and 2-way splitter by EPC Agilent 7890 GC detectors supported are: Flame Ionization Detector (FID) Thermal Conductivity Detector (TCD) Micro-Electron Capture Detector (micro- ECD) Agilent 7890 GC system PTV, COC, Split/Splitless, Purged Packed Volatile Interface and Multimode inlets. Agilent 7683B Autosampler Agilent 7693A Autosampler GC PAL and Combi PAL Autosampler Agilent 7890GC Dean Switch and 2-way splitter by EPC Agilent 7890 GC detectors supported are: Flame Ionization Detector (FID) Thermal Conductivity Detector (TCD) Micro-Electron Capture Detector (micro- ECD) Other options: PCM control of Dean Switch via GC panel only Gerstel CIS-4 injector pneumatic control only. Operating Systems: Microsoft Windows 7 Professional 64 bit with Service Pack 1 Security: MassLynx security is not supported. Page 4 of 19 Document No: 46154_1

5 SCN 916 Installation Procedure: MassLynx 4.1 SCN 916 is a complete installation of MassLynx 4.1. If MassLynx or any MassLynx SCNs are already installed they must be uninstalled before installation of MassLynx 4.1 SCN 916. NOTE : Detector Setup and Calibrations from previous software versions are not maintained when an installation is performed. All IntelliStart configurations must be repeated. 1. Close MassLynx and any other software applications. 2. If any previous versions of Waters Pump Control or ACQUITY Components have been installed they should be removed using Windows Programs and Features before installing SCN If MassLynx (including V4.1) is installed, it should be removed using Windows Programs and Features and the PC should be rebooted after the removal is complete. 4. If the "C:\Program Files\Micromass Utilities\ICOP" folder still exists after uninstalling existing MassLynx versions it must be manually deleted prior to installation of SCN Install MassLynx V4.1 SCN 916 following the remaining installation instructions 6. Select Start >Run from the windows start menu and type: <DVD Drive>:\setup <return> Where, <DVD DRIVE> is the drive letter of the DVDROM. 7. Follow the instruction of the program. 8. Click Finish to complete installation of the SCN files. 9. Reboot the instrument embedded PC. If an inlet system is being used: 10. Launch MassLynx and open the Inlet Editor. Select Instrument Configuration from the Tools menu. 11. Install any required Waters instrument drivers (ICS) using the Deployment Manager by clicking Setup Instruments. If any drivers are installed it is recommended that the PC is rebooted afterwards before continuing the inlet system configuration. 12. Click Configure to launch the Inlet Configuration Dialog to complete the configuration of the inlet system. NOTE : MassLynx, Java3D may fail to install. The following actions should be completed prior to loading SCN 916; a. Remove all Java components (J2SE Runtime Environment, Java 2 Runtime Environment, Java 3D from Add/Remove programs. b. Delete the folder C:\Program Files (x86)\java. c. Continue with the installation of SCN 902. Page 5 of 19 Document No: 46154_1

6 NOTE : Modifying or repairing an installation is not supported. Installation of Stand Alone Applications This instruction is for installation of OALogin, OAToolkit, and OpenLynx Browser. If any of these applications are already installed they must be uninstalled using Windows Programs and Features before installing the SCN 916 version. 1. Close any open software applications. 2. Insert the MassLynx SCN 916 DVD into the DVD ROM drive. 3. Navigate to the Applications folder on the DVD and select the folder for the Application required. 4. Run setup.exe 5. Follow the instruction of the program. 6. Click Finish to complete installation of the SCN 916 files. Installation of nanoacquity NOTE : We recommend the use of separate instrument PCs when regularly using ACQUITY and nanoacquity with the same instrument. When using nanoacquity the following steps must be to be performed prior to configuration of the nanoacquity : 1. Uninstall all previously installed ACQUITY components and versions of Waters Pump Control software. 2. Reboot the instrument PC. 3. Install the nanoacquity ICS and WPC v by running "c:\program files\micromass utilities\icop nanoacquity\dm.exe" 4. The nanoacquity inlet is now configured. There is no need to open the Inlet Configuration Wizard. 5. You may be prompted for some additional configuration information when first opening the console. SYNAPT G2-S/G2-Si MS and HDMS EPC Reset Occasionally after a reboot of the SYNAPT G2-S/G2-Si MS/HDMS it may prove difficult to reestablish communications to the instrument. This appears to be caused by Symantec Endpoint Protection V12.1 being installed on the MassLynx PC. A solution to this is: 1. Run C:\Program Files (x86)\waters Instruments\DHCP Server Configuration.exe. 2. Observe the IP address listed for the SYNAPT G2-S/G2-Si MS/HDMS which will have the format x (where x is a number) Page 6 of 19 Document No: 46154_1

7 3. Select Start > Run and type ping x 4. Communications will re-establish shortly afterwards (or after one further press of the reboot switch) and a chime will sound from the instrument. LCMS System Check LCMS System Check files can be found in the SystemQC.pro folder in the MassLynx installation folder. Installation of 7890 GC Systems 1. Follow the general installation instructions for installing the 7890 driver and configuring the inlet system. 2. Close MassLynx. 3. If using one LAN card and a hub go to step 4. If using two LAN cards instead of a hub, follow the steps below. a. Make a note of the IP address of the A7890 GC instrument connected to the host PC. The IP address of the instrument is available on the A7890 instrument control panel. Use <Options> key and scroll to the Communications section and press <Enter>. The IP address should be in the form of xxx. b. Launch Control Panel from the Windows Start Menu c. Double click on the Network Connections application listed in Control Panel d. In the Network Settings window right click on the Ethernet device connected to the GC instrument and select the Properties option. The LAN properties dialog pops up. e. Select Internet Protocol (TCP/IP) option on the LAN properties dialog and click on the Properties button. Internet Protocol (TCP/IP) Properties dialog pops up f. Ensure that the IP address and sub-net mask on the Internet Protocol (TCP/IP) Properties dialog are set as defined below: i. Select Use the following IP address. ii. Set the IP Address: xxx (Doesn't have to be specifically this value, but must not be the same as the IP address of the GC instrument). The IP address of the GC instrument was obtained in step 3(a). iii. Set up Subnet mask: g. Click on Ok button to close Internet Protocol (TCP/IP) Properties dialog. h. Click on the OK button on the LAN Properties window to complete the LAN configuration set up. i. Go to step Configure the Waters DHCP for the A7890 as shown in the steps below. a. Ensure MassLynx is closed. b. Ensure that A7890 GC instrument is connected to host PC. Page 7 of 19 Document No: 46154_1

8 c. Make a note of the GC IP address, MAC address and serial number of the A7890 GC instrument connected to the host PC. These details can be obtained as follows:- i. The IP address and MAC address of the instrument are available on the A7890 instrument control panel. Use <Options> key and scroll to the Communications section and press <Enter>. The IP address should be in the form of xxx and the MAC address should be in the form of 00-XX-XX-XX-XX-XX. ii. A7890 instrument serial number is seen on the bottom left of the instrument front body panel. (Below the control panel). d. Run C:\Program Files\Waters Instruments (x86)\waters DHCP Server Configuration.exe. Waters DHCP Server configuration window pops up. e. Click on Add button to add a new DHCP entry for A7890 instrument. The Add IP Address dialog pops up. i. Update the Add IP Address dialog with the below details: ii. Update the IP Address and MAC Address fields with the corresponding values noted in Step 4(c). iii. Select the Instrument Type as A7890 from drop down option. f. Enter the serial number noted in Step 4(c.ii) into the Serial Number/Unique Name field. g. Click on OK button to complete the Waters DHCP configuration for A7890 GC instrument. 5. Start MassLynx, open the Inlet Editor and reset the GC communication. Un-installation: MassLynx can be removed by using the Windows Programs and Features facility in the Windows Control Panel. Page 8 of 19 Document No: 46154_1

9 MS Enhancements: The following table contains a list of software enhancements included in SCN 916. The following enhancements are incorporated for the Synapt G2-S instrument. Improved acquisition methods for targeted experiments: a. Discovery - Improved FastDDA (MS mode) and new HD DDA methods (HDMS only). b. Quantitation - New Tof-MRM (MS mode) and HD-MRM (HDMS only) modes and TargetLynx Support. New CCS-based (HDMS only) screening workflow for small molecule screening applications a. IntelliStart support for CCS calibration and LockCCS functionality b. Data compatible with UNIFI CCS Research Edition Informatics and TransOmics (v2.0) Enhanced Imaging capabilities a. Enhanced pixel acquisition rates b. Statistics based image generation in HDI MALDI (v1.2) The following enhancements are incorporated for the Synapt G2-Si instrument. Improved acquisition methods for targeted experiments: a. Discovery - Improved FastDDA (MS mode) and new HD DDA methods (HDMS only). b. Quantitation - New Tof-MRM (MS mode) and HD-MRM (HDMS only) modes and TargetLynx Support. New CCS-based (HDMS only) screening workflow for small molecule screening applications a. IntelliStart support for CCS calibration and LockCCS functionality b. Data compatible with UNIFI CCS Research Edition Informatics and TransOmics (v2.0) Enhanced Imaging capabilities a. Control of a new 2.5kHz solid state laser b. Enhanced pixel acquisition rates c. Statistics based image generation in HDI MALDI (v1.2) Resolution a. Enhanced Resolution mode for 50,000 FWHM mass resolution Page 9 of 19 Document No: 46154_1

10 Concessions: The following table contains a list of known software issues and workarounds for SCN 916. CCS Ensure that the sample syringe has enough sample before performing a CCS or mass calibration setup. Should there not be sufficient sample, it will incorrectly prime the reference fluidics rather than filling the sample syringe. It is possible to create a new CCS calibration profile with the same name as an existing mass calibration profile, which will result in the existing profile being deleted. The same problem occurs when creating a mass calibration profile with the same name as an existing CCS calibration profile. Avoid using the same name for calibration profiles. The Curve Fit option is redundant for CCS calibrations and will not have any effect. If a LockSpray setup for LockCCS is run without a valid CCS calibration profile applied the cone voltage and reference capillary voltage will be set to 0. Ensure that a CCS calibration profile is applied before running a LockSpray setup. The Synapt G2-S/G2-Si must be in Operate in order to setup a CCS calibration in IntelliStart using pre-existing data. When searching for help on CCS in the online help do not refer to the CCS Automatic calibration and CCS manual calibration pages that are returned. Use the CCS calibration page instead. In the CCS calibration help page, item 3 in the section titled Acquiring spectrum for manual calibration should read: 3. Acquire 2 minutes of TOF MS Mobility data for the Polyalanine CCS calibration solution across the desired mass range In the CCS calibration help page, item 6 in the section titled Manual CCS Calibration should read: 6. Select the saved spectrum Prior to performing a CCS calibration please ensure the Synapt G2-S/G2-Si has been in mobility mode for at least 1 hour. HDMS The intensity of reference signal displayed on the tune page may be different to that displayed when performing a Mobility acquisition method. This is due to the flat transfer mode of operation used for acquisition of LockSpray data within a Mobility method. Extending the scan time used of LockSpray scans within the method will minimise this issue. The peak saturation indicator flags (shown as? in the spectra, indicating mass shift due to intensity saturation) are not shown for mobility drift time functions generated during MS acquisitions. They are shown for drift time functions exported from the Driftscope application. The Dynamic Range option for the Tune Page acquisition for Mobility mode should only be used with Normal selection. To reduce CID fragmentation in ETD mobility mode the IMS DC Entrance voltage should be reduced from 20V to 10V and He cell DC should be reduced from 50V to 35V. When returning to CID mobility mode the values should be reverted to their original settings (that is IMS DC Entrance voltage should be 20V and He cell DC should be 50V). Page 10 of 19 Document No: 46154_1

11 MALDI Minor distortion in the image may be seen at a spatial resolution of 15 µm ETD acquisitions are not supported when the MALDI source is engaged. When MassLynx is configured with a MALDI source an Inlet may be displayed as configured within the MassLynx main window. This is a result of the MALDI sample plate definition processing and should be ignored. Lockspray profiles are not compatible with MALDI methods. Ensure that MALDI methods are always created from new. MALDI survey methods with real-time lock mass correction only have the first survey scan lock mass corrected. The second scan is a side effect of the DDA process, and as it is not corrected can lead to spiky data being displayed when the data regions are combined. MALDI Mobility data cannot be processed in HDI MALDI v1.0. Real time MALDI accurate mass functionality is not supported. After stopping a MALDI tune page acquisition the dialog can re-open automatically. Close the dialog again should this occur. IntelliStart - General If acquiring data that will be used to create a manual custom mass calibration then this data must be acquired without a calibration applied to ensure reliable behaviour. Load the Uncal profile to ensure the calibration is removed prior to acquisition of data for use in performing manual calibrations. Ensure that the sample syringe has enough sample before performing a CCS or mass calibration setup. Should there not be sufficient sample, it will incorrectly prime the reference fluidics rather than filling the sample syringe. When selecting a raw file for manual custom calibration the data must have been manually processed to a centred spectrum using Automatic Peak Detection. IntelliStart describes this as "an accurate mass function". IntelliStart does not allow loaded calibration profiles to be edited or reset. In order to edit or reset the active profile an alternative profile must be loaded using the Use Calibration Profile option. If the fluidics system fails to respond when performing create calibration operations through IntelliStart using automatic fluidics control follow the steps below: A. Stop the IntelliStart operation. B. Check your fluidics system is responding through the tune page. C. Repeat the IntelliStart operation. If the system continues to fail to respond either re-start MassLynx or run your operation with tune page fluidics until it is convenient to re-start MassLynx. IntelliStart Calibration acquisitions run from the console should only be stopped from within the console. IntelliStart checks may need to be configured to suit your application. This can be performed within the IntelliStart configuration window. Checks specific to a polarity will be reported regardless of the current instrument polarity. In Detector Setup, on the rare instance where the tolerance (%) passes but the stability fails, the Ion Area Setup reports a pass but the console reports a failure. The console log records that there was a "BEAM ERROR - Not enough signal stability" but this is not recorded in the XML log. Page 11 of 19 Document No: 46154_1

12 If parameters are changed in the System View, ensure that they are saved to the EPC in order for IntelliStart resolution optimisation to operate correctly. IntelliStart LCMS System Check Only specify LCMS System Check to operate with MS methods defined with a single Tof MS/Tof MSMS function of Centroid data type. Failure to do so will cause unreliable behaviour. When stopping an LCMS System Check operation it will also be necessary to stop queued acquisitions from the sample list. LCMS System Check should be performed referencing all methods from within the SystemQC.pro project. Failure to do so will result in the system being left in an undesired state and will require MassLynx to be restarted. In APGC mode the option for LCMS System Check is available in IntelliStart. LCMS If System Start Up is run from the ACQUITY Console and the UV Lamp is set to "Off" the MS instrument can switch from Operate to Standby. Ignore the UV Lamp within the Start Up list. To acquire data without using an LC, the LC must be de-configured through the Inlet Editor application to prevent the system attempting to control the LC. If a MassLynx sample list configured with an ACQUITY system is stopped, ensure that any inlet methods are correctly stopped before attempting to close MassLynx. When purging the sample fluidics with LC flow via the sample divert valve, the inlet tubing fitting may over-pressurise and release from the sample divert valve. When stopping a sample list before completion any inlet systems must also be stopped through the Inlet Editor application or left to complete before another sample list may be started. Method Editor For Fast DDA acquisitions ensure that the mass range of the Survey and MSMS acquisitions are identical. If they are different then an incorrect pusher frequency will be applied, causing artefacts in the data. The maximum number of supported method events is 20. Only the final 20 events defined will actually be processed during the MS acquisition. When configuring multi-function MS experiments, the first function specified must have a mass range large enough to cover the selected lock mass compounds. Lock Mass data will only be acquired when a method has an active function. When using staggered functions within a method Lock Mass data will not be acquired during the regions of the method where no functions are active. When an MRM file is created from the output search results of a prior MSe acquisition, the format is not exactly the same as that produced from the method editor, duplicate lines may be generated and variations in decimal values for masses. Ensure the format for files produced from the MSe acquisition is the same as that produced from the method editor. Page 12 of 19 Document No: 46154_1

13 Fluidics Ensure that the sample syringe has enough sample before performing a CCS or mass calibration setup. Should there not be sufficient sample, it will incorrectly prime the reference fluidics rather than filling the sample syringe. After a reboot of the EPC, the reference fluidics will prime from vial C, even if LockMass is set to vial B in IntelliStart. Once the first prime is performed it will behave correctly. The pre-compression functionality built into the fluidics system results in short periods of high flow rates when the fluidics starts flowing. A solvent delay (in an acquisition method) can be used to at the start of an acquisition so that this high flow data is not recorded. Stopping an acquisition when fluidics method events are being processed may result in these operations continuing to completion after the end of the MS acquisition. Ensure the fluidics have been returned to the required state via the tune window controls prior to performing any further MS acquisitions. If the fluidics system fails to respond when performing create calibration operations through IntelliStart using automatic fluidics control follow the steps below: Stop the IntelliStart operation. Check your fluidics system is responding through the tune page. Repeat the IntelliStart operation. If the system continues to fail to respond either re-start MassLynx or run your operation with tune page fluidics until it is convenient to re-start MassLynx. Page 13 of 19 Document No: 46154_1

14 General If parameters are changed in the System View, ensure that they are saved to the EPC in order for IntelliStart resolution optimisation to operate correctly. When zooming in on integrated peaks in Chromatogram, peaks are no longer integrated. When setting integration parameters for calibration curve use the Quanref column in the sample list to automatically define integration parameters in the TargetLynx method. Chromatographic data is not annotated with RT/area after being integrated. When setting integration parameters for calibration curve use the Quanref column in the sample list to automatically define integration parameters in the TargetLynx method. When using Lock Mass Profiles a separate profile should be used for each source type. The Mass Measure operation is not supported for ADC data and is therefore disabled within the MassLynx user interface. Use of Automatic Peak Detection or Center is recommended for ADC data. The function description used for selecting TICs for MSMS methods does not report the collision energy correctly. The value 0eV reported at the end of the function description does not describe the collision energy correctly. The correct collision energy for Trap and Transfer can be displayed using the Spectrum and Chromatogram header editor. Large intensity signals may exhibit artefact peaks. The optimisation of the detector allows for a small degree of overshoot in the single ion response. When signal intensities are large the overshoot may exceed the ADC baseline thresholding and as such appear in the data as small signals typically within 0.1m/z of the peak of interest. This effect is more pronounced in Mobility Tof mode than in Tof mode. Playback of recorded camera data may appear faster than the rate at which it was recorded. It is recommended to use the PAL option to match the playback speed to the record rate. Transfer T-Wave parameter must not be modified during Wideband Enhancement calibration. In ASAP mode, the sample List acquisitions will not proceed if sample fluidics is in stopped state. If the instrument electronics need resetting, follow the procedure below: A. Close MassLynx and place the Synapt G2-S/G2-Si into Pump Override B. Turn off the EPC power switch C. Turn off the Electronics power switch D. Turn on the Electronics power switch E. After 20 seconds, turn on the EPC power switch If Auto Detector Check is enabled, and the detector value has automatically been adjusted by over 25 volts during a batch sample list acquisition, Detector Setup will have to be re-run Page 14 of 19 Document No: 46154_1

15 Informational: Tri Wave Transfer Wave Velocities General The table below defines the recommended tri wave transfer wave velocity settings for the following modes\mass ranges: Mode Mass range(da) Twave velocity(m/s) HDMSe (proteomics) (default) HDMSe (small molecules) HD-DDA (proteomics) 5000(Wideband Enhancement) 110 HD-MRM (proteomics) 5000(Wideband Enhancement) 110 Individual instruments may demonstrate some variance and require tuning around these values. Page 15 of 19 Document No: 46154_1

16 INLETS Concessions: The following table contains a list of known software issues and workarounds for SCN 916. General ACQUITY QSM can occasionally freeze during priming. Rebooting QSM module and resetting communications to the instrument in MassLynx will recover from this problem. Do not uninstall QSM/FTN ISC/ICOPs as it removes common components which would require a complete MassLynx reload. If needed the modules should be deconfigured within the Inlet Editor Configuration and the modules removed from WatersDHCPConfig. Informational: Notes for Agilent 7890 Systems Any new inlet file must be based either on the default inlet file, or on another inlet file that itself is based on the default inlet file. Otherwise the method may not download successfully. The default inlet file, default.a7890, must not be deleted from the system. If any changes are made to the default.a7890 file then it is recommended that the changes are saved with a different file name. If a new MassLynx project is created, it must be based on the default MassLynx project (or on another MassLynx project that is itself based on the default MassLynx project). If not, any necessary files (e.g. default.a7890, CTC autosampler macros) must be manually copied into the new MassLynx project. The A7890 method editor can be used to edit existing A7890 methods or to create new A7890 methods. The A7890 method editor can be invoked from inlets buttons (Pump, Autosampler or Detector button) available on the left side of the Inlet Method Editor. To print an A7890 method, the A7890 method file must be opened once in the A7890 method editor. Sampler offset must not be activated in dual injection tower mode. Otherwise the autosampler parameters will not download. On the Agilent 7683 and 7693 ALS, the Allow Sampling Offset option available in the Front/Back Injector tab of the A7890 method editor does not work as expected. Even when the sample offset option is disabled in the A7890 method editor, a static value of 10mm is downloaded to the instrument. If the sample offset is not required to be used in routine sample analysis, then the Allow Sample Offset option should be enabled in the method editor and should be set to value 0.0mm. This will ensure that the offset option is switched off on the instrument. AutoPrep functionality is not supported with MassLynx. To stop the current inlet method, the run must be manually stopped from the GC instrument front panel. However, when using a GC PAL, do not stop the method until after the Running LED has changed to green, otherwise the next sample will go straight to Acquire and the inlet method will not be run. The Running LED is on the inlet method editor. To control a GC PAL or Combi PAL with the 7890 GC, the PAL must be configured with an Out signal called Prep. Page 16 of 19 Document No: 46154_1

17 The sample list may randomly stop with Waiting for Prep Run status when using a CTC PAL. The inlet method is not run, and there is no error message. The sample batch can be restarted by pressing Prep on the GC. The workaround is to increase the length of the Pulse Times for the Prep signal on the PAL to 500 ms. The Pulse Times for CTC PAL can be set on CTC PAL instrument control panel through: Setup/Objects/Out Signals/Prep menu. If an FID, TCD or micro-ecd detector is connected on the A7890 GC instrument and data is to be acquired from the detector, the detector must be configured as A7890 from the Inlet Method editor ->Tools -> Instrument Configuration menu option. When the detector is configured, the Channel 1 or Channel 2 option must be enabled. Also, Front Detector or Back Detector must be selected as the Output channel in the Channel 1 tab of the A7890 method file (or Channel 2 tab if Channel 2 is selected). Attempting to acquire data with a detector configured but the Channel 1 or Channel 2 option disabled in the A7890 method, will result in the sample list pausing at the end of each sample with the error No data was acquired on detector. If an FID, TCD or micro-ecd detector is connected on the A7890 GC instrument but there is no intention to acquire the detector data, de-configure the detector from the Inlet Method editor ->Tools -> Instrument Configuration menu option and ensure the Channel 1 and Channel 2 option is disabled in the A7890 method file. Alternatively, the Channel 1 or Channel 2 option can be left enabled but a valid source option (such as Oven Temperature or Front Inlet Pressure etc) must be selected in the Channel 1 or Channel 2 tab accordingly. Note that in a new A7890 method file the Channel 1 option is enabled and, on the Channel 1 page, the Source field is configured to Front Detector Output by default. The Channel 1 option will need to be disabled or a valid source option must be selected. If an FID, TCD or micro-ecd detector is not connected on the A7890 GC instrument and there is no intention to acquire the detector data, de-configure the detector from the Inlet Method editor ->Tools -> Instrument Configuration menu option and ensure the Channel 1 and Channel 2 option is disabled in the A7890 method file. If the A7890 GC column is connected to the MS then ensure that the output of the column is set to MSD in the A7890 method. It allows the column to maintain proper backing pressure If the outlet of the A7890 GC column is connected to the MS through an APGC interface, then ensure that the outlet of the column is set to the Other option in the A7890 method file. The A7890 GC instrument supports different hardware configurations as stated in the Supported Hardware Configurations section above. The parameters that are configured in the A7890 method file should match the hardware configurations that are available on the A7890 GC system. Failing to do so will cause an error in the Inlet Method editor. Selecting Reset Communication from the Inlet Method tools menu will reset the error. Page 17 of 19 Document No: 46154_1

18 APPLICATIONS: General Note(s): Application managers should not be installed from SCN 916. Application managers should be installed on a separate PC using SCN 901 MassLynx Desktop. Data must be processed using MassLynx Desktop. Supported Computers, Operating systems, Hot fixes and Anti-Virus software: MassLynx 4.1 SCN 916 was tested and validated with Lenovo ThinkStation C30X Workstations on Microsoft Windows 7 Professional 64 Bit SP1. The following Windows Updates are supported with MassLynx v4.1 SCN 916: Windows Bit Professional Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Page 18 of 19 Document No: 46154_1

19 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Security Update KB /14/2013 Update KB /14/2013 Update KB /14/2013 Update KB /14/2013 Update KB /14/2013 Update KB /14/2013 Update KB /14/2013 Update kb /14/2013 Update KB /14/2013 Update KB /14/2013 Update KB /14/2013 Update KB /14/2013 Update KB /14/2013 Antivirus Symantec Endpoint Protection v12.1 anti-virus software is supported. It is recommended that Network Threat Protection is disabled on the Acquisition PC. Windows Updates The PC firewall can occasionally be re-enabled by windows updates, after every update the firewall should be checked to ensure it is still disabled. Page 19 of 19 Document No: 46154_1