Shimadzu LC-40D X3 CL User manual

228-97197B
Sep. 2022
Solvent Delivery Module for Shimadzu
Liquid Chromatograph
LC-40D X3 CL
LC-40D XR CL
Instruction Manual
Read this manual thoroughly before you use the product.
Keep this manual for future reference.

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Read this Instruction Manual thoroughly before using
the product.
Thank you for purchasing this product.
This instruction manual describes the basic operation, and accessories and options for this
product. Read this manual thoroughly before using the product and operate the product
in accordance with the instructions in this manual.
The following instruction manuals are included with the product in booklet form or in
PDF format. The PDF documentation is on the instruction manual DVD-ROM (Part No.
228-97193-41).
Document Name Document No. Description
Instruction Manual (PDF) 228-97197 This instruction manual.
System Guide (PDF) 228-97194
This manual provides details on how to use
the system:
system performance optimization, analysis
procedure, troubleshooting, validation,
installation, etc.
Safety Guideline
(Booklet/PDF) 228-97195 Describes the precaution instructions to ensure safe operation.
Read "Safety Guideline" thoroughly before using the product.
"Safety Guideline" describes the information about the warranty, after-sales service,
safety instructions and precautions to ensure safe operation of the instrument. Keep this
manual for future reference.
Important
• If the user or usage location changes, ensure that this Instruction Manual is always
kept together with the product.
•If this manual or a product warning label is lost or damaged, immediately contact
your Shimadzu representative to request a replacement.
•To ensure safe operation, read the accompanying booklet "Safety Guideline"
before using the product.
•To ensure safe operation, contact your Shimadzu representative if product
installation, adjustment, re-installation (after the product is moved), or repair is
required.
ã 2020-2022 Shimadzu Corporation. All rights reserved.
Original version is approved in English.
Introduction
LC-40D X3 CL LC-40D XR CL i

Notice
• Information in this manual is subject to change without notice and does not represent
a commitment on the part of the vendor.
• Any errors or omissions which may have occurred in this manual despite the utmost
care taken in its production will be corrected as soon as possible, although not
necessarily immediately after detection.
• All rights are reserved, including those to reproduce this manual or parts thereof in
any form without permission in writing from Shimadzu Corporation.
•Nexera and LabSolutions are trademarks of Shimadzu Corporation.
Windows is a registered trademark of Microsoft Corporation in the United States and/or
other countries.
Third-party trademarks and trade names may be used in this publication to refer to
either the entities or their products/services, whether or not they are used with
trademark symbol "TM" or "®".
Indications Used in This Manual
Precaution symbols are indicated using the following conventions:
Indication Meaning
Indicates a potentially hazardous situation which, if not
avoided, could result in serious injury or possibly death.
Indicates a potentially hazardous situation which, if not
avoided, may result in minor to moderate injury or equipment
damage.
Emphasizes additional information that is provided to ensure
the proper use of this product.
The following symbols are used in this manual:
Indication Meaning
Indicates an action that must not be performed.
Indicates an action that must be performed.
Indicates information provided to improve product performance.
Indicates the location of related reference information.
ii LC-40D X3 CL LC-40D XR CL
Introduction

Electromagnetic Compatibility
Descriptions in this section apply only to the following models:
•228-65076-55 LC-40D X3 CL
• 228-65000-55 LC-40D XR CL
This product complies with European standard EN61326, class B for electromagnetic
interference (Emissions) and industrial electromagnetic environment (Immunity).
nEN55011 Emissions (Electromagnetic Interference)
This is a class B product. When this product causes an electromagnetic disturbance to
devices being used near this product, create an appropriate distance between those
devices and this product in order to eliminate the disturbance.
Operating Nexera CL System
nIntended Use
This system is designed to perform qualitative and quantitative analysis of target
compounds in a sample matrix and can be used as a liquid delivery unit of the liquid
chromatograph for general in vitro diagnostic applications. However, only personnel who
have received appropriate training on use of the system can use it for these purposes.
nCalibration
A calibration curve should be generated for each analyte in appropriate methods. At
least four out of six non-zero standards should meet the appropriate criteria, including
the calibration standard lower than the assumed LOQ and the calibration standard at
the highest concentration.
nQuality Control
Implement quality control of the instrument by routinely measuring at least one each of
four types of quality-control samples (a sample with a normal concentration level, a
sample with a concentration level higher than normal as well as a sample lower than
normal, and a blank sample). Check the selectivity/specificity in the matrix used for the
actual sample, the accuracy, correctness, recovery rate, dynamic range, linearity, and lower
limit of quantitation.
Based on these assessment results, check that the results are within the permissible range.
If the assessment results are out of range, the measured data may be invalid, so do not
use analysis results obtained from the instrument in question until it can be confirmed
that it is functioning normally. When, for example, analyzing samples that contain
complex sample matrices such as serum, plasma or urine, it may be possible to obtain
stabilized data by using an appropriate pre-treatment or an internal standard.
LC-40D X3 CL LC-40D XR CL iii
Electromagnetic Compatibility

Contents
Introduction Indications Used in This Manual ......................... ii
Electromagnetic Compatibility ............................ iii
Operating Nexera CL System .............................. iii
1Overview 1.1 Features ............................................................. 1
1.2 Component Parts ................................................. 2
1.3 Optional Parts ..................................................... 3
2Parts Identification
and Function
2.1 Front .................................................................. 7
2.2 Behind Front Cover ............................................. 8
2.3 Back ................................................................... 9
2.4 Right Side and Bottom ...................................... 10
2.5 Name and Functions of the Operation Panel ....... 11
2.5.1 Display Area ................................................... 13
2.5.2 Operation Area ............................................... 14
3Operation 3.1 Settings for the Basic Operation ......................... 16
3.1.1 Prior to Key Operation ........................................ 16
3.1.2 Setting Flow Rate ............................................. 16
3.1.3 Setting Compressibility ........................................ 16
3.1.4 Setting Maximum Pressure Limit .............................. 17
3.1.5 Setting Minimum Pressure Limit .............................. 18
3.2 Operation ......................................................... 19
3.2.1 Preparation before Operation ................................. 19
3.2.2 Operation in Constant Flow Delivery Mode .................. 20
3.2.3 Operation in Constant Pressure Delivery Mode .............. 21
3.3 Types of Screens ................................................ 23
3.4 Monitoring Screens ............................................ 24
3.5 Auxiliary Functions Screen (FUNCTION) ................ 28
3.5.1 Auxiliary Functions (FUNCTION) List .......................... 28
3.5.2 [PARAMETER] Setting Group .................................. 31
iv LC-40D X3 CL LC-40D XR CL

3.5.3 [CONTROL] Setting Group .................................... 37
3.5.4 [SYSTEM] Setting Group ...................................... 38
3.5.5 [UTILITY] Setting Group ....................................... 44
3.5.6 [FILE] Operation Group ........................................ 46
3.6 VP Functions Screen ........................................... 47
3.6.1 List of VP Functions .......................................... 47
3.6.2 Product Information Group (PRODUCT INFO) ................ 49
3.6.3 Maintenance Information Group (MAINTENANCE) ........... 49
3.6.4 Validation Support Information Group (VALIDATION) ........ 53
3.6.5 Calibration Support Information Group (CALIBRATION) ...... 61
3.7 Creating Time Program ...................................... 69
3.7.1 Time Program Command List ................................. 69
3.7.2 Time Program Setting Screen ................................. 70
3.7.3 Creating a Time Program ..................................... 71
3.7.4 Creating a Low-Pressure Gradient Program .................. 73
3.7.5 Deleting a Step ............................................... 74
3.7.6 Starting and Stopping a Time Program ...................... 74
3.7.7 Commands Used for Time Programs Only ................... 75
3.8 Delivery in the Low-Pressure Gradient Mode ....... 76
3.8.1 Set Value ...................................................... 76
3.8.2 Preparation for Delivery ....................................... 76
3.9 Connection with the System Controller or
Workstation ...................................................... 78
3.9.1 Setting the Instrument ........................................ 78
3.9.2 Basic Parameters .............................................. 78
3.10 Connection to External Input/Output
Terminals .......................................................... 78
4Maintenance 4.1 Periodic Inspection and Maintenance .................. 79
4.1.1 Prior to Inspection and Maintenance ......................... 79
4.1.2 List of Periodic Inspection and Maintenance ................. 82
4.1.3 Check after Inspection and Maintenance .................... 83
4.2 Removing the Right Panel Cover and the Filter
Holder .............................................................. 84
4.3 Removing/Installing the Pump Heads ................... 85
LC-40D X3 CL LC-40D XR CL v
Contents

4.4 Replacing the Plunger Seal ................................ 92
4.4.1 Replacing the Plunger Seal and Backup Ring ................ 92
4.4.2 Resetting the Delivery Amount ............................... 99
4.4.3 Check after Replacement ..................................... 99
4.5 Cleaning/ Replacing the Plunger and
Diaphragm ...................................................... 100
4.5.1 Removing the Pump Head and the Head Holder .......... 101
4.5.2 Cleaning and Replacement of the Plunger and the
Diaphragm ................................................... 103
4.6 Rinsing the Check Valve ................................... 107
4.7 Performing an Ultrasonic Cleaning of the
Check Valve .................................................... 110
4.8 Replacing the Check Valve ............................... 112
4.9 Inspecting the Line Filter ................................. 114
4.10 Replacing the Line Filter .................................. 115
4.11 Cleaning/Replacing the Suction Filter ................. 117
4.12 Replacing the Drain Valve ................................ 119
4.13 Replacing the Air Filter (Right Panel) ................ 120
4.14 Cleaning of the Leak Tray ................................ 122
4.15 Cleaning the Exterior ....................................... 122
4.15.1 Usual cleaning ............................................... 122
4.15.2 Decontamination cleaning .................................. 123
4.16 Cleaning of the Automatic Rinsing Kit .............. 123
5Technical
Information
5.1 Specifications ................................................... 125
5.1.1 LC-40D X3 CL Specifications ............................... 125
5.1.2 LC-40D XR CL Specifications ............................... 126
5.1.3 High-Pressure Gradient System .............................. 127
5.1.4 Low-Pressure Gradient System .............................. 127
5.1.5 Other Specifications ......................................... 128
5.2 Maintenance Parts ........................................... 130
5.2.1 Consumable Parts ........................................... 131
5.2.2 Replacement Parts ........................................... 132
5.2.3 Maintenance Kit ............................................. 133
vi LC-40D X3 CL LC-40D XR CL
Contents

Index ......................................................... 134
LC-40D X3 CL LC-40D XR CL vii
Contents

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This instrument is a liquid delivery unit for liquid chromatography using a parallel double
plunger reciprocating-type pump developed to improve the precision and sensitivity of
analysis.
By pumping alternately from two pump heads arranged in parallel, it can perform
continuous pumping. The stepping motor's torque is transmitted to the cam, causing the
plungers to perform a piston motion.
1.1 Features
nLow Flow Pulsation and Pulsation Period Enable Precise Delivery
By reducing the discharge volume per plunger stroke to the microvolume level (10 µL),
and applying high-speed drive, the flow pulsation and pulsation period have been
reduced to levels significantly lower than those for other instruments.
nChoice of Gradient Modes and Control Options
LC-40D X3 CL/LC-40D XR CL can be used in both low- and high- pressure gradient modes.
The high-pressure gradient mode uses two pumps and is highly accurate with minimal
time lag. In low-pressure gradient mode, a single pump unit plus the gradient unit
provides a low cost option to combine up to four solvents.
There are two gradient modes available: fast LC mode or normal mode under control of
the system controller.
The fast LC mode for binary high-pressure gradient delivery supports ultra high speed
high separation analysis with minimized gradient control steps.
nAutomatic Plunger Rinsing
An automatic rinsing kit is provided as standard for LC-40D X3 CL/LC-40D XR CL . It can
rinse the plunger in the back of the plunger seal. When high-salt-concentration buffer
solutions are used, in particular, it prevents premature seal failure due to crystallization,
extending the service life of plunger seals.
nHigh-pressure Flow is Available
LC-40D X3 CL enables ultra high pressure solvent delivery up to 130 MPa supporting ultra
fast high separation analysis in combination with Shim-pack XR-ODS III or other ultra fast
high separation columns. For LC-40D XR CL, high-pressure solvent delivery up to 70 MPa
is possible so high speed high separation analysis is supported in combination with
Shim-pack XR-ODSⅡcolumns.
1Overview
LC-40D X3 CL LC-40D XR CL 1
1

1.2 Component Parts
This instrument consists of the standard parts listed below. Check the parts against this
list after unpacking.
No. Part Name Part No. Q'ty Remark
-
Main Unit
LC-40D X3 CL/LC-40D XR
CL
- 1
-Safety Guideline
(Booklet)*1 228-97195 1
-Instruction manual/
System Guide (CD-ROM) 228-97193-41 1
- Bottle, 250 mL 228-74372 1
1 Suction Filter Assy 228-45708-91 1 Including a tube
2 REMOTE CABLE ASSY 228-28253-91 1 Not used in CL model.
3 DRAIN TUBE SI(L1000) 228-25162-03 1
4STOP JOINT ASSY,B,D 228-46054-91 1
SYRINGE TUBE ASSY,B,D 228-46055-91 1
5
SYRINGE,SS-20ESZ 228-66048 1
NEEDLE ASSY,FOR
SYRINGE 228-18216-91 1
6 CLAMP,M9120 046-05522-02 1
7 DRAIN ADAPTER 228-42204 1
8 STANDARD OUT DRAIN 228-42205 1
9 CTO OUT DRAIN 228-42206 1
10 STRAIGHT JOINT 228-28163 1
11 FITTING,L-TYPE 1253 035-61561-12 1
*1 It contains cautions for use regarding the instrument.
2LC-40D X3 CL LC-40D XR CL
1 Overview

1.3 Optional Parts
Optional units available for this instrument are listed below.
For information about other optional units listed below, contact your Shimadzu
representative.
nCommon Optional Parts for LC-40D X3 CL/LC-40D XR CL
Option Part No. Features
Low pressure gradient
kit 228-65016-58
Switches between up to 4 liquids of low-pressure
gradient or mobile phase. It also can be used for
auto rinsing of column flow lines.
Installed inside of the instrument.
Reservoir switching
valve 228-65017-58
• Switches between 2 liquids (for example,
switches between mobile phase and rinse
solution) or two mobile phases.
• Installed inside of the instrument.
Mixer installation kit
(MR40 LPGE, to be
built in)
(w/ mixer
recognition
device)
228-65020-41
Gradient mixer (40 µL internal capacity)
exclusively for low-pressure gradient analysis.
Fixed inside of the instrument.
Mixer MR40 LPGE
(fixed inside column
oven)
(w/o mixer
recognition
device)
228-45210-41
Gradient mixer (40 µL internal capacity)
exclusively for low-pressure gradient analysis.
It can be installed inside of the CTO-40C CL.
Mixer MR300 LPGE
(w/ mixer
recognition
device)
228-72653-42
(w/o mixer
recognition
device)
228-45210-42
Gradient mixer (300 µL internal capacity)
exclusively for low-pressure gradient analysis.
It can be installed inside of the CTO-40C CL.
This option can be used for solvents that are
hard to mix, such as TFA (trifluoroacetic acid), or
for reducing the baseline fluctuation of the
photo diode array detector.
Gradient Mixer for
High-Pressure Gradient
Analysis
"Gradient Mixer for High-Pressure Gradient Analysis" P.5
LC-40D X3 CL LC-40D XR CL 3
1.3 Optional Parts
1

Option Part No. Features
RINSING PUMP XR 228-39625-42
The rinsing pump kit is intended for
continuously rinsing the back part of the plunger
seal with rinsing solution. The rinsing volume
can be selected.
Tool Kit 228-57647-43 Kit containing the necessary tools for
preparation, inspection, and maintenance.
SUS Pipe (0.3´600) 228-53184-54 Plumbing for the pump outlet. ID 0.3 mm
´600 mm, pre-bent
SUS Pipe HP (0.3´1,000) 228-53184-96 Plumbing for the pump outlet. ID 0.3 mm
´1000 mm
Plunger Seal GFP 228-52711-94
The maximum available pressure is 44MPa.
When using a non-polar organic solvent such as
hexane or a solvent of alkyl sulfonic acid with
TFA, use the standard plunger seal.
SUCTION FILTER ASSY 228-61905-49 Suction filter with tube and fittings for the low
pressure gradient kit or the degassing unit.
n Optional Parts for LC-40D X3 CL
Option Part No. Features
MAINTENANCE
KIT,LC-40D X3 228-53265-45
A set of consumable parts and plumbing parts
for LC-40D X3 CL.
"Maintenance Kit for LC-40D X3 CL (Parts
No. 228-53265-45)" P.133
nOptional Parts for LC-40D XR CL
Option Part No. Features
MAINTENANCE KIT,
LC-40D XR 228-45593-49
A set of consumable parts and plumbing parts.
"Maintenance Kit for LC-40D XR CL (Parts
No. 228-45593-49)" P.133
4LC-40D X3 CL LC-40D XR CL
1 Overview

nGradient Mixer for High-Pressure Gradient Analysis
The following gradient mixers for high-pressure gradient analysis are available for liquid
chromatographs.
Part Name Part No.
MIXER,MR 20 µL (w/ mixer recognition device) 228-72652-41
(w/o mixer recognition device) 228-45209-41
MIXER,MR 40 µL (w/ mixer recognition device) 228-72652-42
(w/o mixer recognition device) 228-45209-42
MIXER,MR 100 µL (w/ mixer recognition device) 228-72652-43
(w/o mixer recognition device) 228-45209-43
MIXER,MR 180 µL Ⅱ(w/ mixer recognition device) 228-72652-44
(w/o mixer recognition device) 228-45209-44
Mixers described above are packaged in a set
Part Name Part No.
Set of Two Mixers MR 40 µL and MR 180 µLⅡ228-45292-41
Set of Two Mixers MR 100 µL and MR 180 µLⅡ228-45292-42
Set of Three Mixers MR 40 µL, MR 100 µL and MR 180 µLⅡ228-45292-43
Recommended Mixers
The table below lists the mixers with the smallest volume among mixers that can be used
in individual combinations of detectors and mobile phases.
Mobile Phase
Solvent Containing
Trifluoroacetic
Acid (TFA)
Solvent Containing
Formic Acid,
Acetic Acid, etc.
Water (Including
Buffer Solution),
Organic Solvent,
or Its Solvent
Mixture
Detector
Photo Diode Array
Detector MR 180 µL MR 180 µL MR 180 µL
UV Detector MR 180 µL MR 100 µL MR 40 µL
LCMS, LCMSMS - MR 20 µL MR 20 µL
Using a mixer with a volume smaller than the recommendation shown above may cause
excessive fluctuation of the baseline.
When connecting multiple detectors, use a mixer with the largest volume among the
applicable mixers. For example, if using a Photo Diode Array and an LC/MS, the MR 180
µLⅡmixer is recommended.
A larger than recommended mixer can be used to improve mixing performance, but will
also increase the gradient delay volume.
LC-40D X3 CL LC-40D XR CL 5
1.3 Optional Parts
1

nAutomatic Rinsing Kit
The plunger can be rinsed with the automatic rinsing kit at the back part of the plunger
seal. LC-40D X3 CL/LC-40D XR CL has the automatic rinsing kit as standard. When using
buffer solution, be sure to attach the automatic rinsing kit.
See the table below for the necessity of the automatic rinsing kit and rinsing solution.
Mobile Phase
LC-40D X3 CL/LC-40D XR CL
Necessity Recommended Rinsing
Solution
Buffer Solution Necessary 10 % 2-propanol water
Normal-phase solvent such as hexane Not necessary -
Other Solutions Necessary 10 % 2-propanol water
Necessary: The rinsing kit is necessary.
Not necessary: The rinsing kit should not be used.
• For the application system, refer to the instruction manual of the application
system.
• If the rinse solution is dirty, replace with new solution. If getting significantly
dirty, replace with new solution once a day. Even if it does not appear dirty,
replace with new solution once a week.
If using distilled water as rinsing solution, replace it once a day.
6LC-40D X3 CL LC-40D XR CL
1 Overview

2.1 Front
No. Name Description
1 Operation Panel
Configure or operate the instrument with the operation keys.
Touching the center part on the operation panel displays the
operation keys.
2 Front Cover This is the cover for the flow line.
3 (Power button)
Switches ON/OFF the power.
Pressing the switch turns on the power and pressing it again
turns off the power.
The switch is enabled only when the main power switch on
the back is on.
2
Parts Identification and Function
LC-40D X3 CL LC-40D XR CL 7
2

2.2 Behind Front Cover
No. Name Description
1Pump Head*1 The plunger inside it reciprocates to deliver solvent.
2Head Holder*1 It has the rinsing flow path of the plunger inside. The
pump head is attached to this part.
3Check Valve OUT*1 A check valve on the outlet side.
4 Drain Valve
It is used to replace mobile phase solvent or remove
air from the flow path. It has an internal pressure
sensor.
5 Line Filter A column protection filter for removing contaminants
from mobile phase solvent.
6 Pump Outlet A connection port of the tube connected to the
autosampler/manual injector.
7Check Valve IN*1 A check valve on the inlet side.
8 Pump Inlet A connection port of the tube from the suction filter.
9 Leak Sensor
It detects liquid leaks.
If the leak sensor detects a leak, delivery automatically
stops, causing an alarm and message on the display.
*1 This is common to the right and left pump heads.
8LC-40D X3 CL LC-40D XR CL
2 Parts Identification and Function

2.3 Back
No. Name Description
1 [REMOTE] Connector A connector for connecting the system controller.
2External Input/Output
Terminals Connect to external equipment.
3 [DGU PRESS IN] Connector To input the pressure signal from the external
degassing unit.
4 [DGU/SV] Connector A connector for connecting rinsing pump or degassing
unit.
5 [PC] Connector A connector for service personnel. Normally unused.
6 Power Cord Connector Connect the power cord.
7 Main Power Switch It turns ON/OFF the power to the instrument. Normally
keep it on.*1
*1 Normally use (power button) of the operation panel or system controller to turn ON/OFF the
power. If the system controller is connected and the main power switch is on, the user can use
(power button) of the system controller to turn ON/OFF the power from the front of the instrument.
If the instrument is not used for a long time, turn off the main power switch. Before turning off
the main power switch, be sure to turn OFF the power using the power button.
"2.5 Name and Functions of the Operation Panel" P.11
LC-40D X3 CL LC-40D XR CL 9
2.3 Back
2

2.4 Right Side and Bottom
No. Name Description
1 Mixer Mounting Holes Used to install mixer and column holder.
2 Shipping Screws (Red)
To prevent damage during transportation. LC-40D X3
CL has three screws, and LC-40D XR CL has two screws.
Remove before installation.
3 Leakage Drain Outlet Connect the provided drain tubing.
10 LC-40D X3 CL LC-40D XR CL
2 Parts Identification and Function