Agilent Technologies G1982-6700 User manual

HPLC-Chip/Nanospray
Upgrade Installation
Guide

Page 2 of 33 18 July 2011
Notices
© Agilent Technologies, Inc. 2011
No part of this manual may be reproduced in any form or by any means (including electronic storage and retrieval or translation into a foreign
language) without prior agreement and written consent from Agilent Technologies, Inc. as governed by United States and international
copyright laws.
Manual Part Number
G1982-90000
Edition
First edition, July 2011
Printed in USA
Agilent Technologies, Inc.
Warranty
The material contained in this document is provided “as is,” and is subject to being changed, without notice, in future editions. Further, to
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warranty terms covering the material in this document that conflict with these terms, the warranty terms in the separate agreement shall
control.
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Restricted Rights Legend
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“Commercial computer software” as defined in DFAR 252.227-7014 (June 1995), or as a “commercial item” as defined in FAR 2.101(a) or as
“Restricted computer software” as defined in FAR 52.227-19 (June 1987) or any equivalent agency regulation or contract clause. Use,
duplication or disclosure of Software is subject to Agilent Technologies’ standard commercial license terms, and non-DOD Departments and
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Government users will receive no greater than Limited Rights as defined in FAR 52.227-14 (June 1987) or DFAR 252.227-7015 (b)(2) (November
1995), as applicable in any technical data.

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Contents
1Introduction 4
Kit Contents 4
Required Tools 6
Prepare for the upgrade 7
2Installation 8
Upgrade the HPLC-Chip Interface 8
Replace the gas distributor inside the desolvation assembly 9
3New Default Method Set Points and Reference Mass Introduction Procedure 22
4New Reference Mass Introduction Procedure 24
Preparation of the IRM solutions 24
Low Mass IRM stock solution: 1000 µg/ml methyl stearate in ACN 25
IRM Working Solution: 100 µg/ml methyl stearate and 2% (v/v) HP-1221 in ACN 25
Use of the IRM Solutions 25
Troubleshooting Tips 28
5Calibration or Auto Tuning Using CDS and Infusion Chip 31
6Static Needle Holder Installation and Use 32
Use of Proxeon (Thermo Fisher) Nanospray Emitters 32

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1 Introduction
This document describes the installation of the HPLC-Chip/Nanospray Upgrade Kit. This
upgrade is designed for all Agilent LC/MS instruments utilizing the HPLC-Chip interface in
either the HPLC-Chip configuration or Nanospray configuration.
This document and procedure assumes that air is present in the drying gas supply. If no air is
available, the HPLC Chips will charge which appears as unstable spray on the video capture
device or black/white monitor.
Please note that this document is best viewed when printed in color.
Kit Contents
The HPLC-Chip/Nanospray Upgrade Kit includes the following items:
G1982-67000
HPLC-Chip/Nanospray Upgrade Kit
Part Number Part Description
Quantity
Part
Picture
G1969-20148
End Plate Screw, Gold, M3 x 0.5 x 8mm long
flat head screw
2
2680-0217 Button head screw 1
G1982-20005 Contact spring 1
G1982-20006 Radial Gas Diverter 1
G1946-20111 T-nut 2
G1946-20156 End Plate, Counter Bored Holes 1
G1964-20303 Capillary Insulator 1

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G1982-67000
HPLC-Chip/Nanospray Upgrade Kit Cont.
Part Number Part Description
Quantity
Part
Picture
G1982-20008 Holey Counter Electrode 1
G1982-20011 Wing Nut, Stainless Steel 1
G1982-20111 End Cap Nano Spray Shield 1
G1982-20012 Wave washer, Gold plated 1
G1982-60004
Cover with flex steel
1
GT430-20358
Electrode Spacing Tool
1
59987-20040 Dielectric Capillary 1
0515-1644 Screw, M3 x 0.5 x 12 mm 1
G1982-20152 Emitter Cover 1
5022-2145 ZDV Union 2
9301-6477 Glass Tip Pkg – Nanospray Emitters 1
0515-5373 M4 Thumb Screw 1
G1982-20316 Needle Holder 1
G1982-60025 Nano Nut Assy 1
0100-2609 Tefzel Ferrule 2
G1982-90000
Field Upgrade Installation Manual
1
0100-2436 Ferrule 1

Page 6 of 33 18 July 2011
G1982-67000
HPLC-Chip/Nanospray Upgrade Kit Cont.
Part Number Part Description
Quantity
Part
Picture
0100-2437 PEEK Nut 1
0100-2611 ZDV Union 1
5065-9906 LC-MS Capillary Connector 1
G1982-85001 Chip Cube High Mass Reference (HP-1221) 1
Not
Shown
G1982-85002 Chip Cube High Mass Solvent (FC-70) 1
Not
Shown
G1982-85003 Chip Cube Low Mass Reference Sample 1
Not
Shown
Required Tools
The following tools are required for the installation of the HPLC-Chip/Nanospray Upgrade Kit.
Not all of the required tools are supplied with the kit:
Included in Kit
8710-2624
0.9 mm Allen Wrench
1
8710-2623
1.5 mm Allen Wrench
1
Not included in Kit
8710-1623
Torx T-10 driver
1
8710-1615
Torx T-20 driver
1
8710-1029
Flat blade screwdriver
1

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Prepare for the upgrade
1. If installed, remove the HPLC-Chip Cube and HPLC-Chip Cube interface from the LC/MS
instrument.
2. Remove the HPLC-Chip interface spray shield and gas diverter. Properly dispose these
parts as they will no longer be used and are not compatible with the new gas diverter.
3. Before beginning the upgrade procedure, it is important to verify the current performance of
the LC/MS System. With a standard source installed including the standard capillary cap
and spray shield, perform a Positive and Negative ion mode autotune. Examine the tune
reports to verify that the LC/MS system is meeting tune specifications.
4. Right-click on the LC/MS icon in the Status pane and select “Vent”.
•After the LC/MS system has completed the vent process, switch off the front switch
and unplug the instrument.
•It is suggested that since the instrument is being completely vented, that an Ion Optics
Servicing be performed. This would involve removing the desolvation assembly and
cleaning Skimmer 1 and possibly cleaning Lens 1 and Lens 2 of the Ion Optics
Assembly.

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2 Installation
This section describes the installation of the HPLC-Chip/Nanospray Upgrade Kit hardware.
Upgrade the HPLC-Chip Interface
1. While the LC/MS instrument is venting, remove and properly dispose of the following parts
from the HPLC-Chip interface:
•Counter Electrode – Use the supplied Hex Wrench (part number 8710-2623) to
remove the counter electrode. The set screw only needs to be loosened to remove
the counter electrode.
•Existing Top Plate – The existing top plate may or may not contain the IRM wick
used to introduce IRM compounds into the spray chamber. The new Top Plate will
contain the IRM wick but also has been modified to provide additional standoff
clearance for the high voltage spray shield.
The items circled in red are to be removed and discarded.

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2. Locate the new Holey Counter Electrode (part number G1982-20008).
3. Using the hex wrench, install the new counter electrode. Set the Holey Counter Electrode
flush against the Electrode Mounting Bracket. Temporarily tighten the set screw to keep
the new counter electrode in place. The final spacing adjustment will be performed with
the interface installed on the instrument.
Replace the gas distributor inside the desolvation assembly
1. Once the instrument has vented, remove the spray shield and the existing endplate. The
stainless steel endplate cannot be used with this upgrade kit. Please dispose it in the
proper disposal container. The new endplate that is part of this upgrade kit is compatible
with all source types.
Please note: If the instrument type is a TOF or Q-TOF and the instrument has the UIRM,
remove the UIRM hardware. Place this hardware in a clean bag as this hardware will no
longer be used with the HPLC-Chip interface. However, it can still be used with the
standard source types supported with the TOF or Q-TOF.

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2. Remove the Chamber and Capillary High Voltage cables from the T-nut connectors.
3. Remove the two existing high voltage T-nut connectors that are used to secure the end
plate and discard.
4. Remove the currently installed capillary. A new capillary is supplied as part of this upgrade
kit.
Please Note: This capillary will not be used after installation of this kit. Destroy this
capillary so that it cannot be reused in the instrument or any other instrument.
5. Remove the four T-20 torx screws used to secure the metal ring that holds the Teflon spray
shield support block.
Save the UIRM Union for
use with other sources.
Discard the existing
endplate.

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6. Remove the Teflon endplate insulator block to access the vespel gas distributor. Remove
and discard the old gas distributor.
7. Locate the new dielectric capillary (part number 59987-20040). Dip or wet the capillary with
Isopropanol before installing to lubricate it. Install the new capillary.
CAUTION
Do not twist the capillary while installing it. Doing so will
permanently damage the platinum coating of the capillary.
Be careful not to damage the canted coiled spring located inside the capillary cap at the
fragmentor end of the desolvation assembly. It is suggested to remove the desolvation
assembly to ensure that the canted coiled spring has remained in place.

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8. Locate the new gas distributor (part number G1964-20303). With the solid side facing the
Teflon wall, slide the new gas distributor over the new capillary. Push it on until it is flush
with the Teflon block.
9. Reinstall the Teflon support block for the end plate with the stainless steel ring. Make sure
that the new gas distributor is positioned properly before reinstalling the screws. Be
careful during the reinstallation not to damage the URIM vespel union.
10. Reinstall the 4 T-20 torx screws to secure the metal ring in place.
11. Locate the two T-nut high voltage connectors (part number G1946-20111) and install them
into the Teflon block.
12. Locate two gold pan head screws (part number G1969-20148) and the new end plate (part
number G1946-20156). Install the new end plate and secure in place with the two pan head
screws. Make sure that the screws are snug but not over-tightened.
G1964-20303
Gas Distributor

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13. Reinstall the standard spray shield and capillary cap. When installing the capillary cap, do
not twist or the capillary can be permanently damaged.
14. Plug the instrument back into the wall outlet and begin the pump down procedure.
15. For TOF and Q-TOF Instruments ONLY: Locate the Button Head Cap Screw (part number
2680-0217). On the outside of the desolvation assembly, thread the plug into the UIRM
union. Do not over-tighten or the Vespel union will crack.
16. For TOF and Q-TOF Instruments ONLY: Start Diagnostics and performed a 2 hour HV
conditioning procedure.
17. Once the LC/MS instrument has pumped down and stabilized, perform a standard
autotune. Compare the tune report to the one previously obtained. The results should be
approximately the same when comparing reports.
Do not over-tighten these screws!

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Assemble the new spray shield and gas diverter assembly
1. While the instrument is tuning or pumping down, locate the following parts:
•Winged Nut (part number G1982-20011)
•End Cap Nano Spray (G1982-20111)
•Radial Gas Diverter (part number G1982-20006)
•Wave Spring, Gold Plated (part number G1982-20012)
•Contact Spring (part number G1982-20005)
When assembling these parts, wear powder free or lint free gloves. Treat all parts as
ultra clean parts.
2. Start assembling the new spray shield by sliding the Wave Spring (part number G1982-
20012) over the End Cap Nano Spray part (part number G1982-20111).
3. Locate the Radial Gas Diverter (part number G1982-20006) and insert into the End Cap
Nano Spray. Make sure to align the pin in the Radial Gas Diverter with the notch on the
End Cap.

Page 15 of 33 18 July 2011
4. Thread the vespel Radial Gas Diverter into Winged Nut (part number G1982-20011). Make
sure to thread the Radial Gas Diverter completely into Winged Nut.
5. Once all of the parts have been assembled, rinse all of these parts with Isopropanol in a
clean, glass beaker at least three times.
6. Once the parts have been rinsed, remove the parts from the beaker and place them on a lint
free cloth.
7. Locate the Contact Spring (part number G1982-20005) and insert it into the cleaned spray
shield assembly.

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8. Allow the instrument to complete the High Voltage Conditioning and Check Tune process
before proceeding. Once the tune process has completed, convert the system back to Chip
Cube mode.
9. Remove the currently installed spray shield and capillary cap. Store them in a clean, lint
free bag.
10. Before installing the new spray shield assembly, confirm that the two pan head screws
securing the end plate are not loose. Once the new chip cube spray shield is installed,
access to these two screws is not possible. Thread the spray shield assembly with contact
spring onto the End Plate. Make sure to thread the spray shield completely onto the End
Plate. Otherwise, the spacing between the Spray Shield and Counter-Electrode will not be
correct.
11. The new spray shield assembly will now appear as the picture below.
Set the Holey Counter Electrode Distance
CAUTION
This procedure will be performed with the HPLC Chip Cube Interface
installed. Make sure that the instrument is in either Standby or Off.
Otherwise, the Spray Chamber High Voltage Electronics will be
energized and present a shock hazard.

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1. Install the HPLC Chip Interface onto the desolvation assembly. Please note that the Top
Plate should not be installed at this time.
2. Connect the power cables for the illumination LED and video cable for the camera.
3. Locate the Electrode Spacing Tool (part number GT430-20358).
4. Loosen the set screw securing the Holey Counter Electrode. Be careful not to over-loosen
the set screw or the Holey Counter Electrode will fall out of its holder
5. Insert the Electrode Spacing Tool between the counter electrode and the spray shield. The
Electrode Spacing Tool must touch the Holey Counter Electrode AND the new spray shield
assembly. This means the spacing is set correctly. See the figure below as an example.

Page 18 of 33 18 July 2011
6. Once the spacing is set correctly, tighten the set screw that secures the Holey Counter
Electrode in place. Once the set screw has been tightened, recheck the spacing to ensure
that there is no extra space. Otherwise, the high voltage field will not be correct.
Realign the Illumination LED and Camera
Because the Holey Counter electrode has different depth dimensions, the illumination LED
will not be pointing at the right location. This will result in poor illumination of the spray
from the chip. Therefore, the illumination LED position will need to be adjusted. This
procedure must be performed with the HPLC Chip Cube Interface not installed on the
LC/MS instrument. If this adjustment procedure is performed while the interface is
mounted on the instrument, the interface can be pushed off of the instrument by the I-
button reader. This results in the interface dropping on the floor which will damage the
interface.
1. Open the spray chamber and place on a flat surface.
2. Locate the set (grub) screw that secures the illumination LED assembly in place.
3. Using the supplied 0.9 mm Allen wrench (part number 8710-2624), loosen the set screw
slightly.
4. Use the spacing tool between the Holey counter electrode and the spray shield to make
visualizing the LED easier.
5. Rotate the LED assembly to where 1/3 of the beam is striking the edge of the Holey
Counter Electrode. See the figure below.
This is a simulated
illumination spot showing
the desired alignment.

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6. Once the best position has been achieved, tighten the set (grub) screw.
7. If the camera power cable and video cable have been disconnected, reconnect those
cables.
8. Reinstall the HPLC Chip Cube Interface on the LC/MS instrument.
9. The new top plate can now be installed.
10. Locate the new top plate (part number G1982-60004) and install it on the HPLC interface.
Use the new screw (part number 0515-1644) to secure the top plate in place.
This is the actual
illumination LED spot
showing the desired
alignment.

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11. With the top plate installed, examine the image on the video monitor. If the image is not
clear or appears blurry, the camera is not focused correctly.
12. To refocus the camera, using the supplied 1.5 mm Allen Wrench (part number 8710-2623)
loosen the set (grub) screw that secures the camera in place.
13. In order to focus the camera, examine the image on the monitor while either inserting or
pulling out the camera relative to the HPLC Chip Cube Interface. When the camera is
properly focused, the image on the monitor should appear as below.
14. Once the camera has been focused, tighten the set (grub) screw. Recheck the image on
the video monitor to ensure that the camera has not moved while tightening the set screw.
15. Reinstall the HPLC Chip Cube on the instrument. Be careful not to damage any of the
camera or video cables.
16. Restart the MassHunter Acquisition software if needed to have the HPLC Chip Cube
recognized.
17. Insert a chip into the HPLC Chip Cube. The image on the video monitor should resemble
the image below.