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Center for Molecular AnalysisCarnegie Mellon UniversityThermoFisher LCQ ESI Ion Trap MSQUICK USER GUIDEBy: Logan Plath, Teaching AssistantProf. Mark BierModified: 04/21/20151
Introduction: The Finnigan LCQ is a quadrupole field ion trap mass spectrometer withelectrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) sources. TheLCQ has MSn capabilities, which is a powerful analytical tool for use in structural analysis. Thismass spectrometer can provide molecular weight and sequence information for small peptides(MW below 2000 Da) at the femtomole level with proper analyte introduction.Steps: Reserve time in iCal for the ESI ion trap MS!Before you start using the ESI ion trap MS, please wear goggles!Log onto the workstation PC using the your generated username and password.Sign up for the Excel spread sheet with oracle number or #POTurn on the N2OFFONThe front view of the LCQ instrument2
Remove the plug shown below Remember to bring two syringes. One is for the injection of the sample and the other one isfor the solvent pump.Only HPLC 22G square tip needle can be used.3
The needle needs to plug into the tubing, which squeezes down the tip a little bit. Push thesyringe needle into the tubing gently until you feel it reach the back of the fitting. Close the probe head and vacuum should initiate within the source. The vacuum LED lighton the right front panel should now be illuminated (not flashing).4
Double click the LCQ Tune icon on the Desktop of the PC workstation. Click the on/standby button to turn on the instrument5
Click the red circled button.6
This window will pop up, adjusting the parameters according to the sample. Click the red circled button to set the syringe pump’s parameters The flow rate is usually between 5-15 ul/min (make sure you indicate the volume of thesyringe in the “Type” inset)7
Click the red circled button and adjust the ESI source parameters if needed. To save the data, click the camera button. This window will pop up. Then click the red circled button.8
This window will pop up. Then choose the appropriate file directory. Then open the syringe pump. You will see the window shown above. Click the “On” radio button and apply to start thesyringe pump.9
You should begin scanning the instrument and will see spectra being acquired of the background. Then you acquire the data by clicking the start. Then injecting the sample in the load position10
Then put to the inject position11
Then click the view button. This window will pop up. (Hitting F5 will refresh this view.)12
You will see the sample’s chromatogram and mass spectrum To save spectrum as data points, right click the mouse, go to export and then clipboard (exactmass). Then paste into Excel, Wordpad, Notepad, etc. You can process data in your ownsoftware or in xCalibur.13
Then click the stop to stop the data recording. Turn the syringe pump off.Then use the solvent to wash the line.Then turn the instrument into the standby mode.14
Open the probe head and clean up the probe head using methanol.Put the plug back into the heated capillary.Close the N2.Record your time in the Excel spread sheet and log off the computer. If you do not logoff,you may be charged for the time.15
2" " Introduction: The Finnigan LCQ is a quadrupole field ion trap mass spectrometer with electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) sources. The LCQ has MSn capabilities, which is a powerful analytical tool for use in structural analysis. This mass spectrometer can provide mol
