For QTRAP® Systems System Integration Test and Data Log

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System Integration Test and Data Log RUO-IDV-05-8311-A

System Integration Test and Data Log RUO-IDV-05-8311-A

This guide describes the steps for preparing for and performing an LC-MS/MS system integration test for a NanoLC ® System combined with the SCIEX 4000, 4500, 5500/5500+, or 6500 QTRAP mass spectrometer. The system might ® include the cHiPLC System or an external column and one of the following NanoLC Systems: TM • NanoLC Ultra System TM • Tempo System Note: Read the safety instructions in the Operator Guide prior to running the system integration test. ® Note: For information about assembly and operation of the NanoSpray or OptiFlow Turbo V Ion Source, refer ® to the Ion Source Operator Guide....

Note: The test in this document is written with Gradient 1 as the low-flow channel. If this is not true for the system being tested (for example, a 2D system), then make the appropriate changes throughout the test. Refer to Table 1-1. Table 1-1 Channel Flow Rate NanoLC™ Systems System Integration Test and Data Log

Table 1-3 Required Materials for a NanoLC System with a cHiPLC® System This column only available for purchase by users from Phenomenex. The equivalent SCIEX part is only available to Field Service Employees (FSEs).

Create the autosampler and LC methods in the Eksigent Control Software and the acquisition method in the Analyst Software. 1. Plumb the autosampler valve with a 10 pL sample loop. 2. Open the Analyst® Software. 3. In the Autosampler control window, click Method Editor. 4. Create the autosampler method for a trap-elute configuration. Refer to the appropriate appendix for the system. • Methods for NanoLC™ 400 Systems with a cHiPLC® System • Methods for NanoLC™ 400 Systems with an External Trap and Column • Methods for NanoLC Ultra® Systems with a cHiPLC System • Methods for NanoLC Ultra® Systems...

LC-MS System Integration Test Table 2-1 Mobile Phase Mixtures In this method, the loading pump is the channel with the microflow module. 1. Open the Analyst® Software. 2. In the Acquisition window that opens (from the Eksigent Control Software), click the arrow in the top, right corner of the window to select the high-flow or loading pump. 4. Create the loading pump method. Refer to the appropriate appendix for the system: • Methods for NanoLC™ 400 Systems with a cHiPLC® System • Methods for NanoLC™ 400 Systems with an External Trap and Column • Methods for NanoLC Ultra® Systems with a cHiPLC®...

LC-MS System Integration Test • Methods for NanoLC™ 400 Systems with a cHiPLC® System • Methods for NanoLC™ 400 Systems with an External Trap and Column • Methods for NanoLC Ultra® Systems with a cHiPLC® System • Methods for NanoLC Ultra® Systems with an External Trap and Column • Methods for NanoLC™ and Tempo™ Systems with a cHiPLC® System • Methods for NanoLC™ and Tempo™ Systems with an External Trap and Column 4. Type the method name as specified in the appropriate appendix. 1. Close the Eksigent Control Software, if it is open. 2. Verify that the Analyst® Software drivers are installed. Refer...

LC-MS System Integration Test Table 2-2 Acquisition Method Parameters—Analyst® Software (continued) System Integration Test and Data Log NanoLC™ Systems

Table 2-3 MRM Transitions for Beta-galactosidase (continued) 7. Save the Analyst® software method (for example, System Integration Test). 2. Click the autosampler (for example, Eksigent AS2 or AS3) and then select the appropriate autosampler method. Refer to Create the Autosampler Method.

LC-MS System Integration Test 3. If Eksigent Gradient 2 appears in the device list, right-click Eksigent Gradient 2 and then clear the "Use" selection as it is not being used. Figure 2-2 Software Application Properties Tab—Autosampler Method 4. Click Eksigent Gradient 1 and then select the appropriate gradient pump method. Refer to Create the Gradient Method. 5. Click Eksigent Loading Pump and then select the appropriate loading pump method. Refer to Create the Loading Pump Method. 6. Save the acquisition method. Plumb the system in trap-elute configuration to perform the pre-column desalting...

WARNING! Toxic Chemical Hazard. Refer to the chemical product Safety Data Sheets and follow all of the recommended safety procedures when handling, storing, and disposing of chemicals. For health and safety precautions, refer to the Operator Guide. 1. Add 625.0 pL of buffer A (100% water:0.1% formic acid) to the beta-galactosidase vial. 2. Vortex the vial for at least 30 seconds. 3. Using a centrifuge, spin the vial to bring the liquid down to the bottom of the vial before opening. 4. Repeat step 2 to step 3 to confirm dissolution. 5. Aliquot the stock solution into 50 pL volumes and then store...

LC-MS System Integration Test This step produces a 1:5 dilution, with a concentration of 200 fmol/pL. 3. Transfer the solution to the autosampler vial, making sure there is no bubble on the bottom of the vial. Required Materials • Beta-galactosidase stock solution, prepared in Prepare the 1 pmol/pL Stock Solution of Beta-Galactosidase Digest Solution • Water with 0.1% formic acid (Buffer A) 1. Combine the specified amount of the 1 pmol/pL beta-galactosidase stock solution with Buffer A in clean vial. Refer to Table 2-4. Table 2-4 Sample Dilutions by Mass Spectrometer 2. Mix the solution for at...