UNIVERSITEIT GENT

Faculteit der Toegepaste Wetenschappen

Vakgroep Chemische Proceskunde en Technische Chemie

Laboratorium voor Petrochemische Techniek

Directeur: Prof. Dr. ir. G. B. Marin

How to use GC-MS?

Raquel García Bolado

February 2003

Equipment

A quadrupole MS, HP 5989A is used. The ionization of the molecules is obtained by electronic impact at a high voltage. The quadrupole temperature is 100°C, the ion source temperature 250°C and the transfer line temperature 250°C. The GC separation is performed with an HP 5890 Series II instrument on a 100 m x 0.25 mm fused silica capillary column coated with a 0.5 m film of HP-PONA. Hydrogen was used as carrier gas.

1. To log in and to start up a session (Pages 16-18 User’s Guide)

To log in:Username: user1

Password: 69holbach

To start up a session you have to hold the left mouse button down in the background area of the window:

Root Menu
ChemSystem / ChemSystem Menu
Admin 
Tools 
Toys  / Session Startup…
Session Shutdown…
Show Status…
Configure Instrument…
Show Configuration
Refresh
Restart
Help… / Data Analysis…
File Manager…

The Startup a Session panel allows you to initiate an online or offline session:

-Online session:to communicate directly with an instrument

access to instrument control and data acquisition

-Offline session:cannot communicate directly with an instrument

no access to instrument control and data acquisition

The ChemSystem’s Top Level Window will be displayed:

hp1(online1):/chem/hp1/default.m
Run Control / Instrument / Data Analysis / Methods / Sequence / Utilities / Help

2. Setting of the analysis parameters (Chapter 2 User’s Guide)

  • There is always a method loaded in ChemSystem memory.
  • All aspects of running a GC/MS analysis are controlled by the current method (its name is displayed in the title bar of the top level window).
  • A method specifies which steps will be performed in an analysis and contains the instructions and parameters for carrying out the specified steps.
  • Creating a new method always consists of modifying the current method.

Methods
Load…
Print…
Save…
Edit Method Information…
Edit Run Time Check List…
Edit Sequence Recalibration Table…
Edit Entire Method…
Edit method

Deselect “Customize Data Analysis Macro” and “Sequence Recalibration Table”.

Click the Edit pushbutton, and a sequence of panels will be displayed (you can also access to each panel individually).

Method information

Type the comments you want to save with the method in to the Method comments field. Usually the option “no save or overlap” is selected.

Data acquisition: mode

-Acquisition mode:

SCAN- The MS scans linearly across every mass in the specified range. It is used to obtain complete spectral information for components in a sample. You must select Scan mode if you intend to look up chemical compounds in a spectral library.

SIM- The MS looks only at the specified ions entered on the panel. It is used to maximize sensitivity when looking for particular ions in known compounds.

-Tune file: It specifies the mass spectrometer tune file to be used during the acquisition run. If you wish to use tune results other than those from the displayed tune file, type the name of another tune file into the Tune file text box.

Data Acquisition: SCAN Acquisition

-Solvent delay: Time (min) to turn on the MS after the start of the run. Use a value of 2-3 minutes if you are making a splitless injection.

-Resulting voltage: The electron multiplier voltage is calculated with the values you entered for EM Volts and Relative/Absolute.

-Scan Acquisition group: This portion of the panel specifies the scan conditions during the run:Start time, low mass (>35), high mass (<350), scan threshold (20), a/d (2), scans/second (estimated from the previous values).

-Real time plots parameters: This part of the panel is used to select options for the display of information on the screen while data is being acquired: Num. of plots (1), initially ON/OFF (ON), t window, plot #, low mass, high mass, scale.

Data Acquisition: GC/MS Temperatures

-GC Temperatures: Fill out the panel with the GC parameters appropriate to your analyses: Inj., Set point (< 300°C: max oven temperature), Oven tracking (off).

-MS Temperatures: Setpoint, actual and maximum temperatures of the source and the quadrupole.

-Oven Program: Initial temperature, initial time, temperature profile, total run time.

-Oven Parameters: Equib. Time, oven max (300°C), cryo.

Data Acquisition: Inlet Programming

-Inlet Program Select: Select between a temperature program and a pressure program. The selection determines the appearance of the Inlet Program area. Usually “Inj. A Temperature” is selected.

-Oven Program: The temperature program parameters for the GC oven.

-Inlet Program: Temperature program conditions for the selected inlet.

-Pressure Units: (psi)

Data Acquisition: Injector control

-Injection source: Determines the mode of injection (Rear Auto).

-Parameters:

- Sample washes: number of times to wash the syringe with the sample before taking an aliquot for injection (3).

- Sample pumps: number of times to pull the sample into the syringe and expel it before the sample to be injected is drawn (3).

- Sample volume: % of syringe capacity (1).

- Viscosity delay: number of seconds the plunger will pause at the top of the sample to be drawn in the syringe (1).

- Solvent A, B washes: number of times the syringe will wash with the solvent bottle after the injection. Each wash is emptied into one of the waste bottles (3).

-Purge A/B:

For splitless injection:Init value: off

On time: t (min) after injection that you want the purge valve to be turned on (typically 0,75)

Off time: 0

For split injection:Init value: on

On time: 0

Off time: 0

Data Acquisition: Run Table

Shows the time-programmed events entered on SCAN acquisition panel. You don’t need to edit this panel unless you wish to add additional timed events.

Method integration

This panel is used to set up the various signals you wish to integrate as part of the method. You don’t have to change the integration parameters

Specify Report

In this panel the report format and its output can be chosen. Usually, the report will be presented in ascending order by retention time. The report format determines what information will be included on the report. Calculations are usually based on peak area data.

Run Time Checklist

The panel is used to select which parts of the method will be executed during the run. Select “Data acquisition” and “Data Analysis”.

Save Method

Type a name for the method you just created. The system will add .m to the file name you specify, to distinguish the file as a method. The method you created is now available for use. Its name will appear in the title bar of the Top Level window, indicating that it is the current method.

3. Starting up of the analysis(Chapter 7 User’s Guide)

After a method has been set up, you may begin to use that method to acquire data.

Select Start Run from the RunControl menu of the Top Level window.

Run Control
Start Run…
Run Sequence…
Pause Sequence…
Resume Sequence…
Stop…
Abort…
Start Run

-File name: The system will add the extension .d to distinguish the file as a data file. The ChemSystem software distinguishes between upper and lower case letters. File names may contain both letters and numbers but cannot start with special characters such as . or *. The number of characters in the file name has to be less than 14.

-Operator: Optional information.

-Sample name

-Vial: Tray location of the sample vial.

The fields Sample Amount, Multiplier, and ISTD Amount are used only with quantitative methods and even then are optional.

When you have completed the Start Run panel, click the Run Method pushbutton. The system will down load the parameters to the MS, check the GC temperatures, and load the appropriate vial from the tray into the injector. When the instrument parameters have been downloaded and the instrument is ready, the message Acquisition: Run Ready. Waiting for start… will be displayed.

If all instrument temperatures specified in the method have stabilized, the sample injection will be made immediately. Otherwise, the Prepare to Inject panel will be displayed with the message Waiting for Ready displayed.

To monitor the system during a run

During a sample run, the system will display a real time display panel on the screen. The plots that you see are those that are specified in the SCAN or SIM Acquisition panel for the method. The panel shows the elapsed time, the time remaining in the run, the number of the scan most recently completed, the current scan rate and the current setting for the electron multiplier voltage. The scroll bar to the right of a plot change that plot’s scale during a run.

To view data before the end of a run

Select Snapshot from the Instruments menu of the Top Level window. The data acquired so far in the run will be saved to the data file specified in the Start Run panel.

Access standalone Data Analysis opening the ChemSystem Menu (root sub-menu) and selecting the Data Analysis menu item. Select Load Data File from the Files menu of Data Analysis and load the data file for the current sample. Use Data Analysis features such as selecting spectra or doing library searches on the acquired data. The system will continue to acquire data for the run.

To terminate a run

The current run will terminate automatically when the run time specified on the GC/MS Temperatures panel is reached.

There is a procedure to stop a run prior to the specified run time during data acquisition:

-Make sure that all Data Acquisition panels except the real time display are closed.

-Select either Stop or Abort from the Run Control menu. For a GC run, pressing the Stop button on the GC will stop the run also. The following table shows the effect of using each of these methods of prematurely terminating a run.

What it stops
Procedure / MS acquisition / GC run acquisition / Method
Stop menu item
Stop button on GC
Abort menu item / Yes
Yes
Yes / No
Yes
Yes / No
No
Yes

All data acquired for the run before its termination will be saved to the data file specified on the Start Run panel.

4. Analyzing data (Chapters 9-10 User’s Guide)

The Data Analysis program allows you to manipulate and display data acquired from a mass spectrometer or a gas chromatograph.

There are two ways to access Data Analysis window:

  1. From an online or offline session: Open the Data Analysis menu of the Top Level window.

DataAnalysis
Main Panel…
Integration Parameters…
Specify Report…
Edit Calibration Table…
Edit Calibration Settings…
  1. To access standalone Data Analysis: The standalone version of Data Analysis uses fewer system resources than an online or offline session. Use standalone Data Analysis while a method or sequence is running. To do it, open the ChemSystem Menu (root sub-menu) and select the Data Analysis menu item.

The Data Analysis window title bar and menu bar are shown below:

hp1(online1) Data Analysis
Files / Graphics / Integration / Reports / Spectra / LibrarySearch / Structures / Help

To load a data file, select Load data file from the Files menu. The Select New Data File Panel will be displayed. Type in the name of the data file you want to load or click on its name in the list box. The total ion chromatogram (TIC) for the data file you selected will be drawn to the screen.

To integrate the chromatogram

Double click the middle button. The system will redraw the chromatogram showing the retention times for each peak detected.

To generate a report

Select Specify Report from the Reports menu. The Specify Report panel will be displayed. Select the options you want for the report and click the Print Report (text only) pushbutton. To interpret the items considered in the report and their description see p.258 User’s Guide.

To identify peaks

Peak identification is done searching in spectral libraries. A library search is a procedure that compares the spectrum of an unknown compound against a library of reference spectra.

There are two types of library search:

-Probability-based matching (PBM) search: The search algorithm compares an unknown spectrum to each reference spectrum in the library. PBM search is used to do qualitative analysis of unknown samples.

-Parametric retrieval: It searches the header information in a PBM library and produces a list that contains those entries that match the criteria that you specify.

First select Select Library from the Library Search menu. Select WILEY138.l.

The identification can be done using the mouse buttons:

1. TIC  Left button  click and drag:Zoom in

2. TIC  Right button  double click:Select the central area of a peak in the

TIC to get a spectrum at that scan

3. SpectrumMiddle buttondouble click:The result of the search and its quality

will be displayed

4. TIC  Left button  double click:Zoom out

To interpret PBM research results, select Tab Results from the Library Search menu and a tabular report from the last PBM search will be displayed. To interpret the items considered in the report and their description see p.258 User’s Guide.

To draw the chemical structure of a compound in the hit list from a PBM search, select the PBM Structures item on the Structures menu. To clear the drawing from the screen select Clear Last Drawing or Clear All Drawings from that same menu.

5. Managing Files (Chapter 13 User’s Guide)

You can use the File Manager to copy, move, rename, and delete files. To access the File Manager, open the ChemSystem Menu (root sub-menu) and select the File Manager item. A window with a list of files and directories will be displayed. Use the following guidelines to interpret the listing:

ExtensionMeaning

.dContains data acquired from the instrument

.mContains method information

.sContains sequence information

.uContains tuning information for the instrument

To copy filesp.366

To create a directoryp.368

To delete filesp.369 User’s Guide

To list a directoryp.371

To move filesp.373

To print a filep.375

6. Tuning (Chapters 4-5 User’s Guide)

Tuning is the process of adjusting mass spectrometer parameters to meet certain performance criteria. The instrument needs to be tuned periodically. Tune the instrument prior to acquiring data for a new batch of samples.

To acces Tune window, open the Utilities menu of the Top Level Window. Select Tune, and then select a tune file from the list.

Autotuning

Several automatic tuning procedures are supplied with the MS ChemSystem software. When you select Autotunes from the menu bar, the Autotunes menu will be displayed:

Autotunes
User Tune /  Allows you to specify une masses and other parameters
Auto Tune (EI)
MidMass Tune (EI)
HighMass Tune (EI)
Quick Tune (EI) /  General purpose tune
 More accurate calibration over the low-to-mid mass range
 More accurate calibration over the high mass range
 Subset of the Auto Tune (EI)
Auto Tune (PCI)
Auto Tune (NCI)
Auto Tune (PTS)
Auto Tune (NTS)

Some features of autotune are:

-Perfluorotributylamine (PFTBA) is used as tuning standard.

-Adequate sensitivity and peak shape for any mass in the range 10 to 1000 amu are obtained.

-A tune report is generated at the end of an autotune.

-A red stop sign is displayed on the screen during the autotuning that allows you to interrupt the autotune.

Manual Tuning

Manual tuning allows to interactively set the MS parameters to values that meet the needs for a particular analysis.

Select Mass Spectrometer Parameters from the Edit Parameters menu in the Tun e window. Manual tuning allws you to ramp parameters and to specify the range and step size for the ramp. You can acquire two types of data in manual tune: profile sacns and spectrum scans. Tune parameters set in manual tune can be saved to a file and later retrieved for data acquisition or as a starting point for the next tuning session.

7. To shut down a session and log out (Pages 25-27 User’s Guide)

Open the ChemSystem Menu (root sub-menu) and select the Session Shutdown item. The Shutdown a Session panel will be displayed. Click on the name of the session you wish to close and then click the Ok pushbutton.

To log out:Ctrl + Shift + Reset

 HP 5989A MS Engine Hardware Manual:

Chapter 4: Operation

-Startup and pumpdown

-Shutdown and venting

Chapter 5: Troubleshooting

-Symptoms, possible causes and actions

-Error messages

 ChemSystem User’s Guide:

Explanation of ChemSystem Software:

 ChemSystem Reference:

Explanation of ChemSystem’s screens and windows