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EASY-nLC 1000 User Guide Version C

1. Gradient 00 00 f Administr BETTE i 11 May 2011 1 0 A1 Sample 1 admin 20110511 13 07 Current BSA 40 min RePlay 1 Samples 11 5 14 03 11 5 14 03 admin STOP Exit RePlay method readback Thermo Scientific EASY nLC 1000 User Guide 189 A External Devices Additional Run Time for a RePlay Experiment Additional Run Time for a RePlay Experiment For a typical RePlay application injecting and loading 5 pL of sample with a gradient of 60 minutes 30 minutes RePlay the full timing is as follows 2 minutes Refilling pumps at 100 pL min 2 minutes Injecting 5 pL at 20 pL min and waiting for pressures to settle 12 minutes Loading the sample onto the analytical column with 15 pL at 1 25 pL min 60 minutes Gradient autosampler wash 30 minutes RePlay while also reequilibrating the analytical column In total you can achieve an MS utilization rate of close to 85 percent 90 106 despite the fact that the EASY nLC system cannot overlap parts of two runs in parallel 190 EASY nLC 1000 User Guide Thermo Scientific Oo OE Returning the EASY nLC Instrument If it is necessary to return the EASY nLC system to the factory follow the instructions in this appendix Contents Transport Instructions Declaration of Contamination Transport Instructions To prepare the instrument for transport 1 Press Home Overview 2 Press Eject Plate 3 Remove the
2. Status Connected e Depending on the connection status do one of the following f the status changes from Not Connected to Connected go to step 3f Ifthe connection fails see To troubleshoot a failed connection to the support server When the connection fails the SSH Connection Error dialog box might appear with this message Not able to determine connection status See message log for details The message log file is in the admin WsystemLog folder on the EASY nLC system For information about accessing the admin folder from another computer on your local network see To access the admin folder on the EASY nLC systems computer hard drive from another computer on the network on page 63 While this file might provide useful information to a member of Thermo Scientific Technical Support users should follow the suggested troubleshooting procedure To troubleshoot a failed connection to the support server f After the status changes to Connected allow enough time for the EASY nLC system to create the zip file in the admin folder and for the support server to retrieve the zip file Then go to step 4 After you send a message with the appropriate contact information through the remote support feature a member of the Thermo Fisher Scientific Technical Support team will contact you 4 To close the communication link press Disconnect 5 To return the system to normal operation reconnect the Ethernet
3. 2012 Thermo Fisher Scientific Inc All rights reserved EASY nLC AFC IFC LCQ Fleet LXQ LTQ nanoViper and PepMap are trademarks and Acclaim Dionex and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc PEEK and PEEKsil are trademarks of SGE International Pty Ltd Corp This product uses FreeRTOS from www freertos org available upon request FreeRTOS is a registered trademark of Real Time Engineers Ltd The following are registered trademarks in the United States Advion and RePlay are registered trademarks of Advion Biosystems Inc Agilent and Varian are registered trademarks of Agilent Technologies Inc Bruker is a registered trademark of Bruker Corporation CMOSens is a registered trademark of Sensirion AG Corp Duran is a registered trademark of Schott AG Micromass and Waters are registered trademarks of Waters Corporation PhotoMOS is a registered trademark of Panasonic Electric Works Co Ltd Sciex is a registered trademark of Applied Biosystems Life Technologies Teflon is a registered trademark of E I du Pont de Nemours and Company VICI and Valco are registered trademarks of Valco Instruments Co Inc Microsoft and Windows are registered trademarks of the Microsoft Corporation in the United States and other countries All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries Thermo Fisher Scientific Inc provides this document to its customers with a product purchase
4. Step Event 1 The pump refills 2 The associated valve centers blocking the solvent flow through the valve 3 The pump builds pressure to 980 bar 4 When the pressure stabilizes at 980 bar the pump calculates the flow loss based on the pump piston movement required to maintain a pressure of 980 bar If the flow loss is less than 400 nL min the pump passes the leak test During a leak test of the system the script pressurizes the flow paths shown with red dashed lines in Figure 105 and monitors the flow sensors and pump piston movement Thermo Scientific EASY nLC 1000 User Guide 171 10 Maintenance Maintenance Scripts Figure 105 Pressurized lines for a system leak test Pump S Pressure S sensor To the autosampler needle Pump A x Pressure sensor Sample loop 1 2 6 A one Flow AA sensor 1 2 6 S 90105 Mixing Tee Pump B x Column Out line Union Pressure Flow Waste In line sensor sensor 1 1 2 6 2 6 8 B W SEES 345 O ww Centered d 172 EASY nLC 1000 User Guide Thermo Scientific 10 Maintenance Maintenance Scripts To set the Leaks script parameters 1 Select the Leaks script as follows a Press Maintenance gt Scripts b In the Category list select Test c Inthe Name list select Leaks 2 Set the parameters see Figure 106 for this script as follows a Press the Parameters tab b To select pump A or B both pumps or the entire system flow path for th
5. This value as shown in Figure 118 indicates how long into the gradient to switch back to playback mode At the end of the gradient the contact closure control reverts to capture mode Figure 118 RePlay Playback Delay setting Thermo Home sElweg site Method Editor Maintenance Configuration SCIENTIFIC File E JI a Name BSA 40 min RePlay Open f Close ES RePlay Capture Playback Eluent Playback delay 45 00 min sec Timing Job 00 15 48 11 May 2011 13 05 admin Exit S 6 6 5 Thermo Scientific A External Devices Monitoring the Run of a RePlay Method Monitoring the Run of a RePlay Method The readback for a RePlay method displays Capture or Replay To monitor the run of a RePlay method 1 When running a sample using a method with the RePlay extension open the Home Overview page 2 View the RePlay RP mode readback in the center status box see Figure 119 Figure 119 RePlay method readback Thermo Home Batch Setup Method Editor NES Maintenance Configuration LSP disabled Idle flow disabled Graphs 0 2 bar 0 0 nl min 127 8 140 0 ul Queue Solvent A 8 2 bar 0 0 nl 137 0 min 140 0 yl T 2 B LI l la a ickup sam ple Initialize system Refill AB Nes Loa ple E rate precolum n RP Capture Prealign A E brate analytica Gradient Solvent B 00 00 08 in f Eject plate f Insert plate t amp f ance Sample 00 00 08
6. 8 Troubleshooting Manual Controls To empty pump A or B to waste 1 Check the position of the pump valve on the Home Overview page 2 Doone of the following To empty pump A or B directly to waste make sure that its valve is in position 1 2 To empty pump A or B to waste by way of valve W place the pump valve in position 1 6 and valve W in position 1 6 Valve Position Solvent flow A or B 1 2 Empties to the waste beaker 1 6 Passes through valve S and into the Column Out line S 1 2 Bypasses the sample loop 1 6 Passes through the sample loop W 1 2 Passes through the installed columns 1 6 Exits the Column Out line to waste for a one column setup or passes through the precolumn and then exits the system to waste for a two column setup 3 Press the pump icon for the pump you want to control The Pump dialog box see Figure 89 on page 143 opens 4 In the flow rate box enter the flow rate 0 01 to 300 nL min When valve A or B is in position 1 6 the maximum system pressure limit constrains the maximum flow rate 5 In the volume box enter the volume that you want the pump to empty to waste 6 Press Start The pump empties until it pumps the requested volume or reaches the empty position whichever occurs first 144 EASY nLC 1000 User Guide Thermo Scientific 8 Troubleshooting Manual Controls Using the Manual Controls to Fill or Empty Pump S Thermo Scientific Before using the manual con
7. Connecting to Line Power Connecting to the Mass Spectrometer through Contact Closure Connecting the Ethernet Communication Cables Attaching a Mouse and Keyboard to the USB Connections Attaching Add on Devices through the P Bus and RS 232 Figure 25 shows an LC MS system with an EASY nLC system an LTQ Series mass spectrometer and a data system computer The LC system mass spectrometer and data system hardware are connected to three separate fourplex outlets that are hardwired to a common protective earth ground This figure does not show the monitoring system for the nanoflow ion source or the external rotary pumps for the mass spectrometer Figure 25 LC MS system with an EASY nLC system an LTO Series mass spectrometer and a data system computer Data system computer EASY nLC system LTO Series mass spectrometer and Ethernet switch back panel right panel Contact closure cable Fourplex outlet for the data system hardware Laboratory LAN port Fourplex outlet for the mass spectrometer Fourplex outlet for the EASY nLC system Thermo Scientific EASY nLC 1000 User Guide 37 2 Installing the EASY nLC Instrument Back Panel Connections Connecting to Line Power Each EASY nLC system comes with a 2 5 m 8 2 ft long power cord CAUTION Power cords can become frayed and damaged with use If the power cord is frayed or damaged replace it with an eq
8. Network Access Table 25 contains troubleshooting tips for network access problems For information about setting up the network connection see Setting Up the Ethernet Connection to a Local Network for Data Exchange on page 42 and Setting Up the Local Area Network Connection on page 61 Table 25 Network access problems Symptom Cannot access the EASY nLC system through the network Possible causes Unsaved network information on the Configuration gt Network page Action Press Configuration Network Check the network settings and then press Save Configuration No physical connection to the local area network Check the Ethernet cable connections see Setting Up the Ethernet Connection to a Local Network for Data Exchange on page 42 Broken Ethernet cable Replace the Ethernet cable Incorrect address in Windows Explorer Verify the IP address of the EASY nLC system and then retype file WP address in the Windows Explorer address list Incorrect network information for the EASY nLC system on the Configuration Network page Press Configuration Network Check the network settings and then press Save Configuration System Component States Valves Pumps Autosampler and Plate Cooler Table 26 contains troubleshooting tips for the system component states Table 26 LED state troubleshooting tip Symptom The LED on the device is blinking red 138 EASY nLC 1
9. i tubing with sleeves L and emitter Waste beaker Waste In tubing 10 EASY nLC 1000 User Guide Thermo Scientific 1 Introduction Solvent Delivery and Sample Pickup Systems Solvent Delivery and Sample Pickup Systems Syringe Pumps Pressure Sensors Flow Sensors Thermo Scientific These topics describe the components of the solvent delivery and sample pickup systems Syringe Pumps Pressure Sensors Flow Sensors Six Port Valves Pump A and Pump B Solvent Delivery System Sample Pickup and Autosampler Wash System The syringe pumps perform these functions Component Function Pumps A and B Draw solvent from solvent bottles on top of the instrument empty solvent to the waste beaker and deliver solvent to the mixing Tee Pump S Draws solvent from the W3 bottle draws sample from the specified sample location into the needle and empties solvent to the W4 bottle in the autosampler tray compartment For maintenance purposes the system tracks the volume pumped by each pump see Checking and Resetting the Device Usage Counters on page 181 The three pressure sensors are connected to the solvent path between the syringe pump outlets and the six port three position valves Two flow sensors provide feedback control for pumps A and B The two flow sensors are liquid mass flow meters with a patented technology Each flow meter consists of a length of fused silica capillary a sensor chip a
10. W3 bottle W4 bottle Sample vial 1 uL front air segment From the mixing Tee y Figure 18 Pickup Sample step with the requested sample volume loaded into the loop and bracketed by two air segments lt m 1 uL front air segment W Y W3 bottle WA bottle Sample vial N Column Out line Pressure Sensor 1 uL rear air segment t Column Out line From the mixing Tee x 22 EASY nLC 1000 User Guide Thermo Scientific 1 Introduction Predefined Steps for Sample Runs Autosampler Wash Step The standard autosampler wash step includes this sequence of actions Action 1 The autosampler needle moves to the W4 bottle see Figure 15 on page 20 2 Pump S pushes the specified volume of solvent through sample loop and the needle As the wash solvent exits the needle it overfills the needle insert and washes the exterior surface of the needle 3 Pump S refills with solvent A from the W3 bottle Predefined Steps for Sample Runs Step Refill A B During sample runs the EASY nLC system goes through a series of predefined steps Pumps A and B draw solvent from the solvent bottles on top of the instrument Precolumn and analytical column Pump A delivers solvent to the system For a two column system solvent A passes through the precolumn and then out to the waste beaker After the precolumn equilibration finishes equilibration the sy
11. Non togliere i coperchi a protezione dalle schede di circuito stampato PCB Prodotti chimici Possibile presenza di sostanze chimiche pericolose nell apparecchio Indossare dei guanti per maneggiare prodotti chimici tossici cancerogeni mutageni o corrosivi irritanti Utilizzare contenitori aprovo e seguire la procedura indicata per lo smaltimento dei residui di olio Calore Attendere che i componenti riscaldati si raffreddino prima di effetturare l intervento di manutenzione Incendio Adottare le dovute precauzioni quando si usa il sistema in presenza di gas infiammabili Pericolo per la vista Gli schizzi di prodotti chimici o delle particelle presenti nell aria potrebbero causare danni alla vista Indossare occhiali protettivi quando si maneggiano prodotti chimici o si effettuano interventi di manutenzione sull apparecchio Pericolo generico Pericolo non compreso tra le precedenti categorie Questo simbolo e utilizzato inoltre ull apparecchio per segnalare all utente di consultare le istruzioni descritte nel presente manuale co Quando e in dubbio la misura di sicurezza per una procedura prima di continuare si prega di mettersi in contatto con il Servizio di Assistenza Tecnica locale per i prodotti di Thermo Fisher Scientific San Jose CAUTION Symbol PPP PRP o CAUTION Electric Shock This instrument uses high voltages that can cause personal injury Before servicing shut down the instrument
12. Position 15 84 ul Readbacks Real flow 549 6 nl min Close Note Because pump S does not have an associated flow sensor the Pump S dialog box does not include a Real Flow readback Using the Manual Controls to Fill or Empty Pump A or B Before using the manual controls to fill or empty pump A or B make sure that the valves are in the appropriate position For information about controlling the position of the valves see Using the Valve Controls on page 141 IMPORTANT Before you fill pump A or B make sure that the pumps associated valve is in position 1 2 You can contaminate the pump by attempting to fill the pump when its associated valve is in position 1 6 To fill pump A or B with solvent 1 Check the position of the pump valve on the Home Overview page 2 Make sure that the corresponding valve is in position 1 2 When valve A or B is in the 1 2 position the corresponding pump draws solvent from the solvent bottle on top of the instrument see Figure 12 on page 14 3 Press the pump icon for the pump you want to control The Pump dialog box see Figure 89 opens 4 In the flow rate box enter the filling flow rate 20 01 to 2300 nL min 5 In the volume box enter the volume that you want pump A or B to draw 6 Press Start The pump draws solvent until it draws the requested volume or reaches the full position whichever occurs first Thermo Scientific EASY nLC 1000 User Guide 143
13. The Name Password and Re enter boxes also become available for data input Make entries in the User Login and Name boxes Select the privileges for the user by level Normal Super or Admin For user privileges by user type see Table 14 on page 63 If you want the user to carry out instrument maintenance you must select Super user as the user type If you want the user to restore data to the system select Admin as the user type Create an initial password for the defined user by using the Password and Re enter boxes Users can change their passwords from the Login Exit menu Press Save Changing Your Password from the Exit Menu 66 After logging in all users can change their password from the Exit menu EASY nLC 1000 User Guide To change your password Press Exit in the lower right corner of the touch screen The Exit dialog box for the current user opens see Figure 41 Figure 41 Exit dialog box for the current user dministrator f Logout gt Change password J Stop Application J Power Down Cancel J 4 J X Press Change Password The Change password for current user dialog box opens Make the appropriate entries Press Accept to accept the new password and close the dialog box Thermo Scientific 4 Configuring the EASY nLC System Modifying the Time Settings Modifying the Time Settings Use the Configuration gt Time page Figure 42 to se
14. c Inthe Name list select Valve Check 2 Set the parameters see Figure 107 for this script as follows a Press the Parameters tab b Select the check boxes for the valves that you want to test Figure 107 Figure 107 Valve Check script parameters Thermo Home Batch Setup Wicadeemaclioem Maintenance mi ersitelele iaielg SCIENTIFIC No graph Support Devices m graph J Job 00 15 48 11 May 2011 12 47 cQ 174 EASY nLC 1000 User Guide Thermo Scientific 10 Maintenance Maintenance Scripts Test Back Pressure The Back Pressure script determines instrument back pressure for solvent A and B The script runs at a preset flow and measures the back pressure on the system IMPORTANT Before you perform the Back Pressure script ensure that the solvent A bottle contains water and the solvent B bottle contains acetonitrile This test is not valid for other solvents Use this script when testing for instrument flow path blockage Before running the script connect column output to waste input as shown in Figure 105 on page 172 To set the Back Pressure script parameters 1 Select the Back Pressure script as follows a Press Maintenance gt Scripts b In the Category list select Test c Inthe Name list select Back Pressure 2 Set the parameters see Figure 108 for this script as follows a Press the Parameters tab b Test solvent A solvent B or both A and B by se
15. see Figure 79 on page 122 The Autosampler Plate Calibration dialog box opens Figure 81 shows the dialog box at the beginning of the plate calibration routine The top left and bottom right positions are highlighted in green The position readbacks for the xyz axes are unpopulated Thermo Scientific EASY nLC 1000 User Guide 125 7 Calibrating the Autosampler s XYZ Robot Calibrating Plates Figure 81 Plate view in the Autosampler Plate Calibration dialog box Autosampler Plate Calibration Calibrate Plate HT MTP Needle In Out Needle Up Down E LeftRight 4 m p Capture gae 3 Press the green vial or well in the upper left corner of the plate view 1 The needle moves to the current saved coordinate The saved coordinates for the x and y axis appear on the left side of the slash the needle does not descend into the vial or well and the z axis value on the left side of the slash remains at 0 The values on the left side of the slash change as you adjust the needle position 4 Center the needle above the vial or well as follows Press the Needle In Out 3 buttons to adjust the x axis position Press the Needle Left Right 4 buttons to adjust the y axis position yaxis 1 In A X axis Out Right left 126 EASY nLC 1000 User Guide Thermo Scientific 7 Calibrating the Autosampler s XYZ Robot Calibrating Plates 5 Using the step buttons in the Ne
16. select Purge Solvent Select the check boxes for the appropriate pump or pumps Press Purge Iterations to specify the number of empty fill cycles to be performed Note Entering a value of zero 0 for purge iterations will just refill the pumps Figure 98 Purge Solvent script parameters Thermo gm SCIENTIFIC etup Name Method Editor Log Book Poe 7 fe solvent Support cription Devices 10 x x Job 00 00 21 11 May 2011 11 36 EJ admin Schedule Exit Flow nl min Flow nl min Configuration Fr J Desired flow Real flow Pressure 300 000 0 250 000 0 200 000 0 150 000 0 100 000 0 50 000 0 0 0 1 000 0 750 0 500 0 req sunssa4 250 0 0 0 0 1 2 3 Time min 5 oup B J Desired flow Real flow Pressure 300 000 0 250 000 0 200 000 0 150 000 0 100 000 0 50 000 0 0 0 Time min 1 000 0 750 0 500 0 eq sunssaJd 250 0 0 0 Thermo Scientific 10 Maintenance Maintenance Scripts Prepare Flush Air Thermo Scientific The Flush Air script pressurizes the pump and then releases that pressure into the flow lines toward the waste container which is effective for removing air from inside the pump head Pressurization time is calculated dynamically while the script is executed and is based on measurements from previous iterations The pump pressurizes
17. 0 to 980 Tip If you specify both a flow rate and a maximum pressure the pump flow is limited by the parameter that is reached first If you leave the flow and max pressure boxes empty the IFC algorithm allows pump A to run at 980 bar IMPORTANT If you enable the LSP feature and specify a maximum pressure the batch run stops if the system reaches the maximum pressure setting before it reaches the specified flow rate during sample loading To continue setting up the method go to the Edit 3 5 page by pressing the right arrow Thermo Scientific EASY nLC 1000 User Guide 95 6 Running Samples Using the Integrated Software Creating a Method Building the Gradient Use the Method Editor gt Edit 3 5 page to build the gradient This page consists of a schematic view for setting parameters and a graph view showing the gradient as a function of time see Figure 63 Use the four buttons at the bottom of the page to add lines to the gradient move lines up and down and delete lines To move or delete lines first select the line by pressing it The rest of this tutorial guides you through building a gradient for analyzing a BSA digest on a C18 column Because this procedure is intended to help you set up a method make sure to set the parameters appropriately for your analyte and column characteristics Figure 63 Edit 3 5 page of the Method Editor wizard Thermo melaa uM use Method Editor Matetigu iar ine mumme elanielele ial
18. 1 Introduction Specifications Specification 140 pL volume enough for a gt 10 h 0 10096 B 300 nL min gradient 1 nL min to 300 pL min flow range External pressure sensor Valves VICI Valco rotor stator 6 ports 3 positions 1 6 1 2 or CENTERED Autosampler Peltier cooled Capacity is maximum 20 C below ambient temperature measured at 60 RH Expect less if you remove the side panels use an adapter plate in the autosampler other than the standard plate or both Plate holder ejects through spring mounted autosampler door 4 containers for waste or wash liquids EASY nLC 1000 User Guide 31 LLL m Installing the EASY nLC Instrument To install the EASY nLC system or move the system from one laboratory benchtop to another follow the installation instructions in this chapter after reviewing the Safety and Special Notices on page xiii Note This chapter describes the laboratory requirements and the back panel connections for the EASY nLC system For information about installing the LC columns the sample plates the solvent bottles and the wash bottles see Chapter 5 Preparing the EASY nLC Instrument for Use e For information about connecting the column assembly to the mass spectrometer s ion source refer to the manual provided with the ion source For information about the internal solvent lines see Solvent System Schematic on page 194 Contents Lifting Inst
19. 24 To minimize the cycle time the system runs these steps in parallel Refill A and B and Pickup Sample Column Equilibration and Pickup Sample Prepare Gradient after valve S switches to position 1 2 Gradient and Autosampler Wash Refill S Figure 20 on page 24 shows a flow chart of the sample run steps Figure 20 Flow chart of the sample run steps Initialize system check that the hardware is ready Pick up sample Refill pump A Refill pump B Equilibrate precolumn for a two column setup Equilibrate analytical column 3 Load sample Prepare gradient a Prealign pumps A and B b Switch valve S to position 1 2 i Autosampler wash EASY nLC 1000 User Guide Thermo Scientific 1 Introduction Pump Flow Control Pump Flow Control The EASY nLC system contains split free high pressure syringe pumps capable of delivering flows from 1 nL min to 300 pL min These flow control systems optimize the system performance Automatic Flow Control System Intelligent Flow Control Load Speed Protection Automatic Flow Control System The Automatic Flow Control AFC system see Figure 21 is active during theses processes The gradient step of a sample run The execution of the isocratic flow maintenance script The AFC system uses the output of the flow sensors to regulate the flow and accurately maintain the programmed flow from each channel even during sudden pressure changes cause
20. Action 1 The system calculates the volume of solvent A required to complete the gradient program Pump A refills if it does not contain a sufficient volume of solvent to complete the gradient program 2 With valves A W and S in position 1 6 and valve B in the centered position the system vents through the Waste In line to a precalculated pressure Pump B builds up pressure to match the precalculated pressure of pump A Note Because the mobile phase bypasses the sample loop during the gradient program the sample loop does not add any gradient delay volume to the system 3 The AFC system takes control of pump A and the solvent flow from pump A stabilizes 4 The AFC system takes control of pump B 5 Valve B moves to position 1 6 and the system sends the closure signal to the mass spectrometer Gradient Step The gradient step includes this sequence of actions Action 1 The system runs the gradient program Note With valve S in position 1 2 the mobile phase bypasses the sample loop during the gradient program So the sample loop does not add any gradient delay volume to the system Thermo Scientific If either pump runs out of solvent during the gradient run both pumps refill The refilling process takes approximately 2 minutes EASY nLC 1000 User Guide 19 1 Introduction Solvent Delivery and Sample Pickup Systems Figure 15 shows the gradient step of a sample run Mobile phase from the mixing Tee bypasses the sampl
21. Desired flow Real flow Pressure Job 00 00 21 300 000 0 1 000 0 250 000 0 A 750 0 mw 200 000 0 m E du a a 11 May 2011 150 000 0 5000 5 11 51 100 000 0 T B 2500 3 admin 50 000 0 Schedule 0 0 a Exit GE EE NE E UE Time min Prepare Precolumn Equilibration The Precolumn Equilibration script equilibrates the precolumn with solvent from pump A Use this script to equilibrate or flush the precolumn and to determine a suitable flow rate for the sample loading step in your method To set the Precolumn Equilibration script parameters 1 Select the Precolumn Equilibration script as follows a Press Maintenance Scripts b In the Category list select Prepare c In the Name list select Precolumn Equilibration 2 Set the parameters see Figure 100 for this script as follows a Press the Parameters tab b Press Volume to set how much solvent A to use for reequilibration of the precolumn For best results use 10 column volumes for reequilibration c Press Flow to set the flow rate for performing the reequilibration of the precolumn If the flow field is left empty the pump operates at the set pressure 164 EASY nLC 1000 User Guide Thermo Scientific Thermo Scientific If the pressure field is left empty the pump operates at the set flow as long as it is below the instrument maximum pressure of 1000 bar If both a flow and a max pressure are specified the pump flow is limited by whic
22. Protection When the LSP system is on the batch run stops if the system reaches the set max pressure before it reaches the set flow during the sample loading step Stopping the batch run when the system pressure rises above an acceptable level prevents the system from running the remaining samples when the column or tubing has become clogged For instructions about how to turn on the Load Speed Protection system see Setting Up the Properties for the HPLC Device on page 70 Thermo Scientific EASY nLC 1000 User Guide 27 1 Introduction Specifications Specifications These topics describe the performance and technical specifications for the EASY nLC system Performance Specifications Technical Specifications Performance Specifications 28 Table 6 lists the performance specifications for the EASY nLC system Table 6 Performance specification Item Flow range gradient Flow while loading and equilibrating Specification 20 to 2000 nL min Recommended 100 to 1000 nL min Up to 25 pL min Pressure range 0 to 1000 bar Retention time reproducibility RT RSD Within the recommended flow range 0 1 to 0 4 Outside the recommended flow range typically better than 1 Peak widths Carryover Typically 3 to 5 seconds full width at half maximum fwhm using PepMap nano bore columns as supplied at delivery Typically lt 0 05 Conditions Injection of 100 fmol tryptic digests of BSA
23. autosampler needle moves to the W4 position EASY nLC 1000 User Guide 145 8 Troubleshooting Manual Controls c Press Needle Down The autosampler needle descends into the W4 bottle d Press Close to close the Autosampler dialog box 3 Dispense solvent from pump S as follows a Press the pump S icon The Pump S dialog box opens b In the flow rate box enter the flow rate 0 01 to 300 pL min c Inthe volume box enter the volume that you want the pump to empty to waste d Press Start The pump empties until it pumps the requested volume or reaches the empty position whichever occurs first Using the Autosampler Controls You can manually control the XYZ robot and the cooler temperature from the Home gt Overview page To open the Autosampler dialog box Press the autosampler icon on the Home Overview page D A m Finish ed Ed ed oooooooo O The Autosampler dialog box opens see Figure 90 oooooooo o E z Figure 90 Autosampler dialog box Autosampler XYZ Robot C C Eject Plate Insert Plate 8x12 Abgene AB 0800 Goto Calibration eae Goto Well Vial or well position box Needle Up Needle Down Wash C C WA we v WA Cooler I Temperature input box j 7 0 Set Disable Temperature GL Temperature readback Close 146 EASY nLC 1000 User Guide Thermo Scientific Thermo Scientific 8 Tro
24. cables as appropriate see Connecting the Ethernet Communication Cables on page 40 152 EASY nLC 1000 User Guide Thermo Scientific 9 Remote Support Saving System Files on a USB Removable Storage Device To troubleshoot a failed connection to the support server 1 Check the support server configuration see step 1 on page 150 2 Verify that the Ethernet cable is securely connected to both the LAN port on the back panel of the EASY nLC system and the laboratory LAN port 3 Verify that the Ethernet cable is working 4 Ask your IT administrator if the network firewalls allow outgoing traffic to port 22 through an SSH connection Saving System Files on a USB Removable Storage Device The EASY nLC system includes network capability Through the network you can back up your system export and import batches and methods analyze your system by examining the log files and perform many other tasks However when you are not connected to the network or the network is broken or you do not have a computer with network access that is near the EASY nLC system you can use the copy function to copy all the system files on the system to a USB removable storage device such as a USB flash drive or memory stick The EASY nLC system ships with a USB flash drive for your convenience But you can use any USB storage device formatted with the file system FAT FAT 16 and at least 128 MB of free space To copy system files to a USB storage devi
25. com Wehlistrasse 27b A 1200 Wien Vienna Phone Fax E mail Address Denmark Phone Fax E mail Address 32 2 482 3030 32 53 73 42 41 The city codes for Brussels and Aalst are 2 and 53 respectively 32 2 482 3031 service sid benelux thermofisher com Clintonpark Keppekouter Ninovesteenweg 198 B 9320 ERMEBODEGEM AALST 45 7023 6267 45 7023 6263 service sid dk thermofisher com Fruebjergvej 3 2100 K benhavn Finland see Sweden Norway and Finland Thermo Scientific EASY nLC 1000 User Guide xvii Table 2 Customer Service information for Europe Sheet 2 of 3 France Also representing French speaking North Africa Algeria Morocco and Tunisia Phone 33 1 60 92 49 50 The city code for Paris is 1 Fax 33 1 1 60 92 48 99 E mail service sid lesulis thermofisher com Address 16 Avenue du Qu bec Silic 765 Z A de Courtaboeuf F 91963 Les Ulis C dex Germany Phone 49 6103 408 1050 The city code for Dreieich is 6103 Fax 49 6103 408 1213 E mail service dreieich thermofisher com Address Im Steingrund 4 6 D 63303 Dreieich Italy Phone Numero Verde toll free 800 823 162 Fax 39 02 95320 225 The city code for Milan is 02 E mail assistenza tecnica it thermofisher com Address Strada Rivoltana I 20090 Rodano Milano Netherlands Phone Fax E mail Address EASY nLC 1000 User Guide 31 76 579 55 55 The city code for Bred
26. control and laboratory use Table 8 Physical specifications Item Width Depth Height Specification 35 cm 14 in 38 cm 15 in 45 cm 18 in Weight Weight in the shipping container Thermo Scientific 35 kg 77 Ib 45 kg 99 Ib EASY nLC 1000 User Guide 29 1 Introduction Specifications Table 9 Electrical specifications Item Specification Power requirements 120 Vac 50 60 Hz 250 W 230 Vac 50 60 Hz 250 W For uninterruptible power supply UPS dimensioning assume 250 W Fuses For 120 Vac one T 5 AL 250 V fuse 5 x 20 mm IEC 60127 For 230 Vac one T 2 5 AL 250 V fuse All fuses are UL Listed and CSA certified Table 10 Communication specifications Item Specification Contact closure 3 outputs 3 inputs and 6 ground pins IN circuit TTL Level OUT circuit PhotoMOS relay protected against high voltages Continuous switch current from 0 8 to 5 V is 35 mA LAN 10 100 Mb s BaseT Ethernet USB 2 x USB 1 1 for keyboard and mouse RS 232 Reserved for hardware add ons or high level MS control by using serial communication P Bus Reserved for instrument add ons using the internal EASY nLC instrument protocol bus 8 wire control and limited power at 9 24 V PS 2 Input for connection of keyboard or mouse Monitor Output for connection of external display 30 EASY nLC 1000 User Guide Thermo Scientific Thermo Scientific Table 11 Parts specifications Item Pumps
27. direct control of the valves the pumps the autosamplers XYZ robot and the cooler temperature Page Function Go to Overview Manually control the valves the pumps and Manual Controls on page 141 the autosampler components Monitor the system status Viewing the System Status and Using the Manual Controls on page 50 and Monitoring the Run on page 109 Graphs Display up to four graphs each selectable Using the Graphs Page in the Home Menu from a list with time dependent data for the on page 111 active run The selection list includes Pump A Pump B Pump S Valve A Valve B Valve S Valve W sample cooling and Gradient Queue View a list of the batch jobs currently Editing the Running Batch on page 114 running or waiting Batch Setup Menu Use the two pages of the Batch Setup menu to set up sample processing jobs For information about setting up and submitting a batch run see these procedures Creating a Batch on page 103 and Starting Sample Acquisition on page 108 Page Function Go to File View or change a directory tree of saved Viewing the Batch List and Setting Up a batch jobs You can create or import new Batch Record on page 103 jobs and create or delete directories on this page Edit Set up new batch jobs View Racks view Select the vial or well positions for the batch Specifying the Method Sample Positions job from a graphical view of the configured plate format and Number of Inje
28. folder where you store your batches Thermo Scientific EASY nLC 1000 User Guide 103 6 Running Samples Using the Integrated Software Creating a Batch To specify the batch name and folder location 1 On the Batch Setup gt File page press New Batch The Create New File dialog box opens In the Folder box browse to the folder where you want to store the batch In the New Name box enter a name for the batch A WW N Optional In the Description box enter a description of the batch 5 Press Save The batch name appears under the selected folder To set up the batch go to the next procedure Specifying the Method Sample Positions and Number of Injections Per Sample Specifying the Method Sample Positions and Number of Injections Per Sample A batch lists the sample injection order the vial or well positions where the samples are located the number of injections per sample and the method used to run the sample To create a batch by using the View Racks view 1 Press Batch Setup gt Edit 2 If you do not see a plate overview press View Racks A plate view for the selected plate format appears Figure 67 shows the plate view for the 6x 8 vial plate format 104 EASY nLC 1000 User Guide Thermo Scientific 6 Running Samples Using the Integrated Software Creating a Batch Figure 67 View Racks view on the Edit page of the Batch Setup menu Methods list Thermo SCIENTIFIC File TT 4 f C
29. graph for Pump B Touch the y axis of each graph to cycle the Flow axis through several preset scales Figure 73 Pump B graph enlarged Thermo Home Batch Setup Method Editor M la n tenance Configuration Scripts Pump B Log Book Desired flow Real flow Pressure Su Sont 1 000 0 PP 300 000 04 tes 275 000 0 Devices 2008 250 000 0 850 0 225 000 04 800 0 200 000 0 750 0 700 0 175 000 0 650 0 150 000 04 E 600 0 125 000 0 5500 a E 100 000 0 sooo 75 0000 4500 T u 50 000 0 AORN 350 0 Job 00 02 11 25 000 0 300 0 ie 250 0 25 000 0 200 0 11 May 2011 50 000 0 150 0 12 27 75 000 0 4 100 0 admin 100 000 0 50 0 0 0 Exit 0 0 0 5 1 0 15 2 0 2 5 3 0 35 4 0 4 5 5 0 Time min 112 EASY nLC 1000 User Guide Thermo Scientific 6 Running Samples Using the Integrated Software Stopping Sample Acquisition Stopping Sample Acquisition You can stop the sample acquisition during the run by pressing the red STOP button on the Home gt Overview page This halts all actions on the HPLC system and the following buttons become active Restart Sample Runs the method from its beginning again Only press this button if you are sure you have enough sample in the Microtiter plate Cancel Sample Cancels the current sample and skips to the next sample in the batch job Cancel Batch Cancels the entire current batch job Eject Plate Ejects the plate for your inspection to help you d
30. method editor starting 93 precolumn equilibration parameters 98 microwell plates preparing samples 91 monitoring the run 109 See also RePlay monitoring the run mouse connection 44 MS Connection script 169 nanoViper fittings using 87 needle position calibrating 124 130 network access troubleshooting 138 connection 61 network card installing in data system computer 41 noise and interference cause of 38 North America customer service for xvi Thermo Scientific Index K 0 one column setup configuration check box 70 description 10 installing 84 P password changing 64 initial 57 performance specifications 28 plates calibrating 125 managing formats 121 port 22 firewall setup for 36 43 149 power requirements 36 turning off 58 power cord connection and specifications 38 Power Down button 58 power save feature Ethernet switch 41 precolumn equilibration step method 15 98 installing 84 preparation for use 88 preparing autosampler for the calibration routines 124 solvent bottles and waste containers 74 well plates 91 pressure sensors 11 product description 2 pump flow control description 25 manual control 142 volume pumped usage counter 181 Pump dialog box 143 Purge Solvent script 162 purging and flushing pumps 79 Q quadrant selection box 384 well plate 106 remote desktop connections 41 remote support 43 149 replacement parts 193 EASY nLC 1000 User Guide 199 Index S RePlay additional
31. mm length LC513 3 Pressure sensor outlet to valve S Stainless steel 250 um ID 150 mm length LC514 4 Mixing Tee to valve S nanoViper 20 um ID 350 mm length LC522 Valve A to flow sensor A Valve B to flow sensor B Flow sensor A to mixing Tee 5 Flow sensor B to mixing Tee nanoViper 10 um ID 180 mm length LC543 6 Autosampler needle connected to PEEKsil 150 um ID 550 mm length LC302 port 1 of valve S 7 Column Out tubing connected to nanoViper 20 um ID 550 mm length LC560 port 3 of valve S 8 Waste In line venting Tee to port2 of nanoViper 75 um ID 550 mm length LC562 valve W 9 Sample loop 20 pL nanoViper 250 um ID 410 mm length LC472 D Port 2 of valve A to check valve A Teflon 500 um ID 150 mm length kit LC230 Port 2 of valve B to check valve B E Tubing 2 from check valves to solvent Teflon 500 um ID 390 mm length kit LC230 bottles F Tubing 2 from check valves to waste Teflon 500 um ID 390 mm length kit LC230 beaker G Tubing from valve W to the waste Teflon 500 um ID 330 mm length LC263 beaker 194 EASY nLC 1000 User Guide Thermo Scientific C Consumables and Replacement Parts Solvent System Schematic Figure 120 Physical layout and schematics of the EASY nLC 1000 solvent system Solvent B Pressure sensor Pressure sensor Waste Thermo Scientific EASY nLC 1000 User Guide 195 LLL m ie Index A accessing files on the instrument s hard drive 42 61 support server 43 150
32. need to reequilibrate the columns at the end of the gradient The parameters for reequilibration are entered directly and separately as described in the next procedure The reequilibration runs parallel with the sample pickup at the beginning of a sample execution run To continue setting up the method go to the Edit 4 5 page by pressing the right arrow Thermo Scientific EASY nLC 1000 User Guide 97 6 Running Samples Using the Integrated Software Creating a Method Setting Up the Column Equilibration Steps Use the Method Editor gt Edit 4 5 page to set up the parameters for the column reequilibrations see Figure 64 Figure 64 Edit 4 5 page of the Method Editor wizard Thermo Home Batch Setup SCIENTIFIC Maintenance Configuration File bsa100fm Name Precolumn equilibration Volume 12 0 ul ON Flow ul min 800 Bar d a Max pressure Analytical column equilibration Job 00 00 00 Volume 3 0 Flow ul ul min i 9 May 2014 1553 Max pressure 800 Bar a admin Exit 45 To set up the precolumn equilibration 1 In the Precolumn Equilibration area press the Volume box to set the amount of solvent A to use for reequilibration of the precolumn For best results use 10 column volumes for reequilibration 2 Press the Flow box to set the flow rate for performing the reequilibration of the precolumn If you leave the Flow bo
33. os Pes pac Shares Psp de t iato edt Vd 138 System Component States Valves Pumps Autosampler and Plate Cooleryszude t e ae eode e gate ea al ah ele cie RU it ernie telo caet 138 Miscellaneous ss aens e Brace die Rea dor due sid reei e eb tae ena Adan 139 Mantal Controls ait uis encodes Reg epe EE A RUE RUE AE tre 141 Using the Valve Controls soit cis elcid eater ald abe 141 Using the Pump Controls uide decia d dhe hh Sees Tease x eta 142 Using the Autosampler Controls ints son aioe e ie Ce ea ieu e e pc 146 hire EE PHI 149 Connecting the EASY nLC System to the Support Server luus 150 Saving System Files on a USB Removable Storage Device 153 Lon Jp Pm 157 General Maintenance ur oom eda Deci Leo has bocca wA PE a te ad 157 eleme Materials a ts rice bee Rey Ae A PERI RIM RETE ied PAS 157 Replacing the Main Power Pise i23 ipd 4 br EERRI ROREM RE AR 158 Daily Maintenance 3 oed emat a aea e EE nS A A ape ME Me ose 159 Weekly Miarmtenadni gs d oed abes AR dates M ues dod e AUR docs 160 O uaretbo anten Cer nat cre ea cm e duck e acu a nine da vies 160 Yearly Maintenance ERE 161 Ma intenance Scripts cv trosses sace ace E ate ds eee eS 161 Prepare Purge Solvent sens occas Med ates Area OUR acne edd 162 Prepare Flush Ait re fein re nera db st e KOE dae pea Read 163 Prepare Precolumn Equilibration 0 5 cece ceca meet 164 Prepare Analytical Col Equilibration 5 5r cepere Ret Resa 16
34. plates tubes 4 Remove the waste container and other bottles see Autosampler Wash Bottles and Waste Beaker on page 76 5 Press Insert Plate 6 Close down the system properly see Closing Down the EASY nLC System on page 58 7 Remove the cables on the back side 8 Fill out the Declaration of Contamination of Equipment in Declaration of Contamination on page 192 9 Place the EASY nLC instrument in the original shipping container Thermo Scientific EASY nLC 1000 User Guide 191 B Returning the EASY nLC Instrument Declaration of Contamination Declaration of Contamination To return service or repair the EASY nLC instrument you must complete and submit a Declaration of Contamination of Equipment to Thermo Fisher Scientific with the returned equipment Qualified personnel must review the declaration Contact Thermo Fisher Scientific for additional copies of this form or if you have any questions regarding the contents of this declaration Description of equipment Equipment type model Serial No Date of receiving purchasing equipment Reason for return Maintenance Repair End of test Describe symptoms and problems Equipment condition Has the equipment been used Yes No Has the equipment been exposed to potentially harmful substances Yes No If yes attach list of all known harmful substances including chemical name and symbol and precautions associated with the
35. releases pressure and empties for each iteration of the script The pressurization is limited to 200 bar and the script measures the amount of pumping required to reach 200 bar Because the solvents are slightly compressible and the pump itself expands even an air free pump allows some pumping before reaching 200 bar Depending on the solvents a pumped volume less than 12 pL is acceptable To set the Flush Air script parameters 1 Select the Flush Air script as follows a Press Maintenance gt Scripts b In the Category list select Prepare c Inthe Name list select Flush Air 2 Set the parameters see Figure 99 for this script as follows a Press the Parameters tab b Press Flush Threshold to enter the tolerated threshold for an accepted test result Below 12 pL is satisfactory The script terminates after the first iteration that gives a flush volume below the set threshold EASY nLC 1000 User Guide 163 10 Maintenance Maintenance Scripts Figure 99 Flush Air script parameters Thermo Home Bat setup Method Editor V Ice Easela SCIENTIFIC Beris pa 2 f f f Pump A v Log Book Prepare w Flush air M Desired flow Real flow Pressure Support 300 000 04 1 000 0 Output 1 250 000 0 Devices 750 0 m 200 000 0 m Parameter v Value E a 150 000 0 5000 5 100 000 0 F 2500 3 50 000 0 d 0 0 Do 2 33 45 E Time min Flush threshold ul Pump B J
36. run time 190 configuring 186 connecting to EASY nLC 183 monitoring the run 189 reset pressure sensor script 179 running batch editing 114 S safety calibrating the autosampler 124 handling emitters 86 precautions for the EASY nLC system xiii standards EMC xxi sample loading method parameters 95 pickup check 131 pickup method parameters 94 Pickup script 170 sample loop bypassed during gradient program 19 configuring 71 maximum capacity 21 ordering 194 washing 23 sample runs predefined steps 23 troubleshooting 117 scripts Analytical Col Equilibration 166 Autosampler Torque 176 Back Pressure 175 Flow Sensors 178 Flush Air 163 Isocratic Flow 167 Leaks 171 Maintenance 161 MS Connection 169 Purge Solvent 162 Reset Pressure Sensor 179 Sample Pickup 131 170 Valve Check 174 Valve Tune 177 Secure Shell SSH network protocol 36 149 service log 180 sharp objects autosampler needle 124 emitter 86 solvent A and B bottles preparing 75 solvent system schematic 194 200 EASY nLC 1000 User Guide solvents checking levels 159 filtering 74 ordering Fisher Scientific solvents 75 Source column autosampler wash 101 specifications performance 28 technical 29 SSH Connection Error message box 152 Standard option autosampler wash 101 Start button green 78 110 starting the EASY nLC 46 Stop button red 78 110 113 stopping sample acquisition 113 support server establishing communication with 150 IP address 150 sup
37. sample pick up Please fill plate well with a defined volume before running test Max volume Loop volume 2pl Max flow 40 0 pl min Category Name Frea f pickup Position Parameter v Value pum 10 00 Flow l min 20 00 DL Description Parameters Sample pickup started Prime pump filling Lu 7 After the EASY nLC application finishes the script do the following a Eject the tray b Check all wells one by one with a pipette c Check that there are 2 pL left in all wells You are finished when there are 2 pL left in all wells d If there are more than 2 pL left in some or all of the wells go to step 8 Thermo Scientific EASY nLC 1000 User Guide 131 7 Calibrating the Autosampler s XYZ Robot Checking Sample Pickup 8 Depending on the volume remaining in the wells do one of the following f there are more than 2 pL left in a wells calibrate the autosampler again and then rerun the sample pickup check An excess volume in a wells indicates a problem with the autosampler calibration or the alignment of the autosampler tray adapter plate fthere are more than 2 pL left in some of the wells run the Flush Air script on pump see Figure 86 and then rerun the sample pickup check An inconsistent sample pickup from each well indicates that there might be air in the system Figure 86 Flush Air sc
38. samples that are not yet tested 4 Press Reschedule The batch continues running IMPORTANT If you do not reschedule the batch after you complete the batch edit the instrument stops after the current sample run 5 Optional Check the sample list as follows a Press Home gt Queue b Press Properties see Figure 74 on page 114 c Press Show Samples The Job Properties box opens see Figure 76 and the Show Batch button appears in place of the Show Samples button Thermo Scientific EASY nLC 1000 User Guide 115 6 Running Samples Using the Integrated Software Editing the Running Batch Figure 76 Sample list job properties on the Queue page Thermo SCIENTIFIC Home Batch Setup Method Editor Maintenance Configuration Overview Auto gt Submitter Job name Duration continue 1 C famn famin 201008241 714 11 04 15 Graphs admin 20100825 0002 job properties Position Name Method 2 0 B1 Sampte2 BSA 30 min RePlay 3 op1 sampte4 BSA 30 min RePlay Job 00 00 00 4 oe1 Samples BSA 30 min RePlay s o r1 Samples BSA 30 min RePlay 24 aug 2010 17 14 admin d Click Close 116 EASY nLC 1000 User Guide Thermo Scientific 6 Running Samples Using the Integrated Software Troubleshooting a Sample Run Troubleshooting a Sample Run Ifa problem occurs during a sample analysis the EASY nLC instrument displays the error in a pop up box and sto
39. the Sample Pickup script to check the sample pickup function see Test Sample Pickup on page 170 To check the EASY nLC system for leaks Run the Leaks script for A B and for System to check for and pinpoint instrument leaks see Test Leaks on page 171 IMPORTANT Check the valve rotor shifts regularly When the valve rotor shifts exceed 6000 Thermo Fisher Scientific recommends checking the system for leaks From this point forward perform leak tests every 1000 shifts and exchange the rotor when the leak test fails To check the check valves Run the Purge Solvent script see Prepare Purge Solvent on page 162 and do the following When the pumps are ejecting solvent make sure that solvent is exiting the A and B waste tubing into the waste beaker When the pumps are refilling make sure that no solvents are going into the pump through these tubes Thermo Scientific 10 Maintenance Yearly Maintenance Yearly Maintenance Replace the solvent filters and check the flow sensor calibration once a year To exchange low pressure solvent filters and high pressure inline filters Thoroughly clean new solvent filters before use as these can be a contamination source To check the flow sensor calibration Run the Flow Sensor calibration script with the Inspection Only parameter enabled see Calibrate Flow Sensors on page 178 This checks that the flow sensor calibratio
40. the autosampler automatically empties the pump and refills with solvent from bottle 3 to be ready for the next injection EASY nLC 1000 User Guide 101 6 Running Samples Using the Integrated Software Creating a Method To set up a custom wash program 1 Select the Custom Wash check box The custom wash table becomes available 2 For each row that you want to add to the program press Add Line You can select a different wash solvent for each row 3 Edit each row as follows n the Source column select the wash solvent source The selections are Bottle 1 Bottle 2 or Bottle 3 Note The EASY nLC autosampler holds up to four bottles three for washing solvents and the fourth for ejecting waste and cleaning the outside of the injection needle Bottles 1 and 2 in positions W1 and W2 contain custom wash solvents Bottle 3 in position W3 contains solvent A Bottle 4 in position W4 contains the needle wash insert n the Volume column type a volume from 0 to the sample loop size plus 8 pL In the Cycle column type a value from 0 to 10 4 To edit an existing wash program do the following Press Add Line to add a row to the program Press Delete Line to remove a row from the program Press Copy Line to copy a selected line Press Up or Down to move a selected row up or down respectively When you finish setting up the method parameters save the method as described in the next procedure Saving the Meth
41. the method name To create a new method 1 Open the Method Editor gt File page see Figure 60 on page 92 2 Press New Method The Create New File dialog box opens In the Folder box browse to the directory where you want to store the new method In the New Name box enter a method name Optional In the Description box enter a description of the method N Un A Press Save Starting the Method Editor Wizard and Selecting the Method to be Edited Thermo Scientific The Method Editor wizard consists of five pages that guide you through all the parameters required for a working LC method Use the Method Editor Edit 1 5 page to select the method that you want to edit To start the Method Editor wizard 1 Press Method Editor Edit 2 If you are not already on the Edit 1 5 page see Figure 61 go to page 1 5 by pressing the appropriate arrow near the bottom of the touch screen Figure 61 Method Editor Edit 1 5 page Thermo Home Batch Setup Maintenance Configuration Name BSA 30 min Open Close Save Description Standard 30 min BSA separation Method extensions RePlay Job 00 00 00 23 aug 2010 12 36 admin Exit EASY nLC 1000 User Guide 93 6 Running Samples Using the Integrated Software Creating a Method 3 Press Open The Select Method to Open dialog box opens 4 Select the method that you want to edit 5 Press Accept To continue setti
42. the right of the tray compartment collects solvent delivered by pumps A and B when these pumps empty solvent to waste and solvent delivered by pump A during the precolumn equilibration and sample loading steps for a two column system Thermo Scientific EASY nLC 1000 User Guide 3 1 Introduction Hardware Components Figure 2 Tray compartment front view Solvent bottles T Exit for Aand B Column Out j and Waste In eue solvent lines Tray compartment with vial adapter and wash solvent bottles lt Waste aa beaker Figure 3 Tray compartment viewed from above Well plate 96 or 384 Three 3 positions for Waste bottle with wash Six 6 extra vial positions or vial 6 x 8 adapter wash solvents insert for cleaning of the for standards or regular outside of the needle samples 4 EASY nLC 1000 User Guide Thermo Scientific 1 Introduction Hardware Components Components Behind the Right Panel The EASY nLC nanoflow pump and autosampler system consists of three syringe pumps three pressure sensors four 3 position valves four check valves and a mixing Tee You can access the solvent system components by removing the instrument s right panel see Figure 4 Figure 4 Hardware components behind the right panel of the EASY nLC 1000 instrument Solvent A Solvent B check valve check valve assembly assembly Autosampler needle l Four 3 position 6 port valves L
43. the venting Tee and passes through valve W to the waste beaker EASY nLC 1000 User Guide 15 1 Introduction Solvent Delivery and Sample Pickup Systems Figure 13 Fquilibrate Precolumn step Pump A b Pressure Pump B amp Pressure sensor Mixing Tee S X To the autosampler needle Precolumn Column Out line F Waste In line Venting Tee Analytical column Waste beaker The analytical column equilibration step includes this sequence of actions Action 1 For a two column setup valve A remains in position 1 6 valve B remains in the centered position and valve S remains in position 1 6 Valve W switches to position 1 2 For a one column setup valve A switches to position 1 6 Valve B switches to the centered position Valve S switches to position 1 2 Valve W switches to position 1 2 Pump A pushes the specified solvent volume through the analytical column at the specified pressure or specified flow rate 16 EASY nLC 1000 User Guide Thermo Scientific 1 Introduction Solvent Delivery and Sample Pickup Systems Load Sample Step After pump S draws the sample into the sample loop see Pickup Sample Step on page 21 valve S switches to position 1 6 and pump A pushes solvent A through the sample loop flushing the sample out of the sample loop into the Column Out line and onto the precolumn for a two column setup
44. tips on handling autosampler issues To access the Autosampler control window Figure 87 press Home gt Overview and then press the autosampler plate icon Figure 87 Autosampler control window XYZ Robot f 4 Eject Plate Insert Plate Goto Well z Needle Up Needle Down Cc ow e Cc Cc 7 0 Set Disable i f wa B Cooler i 16x24 HT MTP Uncalibrated Goto Calibration Temperature RC Close Table 23 Autosampler troubleshooting tips Sheet 1 of 2 Symptom Possible causes Action Sample pickup fails Incorrect autosampler 1 Fill some of the wells with a given volume of calibration or air in the sample S pump 136 EASY nLC 1000 User Guide solvent A for example 12 pL Put a plastic film on the microtiter plate Run the maintenance script Test Sample Pickup on page 170 with a pickup volume of 10 pL and your default flow Run the script for each well Eject the tray and check the wells one by one with a pipette Run the maintenance script Prepare Flush Air on page 163 or calibrate the autosampler if the problem still appears Thermo Scientific Table 23 Autosampler troubleshooting tips Sheet 2 of 2 Symptom Possible causes The needle cannot penetrate the Damaged or bent needle tip plastic film on the microtiter plate Cannot run a batch A server warning message about the plate format for the aut
45. top of the screen see Figure 32 on page 49 and each menu has two or more pages tabs along the left side of the screen To access a specific page of the application you first press the appropriate menu tab and then press the appropriate page tab In this guide the following nomenclature describes the navigation to a specific page of the user interface Menu Page Some of the pages have two or more views For example the Batch Setup Edit page has two views View Rack and View List You access these views by pressing View Rack or View List on the page The Method Editor Edit page contains a five page wizard You access the wizard pages by pressing the left and right arrows at the bottom of the touch screen Table 13 User interface structure Home Overview Graphs Queue Batch Setup Method Editor Maintenance Configuration File File Scripts Users Edit with alternate Edit pages 1 5 5 5 Log Book Connections views Rack and List Support Network Devices Time Backup These topics describe the pages and views that you can access from these menus Home Menu Batch Setup Menu Method Editor Menu Maintenance Menu Configuration Menu 52 EASY nLC 1000 User Guide Thermo Scientific 3 Integrated Instrument Control Software Application Menu Structure Home Menu Use the three pages of the Home menu to view the status of your sample runs and the instrument components edit batch jobs in the queue and take
46. using a Thermo Scientific software application to control your liquid chromatograph mass spectrometer LC MS system the plate selection for the EASY nLC system in your Thermo Scientific instrument control software must match the touch screen application selection To delete a plate format Open the Tools view for the autosampler on the Devices page of the Maintenance menu see step 1 on page 121 Select a plate format from the Plate list Note You cannot delete the plate in use When you select the plate in use highlighted in bold text the Delete button becomes unavailable Press Delete The Delete Plate Data dialog box opens Press Accept EASY nLC 1000 User Guide 123 7 Calibrating the Autosampler s XYZ Robot Preparing the Autosampler for the Calibration Routines Preparing the Autosampler for the Calibration Routines To prepare the autosampler for the calibration routines you must remove the left side panel from the instrument and load the appropriate adapter plate vials or microtiter plate wash bottle W4 with insert and optional extra vial into the tray compartment CAUTION Calibrating the autosampler requires removal of the side plate and visual inspection of the autosampler needle holder Because the autosampler compartment contains moving parts and sharp needles make sure to keep hands clear when operating the autosampler during calibration To prepare the autosampler for the plate calib
47. will compromise the performance of the instrument Contact your local Thermo Fisher Scientific representative before running this script Figure 110 Pump Torque script Thermo Home Batch Setup Hede Se ivee Maintenance Configuration SCIENTIFIC fa No graph Log Book rex FI Pump torque Support Parameters omi Parameter Value est pump fx est pump B x Description Devices Fito graph J Job 00 15 48 11 May 2011 12 51 admin 3 Exit Calibrate Valve Tune Thermo Scientific The Valve Tune script automatically retunes the valve IMPORTANT Performing this script incorrectly will compromise the performance of the instrument Contact your local Thermo Fisher Scientific representative before running this script EASY nLC 1000 User Guide 177 10 Maintenance Maintenance Scripts Calibrate Flow Sensors The Flow Sensors script calibrates the flow sensors on pumps A and B Use this script when you change the type of solvent in solvent bottles A or B or you suspect the calibration to be wrong This calibration does not require any additional plumbing IMPORTANT Because the flow sensor calibration requires a stable operating temperature ensure that the instrument s side panels are installed and that the instrument has been on for a minimum of one half hour To set the Flow Sensors script parameters 1 Select the Flow Sensors scr
48. 000 0 iz id 100 000 0 00 o 1 Zo Ug 4 5 00 05 10 15 20 25 30 35 40 45 50 Time min Time min Sample Cooling J Gradient lt Current temperature Target temperature 1 0 d 20 0 Job 00 01 00 zu eno gt 6 0 Sea m 600 3 U 50 E i amp ps 50 0 gp 40 EC ao 9 Sep 2011 e 30 u 30 0 11 52 a 02 X admin 10 10 0 0 0 0 0 0 0 T E E it 00 05 10 15 20 25 30 35 40 45 50 0 00 0 25 0 50 0 75 1 00 XIL Time min Time min Table 19 describes the different types of graphs that are available To change graphs select from their corresponding lists Table 19 Graphical data types Graph Description Pump A Pump B Shows the desired flow black line real flow blue line and pressure and Pump S red line over time for each of the three pumps Valves A B S Shows the valve position over time for each of the four valves and W Gradient Shows the theoretical gradient dotted red line and the actual gradient dynamically calculated on the feedback values from the pumps full red line plus the actual flow calculated on the feedback values from the pumps Temperature Shows the measured temperature on the plate cooler over time Thermo Scientific EASY nLC 1000 User Guide 111 6 Running Samples Using the Integrated Software Monitoring the Run You can change the graph size as follows Touch the graphs to enlarge them and then touch them again to minimize the view Figure 73 shows the enlarged flow
49. 000 User Guide Possible causes Device in bootloader mode The device stopped working This could also block the function of other devices Action Contact Thermo Fisher Scientific us customer support analyzegthermofisher com eu techsupport cms thermofisher com Thermo Scientific Miscellaneous 8 Troubleshooting Miscellaneous For additional issues that might arise while using the EASY nLC system consult these miscellaneous troubleshooting tips Table 27 Table 27 Miscellaneous troubleshooting tips Sheet 1 of 2 Symptom Possible causes Copying log files to a USB Memory stick in wrong memory stick failed format Action Format the memory stick in FAT FAT16 format Memory stick not recognized by the system Copying to the USB memory Too much data to be copied stick does not stop Use one of the memory sticks supplied by Thermo Fisher Scientific or try plugging the stick into the other USB port Contact Thermo Fisher Scientific if neither action works us customer support analyzegthermofisher com eu techsupport cms thermofisher com Remove the memory stick from the EASY nLC system and press Ignore when the error message appears Contact Thermo Fisher Scientific for a system check up us customer support analyze thermofisher com eu techsupport cms thermofisher com Forgot the admin password Thermo Scientific If you are already logged in to the EASY nLC system Thermo Fisher Scientif
50. 1000 User Guide 49 3 Integrated Instrument Control Software Viewing the System Status and Using the Manual Controls Viewing the System Status and Using the Manual Controls EASY nLC 1000 User Guide You can view the system status and access manual controls for the system hardware components on the Home gt Overview page Figure 33 Figure 33 Overview page of the Home menu Pump A status Current sample and status Valve A icon Autosampler icon Flow sensor A readback E ETA LSP disabled Idle flow disabled Graphs 0 3 bar Queue au 0 nl min 140 0 140 0 yl Solvent A 8 9 bar a O nl min 140 0 140 0 yl XB XXX L 0585000 20 0 ul 3 8 nl min sam ple Initialize system Refill A Equilibrate precolum n Equilibrate analytical colum n ash refill 5 uxo EX poss faa OW Autosampler Solvent B Job 00 00 10 _ Sample 11 May 2011 Current as 10 58 Pump B icon quest Login N Mixing Tee readback Thermo Scientific 3 Integrated Instrument Control Software Viewing the System Status and Using the Manual Controls The system readbacks display the following information Readback Information Pump Displays the back pressure flow rate and position for the associated pump The flow rate readback is negative when the pump is refilling Flow sensor Displays the measured flow rate from the a
51. 2010 10 41 58 i Batch admin 20100719 1038 Job 00 00 00 1 205 2010 17 03 40 i Purge solvent 00 00 00 29 04 2010 10 29 34 i Purge solvent 00 00 00 a Mr ad 29 04 2010 10 28 42 Purge solvent 00 00 00 admin gin4 2n1n f Exit Enter Log Entry 2 Press Enter Log Entry The Log Entry dialog box opens 3 In the box at the top of the dialog box enter a description of the service action 4 In the Templates list select a template The Templates list contains the following selections Comment New Part Maintenance Property Change and Precolumn Changed by lt User gt on lt Date gt 5 In the Components list select a hardware component The Components list contains the following selections None Gradient Valve B Valve A Valve S Valve W Analytical Column Precolumn Autosampler Pump A Pump B and Pump S 180 EASY nLC 1000 User Guide Thermo Scientific 10 Maintenance Checking and Resetting the Device Usage Counters Do one of the following e Press Add to add this entry and keep the Log Entry dialog box open Press Add and Close to add this entry and close the Log Entry dialog box Press Close to close the Log Entry dialog box without saving any entries To search the log In the Log Book list select Queue Job or User In the User List select Any Admin or Guest In the Time From list select a time In the Time To list select a time Press Search The search
52. 42 and set up the network configuration for the application you can access the EASY nLC system from other computers on the network IMPORTANT Ask your local IT administrator to help you configure the EASY nLC system on the local network The following information will help you through the process To connect the EASY nLC system to a local network 1 Connect the Ethernet cables as described in see Setting Up the Ethernet Connection to a Local Network for Data Exchange on page 42 2 Press Configuration Network EASY nLC 1000 User Guide 61 4 Configuring the EASY nLC System Setting Up the Local Area Network Connection The Network page Figure 37 contains the configuration address information Figure 37 Network page of the Configuration menu Thermo Home Batch Setup Method Editor Maintenance Users Address Connections Network 9 Dynamic Fixed Network Name c 009815 Domain Time 255 255 o0 ie 16 a2 133 7 sune ass Backup Gateway 10 32 133 254 DNS 10 32 135 28 Support server IP 195 41 108 93 Default IP Job 00 00 21 Save configuration 11 May 2011 11 30 admin Exit 3 For Network type select Dynamic addressing DHCP or use a Fixed IP address Your IT administrator knows which option to select If IT asks about a MAC address for the instrument that is the instrum
53. 6 Prepare Isocratic blown uid So ORE ea IP eR Me Pra edes 167 Test MS Connection iore retten ED sc Je eden b ea TED ek Tet 169 Test Sample Pickup oed Eee ERU S PEDUP WERE FEE bee ee 170 Testes Leaks co dado pos iei aeo dd o ERN oA E aep alor aeons 171 Test Valve Check arrra terr PERRO ed pora Feb Ua dpi Rt 174 Test Back PEessHie a pot esae a ster cb da M aec d T at ti e dea 175 Test Autosampler Torque s sca ters pts REDE tees Gs wag 176 Test Pump Dotques sce skit nates ol oats beg c S C a 177 Calibrate Valve TUBE suero mace xcd aedis ea iba cs aec Auct aov pn 177 Calibrate Flow Sensors o i i deese societ Haale eee tee RE as 178 Calibrate Reset Pressure Sensor uc ces kc bag eo ee ee eee 179 Keeping Servige Records ieusten aah ie togati Qoo aa e did ae eid h 180 Checking and Resetting the Device Usage Counters 000 181 Thermo Scientific Thermo Scientific Appendix A Appendix B Appendix C Contents External Devices sosise ene E ew cones E E a E a A A eaa 183 Connecting the RePlay Device to the EASY nLC Instrument 184 Adding the RePlay Device to the EASY nLC Device List suus 186 Setting Up a Method with the RePlay Device leleeeeeeeee 187 Monitoring ihe Run of a RePlay Method i2 ror eee 189 Additional Run Time for a RePlay Experiment 00020004 190 Returning the EASY nLC Instrument LLuuuuuuuueueesss 191 J EADSDOPETDSUHCEIO
54. C system as close as possible to the high performance liquid chromatography HPLC detector mass spectrometer or both However to avoid exposure to direct heat place the EASY nLC system away from any detector or mass spectrometer vents 34 EASY nLC 1000 User Guide Thermo Scientific 2 Installing the EASY nLC Instrument Laboratory Requirements Figure 24 shows a typical benchtop setup for an EASY nLC system connected to a Thermo Scientific mass spectrometer Connecting the data system computer to your local area network intranet requires an additional network card Using the setup shown in Figure 24 you can control the EASY nLC system from the local data system computer or from another data system computer on the intranet however the EASY nLC system might not be able to communicate with the remote support server For information about connecting the EASY nLC system to the remote support server see Setting Up the Ethernet Connection to the Support Server on page 43 Tip Before you move the EASY nLC system from one benchtop to another exit the EASY nLC system see Closing Down the EASY nLC System on page 58 disconnect the EASY nLC system from line power the detector and the data system computer if applicable For information about installing or removing the column assembly from the mass spectrometer s ion source refer to the manual provided with the ion source Figure 24 EASY nLC system and LTO Series MS det
55. DF documents for the EASY nLC as follows a In the Model list select EASY nLC b In the Document Type list select Manual c Click Submit Search 6 On the Documents page click the link to the right of Download to view the PDF La 7 Click the Save a Copy icon B browse to an appropriate folder and then click Save to save a copy of the document xii EASY nLC 1000 User Guide Thermo Scientific Preface Safety and Special Notices Special Notices Thermo Scientific Make sure to follow the safety practices presented in this guide and observe the safety and special notices that appear in boxes Observe all written safety precautions during all phases of operation service and repair of this instrument Failure to comply with these precautions or with specific warnings elsewhere in this manual violates safety standards of design manufacture and intended use of the instrument and might result in injury or loss of life The following two stickers appear on the EASY nLC instrument This sticker warns you that the instrument includes a sharp needle and moving parts that are accessible to the operator To prevent personal injury or damage to parts of the EASY nLC instrument take care when loading samples into the instruments tray compartment WARNING SHARP NEEDLE AND MOVING PARTS KEEP HANDS CLEAR AVERTISSEMENT A GUILLE POINTURE ET PARTIES MOUVANTES TENIR LES MAINS L CART This sticker alerts you to consul
56. DS ese petes eese Io cde No ito eie eh iin 191 Declaration of Contamitiatl ti is scc Pe pO E EE o ERROR ERES 192 Consumables and Replacement Parts LLuuusuuuuueueseeeue 193 Ordering Intortnatiolt vagos hanes xci ua epa e orare E opas 193 Solvent System Schematic e see erae qu EY E CERRO ee e 194 Indek Loos x xor inn e Ba eee E A E A Fd etd E 197 EASY nLC 1000 User Guide ix LL m Preface This guide describes how to operate and maintain the EASY nLC nanoflow liquid chromatography LC system by using the integrated touch screen software Before you turn on the instrument for the first time read the first three chapters in this guide Before you run your first sample review the chapters that describe how to configure the software prepare the system for operation and submit your first sample set batch Contents Related Documentation Downloading Manuals from the Customer Manuals Web Site e Safety and Special Notices Contacting Us Declaration of Conformity To suggest changes to documentation or to Help Complete a brief survey about this document by clicking the button below Thank you in advance for your help SURVEY Complete a brief survey about this document by going to the following URL Thank you in advance for your help Related Documentation In addition to this guide Thermo Fisher Scientific provides the following documents for the EASY nLC system EASY nLC Virtual Instr
57. EMC This Class A digital apparatus meets all requirements of the Canadian Interference Causing Equipment Regulations EASY nLC 1000 User Guide xxi European Safety and EMC Electromagnetic Compliance Standards Application of Council Directive s 2004 108 EC Electromagnetic Compatibility 2006 95 EC Low Voltage Directive LVD Standard s to which conformity is declared IEC 61010 1 Second edition 2001 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Also conformity with EN 61010 1 2001 UL 61010 1 second edition CAN CSA C22 2 No 61010 1 Second Edition EN IEC 61326 1 2006 Electrical equipment for measurement control and laboratory use EMC requirements Part 1 General requirements EN IEC 61000 3 2 2006 A1 A2 Electromagnetic compatibility EMC Part 3 2 Limits Limits for harmonic current emissions equipment input current lt 16 A per phase EN IEC 61000 3 3 2008 Electromagnetic compatibility EMC Part 3 3 Limits Limitation of voltage changes voltage fluctuations and flicker in public low voltage supply systems for equipment with rated current X16 A per phase and not subject to conditional connection FCC CFR 47 Part 15 Class A Radiated Emissions and Conducted Emissions Manufacturers Name Proxeon Biosystems A S Manufacturer s Address Type of Equipment Edisonsvej 4 DK 5000 Odense Denmark Laboratory Instru
58. ER Add Injections 1 Browse methods X Batch Extensions X l uU b bl a J u uo QOeoooooo O mm lo O0 eoooooo Jy Qe6oooooo w L7 Ia Q6OOOOOO m Qeoooooo Home fBatchSetuph Method Editor Mainten l OOO Oooaoa 23 aug 2010 12 35 18 eR E i Schedule admin Exit 6x8 vials Plate button 3 If the plate format is not set to your installed plate do the following a Press the Plate button Note The Plate button is the rectangular button imprinted with the plate name on the lower left side The default plate is 6 x 8 vials The Autosampler Rack Configuration dialog box opens b Select a plate format from the list c Press Accept The new plate format appears on the rectangular Plate button 4 If you have already created a name and selected a folder location for the batch do the following a Press Open b Select the batch c Press Accept The batch name appears in the batch name box Thermo Scientific EASY nLC 1000 User Guide 105 6 Running Samples Using the Integrated Software Creating a Batch 5 In the Injections box enter the number of injections per sample The default value is 1 injection per sample 6 Browse the methods list next to the Injections box and select the method that you want to use for the entire batch or for a subset of sample runs in the batch If you have not already created a method create one by following th
59. Isocratic Flow script runs solvent A and B at a fixed mixture ratio The script utilizes the AFC system to accurately control the flow Use this script to tune the mass spectrometer at a given B percentage or when cleaning the instrument the columns or both To set the Isocratic Flow script parameters 1 Select the Isocratic Flow script as follows a Press Maintenance Scripts b In the Category list select Prepare c Inthe Name list select Isocratic Flow 2 Set the parameters see Figure 102 for this script as follows a Press the Parameters tab b Press Volume to specify the total volume to be delivered by the pumps C Press Flow to specify the flow rate to be used d Press AB Mix to specify the solvent composition EASY nLC 1000 User Guide 167 10 Maintenance Maintenance Scripts e Ifyou want the solvent flow to continue until you press Stop select the Run Indefinitely check box When either pump runs out of solvent both pumps refill The refilling process takes approximately 2 minutes Figure 102 Isocratic Flow script parameters SCIENTIFIC Log Book Support Devices Job 00 15 48 11 May 2011 12 41 admin Exit 168 EASY nLC 1000 User Guide Home Batch Setup Method Editor Category Name Prepare Isocratic flow J Description Parameter wm 939 Pew s Run indefinitely o se Configuration No graph J No graph Th
60. K 6 Press Save to save the user account information Creating New User Accounts Thermo Scientific Use the Users page to create new user accounts for all the people or groups that will use the instrument Each user has a private file space for batch jobs and methods that other users apart from system administrators cannot see In addition there is a public file space for methods and batch jobs that all users can see and use Only Super users and Administrators can copy files into the public spaces and only Administrators can delete files and directories from the public space To create a new user account 1 Log in as admin otherwise see Logging In to the EASY nLC System on page 57 2 Press Configuration gt Users The Configuration gt Users page opens see Figure 40 Figure 40 Users page of the Configuration menu Thermo SCIENTIFIC Home Batch Setup Method Editor Maintenance Connections Description Name Administrator rm Network Administrator Time Password Backup Re enter Level Job 00 00 00 Graphs f Pump A J f Pump B J f Gradient J f Sample Cooling 24 aug 2010 f f f f paye Open Close New admin Exit EASY nLC 1000 User Guide 65 4 Configuring the EASY nLC System Modifying User Permissions Press New The User box changes to the User Login box and becomes available for data input
61. L TSMR MALTESE RRSTRfEBR ORMISLIEUADS 4 TORRBAETS OL ERLE j Xf HRB COMMA CU 538813 Ev TUVO eS BUCTF amp SU RSMAS AFE bhb FSEE BPPRIEL 5314 0 rIv2knv n Z4Zn420T2 h W R bkt v4 CCuHe EE ARE G2 RERARARPERKRARHESHRRKRER EHEZH gt LAA RERA ERER o EOS EGER E E E NS ELT RH th 3o th 77 HF PCB A HE E LEG RERA TEREA AREE AR o EMH Eo KERAN ADECER WRTTSIESESX Bt HR Bi FT NUR BEF o Hh 6 5 T1500 ALKA EE o KR EA RAE REAR gt WB LD CBE RSE ER RRS RRA Ee Ro ESI AE ee EAE AR SS HK A OF BLM HK SMR HF RKERR LULA i6 dE EXEM UIT HREM ht RS Be ER iE ES UE RA PARAS AP YK o nx de AEE ABE ie TEAR HE N 36 DU SEJE TIR BOR IA D LIK a a E Contents it ee ee ree eT a D ra o a Ter ret xi Related Documentation 2452 24 9 sain 1tuweiosewe idea chy aces ORDER d xi Downloading Manuals from the Customer Manuals Web Site xii Safety and Special Notices nic cep donee eee RES Pbi gard Vae xiii Contacting US cosa sec eer tre e etx b Cae eee eg rd e vea aes xv Declaration of Conformity A Lug aed ngu op OE on D a OEC EORR RD t xxi Chapter Introduction 0c cece cece eee eee eee eee 1 System Overview oko bibit eee ee a a ee qn ed dps 2 System Components dd cada veg rd ea ee ea e ae bares A ed ees 2 External System Connections 45 ackcxe qa acice d pec ce Vac eC Ree 3 Hardware Components 12 a d aie tack arenes ap OR Rl aa Doe ed uat deeok 3 Autosampler Tra
62. LC system directly to the Internet access port using the supplied Category 6 network cable To use the remote support feature the firewalls for your local network must allow outgoing TCP IP traffic from the EASY nLC system to the support server at IP address 195 41 108 93 port 22 Figure 27 EASY nLC system connected to a local network port with Internet capability Network port with Internet capability that allows outgoing traffic to port 22 Supplied Ethernet cable I E L J Thermo Scientific EASY nLC 1000 User Guide 43 2 Installing the EASY nLC Instrument Back Panel Connections Attaching a Mouse and Keyboard to the USB Connections You can use a mouse and keyboard instead of the built in touch screen but Thermo Fisher Scientific recommends using the touch screen interface For more information see Using the Touch Sensitive Screen on page 47 Connect the USB mouse or keyboard by using the USB connectors on the back of the instrument The EASY nLC application detects the mouse or keyboard within 30 seconds The application does not recognize all USB based keyboards or mice Attaching Add on Devices through the P Bus and RS 232 The EASY nLC system can control and power add on devices through the P bus the RS 232 interface or both see Figure 28 Figure 28 EASY nLC back panel top portion og ote htt AA AAAA AAA EE A A edd
63. Lone opa aces dp e ael ce UA ee cs fe i eed bia e ote en 29 Laboratory Requirements vein cies eo aee Pape c Bab et daba et es 34 Benchtop Requirements 1 0 82 22d 0 a Ra d REA C Reb e CAD dna 34 TiO CD ACCESS Societe pret Pes eMe d ates aired quce Res aeq ig 36 Power and Fuse Requirements 529 iii Fact xoa e sedan dis 36 Temperature and Humidity Requirements 00000000 008 36 Back Panel Connechons s y aici tenon eu Ro X eO TD ERG eda 37 Connecting to Line Power 2 cece eh 38 Connecting to the Mass Spectrometer through Contact Closure 39 Connecting the Ethernet Communication Cables 0 40 Attaching a Mouse and Keyboard to the USB Connections 44 Attaching Add on Devices through the P Bus and RS 232 44 Integrated Instrument Control Software Lus 45 Turning On the EASY nLC Instrument ssseeeeeeeeeeee 46 Using the Touch Sensitive Screen oiii pora phi IEEE Sees RE aie Roa 47 Using The BONS o ed unco asini tod Rt ata rati aes aan d 47 Inputune Alphanumeric Text 5c ladda tootsie Pes DS 48 Using Tables and Input Fields sina see hts eb ante e RAO UCK e dU ws 48 Interactive Graphical Controls sta osito b ios tne P iris et dor ett 48 Weyer Interface Lag olg dcos Veces te debat e ea o o UE Ae a eg 49 Viewing the System Status and Using the Manual Controls 50 Application Menu Structure cinis kh webs xad rur d ade Ro REED e pd 52 Home M
64. MS system requires only four connections e Solvent outlet connection to the mass spectrometer ion source Power cable connection to a grounded line power source Contact closure connection between the EASY nLC system and the mass spectrometer see Connecting to the Mass Spectrometer through Contact Closure on page 39 Ethernet connection between the EASY nLC systems built in computer and an Internet access port see Setting Up the Ethernet Connection to the Support Server on page 43 To control the EASY nLC system from the Thermo Xcalibur data system you must also connect the EASY nLC system to the data system computer Hardware Components These topics show the hardware components of the EASY nLC system Autosampler Tray Compartment Components Behind the Right Panel Components Behind the Left Panel Back Panel Autosampler Tray Compartment Figure 2 and Figure 3 show the tray compartment and the waste beaker You can open the tray compartment door manually or by using the touch screen controls The tray compartment holds the sample tray the wash bottles and six extra vials The compartment to the right of the tray compartment holds the waste beaker The autosampler draws solvent from wash bottle W3 to perform a standard wash and ejects the solvent into wash bottle W4 which contains the needle wash insert The autosampler can also perform a custom wash using the solvents from wash bottles W1 W2 The waste beaker to
65. P Table 15 describes the parameters in the Properties view for the EASY nLC instrument on the Devices page of the Maintenance menu 70 EASY nLC 1000 User Guide Thermo Scientific 4 Configuring the EASY nLC System Setting Up the Properties for the HPLC Device Table 15 HPLC parameter descriptions Parameter Description Loop Volume Specifies the nominal size of the installed sample loop Take care to specify the correct loop size If you specify a smaller loop size than the installed loop size the instrument might draw sample into the pump Idle Flow Rate Specifies the solvent flow rate when the instrument is idle This feature activates when the last sample in a batch is done If you do not want a solvent flow through the instrument when it is idle type 0 in the Idle Flow Rate box Maintaining long term emitter stability with glass emitters might require constant flow through the system One Column Setup Specifies the one column setup The diagram on the Overview page of the Home menu displays the column setup Load Speed Protection When this check box is selected the system uses the flow rate entered in Sample Loading area on page 2 5 of the Method Editor wizard see Setting Up the Sample Pickup and Loading Steps on page 94 to load the sample onto the precolumn or the analytical column for a one column system During a batch run the sequence stops immediately if the system reaches the maximum pressure limi
66. Parameters tab b Press Volume to set how much solvent A to use for reequilibration of the analytical column For best results use 10 column volumes for reequilibration c Press Flow to set the flow rate for performing the reequilibration of the analytical column If the flow field is left empty the pump operates at the set pressure d Press Max Pressure to set the maximum allowed pressure If the pressure field is left empty the pump operates at the set flow as long as it is below the instrument maximum pressure of 1000 bar If both a flow and a maximum pressure are specified the pump flow is limited by whichever parameter is reached first CAUTION The maximum pressure rating for the PepMap columns supplied with the EASY nLC 1000 system is 800 bar Running the system at pressures higher than 800 bar reduces the column lifespan 166 EASY nLC 1000 User Guide Thermo Scientific 10 Maintenance Maintenance Scripts Figure 101 Analytical Col Equilibration script parameters Thermo Home Batch Setup Weee Zellers Maintenance Configuration SCIENTIFIC ripts Category Name f P m _ No graph X Log Book Prepare w Analytical col e Support Devices Parameter Value olume pl a p Max pressure bar 800 00 _ No graph Job 00 05 02 Sample 00 05 00 Gradient 00 00 2 May 2011 14 06 admin Schedule Exit Prepare Isocratic Flow Thermo Scientific The
67. Pressure sensor S Lo Flow Mixing Tee sensors l sensors Aand B Three syringe pumps Thermo Scientific EASY nLC 1000 User Guide 5 1 Introduction Hardware Components Components Behind the Left Panel You can access the integrated computer and the autosampler needle fitting that connects to the needle guide by removing the left side panel of the instrument see Figure 5 Figure 5 Internal features behind the left panel ii Integrated computer Needle tubing Needle guide Autosampler Enclosed refrigerated sample compartment 6 EASY nLC 1000 User Guide Thermo Scientific Back Panel Thermo Scientific 1 Introduction Hardware Components The system communication contact closure and power line connections are on the back panel of the instrument see Figure 6 Figure 6 Back panel of the EASY nLC instrument 9 9990990999909000090909000 090008 9709009 PRO YEON eeeeceeeeeerocoeco soe fe eeeeee eeeseeseerecrococe ooo eeceeccecee ras OA 7 i si 2 Qi wv gt IN3 OUT3 IN2 OUT2 IN1 OUTI v 9999999 v900999 e U py HARD 9999999990999 009099 DRIVE This device complies with Part 15 of the FCC Rules Operation is subject to the following two conditions 1 this device may not cause harmful interference and 2 this device must accept any interference received including interference that may cause undes
68. Software Creating a Method 2 Press the Flow box to set the flow rate at which the autosampler picks up sample Range 0 to 40 pL min Set the speed according to the sample viscosity and accuracy needed For aqueous solutions 20 p L min is a good starting point Tosetupthe sample loading parameters 1 In the Sample Loading area press the Volume box and enter the volume of solvent A to be used to load the sample from the sample loop onto the precolumn or analytical column in a one column system Range 0 to 137 Normally it is sufficient to load the precolumn with two times the sample pickup volume 2 pL 2 Press the Flow box and enter the flow rate for sample loading onto the precolumn or analytical column in a one column system If you leave the Flow box empty the pump operates at the set pressure Range 0 to 100 Tip The application accepts values from 0 to 100 pL min but the IFC algorithm see Intelligent Flow Control on page 26 prevents the flow rate for the sample loading step from exceeding 25 pL min based on the back pressure produced by the system tubing alone without the columns attached Use the column equilibration scripts to determine the appropriate flow rate for your application 3 Press the Max Pressure box and set the maximum allowed pressure If you leave the Max Pressure box empty the pump operates at the set flow as long as it is below the instrument pressure of 1000 bar Range
69. TANT For the autosampler to determine the appropriate depth for the needle the wash bottle in position W4 must contain the needle wash insert 4 Remove the left side panel so that you can watch the movement of the needle To calibrate the wash bottle and extra vial positions go to Calibrating the Wash Bottle and Extra Vial Positions on page 129 Calibrating Plates For information about selecting or creating a plate format see Managing Plate Formats on page 121 IMPORTANT When the calibrating the XYZ robot for vial or microwell plates make sure to remove the vial caps or plate covers Keeping the caps or covers on makes the needle susceptible to bending Calibrating plates requires determining the xyz positions for the top left and bottom right vial or well Table 20 lists the top left and bottom right positions for the three plate formats Table 20 Top left and bottom right positions on the plate formats Plate format Top left position Bottom right position 6x8 Al F8 8x12 Al H12 16x 24 Al P24 To calibrate plates 1 If you have not already done so prepare the autosampler for the plate calibration routine see To prepare the autosampler for the plate calibration routine on page 124 2 Open the Autosampler Plate Calibration dialog box as follows a Press Maintenance gt Devices b In the Devices list select the autosampler c Press the Tools tab d In the Plate area press Calibrate
70. Valve rotors and stators All bottles and lids All sample vials microtiter plates and associated lids and mats Columns supplied by Dionex a part of Thermo Fisher Scientific Fuses Autosampler needle Thermo Scientific EASY nLC 1000 User Guide 193 C Consumables and Replacement Parts Solvent System Schematic Solvent System Schematic The pump and valve compartment of the EASY nLC instrument contains all the flow lines between the components see Figure 120 on page 195 In addition to pumps and valves the solvent delivery and waste system includes several filters and four check valves The two check valves on each solvent line ensure that solvent is drawn from the solvent bottles and ejected to waste without switching valve positions Table 28 lists the tubing requirements and identifies the tubing components shown in Figure 120 The Low Pressure Solvent Line Kit P N LC230 contains the Tees check valves and low pressure solvent lines to connect one pump A or B to the waste system and to its corresponding solvent bottle and six port valve The EASY nLC 1000 Flow Line Kit P N LC570 contains all of these flow lines The stainless steel tubing is prebent Table 28 Tubing requirements ID Connections Tubing Part number 1 Pump outlet to pressure sensor inlet Stainless steel 250 um ID 150 mm length LC512 2 Pressure sensor outlet to valve A or B Stainless steel 250 um ID 150
71. a code To contact Customer Service for ordering information For North America see Customer Service Information for North America on Page xvi For Europe see Customer Service Information for Europe on page xvii For Australia and Asia see Customer Service Information for Australia and Asia on page xx Customer Service Information for North America Table 1 lists the Customer Service information for North America Table 1 Customer Service information for North America North America United States Phone 1 800 532 4752 toll free Fax 1 877 373 4006 toll free E mail us customer support analyzegthermofisher com Address 1400 North Point Pkwy 10 West Palm Beach FL 33407 Canada Phone 1 800 530 8447 toll free Fax 1 905 890 9161 E mail us customer support analyzegthermofisher com Address 2845 Argentia Road Unit 4 Mississauga Ontario L5N 8G6 xvi EASY nLC 1000 User Guide Thermo Scientific Preface Customer Service Information for Europe Table 2 lists the Customer Service information for Europe Tip When calling from a different city or area code within the same country the dialing sequence is as follows 0 city or area code local phone number Table 2 Customer Service information for Europe Sheet 1 of 3 Europe Austria Phone Fax E mail Address 43 1 333 50 34 0 The city code for Vienna is 1 43 1 333 50 34 26 service sid austria thermofisher
72. a is 76 31 76 581 09 61 service sid benelux thermofisher com Takkebijsters 1 NL 4817 BL Breda Thermo Scientific Preface Table 2 Customer Service information for Europe Sheet 3 of 3 Norway see Sweden Norway and Finland Spain Phone Fax E mail Address 34 91 484 5965 The city code for Madrid is 91 34 91 484 3598 service sid spain thermofisher com C Valportillo I n 22 1a Planta Edificio Caoba ES 28108 Alcobendas Madrid Sweden Norway and Finland Phone 46 8 556 468 20 The city code for Stockholm is 8 Fax 46 8 556 468 08 E mail service sid nordic thermofisher com Address Pyramidbacken 3 S 141 75 Kungens Kurva Stockholm Sweden Switzerland Phone 41 61 716 77 40 The city code for Basel is 61 Fax 41 61 716 77 20 E mail service sid ch thermofisher com Address Neuhofstrasse 11 4153 Reinach United Kingdom Phone 44 870 241 1034 toll free phone number from outside the United Kingdom Fax 44 1442 233 667 The city code for Aldbury Hertfordshire is 1442 E mail service sid hemel thermofisher com Address Stafford House 1 Boundary Park Boundary Way Hemel Hempstead Hertfordshire HP2 7GE EASY nLC 1000 User Guide xix Preface Customer Service Information for Australia and Asia Table 3 lists the Customer Service information for Australia and Asia Tip When calling from a different city or area code within the same country the dialing sequ
73. a of the Configuration gt Connections page Table 12 Contact closure cables Description Part number Thermo Fisher contact closure cable LC160 ABI MDS Sciex contact closure cable LC161 Bruker Agilent contact closure cable LC162 Waters Micromass contact closure cable LC163 Varian contact closure cable LC164 Varian is now a part of Agilent Technologies Inc EASY nLC 1000 User Guide 39 2 Installing the EASY nLC Instrument Back Panel Connections Connecting the Ethernet Communication Cables How you set up the Ethernet communication cables depends on the type of communication you are trying to establish Follow the appropriate procedure to set up communication between the EASY nLC system and the data system computer the intranet for data exchange or the remote support server Setting Up the Ethernet Connections to the Data System Computer Setting Up the Ethernet Connection to a Local Network for Data Exchange Setting Up the Ethernet Connection to the Support Server Setting Up the Ethernet Connections to the Data System Computer For an LC MS system with an EASY nLC system and a Thermo Scientific mass spectrometer you operate the system from a data system computer with the Xcalibur data system and the device drivers for the EASY nLC system and a Thermo Scientific mass spectrometer Note You can create instrument methods and injection sequences submit and process injection sequences an
74. accounts adding new users 65 acetonitrile solvent requirements 74 adapter plate replacing 120 admin folder accessing 42 63 admin changing password 64 analytical column column setup options 8 equilibration script 166 equilibration step method 16 installing 83 preparation for use 89 application version 49 Australia and Asia customer service for xx Automatic Flow Control AFC description 25 autosampler calibration 119 checking sample pickup 160 manual control 146 sample pickup method parameters 94 Sample Pickup script 131 Torque script 176 tray compartment accessing 3 troubleshooting 136 wash step method 23 100 back panel instrument 7 37 150 back pressure analytical column rating 166 precolumn rating 165 testing 175 Back Pressure script 175 backup system 68 Thermo Scientific batches editing on the Home gt Queue page 114 setting up and scheduling 103 starting 108 troubleshooting 134 beaker waste 4 C calibrating autosampler 119 flow sensors 178 plates 125 carryover reducing 101 specification 28 changing the administrator password 64 checking sample pickup 131 solvent levels 159 valves 160 Column Out tubing 4 9 84 columns See analytical column or precolumn compliance electromagnetic xxi components system 2 troubleshooting 138 computer damage cause of 38 configuring devices 70 global settings 70 RePlay 186 connecting add ons 44 contact closure cable 39 mouse and keyboa
75. ack panel of the EASY nLC instrument see Figure 114 Figure 114 RePlay device connection to the EASY nLC contact closure port RePlay device back panel Remote cable connector P Bus A IN3 OUT3 IN2 OUT2 IN1 OUTI EASY nLC contact closure port LCQ Fleet LXQ or LTQ M MS detector E right side panel Pej pheral Control Peripheral control port 184 EASY nLC 1000 User Guide Thermo Scientific A External Devices Connecting the RePlay Device to the EASY nLC Instrument 3 Connect the solvent lines to the valve on the front panel of the RePlay device see Figure 115 as follows Connect the output end of the EASY nLC analytical column to position 5 of the RePlay valve Connect position 4 of the RePlay valve to the secondary column emitter Note For more information about connecting and using the RePlay device refer to the Advion RePlay Users Manual supplied by Advion Biosystems Inc Figure 115 Valve connections for the standard plumbing configuration Plugged Capture Cartridge ae Secondary column emitter EASY nLC column Flow sensor Waste 4 Turn on the EASY nLC instrument Thermo Scientific EASY nLC 1000 User Guide 185 A External Devices Adding the RePlay Device to the EASY nLC Device List Adding the RePlay Device to the EASY nLC Device List 186 EASY nLC 1000 User Guide To add the RePlay device to the device l
76. ample loop The range depends on the sample loop size For the 20 pL sample loop the range is 30 25 to 100 75 pL For a more thorough wash of the needle and loop select the Custom Wash check box Use this option to set up a user definable procedure for washing the loop and needle Tip The custom wash program automatically ends with a preset volume of solvent A from bottle W3 The Custom Wash table consists of three user editable parameters see Table 18 The order column lists the order in which the autosampler performs the steps To change the order use the Up and Down buttons Table 18 Custom wash parameters Parameter Order Description Defines the order of the wash steps To change the order of the wash steps use the Up and Down buttons Source Specifies the wash solvent source for the current wash step Selections Bottle 1 Bottle 2 or Bottle 3 Bottles 1 and 2 contain custom wash solvents Bottle 3 contains solvent A Volume Specifies the volume that pump S draws from the source location for each wash cycle To avoid drawing solvent into pump S for a 20 pL sample loop the maximum volume is 28 pL needle volume loop volume 2 pL Cycles Specifies the number of wash cycles for the wash step For each cycle the autosampler draws the specified volume of wash solvent from the specified source and then ejects the wash solvent into wash bottle 4 When the custom wash has ended
77. ampler s XYZ Robot Managing Plate Formats Figure 78 Removing the vial adapter plate before installing the microwell plate adapter plate Mounting stud 4 Install the other adapter plate in the autosampler Managing Plate Formats Follow the appropriate procedure to use an existing plate format create your own plate format or delete a plate format you no longer need To create a new plate format 1 Open the Tools view for the autosampler as follows a Press Maintenance Devices b In the Devices list select the autosampler device c Press the Tools tab Figure 79 shows the Tools view for the autosampler Thermo Scientific EASY nLC 1000 User Guide 121 7 Calibrating the Autosampler s XYZ Robot Managing Plate Formats Figure 79 Tools view for the autosampler Thermo Home Batch Setup M SCIENTIFIC hod Editor Maintenance Configuration Scripts Devices Log Book Add Device Suppor Remove Device Devices 1 EASY nLC HPLC HPLC Piston Pump flow feedback Pump A Piston Pump wi flow fee Name Type Cooled Autosampler ASC Autosampler Autosampler Cooled Autosampler ASC Autosampler r Plate r Vials Wash New Calibrate Current Vials Job 00 00 00 Manipulator 6x8 Vials Reset 23 aug 2010 12 38 admin Copy To Calibrate Selected plate format button button 2 Do one of the following To create a n
78. and chemicals review the specific hazards for each substance by reading the MSDSs provided by the manufacturer When working with solvents and chemicals wear the appropriate safety gear CAUTION When working with solvents wear safety glasses CAUTION When working with solvents wear safety gloves Thermo Scientific EASY nLC 1000 User Guide 73 5 Preparing the EASY nLC Instrument for Use Preparing Solvent Bottles and Waste Containers Before shipment the EASY nLC system is flushed with methanol CAUTION Methanol CAS number 67 56 1 is highly flammable and toxic by inhalation ingestion or skin absorption Take appropriate measures to protect yourself and your equipment Make sure that the mobile phases are miscible with methanol or flush the A and B solvent lines with an intermediate solvent To set up the two bottles that contain the mobile phase solvents the four autosampler bottles and the waste beaker follow these topics Solvent Requirements Solvent A and B Bottles Autosampler Wash Bottles and Waste Beaker Solvent Requirements The installation solvents for the EASY nLC 1000 system are as follows Solvent A 0 196 formic acid in water Solvent B 0 196 formic acid in acetonitrile Wash solvent 3 0 1 formic acid in water To prepare these solutions order the appropriate LC MS grade solvents or the pre blended solutions Table 16 lists the solvents that you can order from Thermo Fisher Scientific Table 16 S
79. and disconnect the instrument from line power Keep the top cover on while operating the instrument Do not remove protective covers from PCBs Chemical This instrument might contain hazardous chemicals Wear gloves when handling toxic carcinogenic mutagenic or corrosive or irritant chemicals Use approved containers and proper procedures to dispose waste oil Heat Before servicing the instrument allow any heated components to cool Fire Use care when operating the system in the presence of flammable gases Eye Hazard Eye damage could occur from splattered chemicals or flying particles Wear safety glasses when handling chemicals or servicing the instrument General Hazard A hazard is present that is not included in the above categories Also this symbol appears on the instrument to refer the user to instructions in this manual When the safety of a procedure is questionable contact your local Technical Support organization for Thermo Fisher Scientific San Jose Products EREE US OHWSIMRETERL Ak Att DTE XT RTF EER DGUUOREIRBIEL MRED OTHORMLTFEY EMH AEA LT xXCBASEURHUZUCCTEvs 7Y hR RORMBA 7 IAE STRUCT SV LEDER ERAAN PELTOA HEB 35 0 ET BEE EP ATE PAE fe MRE LOHDSRHERYVRIM RAE MALTFAY EMOANN MEODSBL FMEHRALTFS M WAS ROKMMIMADOL HO TH ORF EBEAOTIS AI MED HADES SBM CL AF ALMETSBSIL KORE EMOTE RET BER CFR RLF ATK L TRE 5017 5 fep TED 5 0 E T EFMRORMYORV HSVILHMBORT SICH
80. anet When you connect the EASY nLC system to a data system computer through an Ethernet switch you can access these files from the data system computer When you connect the EASY nLC system to a data system computer through an Ethernet switch and connect the data system computer to a laboratory LAN port with intranet access you can access these files from other computers on the intranet Note When you control the EASY nLC system in the stand alone mode the chromatographic methods and batches reside on the integrated computer hard drive When you control the EASY nLC system from a data system computer your instrument methods and sequences created with the data system reside on the data system computer To access the files on the EASY nLC system from another computer on the intranet 1 Do one of the following Fora stand alone EASY nLC system use a shielded Ethernet cable to connect the LAN port on the back panel of the EASY nLC instrument to a laboratory LAN port with intranet access Foran EASY nLC system that is part of a Thermo Scientific LC MS system connect the Ethernet cables as described in Setting Up the Ethernet Connections to the Data System Computer on page 40 2 Set up the software connection for the EASY nLC system as described in Setting Up the Local Area Network Connection on page 61 With a Thermo Scientific LC MS system you can access the files on the EASY nLC system from the data system co
81. ardware parts in the system Position pressure and flow for pumps A B and S Valve positions 1 2 1 6 or centered Percentage of solvent B being delivered Actual flow being measured by the flow sensors Note When pumps A and B are delivering solvent to the mixing Tee the flow sensors measure the actual flow rate During the refill A B step pumps A and B are drawing solvent from the solvent bottles Samples to be analyzed plus their current status Current sample and job plus the next sample and job Current step in the sample run When the batch starts the green START button is grayed out and the red STOP button becomes active When the instrument is running three counters measure the time for job sample and gradient 110 EASY nLC 1000 User Guide Thermo Scientific 6 Running Samples Using the Integrated Software Monitoring the Run Using the Graphs Page in the Home Menu The Graphs page displays up to four graphs with time dependent data for the currently active sample see Figure 72 Figure 72 Graphs page of the Home menu Thermo Home Batch Setup Method Editor Maintenance Configuration SCIENTIFIC j f f Overview Pump A X Valve A Graphs Desired flow Real flow Pressure 1 000 0 300 000 09 POS 1 2 Queue y 250 000 0 200 000 0 7500 c S T a E 1500000 v S CENTER 100 000 0 sono S o z ri 3 500000 7 m u 0 0 200 50
82. ce 1 Press Maintenance Support The Support page of the Maintenance menu opens see Figure 92 on page 151 2 Insert the USB storage device into the connector panel on the back of the EASY nLC instrument Choose between one of two USB ports on the upper left side of the panel see Figure 94 Figure 94 USB port location on the back panel of the EASY nLC instrument Thermo Scientific EASY nLC 1000 User Guide 153 9 Remote Support Saving System Files on a USB Removable Storage Device 154 3 4 5 6 EASY nLC 1000 User Guide In the Log File Copy area select the To USB Removable Storage option Note When you select the To Home Directory option the EASY nLC system creates zip files in the admin folder For information about accessing the admin folder from another computer on your local network see To access the admin folder on the EASY nLC system s computer hard drive from another computer on the network on page 63 Press Copy Log Files When the copying is finished the following confirmation appears Copied successfully It is now safe to remove the USB storage Close Press Close and remove the USB storage device from the connector panel Insert the USB storage device into your computer Five zipped files appear on the USB storage device see Figure 95 Figure 95 Windows XP view of the files on the USB memory stick File Edit View Favorites Tools Help Q Back u
83. cess solvent A exits the venting Tee and passes through valve W to the waste beaker see Figure 8 Figure8 Flow path during the sample loading step for a two column setup EASY nLC 1000 system To the autosampler needle Column Out Stainless Venting Tee PEEK union tubing steel union with sleeves and emitter Precolumn Analytical column Waste In tubing re M Waste beaker Thermo Scientific EASY nLC 1000 User Guide 9 1 Introduction Column Setup Options One Column Setup A one column setup consists of an analytical column The Column Out tubing the Waste In tubing and the analytical column connect to the venting Tee Figure 9 shows the sample loading step for a one column setup with an analytical column During the sample loading step valve W is in the 1 2 position and excess solvent A exits through the emitter tip Tip When you install a one column setup select the One Column Setup check box in the EASY nLC device section on the Devices page of the Maintenance menu see Setting Up the Properties for the HPLC Device on page 70 When the One Column Setup check box is selected valve W remains in the 1 2 position during the sample loading step Excess solvent A exits through the emitter tip see Figure 9 Figure 9 Flow path for a one column setup during the sample loading step S To the autosampler needle x To pump S Column Out Venting Tee Analytical column PEEK union gt
84. corresponding check box in the Auto Continue column In the case shown in Figure 69 the admin 20100824 1714 job does not auto continue when the 6 x BSA 30min job is done EASY nLC 1000 User Guide 107 6 Running Samples Using the Integrated Software Starting Sample Acquisition Starting Sample Acquisition Before starting the sample acquisition make sure that the system is properly set up This includes having contact closure see Connecting to the Mass Spectrometer through Contact Closure on page 39 Also make sure that you have set up the mass spectrometer or any other detector to acquire data during the sample run Before starting a batch run consider running the maintenance script described in Test MS Connection on page 169 To start a batch run 1 Create a batch and submit it to the queue as described in the previous procedure 2 Press Home gt Overview The Overview page of the Home menu opens 3 Press START to start running the batch A message box opens prompting you to check that you have installed the sample plate filled solvent bottles A and B installed the W3 bottle with solvent A installed the W4 bottle with the needle insert and emptied the waste beaker see Figure 70 Figure 70 Start Queue message box EASY nLc Is plate ready Check buffer A andB Check waste container Check autosampler bottles f L S a Accept Cancel E J 4 Press Accept The instrument
85. ctions Per Sample on page 104 View List view Thermo Scientific View the batch job as a list of samples in the order of processing Each row in the table holds information about the position name and method for that position Editing the Running Batch on page 117 EASY nLC 1000 User Guide 53 3 Integrated Instrument Control Software Application Menu Structure Method Editor Menu Use the pages of the Method Editor Menu to set up the chromatographic methods for your samples see Creating a Method on page 100 Note If the method controls the Advion RePlay external device the Method Editor wizard includes six pages For information about setting up a method that includes the RePlay device see Appendix A External Devices Page Function Go to File View a directory tree of saved methods You Browsing for a Stored Method or Creating a can create or import new methods and create New Method File on page 92 or delete directories from this page Edit Method Editor wizard with five pages 1 5 Use page 1 5 of the Method Editor wizard to Starting the Method Editor Wizard and select the method that you want to edit and Selecting the Method to be Edited on to enter a description of the method page 93 2 5 Set up the sample pickup and sample Setting Up the Sample Pickup and Loading loading steps of the method Steps on page 94 3 5 Control the liquid chromatography gradient Bu
86. current saved coordinate The saved coordinates for the x and y axis appear on the left side of the slash the needle does not descend into the vial or well and the z axis value on the left side of the slash remains at 0 8 Repeat step 4 through step 6 on that vial or well 9 Press Save and then press Close to close the calibration dialog box 10 Replace vial caps and plate covers as necessary 11 Go to the next procedure to calibrate the W4 bottle position or reinstall the EASY nLC instruments left side panel IMPORTANT To maintain a stable temperature inside the tray compartment the left side panel must be installed 128 EASY nLC 1000 User Guide Thermo Scientific 7 Calibrating the Autosampler s XYZ Robot Calibrating the Wash Bottle and Extra Vial Positions Calibrating the Wash Bottle and Extra Vial Positions In addition to holding the sample trays the EASY nLC tray compartment holds four wash bottles W1 W4 and six extra vials V1 V6 To calibrate the W4 wash bottle position the extra vial positions or both 1 If you have not already done so prepare the autosampler for the extra vial and wash bottle calibration as described in To prepare the autosampler for the V1 and W4 calibration routine on page 124 2 Open the Autosampler Vials Wash Calibration dialog box as follows a Press Maintenance Devices b In the Devices list select the autosampler c Press the Tools tab below the Devices list d In t
87. d Software Creating a Batch To select wells A1 to P1 do the following a In the quadrant selection box press the first quadrant b Press the DOWN ARROW IL above the first column c In the quadrant selection box press the third quadrant 5 d Press the UP ARROW m below the first column Tip You can clear the vial or well selections by pressing them again 8 Press Add to link the selected vials or wells with the selected method 9 To save the batch do the following a Press Save The Save File dialog box opens b Ifyou have not already done so select the appropriate folder and enter a name for the batch C Press Save 10 Press Schedule see Figure 67 on page 105 to submit the batch to the queue 11 The application switches to the Queue page of the Home menu see Figure 69 Figure 69 Queue page of the Home menu showing the queued jobs Thermo Homes Batch Setup Method Editor Maintenance Configuration Overview Auto i Submitter Job name Duration Graphs continue 1 fadmin ladmin 20100824 1714 11 04 15 Job 00 00 00 24 aug 2010 17 14 gt es 3 3 If necessary move any scheduled batch in the job queue by selecting it and pressing Up or Down You can also delete batches from the Queue by selecting the batches and pressing Delete For a batch run to start automatically after the previous batch is finished you must select its
88. d by solvent composition changes For accuracy the AFC system requires a minimum pressure of 20 bar Figure 21 Schematic diagram of the AFC system Flow sensor A ia i a E A B mixing Tee Flow sensor B Thermo Scientific EASY nLC 1000 User Guide 25 1 Introduction Pump Flow Control Intelligent Flow Control The Intelligent Flow Control IFC system see Figure 22 is active during these processes The column equilibration and sample loading steps of a sample run The pressure buildup for pump B during the prepare gradient step The execution of the precolumn equilibration analytical column equilibration leak and backpressure scripts The IFC system uses output from both the flow sensors and pressure sensors A and B to regulate the flow from pumps A and B By controlling the flow rate with both a flow and pressure feedback system the IFC system enhances system performance as follows Reduces the loss of productivity caused by system stoppage related to overpressure for instance stoppage caused by viscous samples during the sample loading step Uses the pressure range of the system 0 1000 bar more effectively For example when you set a maximum pressure for the sample loading and column equilibration steps instead of a flow rate the system automatically adjusts the flow rate to the maximum acceptable value Builds the pressure rapidly during the prepare gradient step Figure 22 Schematic diagram o
89. d from the Exit Menu Thermo Scientific EASY nLC 1000 User Guide 63 4 Configuring the EASY nLC System Modifying User Permissions Changing the Administrator Password The EASY nLC application supplies a simple administrator password Consider changing it to a more secure password as soon as possible To change the administrator password 1 Log in as admin otherwise see Logging In to the EASY nLC System on page 57 2 Press Configuration gt Users The Configuration gt Users page opens Figure 39 Figure 39 Users page of the Configuration menu Thermo Home Batch Setup Method Editor Maintenance SCIENTIFIC Connections nie 2 escription Name Administrator PEE Network Administrator Time Password Backup Re enter Level Job 00 00 00 C g Graphs fr X Pump B v Gradient f Cooling 24 aug 2010 f g f ATUT Open Close New admin Exit 3 Press Open The Select User dialog box opens 4 In the User list select Admin 5 Enter the new password as follows a Press the Password box The Enter Password dialog box opens b Type a new password and then press OK 64 EASY nLC 1000 User Guide Thermo Scientific 4 Configuring the EASY nLC System Modifying User Permissions c Press the Re enter box The Enter Password dialog box opens d Type the password a second time to confirm it and then press O
90. d monitor the instrument status and injection progress with the external data system The external data system does not include maintenance scripts or direct controls for the EASY nLC system To perform tasks such as flushing air from the LC system you must use the built in touch screen software Figure 24 on page 35 and Figure 25 on page 37 show a typical benchtop setup for an LC MS system with an EASY nLC system a Thermo Scientific mass spectrometer a data system computer and an Ethernet switch The EASY nLC system and the Thermo Scientific mass spectrometer communicate with the data system computer through an Ethernet connection routed through an Ethernet switch connected to the data system computer To make the Ethernet connections use the shielded Ethernet cables supplied in the instrument accessory kits When you order the EASY nLC system with a Thermo Scientific mass spectrometer the Ethernet card for the LC MS system is preset at the factory to this IP address 172 16 0 101 While installing the LC or LC MS system your local Thermo Fisher Scientific field service engineer checks the IP address setting If the data system computer has a second network card you can connect the data system computer to the intranet After you connect the data system computer to the intranet you can view the files EASY nLC systems computer hard drive from other computers on the intranet When you also set up a remote desktop connection you can monito
91. de 99 6 Running Samples Using the Integrated Software Creating a Method Setting Up the Autosampler Wash Step Autosampler Wash Use the Method Editor gt Edit 5 5 page for setting up the autosampler washing procedures see Figure 65 The EASY nLC instrument conducts the wash while the gradient is running Use the standard wash step or set up a custom wash cycle as described in these topics e Autosampler Wash Custom Wash For most samples in low concentrations flushing the needle and loop with solvent is sufficient You can set the amount of solvent for this action in the Flush Volume box Use 100 pL as the default flush volume Note The minimum flush volume that you can set is the loop volume needle volume 1 pL Figure 65 Edit 5 5 page of the Method Editor wizard Thermo Home Eeoa Meth or EEEE Configuration SCIENTIFIC File E Name BsA4omin 40 min Open Close Save h Autosampler wash Flush volume 100 0 ul O Custom wash Order Source Volume Cycles Job 00 00 00 11 May 2011 Exit e 5 5 gt 100 EASY nLC 1000 User Guide Thermo Scientific Custom Wash Thermo Scientific 6 Running Samples Using the Integrated Software Creating a Method To set up a standard wash step 1 Do not select the Custom Wash check box 2 In the Flush Volume box type the volume of solvent A from wash bottle 3 that the autosampler uses to flush the needle and the s
92. e Maintenance menu but you can change the selection for a window from its corresponding list These graphs help you to monitor the job Wait for the jobs to end the flush air job continues until the flush air volume values are below the specified threshold Note While a maintenance job or a script is running you cannot start other jobs or scripts Thermo Scientific 5 Preparing the EASY nLC Instrument for Use Installing Columns Installing Columns The EASY nLC 1000 instrument ships with a two column assembly see Figure 53 Figure 53 Two column assembly Stainless steel union Venting Tee PEEK union Precolumn Analytical column 2 cm length 15 cm length Table 17 lists the columns fittings and unions that make up the two column assembly Table 17 Columns and column fittings Item Description Precolumn Acclaim PepMap 100 2 cm length 75 um ID trap column with 3 um particle size C18 column packing nanoViper fittings Dionex part number 164705 Analytical column with Acclaim PepMap RSLC 15 cm length 50 pm ID nanoV iper fittings 2 um particle size C18 column packing Dionex part number 164704 PEEK union with 0 76 in length 0 035 in thru port for 1 32 in OD tubing fittings Stainless steel union For 1 16 in OD tubing part number SC904 Venting Tee Stainless steel 0 15 mm bore for 1 16 in OD tubing part number SC901 PEEK sleeves for 330 um ID 1 32 in OD par
93. e 111 Flow Sensors script parameters Thermo Home Batch Setup Method Editor Aaintenance Configuration SCIENTIFIC i No graph Support Output Devices Parameter v Value 11 May 2011 Exact inspection Fast inspection m graph J 12 54 admin Schedule Exit Calibrate Reset Pressure Sensor Job 00 15 48 This script auto zeroes the pressure sensor IMPORTANT Performing this script incorrectly will compromise the performance of the instrument Contact your local Thermo Fisher Scientific representative before running this script Thermo Scientific EASY nLC 1000 User Guide 179 10 Maintenance Keeping Service Records Keeping Service Records Use the Maintenance gt Log Book page to electronically enter all the service actions that you perform on the instrument To record a service action 1 Press Maintenance Log Book The Maintenance Log Book page opens see Figure 112 Figure 112 Log Book page of the Maintenance menu tab Thermo SCIENTIFIC Home Batch Setup Method Editor Configuration Scripts Log record contains one term per line Time From Log book 3 Log Book First record Queue job Y S Time To pot Last record User Devices Fs 7 f Search Search result Timestamp Source Summary 05 08 2010 17 52 48 i Batch admin 20100805 1751 05 08 2010 17 44 34 i Batch admin 20100805 1742 19 07
94. e B and the autosampler bottle in position W3 and the bottles in position W1 and W2 if used Refill if necessary Tip You can also inspect the purity of the solvent to ensure no visible precipitates have formed that might lead to blockages in the pump line 2 Visually inspect the autosampler wash bottle in position W4 and the waste container in the pump compartment and empty if necessary 3 Run the Purge Solvent and Flush Air scripts with two purge iterations or until flush volumes fall below 12 pL Thermo Scientific EASY nLC 1000 User Guide 159 10 Maintenance Weekly Maintenance Weekly Maintenance Because the vapor pressures of formic acid water and acetonitrile differ the solvent composition changes over time Refill the solvent bottles to maintain a consistent solvent composition Quarterly Maintenance Perform the following procedures quarterly every three months t 160 EASY nLC 1000 User Guide To check the back pressure Run the Back Pressure script for both solvents see Test Back Pressure on page 175 IMPORTANT The script evaluates the back pressure based on using 99 9 water for solvent A and 99 9 acetonitrile for solvent B To check the cooler temperature Check that the plate temperature is at its set point or approximately 18 to 20 C 64 to 68 F below ambient temperature readout on the Home gt Overview page To check the autosampler pickup function Run
95. e instructions in Creating a Method on page 92 Tip To use different methods in the same batch select the method select the vial or well positions that you want to run with this method see step 7 and then press Add 7 Select the vials or wells that contain the samples that you want to run in the order that you want the system to process them To select an individual vial or well press the vial or well position in the graphic To select an entire column press the DOWN ARROW above the column For example press the arrow labeled 1 to select all the vials A1 to F1 or wells Al to H1 from the first column and first quadrant of a 384 well plate To select the well positions on a 384 well plate use the quadrant selection box to move between quadrants see Figure 68 From left to right and top to bottom the four quadrants are Al to H12 A13 to H24 I1 to P12 113 to P24 Figure 68 View Rack view for a 384 well plate Close A f f Add Injections 1 Browse methods J Batch Extensions gt we JOOOOOOCOOOOOO Ka J OO0OOCOOOCDOOD FIO OUOODgOUggoag elc lm N mENMSOoOoooooooooo amp 3 O 0 999900000000 43110 eR OCOOocooooooo Kaf Batch 0 3000000000000 KJO pud ogoOO00000n09020 eo V5 Q v6 rex Titra 84 trm Plate button L Quadrant selection box 106 EASY nLC 1000 User Guide Thermo Scientific Thermo Scientific 6 Running Samples Using the Integrate
96. e leak test press the cell in the Value column and make your selection from the list see Figure 106 Note You cannot perform the leak test for pump S as it does not operate under pressure during normal batch execution Figure 106 Leaks script parameters Thermo Home Batch Setup Method Editor Aainter E Configuration SCIENTIFIC Scripts Category Name f No graph X Log Book Test Leaks X Support Description Devices Parameter f us graph Job 00 15 48 11 May 2011 12 46 Exit 3 For a system leak test connect the Column Out line to the Waste In line using the stainless steel union P N SC904 as shown in Figure 105 on page 172 For information about troubleshooting system leaks contact your local Thermo Fisher Scientific service representative Thermo Scientific EASY nLC 1000 User Guide 173 10 Maintenance Maintenance Scripts Test Valve Check The Valve Check script performs a self test for the selected valves Use this script when valves begin to move slowly or cannot reach the required positions and after exchanging valve parts rotor or stator IMPORTANT Only use this script when instructed to by Thermo Fisher Scientific Make sure to record any numbers that the script generates To set the Valve Check script parameters 1 Select the Valve Check script as follows a Press Maintenance gt Scripts b In the Category list select Test
97. e loop as it enters and exits valve S through ports 4 and 3 respectively The Autosampler Wash and Refill S step occur in parallel with the Gradient step Figure 15 Gradient step with valve A and valve B in position 1 6 and autosampler wash step with valve S in position 1 2 coor ooon Pump S W3 bottle W4 bottle A Pump A Autosampler needle I _ Pressure Sensor Sample loop Connected to check valves N Flow sensor d Mixing Tee k P Y l Column Out line TT Pressure Flow Sensor sensor Waste In line Connected to check valves e Pump B Solvent A HE Solvent B MEE Sample 20 EASY nLC 1000 User Guide Thermo Scientific 1 Introduction Solvent Delivery and Sample Pickup Systems Sample Pickup and Autosampler Wash System Pump S draws and delivers solvent for these sample run steps Pickup Sample Step e Autosampler Wash Step Pickup Sample Step The Pickup Sample step includes this sequence of actions Action 1 Pump S moves to a fixed position filled with approximately 100 pL of solvent for a system with a 20 pL sample loop by either dispensing excess solvent to the W4 bottle or drawing solvent from the W3 bottle Pump S draws 1 pL of air into the needle The XYZ robot moves the needle holder to the specified sample vial or microplate well location The needle descends into the sample solution Pu
98. ector setup Solvent lon source LTO Series lines monitor MS detector Data ind EASY nLC 1000 computer system Ethernet z 2 l E switch 9 TA Q Contact closure cable Power line from the EASY nLC system connection to the MS detector Ethernet cable from Ethernet cable from Ethernet cable from the Ethernet switch the EASY nLC system the MS detector to to the data system computer to the Ethernet switch the Ethernet switch Intranet connection Ethernet jack Thermo Scientific EASY nLC 1000 User Guide 35 2 Installing the EASY nLC Instrument Laboratory Requirements Internet Access For online support and monitoring remote support provide Internet access for the EASY nLC system within reach of the laboratory benchtop IMPORTANT The EASY nLC system uses Secure Shell SSH a network protocol for secure data communication to connect to the support server which uses the Linux operating system Port 22 is the standard TCP port for SSH programs To use the remote support feature the firewalls for your local network must allow outgoing TCP IP traffic from the EASY nLC system to the support server at IP address 195 41 108 93 port 22 For information about using
99. ectrometer Setting Up the Local Area Network Connection e Modifying User Permissions Modifying the Time Settings Making System Backups Setting Up the Properties for the HPLC Device Setting Up Communication with the Mass Spectrometer After the EASY nLC injects sample onto the analytical column it signals the mass spectrometer to start data acquisition IMPORTANT Before you connect the EASY nLC instrument to a mass spectrometer make sure that the protective grounding is shared between the instruments To set up the mass spectrometer connection 1 Press Configuration gt Connections The Connections page of the Configuration menu opens see Figure 36 Thermo Scientific EASY nLC 1000 User Guide 59 4 Configuring the EASY nLC System Setting Up Communication with the Mass Spectrometer 60 EASY nLC 1000 User Guide Figure 36 Connections page Thermo Home Batch Setup Method Editor Maintenance Users Mass Spectrometer i iil a Instrument Thermo Finnigan LTQ OrbiTrap 5 Network Time Communications Use Contact Closure X Backup Contact Closure Settings EASY nLC Thermo Finnigan LTQ OrbiTrap Protocol Two way J Peripheral Control OUTI State at start Open J INT Jsstart In OUT2 Ready Out Start at Gradient J IN2 Ready In Job 00400 OUTS sStart Out Signal width abe TIL GND 23 aug 2010 12 38 f f admin Default Exit From the Instrument l
100. edle Up Down area 5 adjust the needle height as follows a Using the big step button LY lower the needle until it reaches a level of 2 3 mm 0 08 0 12 in above the vial or well b Using the small step button ib slowly lower the needle until it reaches the bottom of the vial or well Note The O ring at the top of the needle holder rises a little when the needle reaches the bottom of the vial or well see Figure 82 Figure 82 O ring pushed slightly above the needle holder Observe when the O ring moves up a bit or gently hold needle tubing as you press the step button c Press the small step button T once to raise the needle slightly off the bottom of the vial or well The appropriate needle height is one small step higher than the bottom of the vial or well 6 When you are satisfied with the current xyz coordinate for the vial or well press Capture The color of the vial or well on the plate graphic changes from green to red and the position readbacks for the xyz axes are unpopulated see Figure 85 Thermo Scientific EASY nLC 1000 User Guide 127 7 Calibrating the Autosampler s XYZ Robot Calibrating Plates Figure 83 Plate calibration captured for the A1 position Autosampler Plate Calibration Calibrate Plate HT MTP Needle In Out Needle Up Down E LeftRight 7 Press the green vial or well in the lower right corner of the plate view The needle moves to the
101. elg SCIENTIFIC File ape eS Gradient Time Duration Flow B 250 01 300 0 Y 100 275 01 225 0 200 0 gt z S 600 3 E 175 0 2 150 0 up E m 125 0 2d ao E 100 0 30 75 0 Job 00 00 00 50 0 oe 25 0 10 0 0 0 D 5 0 15 20 25 3d 735 AD Time min w 11 May 2011 ec c 11 19 Add g admin Exit 3 5 Note When you press a cell in the gradient table the keypad dialog box opens To build a gradient 1 In the first row of the gradient table do the following a Press the Flow column cell and enter 300 nL min Then press ACCEPT b Press the 96 B column cell and enter 10 96 Then press ACCEPT The gradient is now set to start at 300 nL min and 10 B 2 Press ADD to add another row 96 EASY nLC 1000 User Guide Thermo Scientific 6 Running Samples Using the Integrated Software Creating a Method 3 In the second row of the gradient table do the following a Press the Duration column cell and enter 20 minutes Then press ACCEPT b Press the Flow column cell and enter 300 nL min Then press ACCEPT c Press the B column cell and enter 40 Then press ACCEPT Press ADD to add another row In this new row set duration to 5 min flow to 300 nL min and 96 B to 100 Press ADD to add another row N A wv A In this new row set the duration to 15 min flow to 300 nL min and B to 100 Note You do not
102. empty solvent into the waste beaker to the right of the autosampler compartment and deliver solvent by way of a pressure sensor and a flow sensor to the mixing Tee The corresponding six port valves low pressure check valves and pressure sensors control the solvent flow Note Flow sensors provide flow control for pumps A and B The solvent flow from pump S is not controlled by a flow sensor These topics describe the pump A and pump B delivery systems Filling and Emptying Pumps A and B Directing Solvent Flow to the Mixing Tee and through Valve S Thermo Scientific EASY nLC 1000 User Guide 13 1 Introduction Solvent Delivery and Sample Pickup Systems Filling and Emptying Pumps A and B When valve A or B is in the 1 2 position the corresponding check valves control the direction of the solvent flow see Figure 12 When the pump begins to draw solvent from the solvent bottle the check valve opens to the solvent bottle and closes to the waste beaker When the pump begins to empty the check valve opens to the waste beaker and closes to the solvent bottle Figure 12 Valve A in position 1 2 Pump A drawing solvent from solvent bottle A Pump A emptying to waste Pressure sensor valves valves Solvent A Solvent A Waste beaker Waste beaker 14 EASY nLC 1000 User Guide Thermo Scientific 1 Introduction Solvent Delivery and Sample Pickup Systems Directing Solvent Flow to t
103. ence is as follows 0 city or area code local phone number Table 3 Customer Service information for Australia and Asia Australia and Asia Australia Phone 61 3 9757 4300 The area code for the South East region of Australia is 3 Fax 61 9763 1169 E mail analyze augthermofisher com Address PO Box 9092 5 Caribbean Drive Scoresby Victoria 3179 Japan Phone 81 45 453 9100 The city code for Yokohama is 45 Fax 81 45 453 9110 E mail analyze jp thermofisher com Address C 2F 3 9 Moriya cho Kanagawa ku Yokohama 221 0022 P R China Beijing Phone 86 800 810 5118 toll free or 86 400 650 5118 toll free Fax 86 10 88370548 The city code for Beijing is 10 E mail analyze cn thermofisher com Address 7th Floor 7F Tower West Younghe Plaza No 28 Andingmen East Street Beijing 100007 P R China Shanghai Phone 86 800 810 5118 toll free or 86 400 650 5118 toll free E mail analyze cn thermofisher com Address Building 6 No 27 Xin Jin Qiao Road Shanghai 201206 XX EASY nLC 1000 User Guide Thermo Scientific Preface Declaration of Conformity U S Safety and EMC Electromagnetic Compliance Standards Safety This instrument has been reviewed for compliance with standard UL 61010 1 Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements EMC This device complies with Part 15 of the FCC Rules Operation is subject to the
104. ent s unique network identifier it is labeled on the connector panel on the back of the instrument The identifier is a series of numbers and letters and might look like this MAC address 00 E0 4B 07 89 65 External users can now access the file server in the EASY nLC system to look at log files for example Microsoft Windows Explorer might display the file server as shown in Figure 38 Figure 38 File server access through Windows Explorer BM 722050 Biadmin ERES ay File Edit View Favorites Tools Help Qe x B yo Search E gt Folders EJ Address K Yiles 172 22 50 18 admin MPE Name Size Type Date Modified j Galusers File Folder 19 05 2005 11 16 Type amp amp E My Documents gt batches File Folder P a dd ress E E My Computer C batchLog File Folder S my Network Places E maintenanceLog File Folder here amp Entire Network E methods File Folder amp y Microsoft Terminal Services QsystemLog File Folder Microsoft Windows Network 2 statistics 20050519 110358 1KB XML Document 19 05 2005 11 04 gy Proxeon S gy Hplc Gy Hple E Proxeon HPLC 172 22 50 18 EJ 2 admin 62 EASY nLC 1000 User Guide Thermo Scientific 4 Configuring the EASY nLC System Modifying User Permissions To access the admin folder on the EASY nLC system s computer hard drive from another computer on the network 1 Type the IP address of the instrument in the Address list for Windows Explorer for exam
105. ent Bottles and Waste Containers on page 73 Note You cannot execute maintenance scripts when the EASY nLC instrument is running batches Figure 49 Scripts page of the Maintenance menu Thermo Home Batch Setup Method Editor SCIENTIFIT fe _ No graph Log Book repare Purge solvent Support Configuration Parameters Output Devices Purge solvent from pumps Make sure to check solvent levels before running f us graph J Job 00 00 21 11 May 2011 11 24 admin Schedule Exit The green START button is active when a job or script is ready to execute After you press START the STOP button replaces the START button and remains active until the job or script ends During execution you can terminate a job or script by pressing the red STOP button When the Schedule button is available you can automate the start of the Flow Sensor calibration script and all of the scripts in the Prepare category You cannot schedule the remaining scripts because they require supervision or hardware changes to the system 78 EASY nLC 1000 User Guide Thermo Scientific 5 Preparing the EASY nLC Instrument for Use Purging and Flushing the Pumps Purging and Flushing the Pumps Because the EASY nLC pumps are purged with methanol before delivery thoroughly purge the pumps with the mobile phase solvents before doing any analytical runs In addition purge the pumps when switchi
106. enus iura ax pees Pee eee Pa So ba EROR E GE 53 BatchSetup Mena v5 a ee eov eas va ev Ace xD E de tare Patito qs 53 Method Editor Menu sisi ROUES SUE ER reads 54 Maintenance Men s oisi Ronde Rond ass eas d caia E AEE 55 Configuration Menu ivo eoe En EFE DH Cp E web dae ales 56 Logging In to the EASY nLC System oii tc care pekixed ek bd CER E 57 Closing Down the EASY nLC System 0 0 2 eee cc eee 58 Configuring the EASY nLC System 0 0 cee ee cence eee eens 59 Setting Up Communication with the Mass Spectrometer 0 59 Setting Up the Local Area Network Connection 00 0 eee eae 61 Modifying User Permissions 4 i aus bw Fe dO ERR E Rol E E OE Eel C Rite pd 63 Changing the Administrator Password llelel eese 64 Creating New User Accounts 0 0 ccc cece cece eae 65 Changing Your Password from the Exit Menu 0004 66 Modifying the Time Settings dL iis ata ised ate es is a dai utt a caudate 67 Making Syste Backips 22424 oe bee TER cuenta hae Bares 68 Setting Up the Properties for the HPLC Device wo palin deat eee 70 Thermo Scientific Thermo Scientific Chapter 5 Chapter 6 Chapter 7 Contents Preparing the EASY nLC Instrument for Use LLsuuuueuuesese 73 Preparing Solvent Bottles and Waste Containers 0000 ee eee 73 Solvent Requirements ios odores 6 daret Wee pet bipes 74 Solvent A and B Bottles 4 5 air ren Se pci Sar OL ved Paret
107. er Fittings on page 87 d Goto step 4 3 Fora one column setup if you are working with the column assembly shipped with the instrument remove the precolumn from the column assembly Connect the Column Out line directly to the venting Tee 4 Connect the Waste In line to the venting Tee as follows a Remove the plug from the third leg of the venting Tee b Insert the nanoViper fitting at the end of the Waste In line into the free port of the Tee see Figure 54 and Figure 55 c Slowly tighten the fitting until you feel resistance d Tighten the fitting by an additional 1 8 to 1 4 turn Do not tighten the fitting by more than a 1 4 turn see general caution following step 2c 84 EASY nLC 1000 User Guide Thermo Scientific 5 Preparing the EASY nLC Instrument for Use Installing Columns Figure 54 shows the one column setup and Figure 55 shows the two column setup Both setups use the venting Tee Figure 54 One column assembly connected to the EASY nLC system Column Out and Waste In tubing Venting Tee PEEK union Column Out tubing PEEK sleeve Analytical column Waste In 15 cm length tubing Figure 55 Two column assembly connected to the EASY nLC system Column Out and Waste In tubing Stainless steel union Venting Tee PEEK union Column Out tubing PEEK sleeve Precolumn Analytical column Waste In 2 cm length 15 cm length tubing Thermo Scientific EASY nLC 1000 User Guide 85 5 Pre
108. er mass spectrometers refer to the documentation provided with the mass spectrometer or contact Thermo Fisher Scientific Customer Service d In the Start At list select Gradient or Sample Loading Ifyou want data acquisition to start when the mobile phase gradient starts select Gradient Ifyou are running the instrument in the one column mode and you want data acquisition to start when the instrument loads the sample onto the analytical column select Sample Loading Note By setting the Start At value to be the sample loading start you might be able to acquire data for early eluting peptides that would not ordinarily bind to the column material and thus be missed from the actual gradient Moving the Start At point to the start of the sample loading step can lead to small retention time variations due to possible differences in pressure buildup before the A B mixing starts in the actual gradient e Inthe Signal Width box enter an appropriate signal width The default signal width is 1 second This signal width is sufficient for a Thermo Scientific mass spectrometer For other mass spectrometers refer to the documentation provided with the mass spectrometer or contact Thermo Fisher Scientific Customer Service Setting Up the Local Area Network Connection Thermo Scientific If you connect the EASY nLC instrument to the local network see Setting Up the Ethernet Connection to a Local Network for Data Exchange on page
109. ermo Scientific 10 Maintenance Maintenance Scripts Test MS Connection Thermo Scientific The MS Connection script see Figure 103 tests the contact closure function between the EASY nLC system and the mass spectrometer Use this script when testing contact closure There are no parameters associated with the MS Connection script It tests the settings on the Connection page of the Configuration menu see Setting Up Communication with the Mass Spectrometer on page 59 Figure 103 MS Connection script Thermo Home Batch Setup Method Editor v Configuration SCIENTIFIC rw f 9 j 073 No graph Log Book Test v MS connection X Support Parameters Output Devices e Tests the connection to the mass le spectrometer using gradient ready and igradient done events m graph Job 00 15 48 11 May 2011 12 42 admin Exit EASY nLC 1000 User Guide 169 10 Maintenance Maintenance Scripts Test Sample Pickup The Sample Pickup script tests the autosampler pickup function by picking up a set volume from the well plate and ejecting it into waste Use this script when testing the sample pickup function and determining sample pickup flow rates for method setup Tosetthe Sample Pickup script parameters 1 Select the Sample Pickup script as follows a Press Maintenance Scripts b In the Category list select Test c Inthe Name list select Sample Pickup 2 Set
110. es method development the built in diagnostic tests minimize troubleshooting time and the easy access to the solvent delivery system components reduces system maintenance time These topics provide an overview of the system components and connections System Components External System Connections System Components The EASY nLC 1000 system consists of the following components see Table 4 Table 4 EASY nLC 1000 system components Hardware Pumps 3 high pressure pumps 1 to 1000 bar with associated pressure sensors Valves high pressure valves Flow sensor 2 nano flow sensors Autosampler Computer Monitor e Cooled maximum 20 C 68 F below ambient temperature Can hold six fixed vials plus either one Microtiter plate 96 or 384 wells or one 6 x 8 vial adapter for a total of 54 vials 4 liquid containers for solvents rinse and waste Embedded computer Pressure sensitive screen that you can use with gloves Screen size 12 1 in 30 7 cm Resolution 800 x 600 pixels Dimensions Width 36 cm 14 in Depth 38 cm 15 in Height 45 cm 18 in Weight 35 kg 77 2 Ib Utilities Mains power 120 230 Vac 50 60 Hz 250 W Software e EASY nLC stand alone application version 3 0 2 EASY nLC 1000 User Guide Thermo Scientific 1 Introduction Hardware Components External System Connections Installing the EASY nLC system as part of an LC
111. es to download at mssupport thermo com To order consumable and spare parts for the EASY nLC 1000 system Go to www proxeon com productrange nano lc easy nlc 1000 accessories spares index html Contacting Customer Service for Ordering Information This guide includes the contact information for Thermo Scientific offices globally Depending on your location follow these guidelines in making international calls to the appropriate Customer Service office To make an international phone call to a Thermo Fisher Scientific office Dial the following sequence of numbers international access code country code city or area code local phone number The international access code depends on your location and the location you are calling From To International access code United States Canada Other countries 011 or the Caribbean Countries other than the Other countries 00 United States Canada or the Caribbean United States Canada United States Canada 1 or the Caribbean or the Caribbean Thermo Scientific EASY nLC 1000 User Guide xv Preface Whether you dial the area or city code depends on your location and the location you are calling From To Dialing sequence United States Location in the Dial 1 area code local phone number United States with a different area code Countries other than Location within the Dial 0 area code local phone number the United States same country with a different are
112. etermine how to proceed Thermo Scientific EASY nLC 1000 User Guide 113 6 Running Samples Using the Integrated Software Editing the Running Batch Editing the Running Batch You can edit the running batch if you want to add samples or remove samples that the instrument has not already run 114 To edit the running batch 1 Press Home gt Queue The Queue page of the Home menu opens see Figure 74 Figure 74 Queue page of the Home menu Thermo 7777 SCIENTIFIC i Overview Auto Submitter continue Graphs Job 00 02 38 Sample 00 00 08 Gradient 00 00 25 aug 2010 00 05 admin 2 EASY nLC 1000 User Guide Select the batch job from the list and press Edit The Batch Setup Edit page opens see Figure 75 Duration Running admin admin 20100825 0002 06 55 00 f Edit F Properties Thermo Scientific 6 Running Samples Using the Integrated Software Editing the Running Batch Figure 75 Edit page of the Batch Setup menu Thermo Home MBatchiSetup Method Editor Maintenance Configuration SCIENTIFIC File e f f cae A Add Injections 1 BSA 30 min RePlay v Batch Extensions X Method Sample 2 BSA 30 min RePlay Sample 4 BSA 30 min RePlay Sample 5 BSA 30 min RePlay Sample 6 BSA 30 min RePlay Job 00 02 46 Sample 00 00 16 Gradient 00 00 25 aug 2010 00 06 3 Edit the batch that is add change or remove
113. ew plate format go to step 3 To copy an existing plate format copies the format selection go to step 4 3 Create a new plate format as follows a Press New The Create New Plate Format dialog box opens Figure 80 Figure 80 Create New Plate Format dialog box Create New Plate Format Create new plate format Format 16x24 v Name HT MTP oA 122 EASY nLC 1000 User Guide Thermo Scientific Thermo Scientific 7 Calibrating the Autosampler s XYZ Robot Managing Plate Formats b In the Format list select a plate format 6 x 8 vials 8 x 12 96 well plates or 16 x 24 384 well plates c Inthe Name box enter a name for the new plate format d Press Accept The new plate name appears in the plate list with the text uncalibrated appended on the right e Go to Calibrating Plates on page 125 to calibrate the vial or well positions Copy an existing plate format as follows a Select an existing plate format from the Plate list b Press Copy To The Copy Plate Format dialog box opens c Inthe Name box type a name for the new plate format d Press Accept e Goto Calibrating Plates on page 125 to calibrate the vial or well positions To select the plate format that you want to use Open the Tools view for the autosampler on the Devices page of the Maintenance menu see step lon page 121 Select a plate format from the Plate list Press Use Tip If you are
114. f the IFC system Pressure sensor A Flow sensor A A B mixing Tee Flow sensor B 26 EASY nLC 1000 User Guide Thermo Scientific 1 Introduction Pump Flow Control You can program the column equilibration and sample loading steps as follows Specify both a set flow and a maximum pressure The setting reached first which becomes the limiting parameter depends on the dimensions of the attached column or columns If the system reaches the set pressure before it reaches the set flow rate the IFC system reduces the flow rate to maintain the pressure If the system reaches the set flow rate before the pressure limit the pump maintains the set flow rate Specify only a set flow The IFC system maintains the set flow rate unless the pressure exceeds the maximum system pressure of 1000 bar Specify only a maximum pressure The IFC system adjusts the flow rate to maintain the set pressure The duration of both the equilibration and loading steps depends on the total volume of solvent specified and the actual flow rate When the set pressure is the limiting factor the system adjusts the actual flow rate which varies the duration of these steps Tip If the duration of the equilibration and loading steps must be fixed limit these steps by flow rather than by pressure Use the appropriate precolumn and analytical column maintenance scripts to determine the appropriate flow rates for your LC columns Load Speed
115. following two conditions 1 This device may not cause harmful interference and 2 This device must accept any interference received including interference that may cause undesired operation WARNING Changes or modification to this unit not expressly approved by the party responsible for compliance could void the user s authority to operate the equipment Note This equipment has been tested and found to comply with the limits for a Class A digital device pursuant to Part 15 of the FCC Rules These limits are designed to provide reasonable protection against harmful interference when the equipment is operated in a commercial environment This equipment generates uses and can radiate radio frequency energy and if not installed and used in accordance with the instruction manual may cause harmful interference to radio communications Operation of this equipment in a residential area is likely to cause harmful interference in which case the user will be required to correct the interference at his own expense Note You must use shielded cables with this unit to ensure compliance with the Class A FCC limits Canadian Safety and EMC Electromagnetic Compliance Standards Thermo Scientific Safety This instrument has been reviewed for compliance with standard CAN CSA C22 2 No 61010 1 Second edition Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements
116. g appropriate 164 166 gradient 96 manual control 142 measuring 11 monitoring 110 sample loading 95 sample pickup 95 flow sensors calibration script 178 description 11 maintenance schedule 161 Flush Air script 163 formic acid solvent requirements 74 fuse replacing 158 G global configuration settings 70 gloves wearing 84 gradient delay volume 19 method step 19 setting up the method 96 graphical data types 111 grounding requirements 38 H humidity specification 36 l injections number per sample 106 pickup sample step 21 sample pickup volume 94 Insert Plate button using 77 Inspection Only check box 178 Intelligent Flow Control IFC system description 26 interface layout 49 international calls making xv Internet access 36 IP address support server 150 Isocratic Flow script 167 Thermo Scientific K keyboard connection 44 L Leaks script 171 leaks checking for 160 lifting instructions 33 Load Speed Protection option 27 71 log book 180 logging in to the application 57 Logo icon Thermo Scientific 49 Loop Volume box 71 low pressure solvent filters 161 maintenance daily 159 scripts 161 yearly 161 manuals EASY nLC xii mass spectrometer contact closure configuration setting 59 hardware connection 39 troubleshooting 137 169 menu structure 52 message log file 152 method LC accessing from another computer 42 63 analytical column equilibration parameters 99 gradient table 96
117. gef hrliche Chemikalien enthalten Tragen Sie Schutzhandschuhe beim Umgang mit toxischen karzinogenen mutagenen oder tzenden reizenden Chemikalien Entsorgen Sie verbrauchtes OI entsprechend den Vorschriften in den vorgeschriebenen Beh ltern Hitze Warten Sie erhitzte Komponenten erst nachdem diese sich abgek hlt haben Feuer Beachten Sie die einschl gigen Vorsichtsma nahmen wenn Sie das System in Gegenwart von entz ndbaren Gasen betreiben Verletzungsgefahr der Augen Verspritzte Chemikalien oder kleine Partikel k nnen Augenverletzungen verursachen Tragen Sie beim Umgang mit Chemikalien oder bei der Wartung des Ger tes eine Schutzbrille Allgemeine Gefahr Es besteht eine weitere Gefahr die nicht in den vorstehenden Kategorien beschrieben ist Dieses Symbol wird im Handbuch au erdem dazu verwendet um den Benutzer auf Anweisungen hinzuweisen Wenn Sie sich ber die Sicherheit eines Verfahrens im unklaren sind setzen Sie sich bevor Sie fortfahren mit Ihrer lokalen technischen Unterst tzungsorganisation f r Thermo Fisher Scientific San Jose Produkte in Verbindung ATTENTION Choc lectrique L instrument utilise des tensions capables d infliger des blessures corporelles L instrument doit tre arr t et d branch de la source de courant avant tout intervention Ne pas utiliser l instrument sans son couvercle Ne pas enlever les tuis protecteurs des cartes de circuits imprim s Chimique De
118. hat component opens For information about using these manual controls see Manual Controls on page 141 48 EASY nLC 1000 User Guide Thermo Scientific 3 Integrated Instrument Control Software User Interface Layout User Interface Layout The EASY nLC user interface Figure 32 contains five menu tabs at the top of the touch screen When you press a tab at the top of the touch screen a set of side tabs appears on the left Figure 32 EASY nLC user interface layout with menus Top menu tabs Logo icon Thermo Homel Batch Setup Method Editor l a ee mmm mm mmm mmm emm mmm mmm mmm mme m mem Side tabs Job 00 00 00 Current user 23 aug 2010 aeemen st Login Login and Exit button In this guide the term menus refers to the tabs at the top of the touch screen and the term page refers to the screens opened by pressing the tabs on the left side of the touch screen During a session the application tracks which page side tab you selected inside each menu top tab and shows that page when you next choose that menu The Thermo Scientific logo icon in the upper left corner and the Login button in the lower left corner are always available To log in or log off press Login see Logging In to the EASY nLC System on page 57 and Closing Down the EASY nLC System on page 58 To view version information for the application press the Logo icon Thermo Scientific EASY nLC
119. hat its corresponding valve is in position 1 2 before you refill the pump For pump S before you empty or fill the pump use the autosampler s manual controls to insert the autosampler needle into the W4 or W3 bottle respectively Tip To prepare the EASY nLC instrument for operation use the Prepare Purge Solvent script to flush the solvent lines see Prepare Purge Solvent on page 162 As it empties and refills the selected pump or pumps the Prepare Purge Solvent script automatically places the valves and autosampler needle in the appropriate positions To work with the pump s manual controls follow these procedures Opening the Manual Controls for the Pumps Using the Manual Controls to Fill or Empty Pump A or B Using the Manual Controls to Fill or Empty Pump S Opening the Manual Controls for the Pumps Each pump is represented by a pump icon on the Home Overview page To open the Pump dialog box Press the pump icon for the pump that you want to control Its dialog box opens see Figure 89 The Position readback displays the current pump position from 0 pL empty to 140 pL full 142 EASY nLC 1000 User Guide Thermo Scientific 8 Troubleshooting Manual Controls Figure 89 Pump dialog box Pump A Pump A Volume box 0 55 uin 1 Flow rate box A at 1400 pl St Stat 00 u siop J sin Pressure 22 3 Bar
120. he EASY nLC instrument replace the right side panel and check the fuse Attach an external monitor to the VGA connector labeled MONITOR on the back panel of the instrument see Figure 6 on page 7 Startup bar is no longer proceeding Batch Runs Damaged system Switch off the EASY nLC instrument and wait five seconds before switching it on again In some cases this recovers the system Contact Thermo Fisher Scientific if the problem recurs us customer support analyze thermofisher com eu techsupport cms thermofisher com For troubleshooting tips when running a batch see Table 22 Table 22 Running a batch troubleshooting tips Sheet 1 of 2 Symptom Gradient does not start Possible causes Waiting for contact closure Action Check the contact closure connections Maximum pressure is exceeded during sample loading or reequilibration or pressure is maintained but the flow is dramatically decreased Possible blocked column 1 Remove all columns from the system 2 Run the maintenance script Test Back Pressure on page 175 Max pressure is exceeded during gradient 134 EASY nLC 1000 User Guide Back pressure that is too high on the column for the specified flow Reduce the flow in the method and schedule a new batch with the changed method Blocked flow paths Contact Thermo Fisher Scientific us customer support analyze thermofisher com eu techsupport cms thermofis
121. he EASY nLC Instrument for Use Purging and Flushing the Pumps Method Editor Description Schedule 5 Press Schedule e The Queue page Figure 52 of the Home menu appears Flow nl min Flow nl min Configuration Pump A Desired flow Real flow Pressure 300 000 0 250 000 0 200 000 0 150 000 0 100 000 0 50 000 0 0 0 1 000 0 750 0 500 0 t 250 0 0 0 1 2 3 4 5 Time min Pump B Desired flow Real flow Pressure 300 000 0 250 000 0 200 000 0 150 000 0 100 000 0 50 000 0 0 0 1 000 0 750 0 500 0 250 0 0 0 1 2 3 4 5 Time min EASY nLC 1000 User Guide reg aunssaug eg sunssaJd 81 5 Preparing the EASY nLC Instrument for Use Purging and Flushing the Pumps 82 EASY nLC 1000 User Guide Figure 52 Queue page of the Home menu showing the queued jobs Hiri Homes BatchSetup Method Editor Maintenance Configuration SCIENTIFIC Overview Auto Graphs continue Submitter Job name Duration INIT NN seen wm x admin Flush air Job 00 00 00 6 sep 2010 13 14 admin f Exit f Delete f Up f f t Properties In the Jobs list make sure the check box in the Auto Continue column is selected for Flush Air Press Overview The Overview page of the Home menu opens Press START The default selections appear in the two graph windows on the Scripts page of th
122. he Mixing Tee and through Valve S Thermo Scientific When valve A or B is in the 1 6 position the solvent flow from the corresponding pump connects to the mixing Tee by way of a pressure sensor and a flow sensor Valve S controls the solvent path downstream of the mixing Tee e When valve S is in 1 2 position the solvent flow from the mixing Tee bypasses the sample loop Valve S is in the 1 2 position during the sample pickup step and during the column equilibration steps When valve S is in the 1 6 position the solvent flow from the mixing Tee passes through the sample loop Valve S is in the 1 6 position during the sample loading step Pump A or Pumps A and B actively pump solvent toward the mixing Tee during these sample run steps Column Equilibration Steps Load Sample Step Prealign A B Prepare Gradient Step Gradient Step Column Equilibration Steps For a one column setup the sample run includes the analytical column equilibration step For a two column setup the sample run includes both a precolumn equilibration step and an analytical column equilibration step The Equilibrate Precolumn step see Figure 13 includes this sequence of actions Action 1 Valve A and valve W switch to position 1 6 Valve B switches to the centered position Valve S switches to position 1 2 2 Pump A pushes the specified solvent volume through the precolumn at the specified pressure or flow rate Excess solvent A exits
123. he Vials Wash area press Calibrate The Autosampler Vials Wash Calibration dialog box opens see Figure 84 3 Press the bottle container in W4 1 see Figure 84 The needle moves to the current saved coordinate The saved coordinates for the x and y axis appear on the left side of the slash the needle does not descend into the bottle and the z axis value on the left side of the slash remains at 0 Figure 84 Vials Wash view in the Autosampler Vials Wash Calibration dialog box Calibrate Vials Wash Needle Infout Z Needle Up Down 4 3 Needle LeftRight Reset Ugoo og J 98 08 OE Ble Thermo Scientific EASY nLC 1000 User Guide 129 7 Calibrating the Autosampler s XYZ Robot Calibrating the Wash Bottle and Extra Vial Positions 4 Center the needle above the bottle as follows Press the Needle In Out 2 buttons to adjust the x axis position Press the Needle Left Right 3 buttons to adjust the y axis position yaxis X axis Out Right lt left 5 Using the step buttons in the Needle Up Down area 5 adjust the needle height as follows a Using the big step button WV lower the needle until it reaches a level of 2 3 mm 0 08 0 12 in above the bottle b Using the small step button J slowly let the needle enter the hole and lower the needle until it reaches the bottom of the wash insert in the bottle Note The O ring at the top of
124. heating resistor and two temperature sensors see Figure 10 The flow sensors determine the flow rate of solvents passing through the system by measuring the heat transfer through the fused silica capillary Outside the capillary a heating resistor on a thermally optimized membrane is maintained above ambient temperature When liquid flows through the capillary the temperature distribution upstream and downstream of the heating resistor is disturbed The two temperature sensors measure this temperature asymmetry EASY nLC 1000 User Guide 11 1 Introduction Solvent Delivery and Sample Pickup Systems Because the temperature distribution depends on both the solvent flow rate and the solvent mixture you must recalibrate the flow sensors whenever you change the solvent types for solvents A and B For example if you use methanol instead of acetonitrile for the solvent B mixture perform the script Calibrate Flow Sensors on page 178 The flow sensors have a maximum measuring range of 4 5 pL min Figure 10 Flow sensor schematic annt Tubing t Heater Sensor chi p Temperature sensors Based on CMOSens Technology Principle patented US Pat 6 813 944 Six Port Valves The six port valves can be in three different positions 1 2 position 1 6 position and centered see Figure 11 Figure 11 Valve positions 1 2 position 1 6 position Centered 6 For maintenance purpo
125. hecking Sample Pickup Thermo Scientific EASY nLC 1000 User Guide 119 7 Calibrating the Autosampler s XYZ Robot Replacing the Autosampler Adapter Plate Replacing the Autosampler Adapter Plate The EASY nLC system ships with the vial adapter plate installed The microtiter adapter plate comes in the accessory kit To load microtiter microwell plates into the tray compartment you must replace the vial adapter plate with the microtiter adapter plate The vial adapter plate holds 48 vials 6 extra vials The microtiter adapter plate holds one 96 well plate or one 384 well plate Follow this procedure to switch between the two adapter plates as necessary t To replace the adapter plate on the autosampler 1 Press Home gt Overview The Overview page of the Home menu opens 2 Make sure that the area in front of the tray compartment is clear and then press Eject Plate The tray compartment opens Figure 77 shows the vial adapter plate mounted to the tray holder The four studs on the bottom side of the plate fit snugly into the mounting holes on the tray holder Figure 77 Open tray compartment M TA i DI LU WEA J MESEL ui aes Pc E J f TL Ns PPS t x ID ITI NIS gt rr Py DL L7 h 3 Remove the current adapter plate by pulling it up and away from the tray holder see Figure 78 120 EASY nLC 1000 User Guide Thermo Scientific 7 Calibrating the Autos
126. hen connected Show Clear Devices Log file copy To home directory To USB removable storage Copy Log Files Status Contact Job 00 00 00 Thermo Fisher Scientific easysupport proxeon com Edisonsvej 4 http www proxeon com hplc DK 5000 Odense C Phone 45 6557 2300 Denmark Fax 45 6557 2301 30 Aug 2010 14 14 admin Ext b In the Connect to EASY nLC Support area press Connect The Message to Support Team dialog box appears see Figure 93 Figure 93 Message to Support Team dialog box 1 je to s team Support region f Name Email address Phone number Enter message Accept Cancel Thermo Scientific EASY nLC 1000 User Guide 151 9 Remote Support Connecting the EASY nLC System to the Support Server c Select a support region provide valid contact information and describe the problem that you are experiencing Note When you place the cursor in the Phone Number box the program prompts you for a country code and phone number Tip When you place the cursor in the Email Address box the program prompts you to enter an address in this format name company com To enter the symbol press Shift The numbers row changes to the symbols row Then press d Press Accept After you enter the requested information the Status box on the right side of the Support page should change from Not Connected to Connected
127. her com Thermo Scientific Table 22 Running a batch troubleshooting tips Sheet 2 of 2 Symptom It takes an extremely long time for the flow rate to stabilize Possible causes Air in the system 8 Troubleshooting Batch Runs Action Purge air from the system as described in Purging and Flushing the Pumps on page 79 Leakage in the system Run the maintenance script Test Leaks on page 171 XYZ robot error Possible step loss on one of the motors because of a blockage in the movement of the axis Remove the obstacle and try again You might need to calibrate the autosampler for more precise penetration of the microtiter plate or wash waste containers Repetition of the error without any visible reason Contact Thermo Fisher Scientific us customer support analyze thermofisher com eu techsupport cms thermofisher com Time out on flow sensor Air in the pumps Run the maintenance script Prepare Flush Air on page 163 Sample is not being picked up Air in the pumps Run the maintenance script Prepare Flush Air on page 163 Run the maintenance script Sample Pickup Verify that the autosampler removes sample from the vial Valve unknown position Thermo Scientific Valve trimming needed Run the maintenance script Test Valve Check on page 174 EASY nLC 1000 User Guide 135 8 Troubleshooting Autosampler Autosampler See Table 23 for
128. hever parameter is reached first 10 Maintenance Maintenance Scripts Press Max Pressure to set the maximum allowed pressure CAUTION The maximum pressure rating for the PepMap columns supplied with the EASY nLC 1000 system is 800 bar Running the system at pressures higher than 800 bar reduces the column lifespan Figure 100 Precolumn Equilibration script parameters Thermo SCIENTIFIC Log Book Support Devices Job 00 05 02 Sample 00 05 00 Gradient 00 00 2 May 2011 14 02 admin Exit Home Batch Setup Method Editor Category Name fius equil olume pl Flow l min Max pressure bar 800 00 Schedule Configuration _ No graph J No graph EASY nLC 1000 User Guide 165 10 Maintenance Maintenance Scripts Prepare Analytical Col Equilibration The Analytical Col Equilibration script equilibrates the analytical column with solvent from pump A Use this script to equilibrate or flush the analytical column determine a suitable equilibration flow rate for the method or initialize a new analytical column To set the Analytical Col Equilibration script parameters 1 Select the Analytical Col Equilibration script as follows a Press Maintenance gt Scripts b In the Category list select Prepare c Inthe Name list select Analytical Col Equilibration 2 Set the parameters see Figure 101 for this script as follows a Press the
129. ic can extract the password from the system in two ways Ifthe network is set up for remote access press Maintenance Support Enter your contact information and a message requesting your password information Then press Connect or e Run a factory reset see To reset one or all of the settings to the factory values on page 69 EASY nLC 1000 User Guide 139 8 Troubleshooting Miscellaneous Table 27 Miscellaneous troubleshooting tips Sheet 2 of 2 Symptom System is running slower and Possible causes Memory filled with graph Action Press Home gt Graph and disable the graphs by slower data from long gradient run pressing No Graph in each graph window System overload caused by Restart the application or power down power up from other reasons Maintenance Scheduling Unhandled error or SVG Program error in the software In most situations you can continue your work by scalable vector graphics error 140 EASY nLC 1000 User Guide release pressing Ignore or OK More serious error situations might require restarting the HPLC To request a software change do one of the following Send your request to one of these e mail addresses us customer support analyzeghermofisher com eu techsupport cms2thermofisher com Connect to the remote support server and send a message to Thermo Fisher Scientific Technical Support as described in Connecting the EASY nLC System to
130. igure 31 in front of the main window so that you can enter values by pressing the appropriate keys When you press a key it is highlighted in blue until you press another key Figure 31 Touch screen keyboard and numeric keypad userl C b 4 Tab q w e t y u i p Del Caps lock a s d f g h j k 2 Enter j J J Shift z x c v b n m 4 i Shift t 0 A L d L 4 Ji 3t 3t 3 3 Ji B 4 4 Ctrl Alt Space AltGr Ctrl x gt A A i A A A A y Accept Cancel ER e e c M M M I GM J N Using Tables and Input Fields You can edit many tables usually when you have entered the data yourself You can also access single cells by touching the cell twice to open a keyboard keypad display for changing the entry Long tables have vertical scroll bars that you move either by pressing the up or down arrow symbols or by dragging the scroll bar and moving it explicitly In some tables you can select multiple rows by pressing check boxes on several rows or complete columns by pressing the table headings If a screen has blank input fields press inside the field to enter data The application displays a keyboard keypad Interactive Graphical Controls The four valves the three pumps and the autosampler appear as interactive graphical components on the Home gt Overview page When you press a graphical component the manual controls for t
131. iguring the EASY nLC System Setting Up the Properties for the HPLC Device Setting Up the Properties for the HPLC Device Use the Properties page for the EASY nLC instrument on the Devices page of the Maintenance menu to set the global instrument configuration settings such as the one or two column setup loop size idle flow settings and load speed protection itN hod 1 2 3 5 To set up the global instrument configuration for the HPLC device Press Maintenance gt Devices In the Devices list select EASY nLC HPLC Press the Properties tab The Properties view for the HPLC device on the Configuration gt Devices page opens see Figure 44 Figure 44 Devices page of the Maintenance menu showing the HPLC Properties settings Thermo Home Ba up Method Editor Jlaintenance Configuration Scripts Devices Log Book ER Add Device Support Remove Device Ast oevce Cooled Autosampler ASC Autosampler ET msn EASY nLC HPLC E One column setu Loop volume 20 0 ul P 3 Load speed protection LSP joo 0 0621 Idle flow rate 50 nl min Idle mixture 90 B 11 May 2011 11 28 Press the corresponding box to open the keypad and enter the appropriate numeric values for these parameters Loop Volume Idle Flow Rate and Idle Mixture Make the appropriate selections for these check boxes One Column Setup and Load Speed Protection LS
132. ilding the Gradient on page 96 4 5 Control the equilibration of the precolumn Setting Up the Column Equilibration the analytical column or both Steps on page 98 5 5 Control the autosampler wash step Setting Up the Autosampler Wash Step on 54 EASY nLC 1000 User Guide page 100 Thermo Scientific Maintenance Menu 3 Integrated Instrument Control Software Application Menu Structure Perform a number of functions designed to provide and improve system status Page Function Go to Scripts View a collection of useful maintenance Maintenance Scripts on page 161 procedures for keeping the instrument functioning properly and to help diagnose and resolve possible problems Log Book Electronically enter all the service actions Keeping Service Records on page 180 that you perform on the instrument Support Set up support from Thermo Fisher Chapter 9 Remote Support Scientific Devices Add an external device to the system Appendix A External Devices Thermo Scientific Check and reset the device usage counters Set up the global configuration for the HPLC Checking and Resetting the Device Usage Counters on page 181 Setting Up the Properties for the HPLC Device on page 70 Calibrate the autosampler Chapter 7 Calibrating the Autosampler s XYZ Robot EASY nLC 1000 User Guide 55 3 Integrated Instrument Control Software Application Menu Structure Configuratio
133. ing Samples Using the Integrated Software Creating a Method Creating a Method To create a method follow these procedures 1 A WO N MA Browsing for a Stored Method or Creating a New Method File Starting the Method Editor Wizard and Selecting the Method to be Edited Setting Up the Sample Pickup and Loading Steps Building the Gradient Setting Up the Column Equilibration Steps Setting Up the Autosampler Wash Step Saving the Method Settings Browsing for a Stored Method or Creating a New Method File Use the Method Editor File page to browse for stored methods or to select the file folder and enter a name for the new method itN Ww 1 92 EASY nLC 1000 User Guide To browse for a stored method Press Method Editor gt File The Method Editor gt File page opens see Figure 60 Figure 60 File page of the Method Editor Thermo gre Fie New Folder Maintenance Configuration New Method Edit Copy Method Created Modified E BSA 30 min 040240 04 0210 a port E mm Delete S public super user Import Job 00 00 00 BSA 30 min Standard 30 min BSA separation 23 aug 2010 12 36 admin Exit Thermo Scientific 6 Running Samples Using the Integrated Software Creating a Method 2 To view the methods in the folder press the file folder name in the Path column 3 To view a description of the method if available press
134. ipt as follows a Press Maintenance Scripts b In the Category list select Calibrate c In the Name list select Flow Sensors 2 Set the parameters see Figure 111 for this script as follows a Press the Parameters tab b Select the check boxes for the flow sensors A B or both that you would like to either inspect or inspect and calibrate Tip When you clear the Inspection only check box the script inspects the accuracy of the current calibration by performing an exact or fast inspection performs a two point calibration and then stores the new calibration setting For a more accurate evaluation of the calibration select the Exact Inspection option when you are calibrating the flow sensors c Doone ofthe following To check the accuracy of the current calibration only perform an inspection only select the Inspection Only check box Note When you select the Inspection Only check box the program does not recalibrate the flow sensors To inspect and calibrate the sensors clear the Inspection Only check box d Select the inspection speed as follows When you only want a rough estimate of the flow sensor accuracy select the Inspection Only check box and the Fast Inspection option When you are recalibrating the flow sensors clear the Inspection Only check box and select the Exact Inspection option 178 EASY nLC 1000 User Guide Thermo Scientific 10 Maintenance Maintenance Scripts Figur
135. ired operation DEVICE EASY NLC S N AAOZL OLL P N LC100 LAN MAC ADDRESS 00 6 E0 45 4E 28 BEAT Proxeon Biosystems A S C t20 230v 50 60 Hz 250w Web www proxeon com Fuse at 120V T5AL 250V Phone 45 6557 2300 Fax 45 6557 2301 os Fuse at 230V T2 5AL 250V Table 5 lists the function of each back panel element Table 5 Back panel elements Sheet 1 of 2 Element Description RS 232 For communication with add on devices for example a syringe drive USB Port for keyboard or mouse or removable USB storage device two 2 provided PS 2 Input for connection of keyboard and mouse LAN For 10 100 MB sec Ethernet connection MONITOR Output for connection of external display P BUS For communication with add on devices IN OUT pins Contact closure primarily for communication with the mass spectrometer EASY nLC 1000 User Guide 7 1 Introduction Column Setup Options Table 5 Back panel elements Sheet 2 of 2 Element Description I O Power switch Fuse holder below Replaceable fuse ratings I O switch e For 120 V T 5 AL 250 V e For 230 V T 2 5 AL 250 V P N Product order code S N Instrument serial number LAN MAC ADDRESS MAC address of the embedded computer Gives the EASY nLC system a unique network identifier on your local network Column Setup Options Two solvent lines exit from the right side of the instrument The solvent line labeled Column Out connects t
136. irements 74 weight EASY nLC instrument 29 well plates calibrating 125 plate formats managing 121 preparing 91 Windows Explorer 62 138 Thermo Scientific calibrating 124 130 manual control 146 EASY nLC 1000 User Guide Index U 201
137. ist select the correct mass spectrometer see Figure 36 The Instrument list contains the most common mass spectrometers used in proteomics but if you cannot find your particular mass spectrometer select Generic Tip If your mass spectrometer does not appear on the list and you would like to see it supported in a future release of the EASY nLC application provide this information to Thermo Fisher Scientific Customer Service see Contacting Us on page xv If the Use Contact Closure option is not already selected select it In the Contact Closure area do the following a Check the connections on the graphic for the selected mass spectrometer b From the Protocol list select One way or Two way synchronization see Figure 36 f the graphic for the selected mass spectrometer shows only Start In signals select One way synchronization With a one way connection the EASY nLC instrument sends a start signal to the mass spectrometer Ifthe graphic for the selected mass spectrometer shows two way communication between the mass spectrometer and the EASY nLC instrument select Two way synchronization With a two way connection the EASY nLC instrument waits for a ready signal from the mass spectrometer Thermo Scientific 4 Configuring the EASY nLC System Setting Up the Local Area Network Connection c In the State at Start list select Open or Closed For a Thermo Scientific mass spectrometer select Open For oth
138. ist in the EASY nLC application the Devices list If not press Add Device In the Select a Device to Add dialog box locate the Advion RePlay device Advion RePlay Fluid Storage Autosampler ASA Autosampler Autosampler ASC Autosampler EASY nLC HPLC New Era NE 1000 Syringe Drive Liquid Depositor Proxeon EASY SPOTTER Accept Cancel Select the device and press Accept Press Maintenance Devices and check that the RePlay device is not already present in Verify that the RePlay device was added to the system by locating it in the Devices list Selecting the device shows information about the device driver see Figure 116 Figure 116 RePlay About tab under the Devices list Thermo scicuricic Home Batch Setup Method Editor Configuration Maintenance Scripts Log Book Devices Name Type Piston Pump Pump S Piston Pump Fluid Storage Support s pole Rotary Valve Valve A Rotary Valve Add Device Remove Device stk RePlay Manufacturer Advion BioSciences Inc Job 00 00 09 Product RePlay Type Fluid Storage Driver info 0 1 0 Firmware info N A cure Serial Number N A Usages Capture Playback Eluent admin Slaves lt N A gt Exit Thermo Scientific A External Devices Setting Up a Method with the RePlay Device Setting Up a Method with the RePlay Device To set up a method
139. lecting the corresponding check box or check boxes Figure 108 Figure 108 Back Pressure script parameters Thermo Home Batch Setup Method Editor Vaintenance Configuration SCIENTIFIC No graph Log Book Test v Back pressure X Support Devices m graph J Job 00 15 48 11 May 2011 12 50 Exit Thermo Scientific EASY nLC 1000 User Guide 175 10 Maintenance Maintenance Scripts Test Autosampler Torque The Autosampler Torque script Figure 109 measures the torque required to move the XYZ robot on each of its axes IMPORTANT Performing this script incorrectly will compromise the performance of the instrument Contact your local Thermo Fisher Scientific representative before running this script Figure 109 Autosampler Torque script description Thermo Home Batch Setup Method Editor CS punc ETE Log Book Test J Autosampler torque Support Parameters Output Devices Tests the individual torque required for the autosampler manipulator axes Job 00 01 02 24 aug 2010 17 50 admin Exit 176 EASY nLC 1000 User Guide Maintenance Configuration No graph f No graph J Thermo Scientific 10 Maintenance Maintenance Scripts Test Pump Torque The Pump Torque script Figure 110 measures the actuator s ability to generate pressure at predefined torque levels IMPORTANT Performing this script incorrectly
140. longevity of your instrument Contents General Maintenance Daily Maintenance Weekly Maintenance e Quarterly Maintenance Yearly Maintenance Maintenance Scripts Keeping Service Records e Checking and Resetting the Device Usage Counters General Maintenance Maintain a clean working environment for the EASY nLC instrument and replace its fuses as necessary These topics specify the appropriate cleaning solvents and fuses Cleaning Materials Replacing the Main Power Fuse Cleaning Materials When cleaning the outside of the EASY nLC instrument use a mild detergent and a clean cloth Thermo Scientific EASY nLC 1000 User Guide 157 10 Maintenance General Maintenance Replacing the Main Power Fuse The EASY nLC uses these fuses For 120 Vac the instrument uses one T 5 AL 250 V fuse 5 x 20 mm IEC 60127 For 230 Vac the instrument uses one T 2 5 AL 250 V fuse Use only UL Listed and CSA certified fuses All fuses supplied with the system are UL Listed and CSA certified CAUTION Before removing the fuses turn off the instrument and remove the power cable To replace the main power fuses 1 Move the EASY nLC instrument to a benchtop where you can access the back panel Figure 96 shows the steps required to remove the fuse holder 2 Turn off the power and pull out the power plug 3 Place a flat blade screwdriver into the slot in the top of the fuse holder and then twist the screwdrive
141. losing down the instrument in a controlled manner is important to allow all the components to shut down in an orderly sequence Using this controlled method saves important data so that the instrument starts with the correct information the next time you use it WARNING If you turn off the power switch during normal operation you risk damaging essential system components Follow the procedure outlined here whenever possible To turn off the EASY nLC system 1 Press Exit lower left corner of the screen A confirmation dialog box opens see Figure 35 on page 57 2 Press Power Down The EASY nLC application displays a white screen with a small progress bar When the progress bar is filled out and the message appears indicating you can safely turn off the instrument go to the next step EASY nLC The instrument can now be turned off safely SCL e 3 After receiving the message that you can safely turn off the instrument turn off the power switch on the back panel of the instrument 58 EASY nLC 1000 User Guide Thermo Scientific 5 NM Configuring the EASY nLC System After turning on the instrument and logging in as a system administrator you must configure the instrument integrated software application for use and define the network connection for the instrument To set up the application configuration follow the configuration instructions in this chapter Contents Setting Up Communication with the Mass Sp
142. mentation Model Name EASY nLC 1000 Model Numbers LC120 Serial Number LC 010000 and higher Year of Manufacture 2011 I the undersigned hereby declare that the equipment specified above conforms to the above Directive s and Standard s A bee Ole Vorm Site Manager EASY nLC 1000 User Guide July 19 2011 Thermo Scientific LLL m Introduction The EASY nLC 1000 system Figure 1 consists of a compact ultra high performance liquid chromatography instrument designed for split free flows down to the low nanoLiter min range and a built in instrument control software with a touch screen interface The system provides ease of use and ease of service without sacrificing functionality or performance Figure 1 FASY nLC 1000 system To familiarize yourself with the EASY nLC system review the descriptive information in this chapter Contents System Overview Hardware Components Column Setup Options Solvent Delivery and Sample Pickup Systems e Predefined Steps for Sample Runs Pump Flow Control Specifications Thermo Scientific EASY nLC 1000 User Guide 1 1 Introduction System Overview System Overview The EASY nLC system integrates an autosampler and three nanoflow pumps into one compact enclosure An embedded computer controls the system and provides an intuitive user interface through an integrated pressure sensitive touch screen The built in method editor simplifi
143. monitor the progress 3 Monitor the actual flow rate to become familiar with the flow pressure relationship on your particular column 88 EASY nLC 1000 User Guide Thermo Scientific 5 Preparing the EASY nLC Instrument for Use Equilibrating Columns To equilibrate the analytical column 1 Open the Analytical Column Equilibration script and set up the script parameters as described in Prepare Analytical Col Equilibration on page 166 2 Set the desired flow volume and maximum pressure see Figure 59 Thermo Fisher Scientific recommends running the reequilibration at a set pressure rather than a set flow to make sure the column pressure limit 800 bar and the instrument pressure limit 1000 bar are not exceeded If the flow field is left empty the pump will run at the specified pressure For best results use a reequilibration volume of 10 column volumes Figure 59 Analytical column equilibration parameters Thermo Home Batch Setup Method Editor Vaintenanc Configuration SCIENTIFIC Scripts Category Name f f No graph Log Book Prepare Analytical col e w Support Devices Max pressure bar f us graph J Job 00 05 02 Sample 00 05 00 Gradient 00 00 2 May 2011 14 06 admin Schedule Exit 3 Press START The default graphs appear in the two graph windows but you may change the selections from their corresponding lists These graphs help you t
144. mp S draws the requested sample pickup volume into the needle Note The EASY nLC system performs only partial loop injections To avoid drawing sample into pump S the application prevents you from entering a sample pickup volume larger than the sample loop size minus two microliters The extra two microliters are required for the two air segments that bracket the sample The XYZ robot raises the needle out of the sample solution To transfer the sample into the loop pump S draws a fixed volume of air into the needle This fixed volume of air 11 pL is equal to the needle volume plus the valve port to port volume plus an additional 1 pL of air to bracket the sample solution inside the loop Figure 16 through Figure 18 show pump S drawing the first air segment the requested sample pickup volume of 10 pL and the second air segment At the end of the Pickup Sample step the sample loop holds the requested sample volume of 10 pL two 1 pL air segments and approximately 8 pL of solvent A Thermo Scientific EASY nLC 1000 User Guide 21 1 Introduction Solvent Delivery and Sample Pickup Systems Figure 16 Pickup Sample step with pump S drawing the front air segment into the needle Air segment 7 Pressure Sensor pg W3 bottle WA bottle Sample vial 2x Column Out line From the mixing Tee y Figure 17 Pickup Sample step with pump S drawing 10 uL of sample from a sample vial E B
145. mputer If you are already logged in to the EASY nLC system you do not need to reenter the user login and password To access the files on the EASY nLC system s computer hard drive from a computer on the intranet other than the local data system computer for an LC MS system you must know the IP address and the user login and password for the EASY nLC system 42 EASY nLC 1000 User Guide Thermo Scientific 2 Installing the EASY nLC Instrument Back Panel Connections Setting Up the Ethernet Connection to the Support Server You can have Thermo Fisher Scientific Technical Support remotely diagnose problems with your EASY nLC system Thermo Fisher Scientific recommends the following hardware setup when you want to establish a communication link between the EASY nLC system and the remote support server For information about initiating the communication link with the support server see Connecting the EASY nLC System to the Support Server on page 150 To connect the EASY nLC to the local network that has Internet capability 1 If the EASY nLC system is connected to a data system computer or an Ethernet switch as shown in Figure 24 on page 35 disconnect the Ethernet cable from the LAN port of the EASY nLC system 2 Using a Category 6 network cable connect the EASY nLC system directly to the local network that has Internet capability to access the support server see Figure 27 IMPORTANT For remote diagnostics connect the EASY n
146. n Menu Control the instrument setup and manage system configuration Page Function Go to Users Manage user accounts create edit and Creating New User Accounts on page 65 delete Connections Select the mass spectrometer that is Setting Up Communication with the Mass connected to the EASY nLC system set up Spectrometer on page 59 the communications protocol and view a contact closure wiring diagram for the selected mass spectrometer Network Set up or view how the EASY nLC system is Setting Up the Local Area Network identified in a connected computer network Connection on page 61 Consult your IT administrator before making changes to the system Time Set the internal clock in the EASY nLC Modifying the Time Settings on page 67 system and the display format used throughout the application to print date and time information Backup Save and restore backups of the system Making System Backups on page 68 database and configuration A backup includes methods batches instrument configuration and user accounts 56 EASY nLC 1000 User Guide Thermo Scientific 3 Integrated Instrument Control Software Logging In to the EASY nLC System Logging In to the EASY nLC System The EASY nLC application has a user management system that assigns specific access rights to each user When the instrument ships it contains two predefined users guest and admin The default user account is guest and does no
147. n is working Maintenance Scripts KD v 16 2 To select a maintenance script In the EASY nLC application press Maintenance gt Scripts Select a category and then the script for the specific operation you want You can also schedule some of the scripts for execution using the job queue Each of the following topics combines the category with the actual script name Thermo Scientific Prepare Purge Solvent Prepare Flush Air Prepare Precolumn Equilibration Prepare Analytical Col Equilibration Prepare Isocratic Flow Test MS Connection Test Sample Pickup Test Leaks Test Valve Check Test Back Pressure Test Autosampler Torque Test Pump Torque Calibrate Valve Tune Calibrate Flow Sensors Calibrate Reset Pressure Sensor EASY nLC 1000 User Guide 161 10 Maintenance Maintenance Scripts Prepare Purge Solvent 162 The Purge Solvent script fills the selected pump or pumps with solvent and then ejects it into the waste container Use the Purge Solvent script when exchanging solvents removing air from the solvent lines or filling the pumps EASY nLC 1000 User Guide To set the Purge Solvent script parameters Press the Parameters tab To exchange solvents use two iterations To remove air use a minimum of 5 iterations In the Category list select Prepare Press Maintenance Scripts see Figure 98 In the Name list
148. nLC system and the support server 1 If you have not already set up the support server configuration set it up as follows a Press Configuration gt Network b In the Support Server area see Figure 37 on page 62 enter the following IP address 195 41 108 93 c Press Save Configuration 2 Using a shielded Ethernet cable connect the LAN port on the back panel of the EASY nLC system see Figure 91 directly to your local network as described in Setting Up the Ethernet Connection to the Support Server on page 43 The local network must have access to the Internet and allow outgoing traffic to port 22 Figure 91 Ethernet connection between the EASY nLC system and the laboratory LAN port PROXEON Y LAN port with Internet capability 150 EASY nLC 1000 User Guide Thermo Scientific 9 Remote Support Connecting the EASY nLC System to the Support Server 3 Send a support request message and a zip file containing the appropriate log files to Technical Support as follows a Press Maintenance gt Support The Support page of the Maintenance menu appears see Figure 92 Figure 92 Support page of the Maintenance menu Thermo SCIENTIFIC Home Batch Setup Method Editor Configuration Scripts Connectto EASY nLC support Log Book A Remote Port Number 2000 Connect Status Not Connected Support 4 Message window can be used to chat with support w
149. nd Number of Injections Der Sample os ted sud UID bor tat acl Pa Rub dca ec ad ines uf 104 Starting Sample Acquisition ws 1591424 barra UE URS addc pado EE TR 108 Monitoring the RUti dso ete deere taba dackscies E eol Ert ye ede 109 Using the Overview Page in the Home Menu 0004 109 Using the Graphs Page in the Home Menu 000 000s 111 Stopping Sample Acquisition ii 21 ash seein eae EY UR Id EG ROI 113 Editing the Running Batch i iod 9er Res is A do aede Ra rata 114 Troubleshooting a Sample Run z 52e pee a EY ERUIT ERR PEE EE 117 Calibrating the Autosampler s XYZ Robot Luuuuuuueueee 119 Replacing the Autosampler Adapter Plate 1 4 cere Mc 120 Managing Plate Rotates tcc Bion dea ears d an os Aaa Ri ute M dades 121 Preparing the Autosampler for the Calibration Routines 124 Calibrating Plates venis aba 900 ona ane P3 adeo Aero edicere 125 Calibrating the Wash Bottle and Extra Vial Positions leues 129 Checking Sample Pickup os sy shies sea db ex ane ew wees 131 EASY nLC 1000 User Guide vii Contents Chapter 8 Chapter 9 Chapter 10 viii EASY nLC 1000 User Guide Troubleshooting 5 rtu Pete bre Lait ee e Rf ens 133 SYSTEM SCART P m 134 Batch RUNS ese e E eo e nu oed dbaopetide dae dabat ep A cg A 134 Au t sampler eue Asc LUE d aoa aui dac api D arg RO 3 ate aati edd 136 Contact Clostite abdito pube rp COE EO ME EE PER EE ad aod 137 NopVOtRo ese iis
150. ne else is using the EASY nLC system when restoring a backup because this backup also influences user accounts To create a system backup 1 Press Configuration gt Backup The Configuration gt Backup page opens Figure 43 Figure 43 Backup page of the Configuration menu Thermo Home Batch Setup Method Editor Maintenance SCIENTIFIC Users Backup Connections Location backup Network Time Backup Factory reset Reset Job 00 00 00 23 aug 2010 12 41 admin Exit 2 Press Backup The application makes a bak file To restore a backup file 1 In the Location list select the file that you want to restore 2 Press Restore 68 EASY nLC 1000 User Guide Restore Thermo Scientific Thermo Scientific 4 Configuring the EASY nLC System Making System Backups To reset one or all of the settings to the factory values In the Factory Reset area press Reset The Factory Reset dialog box opens Select the check boxes for the items that you do not want the system to reset The check box options are as follows Keep User Data Keep System Log Keep Maintenance Log Keep Backups Press Reset The Factory Reset dialog box closes and the items that you did not select are reset The Factory Reset does not reset the device usage counters see Checking and Resetting the Device Usage Counters on page 181 EASY nLC 1000 User Guide 69 4 Conf
151. nect the EASY nLC system directly to your local network and then open the communication link for remote support through the touch screen software Thermo Fisher Scientific Technical Support cannot initiate this communication link The EASY nLC system uses Secure Shell SSH a network protocol for secure data communication to connect to the support server which uses the Linux operating system To use the remote support feature the firewalls for your local network must allow outgoing TCP IP traffic from the EASY nLC system to the support server at IP address 195 41 108 93 port 22 When you establish the communication link with the support server the support server triggers the file compression utility on the EASY nLC system to build a zip file with the appropriate log files and then retrieves the zip file from the EASY nLC system Meanwhile the EASY nLC system sends an e mail with your supplied message and contact information to Thermo Fisher Scientific Technical Support After you send a message through the remote support feature a member of the Thermo Fisher Scientific Technical Support team will contact you Thermo Scientific EASY nLC 1000 User Guide 149 9 Remote Support Connecting the EASY nLC System to the Support Server Connecting the EASY nLC System to the Support Server Use this procedure to establish a communication link between the EASY nLC system and the support server To open a communication link between the EASY
152. ng prime the filters with methanol or acetonitrile EASY nLC 1000 User Guide 75 5 Preparing the EASY nLC Instrument for Use Preparing Solvent Bottles and Waste Containers Autosampler Wash Bottles and Waste Beaker The autosampler compartment holds the sample trays up to four wash bottles and a waste beaker see Figure 47 You can operate the instrument after installing the wash bottle that the autosampler uses for needle cleaning position W4 the wash bottle that contains solvent A for pump S position W3 and the waste beaker that collects the waste from pumps A and B and from the venting Tee through valve W To access the autosampler compartment you can manually open the tray compartment door or you can press the Eject Plate button on the Home gt Overview screen Figure 47 Autosampler compartment sciENTIFIC Vial tray Waste beaker Wash bottles W3 and W4 To install the waste beaker and prepare and install the wash bottles 1 Fill one of the wash bottles with solvent A and degas it 2 Turn on the system and make sure that the area in front of the tray compartment door is free from obstruction 3 Press Home Overview Then press Eject Plate A confirmation dialog box appears to remind you to remove obstacles from the area in front of the tray compartment before commanding the instrument to open the tray compartment door 76 EASY nLC 1000 User Guide Thermo Scientific 5 Preparing the EASY nLC In
153. ng to a new solvent The purge pump job fills the selected pump or pumps with solvent and then ejects the solvent into the waste container You can specify how many iterations of this job you want performed After purging the pumps flush them to remove any air that might be trapped inside You can specify the maximum number of iterations for this job the period of time that the pumps are being pressurized and the success criteria for stopping the operation earlier than scheduled To purge and flush pumps A and B 1 Press Maintenance Scripts The Scripts page of the Maintenance menu opens 2 Set up the purge solvents job as follows see Figure 50 a In the Category list select Prepare b In the Name list select Purge Solvent C Press the Parameters tab d Press the Purge Iterations box and type 10 with the numeric keypad This is the number of times that the pumps will completely refill and eject the solvent e Select the Purge Pump A Purge Pump B and Purge Pump S check boxes Note The pumps draw and eject solvent as follows Pump S draws solvent from bottle W3 in the autosampler bottle holder and ejects solvent into bottle W4 Pump A and pump B draw solvent from the solvent A and B bottles on top of the instrument and eject solvent to the waste cup Thermo Scientific EASY nLC 1000 User Guide 79 5 Preparing the EASY nLC Instrument for Use Purging and Flushing the Pumps Figure 50 Purge solvent job pa
154. ng up the method go to the Edit 2 5 page by pressing the right arrow Setting Up the Sample Pickup and Loading Steps 94 Use the Method Editor gt Edit 2 5 page see Figure 62 to set the parameters for picking up the sample from the well plate and loading it onto the precolumn Figure 62 Edit 2 5 page of the Method Editor wizard Thermo Home Ew Method Editor EAEan aee mam Ce T dfe Tes ela SCIENTIFIC EN Sample pickup Volume 10 00 ul 33 Flow 20 00 ul min 4 4l Sample loading Job 00 00 00 Volume ul C f AS 5 hy gt uM Flow 5 00 ul min e 11 May 2011 e S e HET 700 Bar TERR Max pressure admin Exit m 2 5 gt To set up the sample pickup parameters 1 In the Sample Pickup area press the Volume box and enter the default amount of sample to be picked up The autosampler withdraws the requested sample volume it does not pick up excess sample To prevent contamination of sample pump S the maximum volume is set to the configured sample loop size minus 2 uL For example the maximum sample pickup for a system with a 20 pL sample loop is 18 pL You can overwrite this setting when you set up the injection sequence from an external Thermo Scientific data system such as the Thermo Xcalibur data system EASY nLC 1000 User Guide Thermo Scientific 6 Running Samples Using the Integrated
155. nstrument uses high voltages that can cause personal injury Before servicing shut down the instrument and disconnect the instrument from line power Keep the top cover on while operating the instrument Do not remove protective covers from PCBs Chemical This instrument might contain hazardous chemicals Wear gloves when handling toxic carcinogenic mutagenic or corrosive or irritant chemicals Use approved containers and proper procedures to dispose waste oil Heat Before servicing the instrument allow any heated components to cool Fire Use care when operating the system in the presence of flammable gases Eye Hazard Eye damage could occur from splattered chemicals or flying particles Wear safety glasses when handling chemicals or servicing the instrument General Hazard A hazard is present that is not included in the above categories Also this symbol appears on the instrument to refer the user to instructions in this manual When the safety of a procedure is questionable contact your local Technical Support organization for Thermo Fisher Scientific San Jose Products VORSICHT Elektroschock In diesem Ger t werden Hochspannungen verwendet die Verletzungen verursachen k nnen Vor Wartungsarbeiten mu das Ger t abgeschaltet und vom Netz getrennt werden Betreiben Sie das Ger t nicht mit abgenommenem Deckel Nehmen Sie die Schutzabdeckung von Leiterplatten nicht ab Chemikalien Dieses Ger t kann
156. o 75 Autosampler Wash Bottles and Waste Beaker 0 0000000005 76 Executing Maintenance Scripts cece eee eee 78 Purging and Flushing the Putnps o6 voor eae nner oe adds 79 Tastalhtig Columns 2 15 o eodd wees an ad E acides ar ire opas 83 Connecting the Column Assembly to the Column Out and Waste In Lines odes Loo ces PLA tes Mo Metu est Bi tere AU 84 Connecting an Emitter to the Analytical Column 00 00 0 86 Using nanoViper Fittings 0 ec eee eee 87 Equilibrating Columns iau v ven dina ben eee cp Ce wa eae ieee 88 Running Samples Using the Integrated Software 91 Preparing Sample Platelet iiis obo Rb et oido x acd deba E Qus 91 Creating a Method iriso ransa pk dd TED pU boe nic ec OP ctor 92 Browsing for a Stored Method or Creating a New Method File 92 Starting the Method Editor Wizard and Selecting the Method to be Edit oae Shenae hee aciem sce oesetalac dtes dite ate E 93 Setting Up the Sample Pickup and Loading Steps lesus 94 Building the Gradient iikd ERE diper E Mowe e dade n Mod nen Ie d 96 Setting Up the Column Equilibration Steps 0 0000 eese 98 Setting Up the Autosampler Wash Step 5125s skype 100 Saving the Method Settings cc eas uer EXON Fla bbs Eja e hae ER er 102 Creatine a Baich poor coto o eoe a use VT dre eic pde Ned 103 Viewing the Batch List and Setting Up a Batch Record Ls 103 Specifying the Method Sample Positions a
157. o monitor the progress 4 Monitor the actual flow rate to become familiar with the flow pressure relationship on your particular column or columns Thermo Scientific EASY nLC 1000 User Guide 89 LLL m Running Samples Using the Integrated Software To create a method and run your first sample batch by using the integrated instrument control software follow these procedures Contents Preparing a Sample Plate Creating a Method Creating a Batch Starting Sample Acquisition Monitoring the Run Stopping Sample Acquisition Editing the Running Batch Troubleshooting a Sample Run Preparing a Sample Plate The EASY nLC instrument ships with adapters for vials 54 vials in a 6 x 8 6 configuration microplates 96 and 384 well and PCR strips To prepare the sample vials or microplates 1 Load some vials or microplate wells with your sample preferably a known standard 2 Make sure that no air is trapped in the sample vials or the microplate wells and that the sample is in the bottom of the vials or wells To do this tap the vial or microplate gently against a hard surface to have the sample move to the bottom 3 Put on the vial cap or plate mat If you are using a new plate format you must add the plate format to the list of configured plate formats and calibrate the plate as described in Chapter 7 Calibrating the Autosampler s XYZ Robot Thermo Scientific EASY nLC 1000 User Guide 91 6 Runn
158. o port 4 of valve S and the solvent line labeled Waste In connects to port 2 of valve W You can connect and enable the EASY nLC system for these column configurations Two column Setup One Column Setup Two column Setup A two column setup consists of a precolumn and an analytical column The EASY nLC 1000 system ships with a two column assembly see Figure 7 Figure 7 Two column assembly shipped with the EASY nLC 1000 system Stainless Venting Tee PEEK union steel union Flow gt Precolumn Analytical column 8 EASY nLC 1000 User Guide Thermo Scientific 1 Introduction Column Setup Options The stainless steel union connects to the Column Out tubing the plugged leg of the venting Tee connects to the Waste In tubing and the red PEEK union connects to the emitter For information about installing the two column assembly see Installing Columns on page 83 Figure 8 shows the sample loading step for a two column setup with a precolumn and an analytical column Excess solvent A exits the venting Tee through the Waste In tubing Tip When you install the two column assembly make sure that the One Column Setup check box in the EASY nLC device section on the Devices page of the Maintenance menu see Setting Up the Properties for the HPLC Device on page 70 is clear When the One Column Setup check box is clear not selected valve W moves to position 1 6 during the sample loading step Ex
159. od Settings Saving the Method Settings After you enter the method settings on page 2 5 to 5 5 of the Method Editor wizard save the method To save the method Press Save in the top right corner of the Method Editor wizard 102 EASY nLC 1000 User Guide Thermo Scientific 6 Running Samples Using the Integrated Software Creating a Batch Creating a Batch Use the Batch Setup gt Edit page to set up and schedule batches for sample acquisition on the EASY nLC system See also Preparing a Sample Plate on page 91 and Creating a Method on page 92 To create a batch follow these procedures Viewing the Batch List and Setting Up a Batch Record Specifying the Method Sample Positions and Number of Injections Per Sample Viewing the Batch List and Setting Up a Batch Record Use the Batch Setup gt File page to view a list of stored batches import a batch from another system and create an empty batch record name a new batch and select its folder location To view a list of batches 1 Press Batch Setup gt File The Batch Setup gt File page opens see Figure 66 Figure 66 File page of the Batch Setup menu Thermo PH Edit Copy Created LastRun m 6x BSA 30min 23 08 10 admin Delete gt public super Edit WEET Schedule Job 00 00 00 6 x BSA 30min 23 aug 2010 12 35 admin Exit 2 To view your batches in the Path column press the
160. olvents Solvent reagent Specification Water LC MS grade Acetonitrile LC MS grade Formic acid 99 5 LC MS grade 0 1 formic acid in water LC MS grade 0 1 formic acid in acetonitrile LC MS grade IMPORTANT Use only LC MS grade solvent Do not filter solvents Filtering solvents can introduce contamination CAUTION Store and handle all chemicals in accordance with standard safety procedures 74 EASY nLC 1000 User Guide Thermo Scientific 5 Preparing the EASY nLC Instrument for Use Preparing Solvent Bottles and Waste Containers To order LC MS grade solvents from Thermo Fisher Scientific Click this icon Go to www FisherLCMS com and click the Solvents tab Solvent A and B Bottles Thermo Scientific Follow these recommended steps to prepare the two solvent bottles bd 1 To prepare the solvent A and B bottles Fill the 25 ml Schott Duran blue cap bottles with the mobile phase solvents Degas the solvents by sonicating the solvent bottles in a sonication bath or by sparging the solvents with helium gas Place the bottles in the holder on top of the instrument solvent A bottle in the front and solvent B bottle in the back position Mount the inline filter assembly on the blue cap lids as shown in Figure 45 and Figure 46 Figure 45 Inline filter assembly exploded view Bu E Figure 46 Assembled inline filter IMPORTANT To establish proper surface wetti
161. on PepMap columns as supplied at delivery and by using the standard wash procedure for the autosampler Autosampler sample pickup volume range 0 1 to 18 pL with the standard 20 pL loop 0 1 to 58 pL with a 60 pL loop Injection reproducibility injection RSD 0 2 at 5 uL pickup 3 096 at 0 1 pL pickup Injection linearity 0 9985 at 0 5 to 10 uL injection volume Autosampler formats 6x 8 Vials 6 Vials 1 x 96 well MTP 6 Vials 1 x 384 well MTP 6 Vials 2x48 PCR strips 6 Vials 4 x 24 PCR strips 6 Vials Autosampler cooling EASY nLC 1000 User Guide maximum cooling 20 C 68 F below the ambient room temperature typical setting 7 C 45 F Thermo Scientific Technical Specifications 1 Introduction Specifications These tables list the technical specifications for the EASY nLC system General specifications Table 7 Physical specifications Table 8 Electrical specifications Table 9 Communication specifications Table 10 Components Table 11 Table 7 General specifications Item Specification Sound pressure level 70 dBA Operating temperature 5 to 30 C Storage temperature 25 to 60 C Humidity 20 to 80 RH non condensing Sample viscosity 0 1 to 5 cP Solvent A Water with 0 1 formic acid Solvent B Acetonitrile with 0 1 formic acid Safety According to IEC 61010 Safety requirements for electrical equipment for measurement
162. or the analytical column for a one column setup The Load Sample step includes this sequence of actions Action 1 Valve S switches to position 1 6 Valve W does one of the following Switches to position 1 6 for a two column system allowing excess solvent A to flow to the waste beaker e Remains in the 1 2 position for a one column system directing the solvent flow through the analytical column 2 Pump A pushes the specified solvent volume through the sample loop at a specified maximum pressure or the specified flow rate In a two column system solvent A vents to the waste beaker through valve W Figure 14 shows the Load Sample step of a sample run for a two column setup Valves A B S and W are in the 1 6 position Thermo Scientific EASY nLC 1000 User Guide 17 1 Introduction Solvent Delivery and Sample Pickup Systems Figure 14 Load Sample step Rear air Pump A segment Pressure my Len J Flow Ss 7 E i Column Out line Mixing Tee Pump B Q Waste In line Pressure Flow sensor sensor Precolumn Venting O r m mo Analytical column lt mo Centered p Waste beaker Solvent A Ec mhi Solvent B ENENEE Sample Thermo Scientific 18 EASY nLC 1000 User Guide 1 Introduction Solvent Delivery and Sample Pickup Systems Prealign A B Prepare Gradient Step Before the gradient begins this sequence of actions occurs
163. osampler configuration pops up when you run the batch Contact Closure Plate format deleted from your configuration with the Delete button from Maintenance gt Devices gt Autosampler gt Tools 8 Troubleshooting Contact Closure Action Do the following 1 Eject the tray 2 Remove the left side panel visually inspect the needle tip The needle tip should not be bent or damaged in any way 3 If there is any residue on the needle tip use tissue with some ethanol to wipe it If you want to run the batch you must create the plate format again Table 24 contains troubleshooting tips for contact closure problems Table 24 Contact closure troubleshooting tips Symptom The mass spectrometer is waiting for a contact closure signal Or The EASY nLC system is waiting for a ready signal from the mass spectrometer Thermo Scientific Possible causes Incorrect contact closure setup Action If you are running two way contact closure with feedback from the mass spectrometer set the contact closure Protocol setting to Two way on the Configuration gt Connections page If you are running one way contact closure that is the EASY nLC system sends a start signal to the mass spectrometer but feedback from the mass spectrometer is ignored set the contact closure Protocol setting to One way on the Configuration gt Connections page EASY nLC 1000 User Guide 137 8 Troubleshooting Network Access
164. paring the EASY nLC Instrument for Use Installing Columns Connecting an Emitter to the Analytical Column 86 Before you mount the column assembly onto the ion source connect an emitter to the analytical column EASY nLC 1000 User Guide CAUTION Because the emitter tip is sharp enough to puncture skin and easily damaged do not touch it To connect an emitter to the PEEK union If you are using the preassembled column assembly disconnect the analytical column from the PEEK union Connect the white distance gauge plug to one end of the PEEK union Using a sleeve connect the analytical column to the other end of the PEEK union Thread the blunt end of the emitter through the adapter sleeve Ensure that the blunt end of the emitter does not protrude from the sleeve by more than 1 mm see Figure 56 Figure 56 Sleeved emitter Blunt end Adapter sleeve Emitter of the tip emitter 5 To ensure proper seating slide the blunt end of the sleeved emitter through the PEEK nut until it protrudes slightly approximately 1 to 2 mm from the front of the fitting 6 As you gently press the sleeved emitter against the union port screw the nut into the port until fingertight Be careful not to overtighten the fitting Thermo Scientific 5 Preparing the EASY nLC Instrument for Use Using nanoViper Fittings Using nanoViper Fittings For the EASY nLC system most of the plumbing connections are made with nanoViper fit
165. ple file 172 22 50 18 and then press ENTER A login dialog box appears You need a valid user name and password to enter the file space The user name and password are the same as those on the EASY nLC system For example if you havent changed the default user name and password the user name is admin and the password is admin 2 Enter the same user name and password that you use to log in locally to the EASY nLC system Modifying User Permissions The four types of users are Guest default Normal Super user and Administrator Each user type has access to different levels of functionality in the EASY nLC application Table 14 User types and permission levels for each menu Menu User type Guest Normal Super user Administrator Home Read only Read Write Read Write Read Write Batch Setup Read only Read Write Read Write Read Write Method Editor Read only Read Write Read Write Read Write Maintenance N A N A Read Write Read Write Configuration N A N A N A Read Write User has read only access b User has read write access Having a Guest user account means you can access the top menu but not enter data or issue commands to the system If a feature is not available the application grays blanks it out so the user cannot access that function Follow these procedures to change passwords and create new user accounts Changing the Administrator Password Creating New User Accounts Changing Your Passwor
166. port server setting up the hardware connections 43 system overview monitoring 109 system startup troubleshooting 134 T technical specifications 29 technical support contacting xv temperature maintaining stable 128 manual control 147 specification 36 time setting 67 touch screen using 47 transport instructions 191 trap column See precolumn tray compartment accessing 3 47 troubleshooting autosampler 136 contact closure 137 network access 138 running a batch 134 sample runs 117 system components 138 system startup 134 tubing requirements 194 turning off the EASY nLC 58 two column setup description 8 installing 84 Thermo Scientific U URLs consumable parts xv customer manuals xii usage counters device 181 USB ports EASY nLC 7 153 USB storage device copying system files 153 user interface layout 49 user permissions 63 V Valve Check script 174 valve position description 12 manual control 141 Valve Tune script 177 venting Tee connections 9 10 84 85 purpose 13 15 version application 49 vials extra vial positions calibrating 129 plate format calibrating 125 preparing sample gJ volume maximum custom wash solvent volume per step 101 sample loading step 95 sample pickup step 94 W warranty 193 wash bottles calibrating W4 bottle with insert 129 description 3 preparing 76 wash step autosampler 23 100 waste beaker description 4 installing 76 Waste In tubing 4 9 84 water solvent requ
167. ps the sample processing In this situation the safest approach is to press Cancel Batch and then go to the Scripts page of the Maintenance menu see Executing Maintenance Scripts on page 78 Here you can try to localize and fix the error by using the maintenance scripts see Maintenance Scripts on page 161 After you fix the problem reschedule the batch possibly changing the number of samples their well positions or both Thermo Scientific EASY nLC 1000 User Guide 117 LLL MM Calibrating the Autosampler s XYZ Robot To calibrate the autosamplers XYZ robot follow the instructions in this chapter The calibration covers the following areas of the autosampler Microtiter plate or vial plate Extra vials Waste bottle with needle wash insert Wash solvent bottles Calibrate the autosampler in the following situations When you want to use a new type of vial or microwell plate When you would like to replace the needle For problems with the sample pickup The needle is not placed in the center of the well or not all of the liquid is picked up from one or more of the vials For problems with the wash waste containers The needle is not placed in the center of the bottle Contents Replacing the Autosampler Adapter Plate Managing Plate Formats Preparing the Autosampler for the Calibration Routines e Calibrating Plates e Calibrating the Wash Bottle and Extra Vial Positions C
168. r and control the LC MS system from other computers on the intranet For information about setting up a remote desktop connection refer to the Microsoft Windows operating system Help 40 EASY nLC 1000 User Guide Thermo Scientific itN v Thermo Scientific 2 Installing the EASY nLC Instrument Back Panel Connections To connect the Ethernet cables for an LC MS system controlled from a data system computer Connect the EASY nLC system and the Thermo Scientific mass spectrometer to the Ethernet switch as follows a Plug a shielded Ethernet cable into the LAN port on the instruments back panel b Plug the other end of the cable into the Ethernet switch Connect the Ethernet switch to the data system computer as follows a Verify that the IP address for the dedicated Ethernet card is set to 172 16 0 101 b Pluga shielded Ethernet cable into the appropriate Ethernet port in the data system computer c Plug the other end of the cable into the Ethernet switch If the Ethernet switch has a power save button make sure that the button is in the Off position The current model of the Ethernet switch that ships at the end of 2011 or later with Thermo Scientific mass spectrometers has a power save button labeled ECO friendly IMPORTANT When the power save feature is on the instruments can lose communication with the data system computer To connect the data system computer to the intranet go to the next p
169. r to loosen the fuse holder 4 Pull the fuse holder out of the power entry module Figure 96 Replacing the main power fuse V es Cod B Using a flat blade screwdriver loosen the Turn off the power and pull the power plug fuse holder out of the power receptacle 158 EASY nLC 1000 User Guide Thermo Scientific 10 Maintenance Daily Maintenance 5 Install the appropriate fuse as follows a Do one of the following Insert the 5 A fuse into the slot that aligns with the white triangle at the end of the 110 120 V line power text nsert the 2 5 A fuse into the slot that aligns with the white triangle at the end of the 220 240 V text b Make sure that the fuse ends align with the mounting brackets Note The fuse holder holds two fuses One fuse is for a 220 240 V line power and the other is for 110 120 V line power 6 Insert the fuse holder into the power entry module in the orientation that corresponds to the operating power The triangle to the right of the voltage rating points toward the white mark at the bottom of the power entry module see Figure 97 Figure 97 Power entry module A 0ZV 0LL AOGZ 30 STIGIN 830 23AY LNSNANOINN M3AO014N3 3 n4 ADSZ HLM AINO 39N 220 240 V 9 Appropriate orientation for 220 240 line voltage Daily Maintenance Check the solvent levels on a daily basis To check solvent levels 1 Visually inspect solvent bottle A solvent bottl
170. rameters Thermo Home Batch Setup Method Editor vlaintenance Configuration seris pases ja f f fr Pump A X v bd Log Book repare Furge so vent w Desired flow Real flow Pressure Support 300 000 0 1 000 0 250 000 0 Devices 750 0 200 000 0 m 150 000 0 500 0 5 100 000 0 Ei 2500 2 50 000 0 0 0 00 ES NEEDED US Time min Pump B J Desired flow Real flow Pressure Job 00 00 21 300 000 0 1 000 0 250 000 0 I 7500 200 000 0 T E 11 May 2011 150 000 0 500 0 5 SET 1000000 F 2500 admir 50 000 0 Schedule 0 0 n Exit NEU ENDE UNES Time min 3 To save these settings and continue press Schedule The Queue page of the Home menu appears 4 Set up the flush air job as follows see Figure 51 a Press Maintenance Scripts b In the Category list select Prepare c Inthe Name list select Flush Air d Press the Parameters tab e Press the Flush Vol Threshold pL box and type 12 with the numeric keypad This values helps to ensure an acceptable amount of solvent compressibility f Select the Flush Pump A Flush Pump B and Flush Pump S check boxes 80 EASY nLC 1000 User Guide Thermo Scientific Thermo Scientific Figure 51 Flush air job parameters Th SCIENTIFIC Log Book Support Devices Job 00 00 21 11 May 2011 11 51 admin Home Batc Category Name 5 Preparing t
171. ration routine 1 Install the appropriate adapter plate 2 To calibrate the vial or well positions on a plate do one of the following To calibrate the 6 x 8 vial positions remove the vial caps from two vials and load them into the adapter plate in positions Al and F8 To calibrate a microwell plate remove the mat or cover from the microwell plate and load the microwell plate onto the adapter plate 3 Open the Tools view for the autosampler as follows a Press Maintenance Devices b In the Devices list select the autosampler c Press the Tools tab 4 In the Plate area do the following a Select the appropriate plate format from the list or create a new plate format To create and select plate formats see Managing Plate Formats on page 121 b Press Use 5 Remove the left side panel so that you can watch the movement of the needle To calibrate the plate go to the next topic Calibrating Plates To prepare the autosampler for the V1 and W4 calibration routine 1 Place an empty vial in position V1 The V1 position is not available for the microtiter plate formates 2 Prepare the bottle for position W4 used for ejecting waste and cleaning the outside of the injection needle See Autosampler Wash Bottles and Waste Beaker on page 76 124 EASY nLC 1000 User Guide Thermo Scientific 7 Calibrating the Autosampler s XYZ Robot Calibrating Plates 3 Install the wash bottle in position W4 IMPOR
172. rd 44 to line power 38 to the data system computer 41 to the network 61 consumable parts list 195 EASY nLC 1000 User Guide 197 Index D contact closure cables ordering 39 configuration setting 59 troubleshooting 137 with the mass spectrometer 39 contamination declaration 192 preventing 142 cooler temperature checking 160 manual control 147 creating amethod 93 new user accounts 65 plate formats 121 Custom Wash sample pickup system 101 customer service contacting xvi Cycles autosampler wash 101 daily maintenance 159 data system computer connecting to the Ethernet switch 41 connecting to the laboratory LAN port 41 using to access folders on the EASY nLC system s computer 42 data types graphs 111 Declaration of Conformity xxi Declaration of Contamination 192 devices configuring 70 usage counters 181 dimensions EASY nLC instrument 29 E EASY nLC description 2 Eject Plate button using 47 76 emitter installing 86 equilibrating analytical column 16 89 precolumn 15 88 Ethernet cables connecting data system computer 41 EASY nLC system to the intranet 42 EASY nLC system to the support server 43 Ethernet switch 41 Europe customer service for xvii Exit button 58 198 EASY nLC 1000 User Guide F Fast Inspection option 178 filling a pump with solvent 143 firewalls laboratory network access 36 fittings and adapters column assembly 9 flow lines tubing requirements 194 flow rate determinin
173. results appear in the Search Result table Checking and Resetting the Device Usage Counters The EASY nLC system tracks the volume pumped by pumps A B and S and the number of valve and rotor shifts for valves A B and S KD v l 2 Thermo Scientific To view the device usage values Press Maintenance gt Devices Do one the following To view the volume pumped by a pump select the pump from the list of devices To view the number of valve and rotor shifts for a valve select the valve from the list of devices Press the Summary tab The Summary view opens To reset the volume pumped or reset the rotor shifts to zero Open the appropriate Summary page Press Reset For a pump the value in the Intermediate Volume box resets to 0 For a valve the value in the Rotor Shifts box resets to 0 EASY nLC 1000 User Guide 181 0 MNM External Devices To install and use the Advion RePlay device follow the instructions in this appendix Note Currently the EASY nLC system supports only the Advion RePlay device Thermo Fisher Scientific might choose to support additional external devices for use with the EASY nLC instrument in future releases The RePlay device was specifically developed for nanoflow LC MS analysis It splits the sample from one injection so a second analysis is provided with no additional sample required The RePlay device consists of a primary column a six port valve a flow sen
174. ript under the Maintenance menu tab Category Name f Prepare J f Flush air Output Parameters Flush air from pumps Make sure to check solvent levels before running Schedule 132 EASY nLC 1000 User Guide Category Name fr J f Flush air Schedule Category Description Parameters Output Flush air started Pump A Iteration 1 Pump B Iteration 1 Pump B Refilling Pump A Refilling Schedule STOP Thermo Scientific LLL mM Troubleshooting To troubleshoot problems with the EASY nLC system follow the troubleshooting tips in this chapter To use the manual controls accessed from the Home Overview page follow the procedures in Manual Controls on page 141 Contents System Startup Batch Runs Autosampler Contact Closure Network Access System Component States Valves Pumps Autosampler and Plate Cooler Miscellaneous Manual Controls Thermo Scientific EASY nLC 1000 User Guide 133 8 Troubleshooting System Startup System Startup Table 21 contains troubleshooting tips for system startup problems Table 21 Startup troubleshooting tips Symptom Dark monitor Possible causes Broken or open main power fuse Defective monitor Action 1 Turn on the power to the instrument 2 Remove the right side panel of the EASY nLC instrument 3 If there is no light on the pumps turn off t
175. rocedure To connect the data system computer to the intranet To connect the data system computer to the intranet If the data system computer does not already have a second network card install one Using a shielded Ethernet cable connect the network card s LAN port to a laboratory LAN port with intranet access When the data system computer is connected to a laboratory LAN port you can access the admin folder on the EASY nLC system s computer hard drive To control the LC MS system remotely from another computer on the intranet Connect the hardware as described in these procedures To connect the Ethernet cables for an LC MS system controlled from a data system computer To connect the data system computer to the intranet Set up a remote desktop connection between the data system computer and the remote local area computer For information about setting up a remote desktop connection refer to the Windows operating system Help EASY nLC 1000 User Guide 41 2 Installing the EASY nLC Instrument Back Panel Connections Setting Up the Ethernet Connection to a Local Network for Data Exchange You can access the chromatographic methods and injection batches stored on the EASY nLC system s computer hard drive after you make the following connections When you connect a stand alone EASY nLC system to a laboratory LAN port with intranet access you can access these files from other computers on the intr
176. ructions Laboratory Requirements Back Panel Connections Lifting Instructions The instrument weighs 35 kg 77 2 lb For safety reasons use two people to move the instrument to a table cart for transport and wear gloves CAUTION At 35 kg 77 2 Ib the EASY nLC instrument is too heavy for one person alone to lift When moving the system use two people to place it on a table cart for transport Thermo Scientific EASY nLC 1000 User Guide 33 2 Installing the EASY nLC Instrument Laboratory Requirements Figure 23 shows the lift points for the EASY nLC instrument Figure 23 Lifting the EASY nLC 1000 system by hand Thermo EASY nl 1000 Laboratory Requirements The following topics describe the laboratory requirements for the EASY nLC system For more information refer to the EASY nLC Preinstallation Requirements Guide Benchtop Requirements Internet Access Power and Fuse Requirements Temperature and Humidity Requirements Benchtop Requirements Place the EASY nLC system on a benchtop or movable table that can support a minimum of two times the system weight Allow for at least 15 cm 6 in of free space at the back of the instrument for proper air circulation The dimensions of the EASY nLC system are as follows e Width 35 cm 14 in Depth 38 cm 15 in Height 45 cm 18 in To minimize extra column volume between the LC column outlet and the detector inlet place the EASY nL
177. s d PP Search le Folders ial Address E vj Go Size Type Date Modified File and Folder Tasks jbatchleg zip 31KB Compressed 24 10 2005 12 23 S 3 etc zip 3KB Compressed 24 10 2005 12 23 LJ export zip 1KB Compressed 24 10 2005 12 23 G Make a new folder Publish this Folder to logfiles zip 35KB Compressed 24 10 2005 12 23 the Web Pus e Share Huc Felder maintlog zip 31KB Compressed 24 10 2005 12 23 4 My Computer Thermo Scientific 9 Remote Support Saving System Files on a USB Removable Storage Device The files are as follows batchlog zip Contains one folder for each batch you have run with information on samples methods and EASY nLC device performance etc zip Contains system configuration files export zip Contains exported batches and methods per user and system backup logfiles zip Contains system log files with information on overall system performance maintlog zip Contains one folder for each maintenance script you have run with information on EASY nLC device performance If you have problems with your system forward the files to Thermo Fisher Scientific Technical Support for assistance Thermo Scientific EASY nLC 1000 User Guide 155 ee AN Maintenance To familiarize yourself with the maintenance schedule and maintenance scripts for the EASY nLC system review this chapter Following the maintenance schedule and using the maintenance scripts will help ensure the
178. s de las tarjetas de circuito impreso Qu mica El instrumento puede contener productos quimicos peligrosos Utilice guantes al manejar productos quimicos t xicos carcinogenos mutagenos o corrosivos irritantes Utilice recipientes y procedimientos aprobados para deshacerse del aceite usado Altas temperaturas Permita que los componentes se enfr en ante de efectuar servicio de mantenimiento Fuego Tenga cuidado al operar el sistema en presencia de gases inflamables Peligro par los ojos Las salicaduras de productos qu micos o particulas que salten bruscamente pueden causar lesiones en los ojos Utilice anteojos protectores al manipular productos qu micos o al darle servicio de mantenimiento al instrumento Peligro general Significa que existe un peligro no incluido en las categorias anteriores Este simbolo tambi n se utiliza en el instrumento par referir al usuario a las instrucciones contenidas en este manual Cuando la certidumbre acerca de un procedimiento sea dudosa antes de proseguir pongase en contacto con la Oficina de Asistencia Tecnica local para los productos de Thermo Fisher Scientific San Jose AVVERTENZA Shock da folgorazione l apparecchio alimentato da corrente ad alta tensione che puo provocare lesioni fisiche Prima di effettuare qualsiasi intervento di manutenzione occorre spegnere ed isolare l apparecchio dalla linea elettrica Non attivare lo strumento senza lo schermo superiore
179. s produits chimiques dangereux peuvent se trouver dans l instrument Portez des gants pour manipuler tous produits chimiques toxiques canc rig nes mutag nes ou corrosifs irritants Utiliser des r cipients et des proc dures homologu es pour se d barrasser des d chets d huile Haute Temperature Permettre aux composants chauff s de refroidir avant tout intervention Incendie Agir avec pr caution lors de l utilisation du syst me en pr sence de gaz inflammables Danger pour les yeux Des projections chimiques liquides ou solides peuvent tre dangereuses pour les yeux Porter des lunettes de protection lors de toute manipulation de produit chimique ou pour toute intervention sur l instrument Danger g n ral Indique la pr sence d un risque n appartenant pas aux cat gories cit es plus haut Ce symbole figure galement sur l instrument pour renvoyer l utilisateur aux instructions du pr sent manuel Si la s ret d une proc dure est incertaine avant de continuer contacter le plus proche Service Client le pour les produits de Thermo Fisher Scientific San Jose PRECAUCION Descarga el ctrica Este instrumento utiliza altas tensiones capaces de producir lesiones personales Antes de dar servicio de mantenimiento al instrumento ste debera apagarse y desconectarse de la l nea de alimentacion el ctrica No opere el instrumento sin sus cubiertas exteriores quitadas No remueva las cubiertas protectora
180. se Equilibrating Columns Equilibrating Columns After you initially install the column assembly equilibrate the column or columns and determine an appropriate flow rate for the sample loading step see Setting Up the Sample Pickup and Loading Steps on page 94 of the chromatographic method To equilibrate the precolumn and determine the flow rate for sample loading 1 Open the Precolumn Equilibration script and set up the script parameters as described in Prepare Precolumn Equilibration on page 164 Thermo Fisher Scientific recommends running the equilibration at a set pressure rather than a set flow to make sure the column pressure limit 800 bar and the instrument pressure limit 1000 bar are not exceeded see Figure 58 If the flow field is left empty the pump will run at the specified pressure For best results use an equilibration volume of 10 column volumes Figure 58 Precolumn equilibration parameters Thermo Rian cue MM o ela Maintenance Eeeeh eiaeia SCIENTIFIC Scripts Category Name f fs f il No graph X Log Book Prepare vw Precolumn equil Support Devices f No qraph Job 00 05 02 Sample 00 05 00 Gradient 00 00 2 May 2011 14 02 admin Schedule Exit 2 Press START The default graphs appear in the two graph windows but you can change the selections from their corresponding lists These graphs help you to
181. ses the system tracks the number of valve shifts for each valve see Checking and Resetting the Device Usage Counters on page 181 12 EASY nLC 1000 User Guide Thermo Scientific 1 Introduction Solvent Delivery and Sample Pickup Systems Depending on the valve position the valves perform these functions Component Valves A and B Function Direct the solvent flow from syringe pump A and B respectively 1 2 position Directs the solvent flow toward the check valve When the valve is in the 1 2 position the pump draws solvent from the solvent bottle on top of the instrument or empties solvent to the waste beaker see Figure 12 1 6 position Directs the solvent flow toward the mixing Tee Centered Prevents backflow into the solvent line upstream of the mixing Tee Valve S Directs the solvent flow from syringe pump S and the solvent flow from the mixing Tee 1 2 position The solvent flow bypasses the sample loop 1 6 position The solvent flow passes through the sample loop Centered N A Valve W Directs the solvent flow through the venting Tee to the waste beaker or provides pressure venting to the system 1 2 position Provides backpressure to the venting Tee 1 6 position Directs the solvent flow from the venting Tee to the waste beaker Centered N A Pump A and Pump B Solvent Delivery System Pumps A and B draw solvent from the solvent bottles on top of the EASY nLC system
182. sor tubing a control panel and a secondary column emitter It performs a second analysis of one sample without a reinjection which allows for twice the analytical possibilities from every nanolC injection For more information visit the Advion Web site www advion com biosystems replay index php Thermo Fisher Scientific does not offer support for or is in any way responsible for the functionality of the RePlay device itself and the associated tubing and columns that it requires Contents Connecting the RePlay Device to the EASY nLC Instrument Adding the RePlay Device to the EASY nLC Device List Setting Up a Method with the RePlay Device Monitoring the Run of a RePlay Method Additional Run Time for a RePlay Experiment Thermo Scientific EASY nLC 1000 User Guide 183 A External Devices Connecting the RePlay Device to the EASY nLC Instrument Connecting the RePlay Device to the EASY nLC Instrument Before you can use the RePlay device with the EASY nLC system you must connect the contact closure cables and the solvent lines The Replay device has a remote port on its back panel and a six port valve see Figure 113 on its front panel Figure 113 Front panel of the Replay device courtesy of the Advion Inc Web site Valve To connect the RePlay device to the EASY nLC system 1 Turn off the EASY nLC instrument 2 Connect the Remote cable port on the back panel of the RePlay device to the Out3 pins on the b
183. ssociated pump see Flow Sensors on page 11 Mixing Tee Display the B solvent composition Autosampler Displays the active pending and finished samples for a batch run and the temperature of the cooling unit The valve icon shows the position of the associated valve see Six Port Valves on page 12 For more information about viewing the system status see Monitoring the Run on page 109 You can access the manual controls for the system by pressing the pump valve and autosampler icons on the Home Overview page Only use these controls for troubleshooting hardware problems For information about using these controls see Manual Controls on page 141 Interactive component Action Pump A B or S Amm Opens the Pump dialog box where you can change the flow rate refill or empty the pump and start and stop the pump flow Valve A B S or W Aa Opens the Valve dialog box where you can E y change the valve position Autosampler z Active efending Opens the Autosampler dialog box where you 22222222 S can work with the XYZ robot change the cooler 000000090 O 22222222 fof temperature or turn off the temperature control oo ooooo o unit 7 0 C Thermo Scientific EASY nLC 1000 User Guide 51 3 Integrated Instrument Control Software Application Menu Structure Application Menu Structure Table 13 lists the structure of the touch screen applications user interface The application has five menu tabs at the
184. starts processing the batch 108 EASY nLC 1000 User Guide Thermo Scientific 6 Running Samples Using the Integrated Software Monitoring the Run Monitoring the Run You can monitor the run and the system status during analysis from two different pages of the Home menu Overview or Graphs Follow these procedures to monitor the run and view the system status Using the Overview Page in the Home Menu Using the Graphs Page in the Home Menu Using the Overview Page in the Home Menu The Overview page provides a full schematic overview of the system complete with real time updating of all critical component data Figure 71 Figure 71 Overview page of the Home menu Pump A status Current sample and status i Current step Valve A position in the sample run Flow sensor A readback Thermo v E etl Configuration i0bar LIP disabled a po din Idle fli w disabled Graphs R 0 2 bar Queue 100 0 yl min 136 9 140 0 ul Solvent A 8 4 bar 100 0 ul min 47 7 140 0 ul Refill A B olum n ical column Solvent B ash refill Job 00 00 08 Sample 00 00 08 Gradient 00 00 11 May 2011 1 O Al Sample 1 admin 20110511 11 56 S113 999JP5A 40 min 1 Samples 11 12 52 11 5 12 52 admin Next Exit Thermo Scientific EASY nLC 1000 User Guide 109 6 Running Samples Using the Integrated Software Monitoring the Run The system schematic provides information on these items H
185. stem lowers the flow rate based on the flow setting pressure setting or both of these settings in the method and equilibrates the analytical column Pickup sample Pump S draws sample from a vial or well position and loads the sample into the sample loop attached to valve S Load sample With valve S in position 1 6 pump A delivers solvent to the system flushing sample out of the sample loop and onto the precolumn or the analytical column Valve W is in position 1 6 for a two column system and position 1 2 for a one column system Prealign A B The system vents through the Waste In line to a precalculated pressure Pump B builds up Prepare Gradient pressure to match the precalculated pressure of pump A Then valves S and W switch to position 1 2 and the AFC system takes control of pumps A and B Gradient Pumps A and B deliver solvent to the system As the percent composition of solvent B increases analytes elute off the column or columns Autosampler wash refill S Thermo Scientific Pump S draws solvent from one or more wash bottles washes the autosampler needle and the sample loop and then refills During sample runs the active steps are highlighted in bold on the Home Overview screen see Figure 19 and Figure 71 on page 109 Figure 19 Current step area of the Home Overview screen Refill AB Pickup sample EASY nLC 1000 User Guide 23 1 Introduction Predefined Steps for Sample Runs
186. strument for Use Preparing Solvent Bottles and Waste Containers 4 Press Accept The tray compartment door opens 5 Put the bottle with the needle wash insert into position W4 see Figure 48 CAUTION You must place the wash bottle with the needle wash insert in position W4 Any other position could lead to instrument malfunction and possible breakdown Figure 48 Wash bottle with needle wash insert and view of the four positions on the autosampler bottle holder eececeosdce soe se soe o6 o o Wash bottle with Autosampler needle wash insert bottle holder 6 Put a wash bottle that contains solvent A into position W3 Pump S draws solvent from this position You can place wash solvents for customized washing procedures in positions W1 and W2 7 Make sure all the bottles are installed with the lids fitting tightly 8 Place the waste container a 250 mL plastic beaker into the compartment on the right side of the autosampler compartment 9 Press Insert Plate to move the plate back into the instrument Thermo Scientific EASY nLC 1000 User Guide 71 5 Preparing the EASY nLC Instrument for Use Executing Maintenance Scripts Executing Maintenance Scripts The EASY nLC application has a set of maintenance scripts that you can access from the Scripts page Figure 49 of the Maintenance menu Before you start any of the maintenance scripts prepare the instrument as described in Preparing Solv
187. substances Were any of the harmful substances e Radioactive Yes No Toxic Yes No e Corrosive Yes No Explosive Yes No Has the equipment been properly decontaminated and or cleaned before being returned Yes No Legally binding declaration I hereby declare that the information supplied on this form is accurate and sufficient to judge any contamination level Name Job title Organization Address Telephone Fax E mail Signature 192 EASY nLC 1000 User Guide Thermo Scientific M Consumables and Replacement Parts To order consumables and replacement parts for the EASY nLC system see the ordering information and solvent system schematics in this appendix Contents Ordering Information Solvent System Schematic Ordering Information To obtain ordering information for the EASY nLC instruments spare parts and accessories go to the following Web site http www proxeon com productrange nano lC easy nlc 1000 accessories spares These EASY nLC parts are consumable parts and not covered by the normal first year Limited Warranty offered by Thermo Fisher Scientific or any other service contract agreement containing extended warranty coverage All flow lines including Tee pieces and fittings nuts ferrules sleeves and valve blank stops Check valves Solvent filters inline filters and all associated filter holders Pump piston seals
188. t entered in the Sample Loading area The LSP feature ensures that the solvent delivery system loads each sample onto the column at the same flow rate Because the flow rate used to load the sample onto the column can affect sample to sample reproducibility for quantitation experiments use the LSP feature to maximize sample to sample reproducibility for quantitation experiments LSP is only active during the sample loading step of a run To use the LSP feature correctly you must enter both a flow and a maximum pressure limit for sample loading in the method file To determine an appropriate flow rate for your LC columns use the precolumn and analytical column equilibration scripts Thermo Scientific EASY nLC 1000 User Guide 71 LLL AM Preparing the EASY nLC Instrument for Use To prepare the EASY nLC instrument for use log in to the system with either Super user or Administrator privileges see Logging In to the EASY nLC System on page 57 and then follow these procedures Contents Preparing Solvent Bottles and Waste Containers e Executing Maintenance Scripts Purging and Flushing the Pumps Installing Columns Using nanoViper Fittings Equilibrating Columns Preparing Solvent Bottles and Waste Containers As you prepare the solvent bottles and empty the waste containers you work with hazardous solvents and chemicals such as methanol acetonitrile formic acid and so on Before working with hazardous solvents
189. t number SC903 fused silica To install the column assembly follow these procedures Connecting the Column Assembly to the Column Out and Waste In Lines Connecting an Emitter to the Analytical Column Thermo Scientific EASY nLC 1000 User Guide 83 5 Preparing the EASY nLC Instrument for Use Installing Columns Connecting the Column Assembly to the Column Out and Waste In Lines Make sure that you connect the venting Tee to the Waste In line for both the one column and two column setups CAUTION Wear gloves when handling the solvent lines To connect the column assembly to the instrument 1 Do one of the following e Fora two column setup go to step 2 Foraone column setup go to step 3 2 For a two column setup connect the Column Out line to the stainless steel union as follows a Slightly loosen the nanoViper fitting connected to the stainless steel union b Insert the nanoViper fitting on the Column Out line into the other end of the stainless steel union and slowly tighten the fitting until you feel resistance c Tighten both fittings by an additional 45 degrees 1 8 turn Do not tighten the fittings by more than a 1 4 turn CAUTION Because the fittings are sealing against each other inside the union do not tighten them by more than 90 degrees 1 4 turn Overtightening the fittings can irreparably damage their sealing surfaces For more information about working with nanoViper fittings see Using nanoVip
190. t require a password With this account you can see Thermo Scientific and monitor the system but you cannot enter any new information To start using or configuring the EASY nLC system In the User list select admin see Figure 34 In the Password box enter admin Press Accept the factory password for the admin account is also admin The first time you start the application it automatically logs you in as a guest Guest appears above the Login button Figure 34 FASY nLC login dialog box 4 User admin gt Password ge mm N Accept Cancel j 1 J IMPORTANT Change the admin password as soon as possible for security reasons If security is an issue change the admin password see Figure 35 To log off the EASY nLC system Press Exit A confirmation dialog box opens see Figure 35 Figure 35 Confirmation dialog box that opens when you press Exit on the lower left corner of the screen dministrator Logout ro B Change password J Stop Application J Power Down Cancel J g X EASY nLC 1000 User Guide 57 3 Integrated Instrument Control Software Closing Down the EASY nLC System 2 Press Logout An administrator can start a controlled power down or exit the application from this dialog box If you are not an administrator you can only log out or change your password Closing Down the EASY nLC System C
191. t the internal clock in the EASY nLC system and the display format used throughout the application for date and time information To set the time zone 1 Press Configuration gt Time The Configuration gt Time page opens see Figure 42 Figure 42 Time page of the Configuration menu Thermo Home Batch Setup Method Editor Maintenance EGonfiguration Users Time Settings Connections f f f Network 4 f Time il Set Time Synchronize NTP seref clock isc org Backup l Set Format ddMM yyyy HH mm ss Presets Y Job 00 00 00 23 aug 2010 12 41 admin Exit Continent city list 2 Select a time zone from the continent city list The Set Time Zone button becomes available 3 Press Set Time Zone To change the display format for the time and date 1 Select a format from the Presets list 2 Press Set Format The time and date format changes immediately on the Maintenance Log Book page Thermo Scientific EASY nLC 1000 User Guide 67 4 Configuring the EASY nLC System Making System Backups Making System Backups Use the Configuration gt Backup page to save and restore backups of the system database and configuration A backup includes methods batches instrument configuration and user accounts You can also remove changes you have made to the system completely or selectively by restoring the factory default settings IMPORTANT Make sure that no o
192. t this manual for instructions on how to operate the instrument The safety and special notices in the documentation include the following CAUTION Highlights hazards to humans property or the environment Each CAUTION notice is accompanied by an appropriate CAUTION symbol CAUTION Highlights electrical hazards to humans or property CAUTION Highlights a sharp object hazard to humans EASY nLC 1000 User Guide xiii Preface CAUTION Highlights an eye hazard to humans CAUTION Highlights a chemical hazard to humans property or the environment CAUTION Highlights lifting hazards IMPORTANT Highlights information necessary to prevent damage to software loss of data or invalid test results or might contain information that is critical for optimal performance of the system Note Highlights information of general interest Tip Highlights helpful information that can make a task easier xiv EASY nLC 1000 User Guide Thermo Scientific Preface Contacting Us There are several ways to contact Thermo Fisher Scientific for the information you need To contact Technical Support for the EASY nLC system Phone 800 532 4752 Fax 561 688 8736 Web site Www proxeon com E mail North and South America us customer support analyze thermofisher com Other continents eu techsupport cmf thermofisher com Address Thermo Fisher Scientific Edisonvej 4 DK 5000 Odense C Find software updates and utiliti
193. tI PRO YEON 99999 29909 v60 eo c 00 rrvYYYXvvfYrYTYTYYYYYTYTYYY Y Y YT Y YY Y Y Y Y Y ron G A y e iv jen ww IN3 OUT3 5uT2 IN1 OUT1 ap a EFEFEF ggg RS 232 P Bus 44 EASY nLC 1000 User Guide Thermo Scientific LLL MM Integrated Instrument Control Software The EASY nLC instrument is controlled by software that runs on an integrated computer this means you can operate the instrument without the aid of a data system computer Note When you are using the EASY nLC instrument as part of a Thermo Scientific LC MS system you can use the Xcalibur data system to create chromatographic methods and batches and to acquire and process mass spectral data from the mass spectrometer For information about controlling the EASY nLC instrument from the Xcalibur data system refer to the data system Help You can access Help from most of the user interface pages by pressing the F1 key on the keyboard connected to the data system computer You can use the built in instrument control application for the EASY nLC instrument to set up instrument methods sample processing protocols schedule batches injection sequences view the system progress and status manage users and carry out maintenance and repair work To familiarize yourself with the touch screen application review this chapter Contents Turning On the EASY nLC Instrument Using the Touch Sensitive Screen User Interface Layout Viewing
194. tem and to a properly grounded electrical outlet 38 EASY nLC 1000 User Guide Thermo Scientific 2 Installing the EASY nLC Instrument Back Panel Connections Connecting to the Mass Spectrometer through Contact Closure Thermo Scientific The EASY nLC stand alone application touch screen software contains preconfigured values for most of the standard mass spectrometers used in proteomics For instructions about setting up the software configuration for the mass spectrometer connection see Setting Up Communication with the Mass Spectrometer on page 59 IMPORTANT Occasionally Thermo Fisher Scientific releases new software for the EASY nLC system Downloading new software files to the EASY nLC system erases the mass spectrometer selection Figure 26 shows the hardwire connections between the EASY nLC system and an LTQ Series mass spectrometer Figure 26 Two way contact closure connection for an LTO Series mass spectrometer EASY nLC 12 pin connector Mass spectrometer P BUS DA input and output pins IN3 OUT3 M rrr INT OUTI i Peripheral Control Us Ready Out T dao Start Out N2 ours TIL GND To connect the contact closure cable Using a contact closure cable provided by Thermo Fisher Scientific see Table 12 connect the cable to the mass spectrometer and the EASY nLC instrument For more information refer to the graphic for the selected mass spectrometer in the Contact Closure are
195. the Support Server on page 150 Thermo Scientific 8 Troubleshooting Manual Controls Manual Controls You can access the manual controls for the instrument s hardware components by pressing the component icons on the Home gt Overview page These topics describe how to use the manual controls Using the Valve Controls Using the Pump Controls Using the Autosampler Controls Using the Valve Controls You can manually change the positions of the instruments three position valves from the Home gt Overview page For more information about the valve positions see Six Port Valves on page 12 To change the position of a valve 1 Press the valve icon for the valve that you want to control The Valve dialog box opens see Figure 88 The readback box lists the current valve position Figure 88 Valve dialog box Valve A Valve A C 7 1 2 J Center 1 6 IN 1 2 Close 2 Press the button for the position that you want the valve to switch to 1 2 Center or 1 6 The readback box displays the new position Thermo Scientific EASY nLC 1000 User Guide 141 8 Troubleshooting Manual Controls Using the Pump Controls You can manually refill and empty the pumps from the Home gt Overview page IMPORTANT Use the pump s manual controls for troubleshooting To avoid contaminating the pumps take care when you use these controls For pump A or B make sure t
196. the System Status and Using the Manual Controls Application Menu Structure Logging In to the EASY nLC System Closing Down the EASY nLC System Thermo Scientific EASY nLC 1000 User Guide 45 3 Integrated Instrument Control Software Turning On the EASY nLC Instrument Turning On the EASY nLC Instrument To turn on the instrument press the On Off I O switch on the back panel of the instrument Figure 29 On Off switch on the back panel A A OZL OLL AGSZ 30 SI aIEN4A 830 M aM ELE a YIAOIINI S3SN4 AOST HLAM AINO 380 220 240 V d E The startup procedure takes approximately 5 to 10 minutes while the instrument does the following 1 Boots the internal computer 2 Initializes the software components 3 Checks the hardware components pumps valves autosampler plate cooler flow sensor and so on 4 Starts the application During this process a status bar indicates progress on the startup screen EASY nLC Please wait SCIENTIFIC 46 EASY nLC 1000 User Guide Thermo Scientific 3 Integrated Instrument Control Software Using the Touch Sensitive Screen Using the Touch Sensitive Screen You control the EASY nLC instrument through the touch sensitive screen Note You can attach a USB based mouse and keyboard to the instruments back panel see Attaching a Mouse and Keyboard to the USB Connections on page 44 but the user interface has been optimized for touch screen interaction The ins
197. the needle holder rises a little when the needle reaches the bottom of the well c Press the large step button TT twice to raise the needle off the bottom of the wash bottle insert Two large steps higher than the bottom of the wash bottle insert is the appropriate needle height 6 Press Capture when you are satisfied with the current xyz coordinate for position W4 The color of the bottle container number changes from green to red 7 Optional To calibrate the extra vial positions for the 6 x 8 plate format do the following a Press V1 vial 5 to select it b Repeat step 4 through step 6 for vial V1 8 Press Save and then press Close to close the calibration dialog box 130 EASY nLC 1000 User Guide Thermo Scientific Checking Sample Pickup 7 Calibrating the Autosampler s XYZ Robot Checking Sample Pickup To check sample pickup from a microtiter plate 1 Identify the positions of the wells where you have problems 2 Fill the wells with a 12 pL of solvent A uo A uU Put a plastic film on the Microtiter plate Insert the tray into the tray compartment Press Maintenance Scripts 6 Run the Sample Pickup script with a pickup volume of 10 pL and your default flow see Figure 85 Run the script for each well you pointed out in step 1 Figure 85 Sample Pickup script under the Maintenance menu tab Category Name f res J fm pickup Parameters Output Test autosampler
198. the parameters see Figure 104 for this script as follows Press the Parameters tab p b Press Volume to specify the volume to be picked up C Press Flow to specify the flow rate that pump S uses to aspirate the sample d Press Position to specify the position of the sample in the autosampler See the Position pop up box in Figure 104 Figure 104 Sample Pickup script parameters Thermo Home Batch Setup Method Editor SCIENTIFIC Category Name f f Fi graph Log Book Test v Sample pickup X Description rameters smt Pa Devices Select position v O Plate vials v A v 1 Accept Cancel Job 00 00 00 6 Sep 2011 11 26 admin Ext 170 EASY nLC 1000 User Guide Thermo Scientific 10 Maintenance Maintenance Scripts Test Leaks The Leaks script tests for possible leaks at the pump seal and in the flow path from the pump to its associated valve The Leaks script can also test for system leaks in the flow path downstream of valves A and B Use this script when you suspect leak problems in the pumps pump seals in the system flow path between the pump outlet and the associated valve or downstream of the pump valves To run a system leak test you must connect the Waste In solvent line to the Column out solvent line using a stainless steel union P N SC904 During the leak test of pump A or B the following events occur
199. the remote support feature see Chapter 9 Remote Support Power and Fuse Requirements Use the EASY nLC system only with properly grounded appliances and power sources You can plug the EASY nLC system into these grounded line power sources 120 Vac 50 60 Hz 250 W 230 Vac 50 60 Hz 250 W Note To determine the appropriate rating for an uninterruptible power supply UPS assume 250 W The fuse requirements for the EASY nLC are as follows For 120 Vac the system uses one T 5 AL 250 V fuse 5 x 20 mm IEC 60127 For 230 Vac the system uses one T 2 5 AL 250 V fuse All fuses supplied with the system are UL Listed and CSA certified Temperature and Humidity Requirements Avoid locations with high air humidity or extreme changes in temperature such as direct sunlight drafts directly below an air conditioning or heating vent or directly next to the mass spectrometer or HPLC detector vent For optimal autosampler plate cooling place the unit in an area where the working temperature is within 5 to 30 C 41 to 86 F The optimal humidity range is between 20 to 8096 RH Avoid condensing humidity 36 EASY nLC 1000 User Guide Thermo Scientific 2 Installing the EASY nLC Instrument Back Panel Connections Back Panel Connections To connect the EASY nLC instrument to a mass spectrometer the intranet within your facility the Internet for remote support and other peripheral hardware follow these procedures
200. tings see Figure 57 Figure 57 nanoViper fitting PEEK sealing surface Screw Removable black knurled tightening tool S Even though nanoViper fittings can withstand UHPLC backpressures of up to 1034 bar 715 000 psi they are fingertight fittings which require only very small torques to seal Therefore it is essential to follow the guidelines below to avoid damage by over tightening To use a nanoViper fitting 1 Insert the nanoViper fitting into the target port and slowly rotate the screw clockwise until you feel the resistance 2 Using the black knurled fitting tighten the screw clockwise to an angle between 0 and 45 degrees 1 8 turn 3 Start operating your system at the desired working pressure and check the back pressure 4 If the back pressure is too low return the system to atmospheric pressure IMPORTANT To extend the lifetime of the nanoViper fittings open and close connections at atmospheric system pressures only Opening and closing connections at high system pressures can reduce the lifetime of the fitting system 5 Tighten the screw by as much as an additional 45 degrees Do not turn the screw beyond an angle of 90 degrees from where you felt the initial resistance IMPORTANT To prevent damage to the sealing surface of the nanoViper fitting take care not to over tighten the nanoViper fitting Thermo Scientific EASY nLC 1000 User Guide 87 5 Preparing the EASY nLC Instrument for U
201. to use in the product operation This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited except with the written authorization of Thermo Fisher Scientific Inc The contents of this document are subject to change without notice All technical information in this document is for reference purposes only System configurations and specifications in this document supersede all previous information received by the purchaser Thermo Fisher Scientific Inc makes no representations that this document is complete accurate or error free and assumes no responsibility and will not be liable for any errors omissions damage or loss that might result from any use of this document even if the information in the document is followed properly This document is not part of any sales contract between Thermo Fisher Scientific Inc and a purchaser This document shall in no way govern or modify any Terms and Conditions of Sale which Terms and Conditions of Sale shall govern all conflicting information between the two documents Release history Revision A October 2011 Revision B October 2011 Revision C January 2012 Revision C contains additional information about connecting to the support server Software version Touch screen software Thermo EASY nLC version 3 0 For Research Use Only Not for use in diagnostic procedures CAUTION Symbol gt PPP e gt CAUTION Electric Shock This i
202. trols to fill or empty pump S make sure that the autosampler needle is inserted into the appropriate wash or waste bottle IMPORTANT To avoid contaminating pump S take care to place the autosampler needle in the appropriate wash bottle before filling the pump To fill pump S Make sure that a wash bottle with the appropriate solvent is installed in position W3 Send the autosampler needle to the appropriate position as follows a On the Home gt Overview page press the autosampler icon The Autosampler dialog box opens see Figure 90 on page 146 b Press W3 The autosampler needle moves to the W3 position c Press Needle Down The autosampler needle descends into the W3 bottle d Press Close to close the Autosampler dialog box Draw solvent into pump S as follows a Press the pump S icon The Pump S dialog box opens b In the flow rate box enter the filling flow rate 20 01 to 300 pL min c In the volume box enter the volume that you want pump S to draw d Press Start The pump draws solvent until it draws the requested volume or reaches the full position whichever occurs first To empty pump S to waste Make sure that a wash bottle with needle wash insert is installed in position W4 Send the autosampler needle to the appropriate position as follows a On the Home gt Overview page press the autosampler icon The Autosampler dialog box opens see Figure 90 on page 146 b Press W4 The
203. trument monitor is a transparent layer of glass Figure 30 that detects finger pressure even while wearing gloves and sends the corresponding commands to the computer Figure 30 Touch screen control for the EASY nLC 1000 instrument Home gt Overview page The touch screen controls consist of buttons tables input fields and interactive graphical instrument components as described in these topics Using the Buttons nputting Alphanumeric Text Using Tables and Input Fields nteractive Graphical Controls Using the Buttons Press buttons only one time for a specific action If the action is irreversible or could cause a system error if the instrument is not prepared for the action the EASY nLC application displays a confirmation dialog box where you can cancel or accept the action For example when you press Eject Plate on the Home Overview page a confirmation dialog box appears to remind you to remove obstacles from the area in front of the tray compartment before opening the tray compartment door To continue the action you must press Accept Thermo Scientific EASY nLC 1000 User Guide 41 3 Integrated Instrument Control Software Using the Touch Sensitive Screen Inputting Alphanumeric Text In most cases pressing a button on the touch screen causes the instrument to carry out a certain operation However when the application requires text or numeric input the application displays a keyboard or numeric keypad F
204. ubleshooting Manual Controls To calibrate the current plate format Press Goto Calibration The Tools view for the autosampler on the Maintenance gt Devices page opens To calibrate the XYZ robot for the plate format follow the instructions in Calibrating Plates on page 125 To move the needle to a vial or well position In the Vial or Well box enter a vial or well position Press Goto To move the needle to a wash bottle position Press W1 W2 W3 or W4 To change the cooler temperature Enter a temperature in the temperature box Press Set Monitor the temperature change in the temperature readback box EASY nLC 1000 User Guide 17 LLL AM Remote Support The EASY nLC system includes a remote support feature that enables Thermo Fisher Scientific Technical Support to diagnose and troubleshoot your EASY nLC system remotely while the system is connected to the support server Technical Support cannot initiate the communication link between your EASY nLC system and the support server You must initiate this communication link from your EASY nLC system To connect the EASY nLC system to the support server or download system files to a removable storage device follow these procedures Contents Connecting the EASY nLC System to the Support Server Saving System Files on a USB Removable Storage Device IMPORTANT To establish communication with the support server you must first con
205. uivalent power cord To meet compliance and safety requirements the replacement power cord must be no longer than 2 5 m 8 2 ft and be certified by recognized organizations for your country for example UL CSA SEMKO VDE or T V Installing an EASY nLC system requires a minimum of one outlet The electrical outlet must be earth ground hard wired to the main panel If you are using the EASY nLC system as an inlet to an MS detector the LC MS system might require two or more fourplex outlets The interconnected electrical outlets for the LC MS system and the data system computer must have a common point to one ground connector see Figure 25 on page 37 CAUTION When using the EASY nLC instrument as an inlet to an LC MS system the EASY nLC instrument the mass spectrometer and the optional data system hardware must have a common ground Connecting the hardware to external grounds at different potentials can do the following Create a ground loop that causes noise and interference Damage the EASY nLC systems built in computer CAUTION Improper grounding of the instrument creates an electrical safety hazard To connect the EASY nLC system to line power 1 If you are moving an existing system from one benchtop to another make sure that the fuse is installed correctly see Replacing the Main Power Fuse on page 158 2 Connect the supplied power cord to the power entry module on the back panel of the EASY nLC sys
206. ument for Xcalibur 2 1 x Quick Reference Guide EASY nLC Preinstallation Requirements Guide Thermo Scientific EASY nLC 1000 User Guide xi Preface Downloading Manuals from the Customer Manuals Web Site For Thermo Scientific software and hardware products Thermo Fisher Scientific provides instructional guides as PDF files on its Customer Manuals Web site Note If you are using a Thermo Scientific software application such as the Xcalibur data system with LC Devices 2 6 or later to control your EASY nLC system the EASY nLC 1000 manuals are also available from the data system computer s Start menu To download the EASY nLC manuals from the Customer Manuals Web site K ld 1 Go to mssupport thermo com 2 On the Terms and Conditions page click I Agree Click Customer Manuals in the left margin of the window A Gd On the right side of the window click Search The Documents Advanced Search page opens Thermo N SCIENTIFIC VUES q 3 ee ae Part of Thermo Fisher Scientific Thermo Fisher Scientific Home gt gt Customer Download Documents Advanced Search Advanced Mass Spectrometry Customer Search for keyword Registration Customer Information Model EASY nLC Service 1 Nanya The VIP vidual Pecument Type Instrument Partner Program Part Number Submit Search Reset to the Default Parameters 5 Open a list of linked P
207. with the RePlay device 1 To use the RePlay device enable the method extension on page 1 of the Method Editor you can also open an existing method and enable its extension An extra RePlay Method Editor page is now available see Figure 117 Figure 117 Page 1 6 of the Method Editor Thermo SCIENTIFIC File cat Name BSA 30 min Open Close Save Description Home Batch Setup WMMetho Of Maintenance Configuration Standard 30 min BSA separation wiRePlay Method extensions fX RePlay Job 00 01 02 Capture Playback Eluent 24 aug 2010 18 34 admin Exit 6 1 6 2 On page 3 of the Method Editor properly set up the gradient For more information see To build a gradient on page 96 RePlay uses a nanoflow splitter and a valve to split the EASY nLC eluent to a direct online analysis and to a Capture Cartridge in the RePlay device The RePlay valve switches to direct the captured chromatogram to the mass spectrometer for a second analysis of the same injection To acquire the second analysis the gradient has to be prolonged Thermo Scientific EASY nLC 1000 User Guide 187 A External Devices Setting Up a Method with the RePlay Device 188 3 On page 6 enter the playback delay relative to the MS START signal which can be the EASY nLC 1000 User Guide start of either sample loading onto the columns or the start of the gradient and set from the Configuration gt Connections page
208. x empty the pump operates at the set pressure during a sample run 3 Press the Max Pressure box to set the maximum allowed pressure If you leave the Max Pressure box empty the pump operates at the set flow as long as it is below the instrument pressure of 1000 bar Note If you specify both a flow rate and a maximum pressure the pump flow is limited by the parameter that is reached first 98 EASY nLC 1000 User Guide Thermo Scientific 6 Running Samples Using the Integrated Software Creating a Method To equilibrate the analytical column 1 In the Analytical Column Equilibration area press the Volume box to set the amount of solvent A to use for equilibration of the analytical column For best results use 10 column volumes for reequilibration Range 0 to 137 2 Press the Flow box to set the flow rate for performing the equilibration of the analytical column If you leave the Flow box empty the pump operates at the set pressure during a sample run 3 Press the Max Pressure box to set the maximum allowed pressure If you leave the Max Pressure box empty the pump operates at the set flow as long as it is below the instrument pressure of 1000 bar Note If you specify both a flow rate and a maximum pressure the pump flow is limited by the parameter that is reached first To continue setting up the method go to the Edit 5 5 page by pressing the right arrow Thermo Scientific EASY nLC 1000 User Gui
209. y Compartment ss vu epa han tape Sea e RU e y 3 Components Behind the Right Panel 4 cis eroe n 5 Components Behind the Lett Patel jc d Er D o che D 6 c dl re T Column Serup Options es dod oot wine epo E ox ee ei ases Rabat s Vatic 8 Two column Setup AE TR T erT edebhe ss 8 One Column Setup iue eoe beta pacta E here Ra ydo ar peb dpa Frag 10 Solvent Delivery and Sample Pickup Systems eee 11 Syringe Pumps oereesacw eer Wea p que ied RO dodo ace iid 11 Pressure Sensors 4 secet ye Rae RR TRA E e RR He XO RR a 11 gh d s aar onana aaa E cee 11 Six Port Valves stebru dtr Rb a beh baat 12 Pump A and Pump B Solvent Delivery System ios Re 13 Sample Pickup and Autosampler Wash System 0 0000s aa 21 Predefined Steps for Sample Bins aay pror ee wise te er 23 Pump Flow Contiml 422 xao order Suida iene oedema aes 25 Automatic Flow Control System odors aaaea aaaea 25 Intelligent Flow Control a 4 o2 da eb Rb da RR qa ER RR 26 Load Speed Protection xdi ad coe roe niet o E acd Kee Rcg 27 Squsei eis NODE 28 Performance Specifications 2 22624 rkbr deer p acoey ean ac baee cesta 28 Technical Specifications cie eod rv boda bo hoi Eae bas Pa eee be eds 29 Thermo Scientific EASY nLC 1000 User Guide v Contents vi Chapter 2 Chapter 3 Chapter 4 EASY nLC 1000 User Guide Installing the EASY nLC Instrument uuuuuuuueuueueuseeeee 33 Lifting Instructions ee

EASY-nLC 1000 User Guide Version C

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