To set up the LCQ Advantage to acquire data in the APCI/MS mode, you dothe following:

.Install the APCI probe assembly

.Set up to infuse your analyte into the MS detector using a syringe pumpconnected to the LC with Tee union

.Set up the MS detector for APCI/MS operation from the Tune Pluswindow

This chapter contains the following topics:

.Removing the ESI probe assembly

.Installing the APCI probe assembly

.Setting Up the Inlet for High-Flow Infusion

.Setting Up the MS Detector for APCI/MS Operation

If the APCI probe is already installed on the API source, go to the topic:Setting Up the Inlet for High-Flow Infusion.

If the ESI probe is installed on the API source, go on to the next topicRemoving the ESI Probe Assembly.

6-1Thermo Finnigan LCQ Advantage Getting Starled

Setting Up to Acquire Data in the APCI/MS ModeRemoving the ESI Probe Assembly

To remove the ESI probe assembly, proceed as follows. See Figure 2-3 forthe location of the components of the ESI probe assembly.

1. Stop the flow of sample solution (from the LC or syringe pump) into theESI probe.

2. Disconnect the high voltage cable from the connector labeled BVon theESI probe. To disconnect the cable, turn the locking ring on the cablecounterclockwise until you can pull the cable free.

3. Disconnect the sample transfer line from the grounded transfer line fittingon the ESI flange. (The sample transfer line is the line that comes fromthe LC, divert/injector valve, or syringe pump. It is not the fused silicacapillary that enters the ESI probe.)

4. Disconnect the sheath gas line and fitting from the inlet labeled SheathGas on the ESI probe by turning the sheath gas line fitting (blue)counterclockwise until you can pull the sheath gas line and fitting freefrom the probe.

5. Disconnect the auxiliary gas line and fitting from the ESI probe byturning the auxiliary gas line fitting (green) counterclockwise until youcan pull the auxiliary gas line and fitting free from the probe. Note thatthe auxiliary gas line might be connected to either the Aux Gas or SweepGas inlets.

6. Loosen the two flange retainer bolts that secure the ESI probe assembly tothe spray shield.

7. Pull back the ESI probe assembly from the spray shield.

8. With one hand holding the ESI flange, loosen the knurled fastener thatsecures the ESI flange to the probe slide adapter.

9. Slide the ESI probe assembly off the probe slide adapter. Store the ESIprobe assembly in its foam storage container.

Go on to the next topic: Installing the APCI Probe Assembly.

Thermo Finnigan6-2 LCQ Advantage Getting Started-

Setting Up to Acquire Data in the APCI/MS ModeInstalling the APCI Probe Assembly

To install the APCI probe assembly, remove the ESI probe assembly using theprocedure in the previous section; then proceed as follows. See Figure 2-1 forthe location of the components of the APCI probe assembly.

1. Remove the APCI probe assembly and corona discharge needle from thestorage container.

2. Insert the corona discharge needle into its socket in the corona dischargeneedle assembly.

3. If your APCI probe assembly does not already contain a sample tube(fused-silica capillary), you need to follow the procedure for installing asample tube that is outlined in the topic: Maintaining the APCI Probe inthe MS Detector Maintenance chapter of the LCQ AdvantageHardware Manual. Ensure that the probe retainer bolt is tight and theAPCI probe is secured to the APCI flange.

4. Slide the APCI probe assembly onto the probe slide adapter. Secure theAPCI probe assembly to the probe slide adapter with the knurled fastener.

5. Connect the sample transfer line and fitting to the inlet labeled LC on theAPCI probe.

6. Connect either Aux or Sweep gas:

.Connect Auxiliary gas: Connect the aUxiliary gas line and (green)fitting to the inlet labeled A on the APCI probe.

.Connect Sweep gas: Connect the auxiliary gas line and (green) fittingto the inlet labeled Sweep on the APCI probe.

7. Connect the sheath gas line and (blue) fitting to the inlet labeled S on theAPCI probe.

8. Connect the high voltage cable to the connector on the APCI probeassembly. Turn the locking-ring on the cable clockwise to secure thecable.

LCQ Advantage Getting Started 6-3

Setting Up to Acquire Data in the APCI/MS ModeInstalling the APCI Probe Assembly

9.

Connect the vaporizer heater cable to the connector on the front panel ofthe MS detector (beneath the APCI probe assembly). Make sure that thered dot on the cable is aligned With the red mark on the connector.

10. Push the APCI probe assembly against the spray shield.

11. Secure the APCI flange to the spray shield with the two flange retainerbolts.

12. In the Tune Plus window, choose Setup I Change to APCI to configurethe software for APCI operation.

Go on to the next topic: Setting Up the Inlet for Tuning Using High-FlowInfusion.

6-4 Thermo FinniganLCQ Advantage Getting Started-

Setting Up to Acquire Data in the APCI/MS ModeSetting Up the Inlet for Tuning Using High-Flow Infusion

6.3

The plumbing connections for APCI/MS sample introduction from thesyringe pump are shown in Figure 6-1.

To make the plumbing connections for APCI/MS sample introduction fromthe syringe pump into solvent flow from an LC, proceed as follows:

1. Connect a4 am (1.5 in) segment of Teflon tubing with a (brown)Fingertight fitting and a (brown) ferrule to the (black) LC union. (SeeFigure 6-2.)

LC Tee

=From lC

-"@)

lC

Syringe

To

-",I I~

Figure 6-1. APCI/MS plumbing connections for sample introductionfrom the syringe pump into solvent flow from an LC

6-5LCQ Advantage Getting Statted

Setting Up to Acquire Data in the APCI/MS ModeSetting Up the Inlet for Tuning Using High-Flow Infusion

2. Load a clean, 500-JiL Unimetrics syringe (PIN 00301-19012) with420 ~L of a 1 ng/~L solution of reserpine or your analyte of interest.(Refer to Appendix B: Sample Formulations for a procedure formaking the reserpine tuning solution.)

3. Insert the needle of a syringe into the segment of Teflon tubing, and placethe s~nge in the syringe holder of the syringe pump.

4. Connect a fused-silica infusion line from the (black) LC union to the(black) LC Tee union, as follows. See Figure 6-2.

a. Connect the infusion line (PIN 00106-10504) with a (brown)Fingertight fitting and a (brown) ferrule to the free end of the LCunion.

Connect the other end of the infusion line with a (red) Fingertightfitting and a (brown) femlle to the side ann of the LC Tee union.

b.

Figure 6-2. APCVMS plumbing connections for the LC Tee union and syringe pump

6-6 LCQ Advantage Getting Starteq

Setting Up to Acquire Data in the APCI/MS ModeSetting Up the Inlet for Tuning Using High-Flow Infusion

5. Connect a segment of PEEK tubing from the (black) LC Tee union to theAPCI LC inlet, as follows. (See Figure 6-2.)

a. Use a PEEK tubing cutter to cut a 4 cm (1.5 in.) length of the PEEKtubing.

b. Connect the PEEK tubing with a (brown) Fingertight fitting and a(brown) ferrule to a free end of the (black) LC Tee union.

c. Connect the other end of the PEEK tubing with a (red) Fingertightfitting and a (brown) ferrule to the LC inlet located on the APCIprobe.

6. Connect an appropriate length of PEEK tubing (transfer line from thedivert/inject valve) from the divert/inject valve to the LC Tee union, asfollows. (See Figure 6-2.)

a. Connect a length of PEEK tubing with a (stainless steel) nut and a(stainless steel) felT\lle to port 3 of the divert/inject valve.

b. Connect the other end of the PEEK tubing with a (brown) Fingertightfitting and a (brown) ferrule to the free end of the LC Tee union.7.

Connect an appropriate length of PEEK tubing (transfer line from the LC)from the divert/inject valve to the LC, as follows:

a. Connect a length of PEEK tubing with a (stainless steel) nut and a(stainless steel) felT\lle to port 2 of the divert/inject valve.

b. Connect the other end of the PEEK tubing with a proper fitting and afelT\lle to the outlet of the LC.

8. Connect an appropriate length of PEEK tubing (waste line) from thedivert/inject valve to a waste container, as follows:

a. Connect a length of PEEK tubing with a (stainless steel) nut and a(stainless steel) felT\lle to port I of the divert/inject valve.

b. Insert the other end of the PEEK tubing in a suitable waste container.

9. Connect an appropriate length of (clear) 3/8 in. ID PVC hose to the ESIprobe outlet drain. Insert the other end of the hose into a suitable wastecontainer (such as a gallon jug). Ideally, the waste container should bevented to a fume exhaust system.

Go to the next topic: Setting Up the MS Detector for APCI/MS Operation.

Thermo Finnigan- 6-7LCQ Advantage Getting Started

Setting Up to Acquire Data in the APCI/MS ModeSetting Up the MS Detector for APCI/MS Operation

6.4

Use the following procedure to set up the MS detector for APCI/MSoperation.

11mStandbyOn

1. In Thne Plus, take the MS detector out of Standby mode and turn it On, asfollows:Click on the On/Standby button in the ControUScan Mode toolbar. TheMS detector begins scanning, and the LCQ Advantage applies highvoltage to the corona needle and shows a real-time display in theSpectrum view.2.

Open the APClTune.LCQTune Tune Method, the Tune Method forhigh-flow APCI operation, as follows:

a. Display the Open dialog box, as follows:Choose File I Open.

b. Select the file APCITune.LCQTune in the directoryC:\Xcalibu~ethods, as follows:Scroll down in the File Name combo box until you seeAPClTune.LCQTune. Then, click on the file name.

c. Open the file, and close the dialog box, as follows:Click on OK. LCQ Advantage downloads the Tune Methodparameters to the MS detector.

3. Verify that LCQ Advantage opened the Tune Method, as follows:

a. Open the APCI Source dialog box, as follows:Click on the APCI Source button in the Instrument Setup toolbar. SeeFigure 6-3.

b. Verify that the settings in your dialog box are similar to those shownin Figure 6-3.

Thermo Finnigan6-8 LCQ Advantage Getting Starled-

Setting Up to Acquire Data in the APC1/MS ModeSetting Up the MS Detector for APC1/MS Operation

Figure 6-3. APCI Source dialog box, showing the proper settings for atypical high flow experiment

Close the dialog box, as follows:Click on OK.

c.

4. Define the scan parameters for tuning the MS detector in the APCI/MSmode, as follows:

a. Open the Derme Scan dialog box, as follows:Click on the Defme Scan button in the Control/Scan Mode toolbar.See Figure 6-4.

b. Select the MS scan mode in the Scan Description group box, asfollows:Click on the Scan Mode: MS option button. Note thatLCQ Advantage sets the Msn power to 1.

c. Select the SIM data type, as follows:Click on the Scan Type: SIM option button. Note thatLCQ Advantage sets the Total Scan Ranges to 1.

d. Set the total number of microscans to 1 in the Scan Time group box,as follows:Double-click in the Total Microscans spin box, then type 1.

e. For this example, leave the maximum injection time set to its defaultvalue of 200.00 ms.

f.

g.

Specify that the ion source fragmentation option is turned off in theSource Fragmentation group box:Confmn that the Turn On check box is not selected ((11).

Set the center mass for the scan range to m/z 609.2 in the Scan Rangesgroup box, as follows:Double-click in the Center Mass text box, then type 609.2.

Thermo Finnigan 6-9LCQ Advantage Getting Started

Setting Up to Acquire Data in the APCI/MS ModeSetting Up the MS Detector for APCI/MS Operation

h. Set the width of the scan range to m/z 2. as follows:Double-click in the Width text box. then type 2.

i. Ensure that the settings in your Defme Scan dialog box are the sameas those shown in Figure 6-4.

j. Save the MS detector scan parameters. and close the Defme Scandialog box. as follows:Click on OK.

Figure 6-4. Define Scan dialog box, showing typical settings for APCVMS operation

5. Select the centroid data type, as follows:Click on the Centroid/Profile button in the Control/Scan Mode toolbar totoggle the data type to centroid. (The picture on the button should be thesame as that shown here).

6. Select the positive ion polarity mode, as follows:Click on the Positive/Negative button in the Control/Scan Mode toolbarto toggle the ion polarity mode to positive. (The picture on the buttonshould be the same as that shown here).

You have now completed setting up your MS detector for APCI/MSoperation. Go to the next chapter: Optimizing the MS Detector with YourAnalyte in APCI/MS Mode.

6-10