225-18427A

Jun. 2014

LCMS-2020 Preparative System

Installation Guide
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CONTENTS

1. Introduction
1.1 Fractionation by LCMS
1.2 Splitter and Delay-time
1.3 Outline of Analog Output
2. System Configuration
2.1 Example Layout
2.2 Connecting Signal Cables
2.3 Flow Line Configuration
2.4 How to Connect the Main Flow Lines
3. How to Check and Adjust the Delay Time
4. Precautions for Using the Preparative System
5. Consumable Parts
6. Service Parts
7. Appendix
8.1 Equipment size and electric requirements
8.2 Footprint

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1. Introduction
This manual is guide for installing the LCMS-2020 Preparative system. Use this guide in
conjunction with the LCMS-2020 instruction manual. For information regarding LC units,
refer to the instruction manuals for respective units. For information regarding how to
operate the software, refer to the LCMS Preparative System Operation Manual, which is
provided with this preparative system.

1.1 Fractionation by LCMS

LCMS-2020 is able to output analog signals in various chromatogram output modes
(total ion chromatograms [TIC], multi ion chromatograms [MIC], mass
chromatograms [MC], or selected ion monitoring chromatograms [SIM]). This allows
collecting fractions of constituent substances based on chromatographic information
obtained from LCMS-2020.

1.2 Splitter and Delay-time

When using UV detectors and PDA detectors for the fractionation, fractions are
collected by connecting the detectors in series to a downstream fraction collector.
When using LCMS System for the fractionation, LCMS cannot recover the sprayed
sample. Therefore, fractions are collected by splitting the flow line to MS and fraction
collector flow lines after the sample passes through the column. (see Figure 1.1).

LCMS Fraction Collector

From Column

Splitter T1
LCMS

From Column Trigger Signal

Fraction Collector
T2 T2＞T1
Adjustment Line of Delay time

Figure 1.1 Diagram of Fractionation Using LCMS System

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When flow lines are split to collect fractions, sample substances diverted by the
splitter must reach the fraction collector after they reach the MS unit. This difference
in arrival times (T2 minus T1) is referred to as “Delay time”, where T2 is the time
required for the sample to flow to the fraction collector and T1 is the time required for
the sample to flow to the MS unit. To become T2>T1, the LCMS-2020 preparative
system provides the adjustment line (Tube for the Delay time) that allows adjusting
the Delay time. (See Figure 1.1.)

We use an active splitter (APV) that has high speed switching valve to split the flow.
The APV can be set to several different split ratio configurations, depending on the
flow rate. (For more details, refer to the APV instruction manual.) Using an APV
(valve) requires a make-up pump (such as the LC-20AD). By using the APV, the
LCMS preparative system has two independent flow lines – the MS line and the
fraction collector line, where the APV diverts part of the sample from the fraction
collector line to the MS line. (See Figure 1.2.)

MS Line LCMS
Make-up Pump

Tube for the Fraction

LC Pump Injector Column UV Detector
Collector
Delay time

FC Line
APV

Figure 1.2 LCMS Preparative System with APV

1.3 Outline of Analog Output

LCMS-2020 is equipped with analog output ports for 2 channels. Each output port
can be set independently to TIC, MIC, MC (in the case of “Scan” analysis), or SIM (in
the case of “SIM” analysis). The system allows setting different analytical parameters
for different time segments. These segments are called scan groups, where the
chromatogram output mode can be changed for each scan group.

The MS detector receives the digital input signal, performs a D/A conversion and
outputs and analog signal. With default settings, one MS count is output as 1 micro V,

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with a maximum count of 1,000,000 (= 1 v). This maximum value can be changed by
editing the method parameters. For example, if the maximum value is set to
10,000,000, then 1 μV will be output for a count of 10. (The maximum analog value
remains 1 volt.) Consequently, even if chromatogram values for an MS detector are
exceptionally large, this maximum value setting can be changed in order to output
appropriate analog values.

The baseline for the analog output is automatically determined from the first three
signal points generated at the beginning of the analysis and for each change in scan
group. Therefore, even if the baseline increases after repeating an analysis or the
baseline varies due to changes in analytical parameters for different scan groups, the
auto-zero function allows ignoring these baseline variations.
Analog output settings are entered via the LCMSsolution software. Refer to the
LCMS Preparative System Operation Manual provided with the system regarding
how to enter these settings.

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2. System Configuration
2.1 Example Layout
Figure 2.1 shows one example of units included in a system and their layout.
Different models can be selected for the pump, autoinjector and fraction collector
units depending on system objectives.

Column holder LCMS-2020

Gilson215 or IFC-PAL CBM-20A

SPD-20A（prep cell）
LC-8A APV
LC-20AD PC Printer

SPD-M20A

（semimicro cell）

Units Included in System Configuration

 LCMS-2020  LC-8A (2 units)
 LC-20AD  Gilson215 or IFC-PAL
 SPD-M20A  SPD-20A
 APV  CBM-20A
 LC-8A Column Holder  PC and Printer

Figure 2.1 System Configuration and Layout Example

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2.2 Connecting Signal Cables

A signal line connection diagram is shown in Figure 2.2.

LC-8A PC
LAN

LC-8A CBM-20A
Optical link 1

M.inj 4 Event COM1

LC-20AD
USB USB
Event
LCMS-2020

ANALOG IN ANALOG OUT

RS232C
SPD-20A （Trigger）
SPD-M20A

APV
OUT 2 IN A (B) (A)

Gilson215 506C Controller

RS232C
GSIOC

Gilson819

A） When Gilson215 is used

LC-8A PC
LAN
CBM-20A 2Ch-RS232C board
LC-8A 1
Optical link
M.inj 2 COM3 COM4
Event
LC-20AD
Event USB
USB

LCMS-2020
Cable of IFC-PAL
ANALOG IN ANALOG OUT
RS232C
SPD-20A （Trigger）
SPD-M20A

A1 A0 APV
INTERFACE 1
NI-6009
IFC PAL USB
P00&G

A/D converter RS232C

RS232C
B） When IFC-PAL is used
Figure 2.2 Signal cables Connection Diagram 7
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(1) Connecting LCMS-2020 and Gilson215 or IFC-PAL

Please connect LCMS-2020 with Gilson215 or IFC-PAL using a remote cable
that is the accessory set of LCMS preparative system.
1. Insert the cable in the predefined position of the connector(Socket type,8pin)
that is accessory of LCMS-2020 and fix it.
2. Please insert it in the analog-out connector (Plug type, 8pin) of the back panel
of LCMS-2020.
3. Please connect the other side of the cable to Gilson506C controller or A/D
converter for IFC-PAL.
(2) Connecting the APV Valve and PC
The USB-RS232C converter is connected with the universal serial bus port of PC
(Please buy the commercial item for the USB-RS232C converter.)
In addition, the USB-RS232C converter is connected between APV with the
RS232C cable attached to the APV starter kit.
(3) Connecting PC or CBM-20A and Gilson215
1. Connect PC and Gilson215 using the RS232C cable provided with
Gilson215.
2. Connect CBM-20A and Gilson215 using a remote cables provided with
LC-20AD and SPD-M20A.(2 lines)
(4) Connecting PC or CBM-20A and IFC-PAL
1. Connect PC and IFC-PAL using the RS232C cables provided with IFC-PAL.
(2 lines)
2. Connect PC and A/D converter for IFC-PAL using the USB cable.
(A/D converter and the LAN cable are not accessories of IFC-PAL. Please
buy them separately.)
3. Connect CBM-20A and IFC-PAL using a remote cable provided with
IFC-PAL.
4. Connect CBM-20A and A/D converter for IFC-PAL using a remote cable
provided with LC-20AD.
(5) Connection of other signal cables
Please connect the cable according to the signal line connection diagram.

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2.3 Flow Line Configuration

Figure 2.3 shows one example of a flow line configuration for a LCMS-2020
preparative system. If an APV unit is used, one MS line pump must be provided in
addition to the standard LC pump. In the case of the preparative line, mobile phase
sent from an LC-8A pump exits the column, then passes through the APV unit before
reaching the fraction collector unit. For the MS line, Mobile phase sent from the
LC-20AD pump (for make-up flow) passes through the APV unit before reaching the
MS unit.

CBM-20A

0.2ml/min
Semimicro cell

LC-8A
SPD-M20A LCMS-2020

Prep-mixer ESI/DUIS
Bypass ASSY
20ml/min

Injector
Prep-column APV bypass kit
APV
LC-8A

Delay time

Gilson215 or
SPD-20A
IFC-PAL
Drain Prep-cell Tube for the Delay time LC-20A

Figure 2.3 Flowline Diagram for LCMS-2020 Preparative System

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2.4 How to Connect the Main Flow Lines

(1) Example of MS Flow Line Connections
① Between LC-20AD, APV, SPD-M20A and LCMS Units

A Tube
LC-8A Column holder

CBM-20A
LCMS-2020
LC-8A Gilson215 or IFC-PAL
SPD-20A APV

LC-8A
LC-20AD SPD-M20A

Connect to inlet tubing of SPD-M20A APV bypass kit

(2) Example of Fraction collector Flow Line Connections

① Between LC-8A, Mixer and Injector Units

LC-8A Column holder

Connect to the bypass tubing installed in the injector.

CBM-20A
LCMS-2020
LC-8A Gilson215 or IFC-PAL
SPD-20A APV

LC-8A
LC-20AD SPD-M20A

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② Example of Flow Line Connections on the injector

Injection port

Sampling loop
Drain port

Tygon tubing

To drain
Drain tubing

From
ﾐｷｻよりmixer

To column
ｶﾗﾑへ

Bypass ASSY（228-20355-92）

A) When Gilson215 is used

Injection port

Sampling loop

Drain tubing

To column
ｶﾗﾑへ

From
ﾐｷｻよりmixer

Bypass ASSY（228-20355-92）

B） When IFC-PAL is used

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③ Between Injector, Prep-column and APV Units

LC-8A column holder

Connect to the bypass tubing installed

in the injector.

CBM-20A
LCMS-2020
LC-8A Gilson215 or IFC-PAL
SPD-20A

LC-8A
LC-20AD SPD-M20A

APV

④ Between APV and the fraction collector Units

Tube for the Delay time

（D Tube） LC-8A column holder
Tubing of the Gilson215
C Tube

B Tube
CBM-20A
LCMS-2020
LC-8A Gilson215 or IFC-PAL
SPD-20A APV

LC-8A
LC-20AD SPD-M20A

Prep-cell

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⑤ Setting of the tube for the Delay time

1) Please fix the tube for the Delay time to the LC-8A column holder as shown
in figure.

About 20mm

About 55mm

Clamp、CKN20

Tube for the Delay time

2) Please attach the cover. It can be fixed with the magnet.

Cover

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3. How to Check and Adjust the Delay Time

(1) Measure the Current Delay Time
Perform one cycle of the fractionation work on the preparative system, using
previously determined analytical conditions, and collect the MS and SPD data. After
acquiring the data, identify peaks by Data analysis and determine the Delay time
from the difference in respective retention times. Given an MS peak retention time of
RT1 and an SPD peak retention time of RT2, the Delay time can be calculated using
the following formula.

Delay Time (min)= RT2 – RT1 + (Delay Time between SPD Detector and Fraction Collector)

= RT2 – RT1 + (Volume of piping between SPD Detector and Fraction Collector / flow Rate)

(2) Adjust the Delay time

If the flow rate of the mobile phase (LC-8A) is changed, such as by changing the size
of the prep column, the flow rate (LC-20AD) of the make-up flow is not normally
changed, so only RT2 will change in the formula for the Delay time shown above.
This creates various problems. For example, if the flow rate is changed from 4
mL/min to 40 mL/min without changing the flow line, then RT2 will become too small,
which could result in a negative the Delay time value. Conversely, if the flow rate is
changed from 40 mL/min to 4 mL/min, then RT2 will become too large, making the
peak widths on the fragmentation side too wide, which could result in worse recovery
rates. In this case, it is necessary to change the tubing kit for the Delay time. Please
contact our sales office. (In the LCMS-2020 preparative system, the standard flow
rate of the MS line is 0.2ml/min and the standard flow rate of the fraction collector line
is 20ml/min.)

4. Precautions for Using the Preparative System

(1) Changing the Split Ratio and Checking the Delay Time
To change the split ratio, change the APV split factor via the LCMSsolution software.
For more details, refer to the LCMS Preparative System Operation Manual. Even if
the split ratio is changed, the Delay time will change very little as long as the mobile
phase or make-up flow rates are not changed, though the Delay time might change
by a few seconds. If the width of target peaks is narrow, changing the split ratio could
affect recovery rates. Therefore, measure the Delay time before collecting fractions.
Also, even if the split ratio is not changed, the Delay time could change if the flow rate
for the mobile phase or make-up flow is changed or if the inner diameter or length of
post-split tubing is changed. Be sure to check the Delay time also after making such

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changes.

5. Consumable Parts
Part Name Part Number Remarks
APV Maintenance Kit 225-10799-02 Includes 3 rotors and 3
stators
Note: For information regarding other consumables, see the instruction manuals for
respective units.

6. Service Parts
For information regarding Service parts, see the instruction manuals for respective units.

7. Appendix
7.1 Equipment size and electric requirements (For IFC-PAL)

Size(WxDxH,mm) Weight(Kg) Electric requirements

LCMS-2020 350x553x726 77.5 200V 10A
Rotary pump 597x276x180 (44) Supplied by LCMS
LC-8A 350x210x450 32x2 100V 7.5A x2
LC-20AD 260x140x420 10 100V 1.5A
SPD-20A 260x140x420 13 100V 1.6A
SPD-M20A 260x140x420 12 100V 1.5A
CBM-20A 260x140x420 5.5 100V 1A
CTC IFC-PAL 1428x912x670 39 100V 4A
APV 78x141x191 2.1 100V 0.4A (24V 1.7A)
Total 223.1 200V 10A、 100V 25A

7.2 Footprint (For IFC-PAL)

400mm
Rotary pump ﾟ

900mm

PC
IFC-PAL Printer

LC
（LC-8A） LC LC
LCMS-2020
APV

4000mm 15