Department of Chemistry, Tufts University
Finnigan LTQ Mass Specrometer–Basic Operation
Part 2. LCMS
Xcalibur Application
Roadmap icon
Real time display icon
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
Instrument Setup
1. Disconnect the direct infusion silica tubing at the grounding union, and replace with PEEK
tubing fron divert valve.
2. Select Tune Plus application, open an appropriate tune method (e.g.
ESI_200ul_50MeOH_50H2O.LTQtune).
3. Select Xcalibur application, then select Instrument setup.
4. Select a previously defined method with File/Open, or create a new method
a. Select an experiment type (usually General MS or MSn). Define one or more scan
events.
b. Click on each of the four units (LTQ MS, Surveyor AS, Surveyor Pump,
Surveyor PDA). Fill in appropriate information.
c. For LTQ MS, select Scan events ,mass range, tune method, and run time. Select
Dependent scan and Settings for zoom scans ans MS-MS if desired.
d. For Surveyor AS the defaults should work in most cases. Change them if desired.
e. For Surveyor MS Pump enter solvent names and gradient program. Turn on pump
to flush column (Surveyor MS Pump from menu). Purge solvent lines with 10 ml
syringe if solvents have changed.
f. For Surveyor PDA turn on lamps (Surveyor PDA/Direct Control from menu,
then Configuration tab). Deuterium lamp needs at least 15 min warmup.
g. For Surveyor PDA enter Run Length. Choose any combination of Collect full
spectra and Channels. Enter wavelength for channels chosen.
h. Save method (File/Save or File/Save as).
Create Sequence file
1. Select Sequence Setup from Roadmap. Open a predefined sequence, or create a new one.
2. For each sample enter datafile name, path, method, position, injection volume. Software bug-you
must specify data file extension .RAW when entering a file name.
Start Acquisition
1. From Sequence Setup, select Run Sample or Run Sequence from toolbar or Action/Run
Sample from menu
Revised 12/28/05
D. Wilbur
Department of Chemistry, Tufts University
2. In the run Sequence window, check that all modules (MS, PDA, AS, Pump) are listed under
Acquisition ions. Select OK
3. For real time data display select View/Real Time Plot View or select real time display icon.
Data processing with Qual Browser
1. Use the Qual Browser to view the data. You can view data as soon as the acquisition starts.
2. Select View/Refresh or type F5 to update the display to all data acquired.
3. Add additional cells by selecting Grid/Insert Cells from the menu bar. Menu and toolbar
selections apply only to pinned cell.
4.
5. Use the View menu to assign a pinned cell as a chromatogram, spectrum, spectrum list, or
parameter list (Report/Status log).
6. Use the Display/Display Options to fine tune the appearance of the pinned cell.
7. Use Display/Ranges to choose mass or UV detector for chromatograms and to change ranges.
The appearance of mass chromatograms will change dramatically, depending on mass range
displayed.
Integrating Cromatograms
1. Pin the desired cromatogram. Use Display/Display Options to choose a peak algorithm
(Genesis is simplest).
2. Select Action/Peak Detection/Toggle Detection…To integrate. Integration limits can be
adjusted by dragging the blue boxes.
3. Select Action/Peak Detection/Add (Delete) Peaks to add or delete peaks manually.
4. To display integration values on chromatogram select Display/Display Options, select the
Labels tab, and check the area box.
Plotting
Same as direct infusion
When Finished
1. Load tune method Standby.LTQTune. Switch the LTQ to standby.
2. Reconnect direct infusion silica tube from syringe pump to source.
3. If you used syringe pump, rinse the syringe with appropriate solvent, usually methanol, replace
on syringe pump, run for 3 min to clear line.
4. If you used LC, be sure lamps are OFF, and pump flow is set to 0.
5. Tidy up.
For more information see the following manuals:
Finnigan Surveyor—Getting Started with Xcalibur 1.3
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 12/28/05
D. Wilbur