dart-agilent vapur interface manual - ionsense · dart-agilent vapur interface manual (si-300-a rev...

DART-Agilent Vapur Interface Manual

For Agilent TOF and Ion Trap Instruments

Rev 2

Document # 7.5.059

IonSense Inc.

999 Broadway

Suite 404

Saugus, MA 01906

DART-Agilent Vapur Interface Manual (SI-300-A Rev 2) 2

Copyright © 2005-2014 by IonSense Inc.

All rights reserved.

The information in this document has been carefully checked and is believed to be

reliable. However, no responsibility is assumed for inaccuracies. Statements in the

document not intended to create any warranty, expressed or implied. Specification and

performance characteristics of the hardware and software described in the manual may be

changed at any time without notice. IonSense Inc. reserves the right to make changes in

any product herein in order to improve reliability, design, or function. IonSense does not

assume any liability arising out of application or use of any product or circuit described

nor does it cover any license under its patent rights or the rights of others.

The apparatus and application of the apparatus described in this document is protected by

US Patent Number 6,949,741 and used under license; additional patents pending.

All trademarks are properties of their respective owners.


This manual details the steps necessary to install a DART source on an Agilent

Instrument. It will focus on the Agilent TOF models, but these instructions are also

applicable for Agilent Ion Trap instruments as well.

Table of Contents

1. Diagram of the Agilent Source and Interface

2. Attaching the DART Vapur Flange to the Instrument

3. Setting the Source Type

a. For New Instruments

b. Old-Style Instruments

4. Optimal Parameters

5. Enabling Contact Closure

6. Calibrating the Agilent TOF with DART


Diagram of the Agilent Source and Interface

All current Agilent sources have an “i-button” attached on the left side (as you are

looking down the capillary of the instrument). The dual ESI source shown below has an

i-button marked “11”.

Figure 1: Dual ESI source view

The desolvation chamber on the Agilent systems has an electronic reader that interprets

the information on the i-button. The reader is shown in the picture below at the right end

of the yellow wire in Figure 2.


Figure 2: Source mounted - hardware side view

The i-button identifies the source attached, so that the parameters associated only with

that source may be displayed and/or controlled in the software.

Before changing the source, make sure the instrument is put in ‘OFF’

mode via the software. Right click on the TOF in the GUI and select ‘OFF’. Ignore

all warnings and press “OK.” Once the DART is installed, place the instrument back into

“standby” mode.

Then remove the ESI source. Do not remove anything else. Detach the source from the

unit by disconnecting it from the LC/MS completely. Leave the i-button attached to the

source to prevent any exposure to high voltage. Complete removal of the source involves

disconnecting the heater and thermocouple connector (multi-pin connector) and the

medium voltage connectors shown below and some gas and solvent connectors shown in

Figures 3 and 4.


Figure 3: Multi-pin Connector leading to Agilent source

Figure 4: Medium voltage connector leading to Agilent source


Attaching the DART Vapur Flange to the Instrument

Attach the DART flange to the Agilent instrument by sliding the two hinge pins on the

left of the flange downward into the two holes on the left side shown circled in red in

Figure 5.

Swing the flange so that it meets the instrument and secure it with the latch. You may

need to unscrew the arm of the latch to extend its length and reach the clamp on the

DART flange.

Figure 5: DART flange attached to the Agilent interface (hinges circled in red)


Figure 6: Rubber stopper in place to create seal with interface (Agilent splash guard still

in place)

Insert the rubber stopper into the waste pumping port as shown in Figure 6 and remove

the Agilent splash guard (pictured below in Figure 7) before closing the Vapur Interface.

Note: If may be necessary to adjust the length of the Agilent clasp used to secure the

Vapur Interface to the front of the instrument. Make sure that the Vapur Interface makes

a good seal against the front of the instrument otherwise there will be vacuum instability.

Figure 7: Agilent splash guard removed


Figure 8: Vapur Interface fully mounted on Agilent MS

Inserting the Ceramic Ion Transfer Tube into the Vapur Interface

Remove the Swagelok nut from the front of the Vapur Interface and insert the ceramic

ion transfer tube into the interface. Secure the ceramic tube with one of the provided

graphite ferrules making sure to set a 2 mm gap inside the interface.

Make sure to set a 2 mm gap inside the Vapur Interface between the end of the ceramic

tube and the Agilent capillary inside the Vapur Interface.

This gap ensures that the excess helium gas will be evacuated and maintain proper

vacuum in the instrument.

Take care to attach the black rubber pumping line from diaphragm pump over the

barbed pumping port fitting on the side of the Vapur Interface.

Refer to the DART SVP Hardware and Network Installation Manual (pages 6-8) for

more specifics on interfacing the DART SVP source to the Vapur Interface.

IonSense website: (http://www.ionsense.com/manuals)

http://www.ionsense.com/manuals


Setting the Source Type

The source setting in the MassHunter software is most likely set to “ESI,” which is the

default setting if the system has not detected an i-button present.

Change the source type to “Dual-ESI”.

The capillary (in the case of ESI) is at high temperature. You can increase/decrease the

temp inside the MassHunter software window (shown below in Figure 9).

Figure 9: MassHunter Control program window

Optimal Parameters IonSense recommends using the following operational settings:

Capillary Voltage: ~1000V

Drying Gas: 8.5 L/min (Important to keep H2O cluster formation low)

Fragmentor Voltage: 150-175V

Octapole Voltage:

o 250V for masses above 100 Da

o 100V for masses below 100 Da

If “Dual-ESI is not an option: On older-version instruments, “Dual-ESI” is not an option in the software.

In this case:

1. Set the source type to “ESI”.

2. On the start button select:

Programs → Agilent- MassHunterWorkstation → Acquisition tools →

Instrument Configuration 3. Deselect LC

4. On the source button select "Do not wait for set-points to equilibrate"

Enter Dual-

ESI source


Enabling Contact Closure

Figure 10: A) Contact closure “Remote” port on Agilent mass spectrometer

B) DART-SVP contact closure cable plugged in

1. Plug in the contact closure cable from your DART-SVP kit into the serial port

on the Agilent mass spectrometer that says “Remote” as shown in Figure 10.

Figure 11: Contact closure cable plugged into the DART-SVP controller

2. Plug the other end of the cable into the “Mass-Spec Interface” port on the

DART-SVP controller as shown in Figure 11.

A B


DART SVP Software Settings for Contact Closure

Navigate in the DART SVP software

to the “Settings” page and click on

the “Contact Closure” button.

On the “Contact Closure” page

check to make sure that “Method

Start Signal” is selected “On”.

Navigate to the “Methods” page and

select the desired method. You can

“Edit” the method parameters or hit

“Start” to initiate the DART

sampling method, which will trigger

the mass spectrometer data

acquisition via contact closure.


MassHunter Data Acquisition: Contact Closure Set-up

Figure 12: Worklist drop down menu

3. Click on the “Worklist” drop down menu and select “Worklist Run

Parameters…” as shown in Figure 12.


Figure 13: Work List Parameters… Menu

4. Select “External Start” from the drop down menu for “Run Type” as shown

in Figure 13.

Figure 14: Worklist tab for sample queue

5. In the “Worklist” tab set up your sample name, method, data file, and sample

type and to begin your run.


Calibrating the Agilent TOF with DART

Thanks to George Dubay of Duke University and Howard Sanford of Agilent

Technologies for their assistance with this section.

While a tune done with the ESI source will remain current with the DART, it is necessary

to calibrate the Agilent TOF with the DART before usage to ensure mass accuracy.

The critical factor for the calibration is ion stability. If the ion current is unstable during

calibration, the system destabilizes and the mass accuracy will drift significantly.

To ensure a stable ion current:

The ions used for calibration must be not too small or large: ~100-700 Da.

IonSense recommends PEG-600 as a calibration compound for achieving

these target ions.

Maintain the instrument vacuum at the lower reaches of 10-7

. At high

vacuum pressures (10-6

and lower), performance decreases. Also, the

vacuum should be relatively constant and not wildly fluctuating.

o To do this, it may be necessary to pull the DART source away

from the ceramic tube inlet so that the gap between the ceramic cap

and ceramic tube is ~8.5mm.

o When using IonSense experiment modules to introduce samples,

attach them to the rail in the position farther away from the API

inlet.

Target ion abundances for calibration ions should be in the range of 200-

500K. Greater abundances will lead to system instability.

It is recommended to use the Agilent instrument’s standard capillary

instead of the resistive-type capillary.


Revision History

REV DCR # Description of Change Effective Date

1.0 43 Initial Release 11/11/2013

2.0 88 Changed distance on page 15 to

8.5mm from 8.5cm.

Removed part number of flange

from document, do not want to

have to update document if part

number changes

Corrected copyright date from 2012

to 2014

3/10/2014

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