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
the maximum extent permitted by applicable law, Agilent disclaims all warranties, either express or implied, with regard to this manual
and any information contained herein, including but not limited to the implied warranties of merchantability and fitness for a particular
purpose. Agilent shall not be liable for errors or for incidental or consequential damages in connection with the furnishing, use, or
performance of this document or of any information contained herein. Should Agilent and the user have a separate written agreement with
warranty terms covering the material in this document that conflict with these terms, the warranty terms in the separate agreement shall
control.
Technology Licenses
The hardware and/or software described in this document are furnished under a license and may be used or copied only in accordance with
the terms of such license.
Restricted Rights Legend
If software is for use in the performance of a U.S. Government prime contract or subcontract, Software is delivered and licensed as
“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
Agencies of the U.S. Government will receive no greater than Restricted Rights as defined in FAR 52.227-19(c)(1-2) (June 1987). U.S.
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.

Page 3 of 33 18 July 2011
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

Page 4 of 33 18 July 2011
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

Page 5 of 33 18 July 2011
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

Page 7 of 33 18 July 2011
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.

Page 8 of 33 18 July 2011
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.

Page 9 of 33 18 July 2011
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.

Page 10 of 33 18 July 2011
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.