Department of Chemistry, Tufts University
Shimadzu QP5050A GCMS –Basic Operation
These directions are meant as a reminder to those who have been trained on the QP-5050A. Contact Dave Wilbur for training.
Basic Operation
This assumes that a suitable column is installed, and helium carrier gas is flowing. This covers only EI operation.
1. Sign the log book. For teaching labs the TA should sign once for each lab session.
2. All modules should be powered on. If not, power on modules in the following order: Autosampler,GC,Mass Spec, Computer
3. Select the GCMS Real Time Analysis icon from the desktop
4. Most navigation within the GCMS applications is via the column of icons on the left side of the screen. Shimadzu calls this the Assistant bar. If the Assistant bar is not visible, select View/Assistant Bar from Menu
Tuning
1. In the Assistant bar, select Tuning, then Start Autotune. Autotune takes about 3 minutes. Save the tuning file as mmddyyEI.qgt
2. To check for leaks, select Peak Monitor View in Assistant bar, enter masses 18,28,32, factor=100, detector voltage 1.00kV. Turn on filament. Intensities of water, nitrogen, and oxygen should all be on scale. Off scale peaks indicates a leak, most likely where the GC column enters the mass spec. Tighten the nut, no more than 1/8 turn.
Define Method
1. In the Assistant bar, select Data Acquisition, then Method Detail.
2. From the menu, select File/Open Method or File/ New Method.
3. In the tab, set desired number of rinses.
4. In tab, set Control Mode (Split or Splitless), carrier gas parameters, Injection/Interface temperatures, and Oven Temp program. If desired, also set pressure program.
5. In tab set Mode (scan or SIM), Start and End times. Note that MS time must be equal or less than GC time. For Scan mode, set m/z range. For SIM mode enter up to 64 m/z values to monitor.
6. Select File/Save Method As to save changes to method.
Data Acquisition- Single Sample
1. Select File/Open Method File from menu. Select the desired method file.
2. Select Sample Login from the Assistant bar. Enter sample information and choose a data file name and tune file (usually the most recent one).
3. Select Standby from the Assistant bar to download parameters to the GC and MS. When all temperatures have stabilized, the Start button will appear green.
4. Select Start from the assistant bar to inject the sample and start acquisition.
5. Once data acquisition starts, select Snapshot from the Assistant bar to start the Postrun Analysis program if desired. All analysis options are available while the run is in progress.
Data Acquisition-Multiple samples
1. Load the autosampler with up to twelve samples, as well as solvent and waste vials.
2. Select Batch Processing from the Assistant bar. Select File/Open Batch File, or select Wizard from the Assistant bar to create a new batch file. The wizard will guide you through the process of creating a sequence list.
Data Analysis-Qualitative
1. Select GCMS Postrun Analysis icon from the desktop.
2. Select File/Open Data File from the menu. Select desired file. The full chromatogram (TIC), zoomed portion of the chromatogram, and selected mass spectrum will be shown.
3. To zoom on a portion of the TIC, drag a box with the mouse. To zoom out right click and select initialize zoom. To display a spectrum, double click on a peak.
4. To integrate the TIC, select Qualitative/Peak Integrate/TIC. Set integration parameters. The easiest way is to use Auto(Area), and enter the desired number of peaks. Select OK.
5. Select Qualitative/Show Qualitative Table. In the TIC tab, select one or more or all peaks, select Edit/Register to spectrum Process Table. Only peaks in the Spectrum Process Table will be included in the report.
6. To do a library search for every peak, go to the Spectrum Process Table, select Edit/Select all, then select Similarity Search. Double click any peak in the spectrum process table to display search results. Select from the hit list and select Process/Copy Marked Compound Name to Process Table
Reports
1. Select Report from the assistant bar. Select File/Open to open a previously saved format file. Format files are in C:\GCMS Solutions\Templates.
2. To create a new report format, Select one or more items from the Item menu, and use the mouse to drag a box on the report page. Only a single spectrum graph or library search is needed on the report format. Spectra for all peaks in the Spectrum Process Table will be printed.
3. Each item in the template has a properties table that determines the appearance of the report. Right click in any item, select properties. Examples include the X,Y range of a chromatogram, and the number of hits printed for each library search.
4. Select File/Print to print the report.
5. Save the format file if desired, with File/Save as.
Exporting Data
1. To export data to .cdf Format, select File/Save Data File as from the Postrun Analysis menu. In the File save dialog window choose type AIA (Andi) .cdf.
2. To export data to a text file, Select File/Export Data from the Postrun Analysis menu. Select data items and filename from the pop-up window. Select OK.
3. To export any report to .pdf format by select File/Print Setup from the menu, then select Primo PDF as the printer type. On the PrimoPDF screen, choose Print as the PDF Setting.
4. To export any chromatogram or spectrum to MS Word or other application, right click in the spectrum window, select Copy, the paste into the other application.
5. To export the chromatogram peak table to Excel, display the spectrum Process Table, select Edit/Select All, then Edit/Copy. Open an Excel file, select Edit/Paste from the Excel menu.
Shutdown
1. If the instrument is to be idle longer than a few hours, select Tools/Daily Shutdown from the menu.
File Structure
.qgd GCMS data files.
.qgm Method files
.qgb Batch (sequence) files
.qgt Tune files
.qgr Report format file
Additional Information:
QP-5050A System User Manual
GCMS Solutions Software Guide
Guide in the Assistant Bar
These manuals are kept near the instrument. Electronic copies, as .pdf files are available. See Dave Wilbur for a copy.
Revised 09/13/2013 D. Wilbur