Department of Chemistry, TuftsUniversity

Finnigan LTQ Mass Spectrometer–Basic Operation

Part 1. Direct Infusion

Tune Plus Application Xcalibur Application

Define Scan Acquire Data Scan Standby

NOTE: These operation notes are meant as a reminder to those who have been trained on the LTQ. Contact the Instrument Specialist, David Wilbur (X72163) for training.

Sample Prep

  1. Fill a clean syringe with sample solution. 50-100ul in a 250ul syringe is usually sufficient.
  2. Insert the needle into the Teflon tube at the end of the silica transfer line.

Instrument Setup

1. Check that the there is a direct connection of silica tubing from the syringe pump to the grounding union to the ESI probe; and that the LC is not connected to the mass spec.

Initial Acquisition

  1. Select the Tune Plus application.
  2. Turn Scan on by selecting the On/Standby icon. The icon will change from yellow to green, and the blue Scanning lights on the mass spectrometer will flash.
  3. Open an appropriate tune method, such as ESI_5ul_50MeOH-50H2O.LTQTune.
  4. Select the syringe pump icon, and turn on the pump, set flow to 10il/min. At 10ul/min there is a 1 min delay before sample reaches the probe.
  5. Tune the instrument for your peak of interest if desired. Select Tune icon. Monitor with Graph view. Automatic tune on base peak or specific mass. Manual tune to optimize flow and temperature.
  6. Select the Define Scan button, Move the resulting window out of the way.Select all desired scan parameters.
  7. Select Centroid or Profile (Full range profile scan can create up to 25MB of data every minute!). Use centroid for peak lists
  8. Select the Acquire Data button. Enter Folder, File name and sample information .
  9. Select .
  10. Change scan parameters in Define Scan window as desired. Select Apply after each change.
  11. Select to terminate acquisition.

Data processing with Qualitative Browser

1.Open the Xcaliburapplication, and select Qual Browser.

2.Open the data file. (File/Open from menu)

3.Apply a predefined layout (File/Layout/Apply from menu), or build your own with Grid/Insert Cells.

4.Pin the spectrum cell (click on the thumbtack icon in the upper right). All changes will be applied to the pinned cell. Clicking a point on the chromatogram will display the corresponding spectrum. Dragging a range on the chromatogram will display a spectrum averaged over that range.

5.Add additional cells by selecting Grid/Insert Cells from the menu bar. Menu and toolbar selections apply only to pinned cell.

6.Use the View menu to assign a pinned cell as a chromatogram, spectrum, spectrum list, or parameter list (Report/Status log).

7.Use the Display/Display Options to fine tune the appearance of the pinned cell.

8.Add annotation to pinned cell with Display/Annotation from menu.

9.Right click any mass label to change to relative labeling.

10.The View and Display Options menus are also accessible by right clicking in a pinned cell.

11.There is a simulation program. Select the A,Y,Z tab to the left of the spectral windows.

12.To change the vertical scale of part of a spectrum, use the amplify icon, . Enter the amplification factor in the pull down menu.

Plotting

  1. Select File/Print or File/Print Preview.
  2. Select Edit/Copy.. to copy cell or entire view to clipboard for export to Word or Power Point.

Exporting Data

1. To export a mass spectrum or chromatogram to a text file , right click and select Export/Clipboard. Paste to Word or Excel.

When Finished

  1. Load tune method Standby.LTQTune. Switch the LTQ to standby.
  2. If you used LC, reconnect silica tube from syringe pump to source.
  3. Rinse the syringe with appropriate solvent, usually methanol/water or acetonitrile/water, replace on syringe pump, run for 3 minutes to clear line.
  4. If you used LC, be sure detector lamps are OFF, and pump flow is set to 0.
  5. Tidy up.

For more information see the following manuals:

Finnigan LTQ—Getting Started

Finnigan LTQ Hardware Manual

Finnigan Xcalibur—Getting Productive: Qualitative analysis

Manuals are kept near the instrument, and are available in electronic form as .pdf files. See Dave Wilbur for a copy.

Revised 11/26/2014D. Wilbur