Waters Prep Series Product manual

Waters Prep Series
Installation and Maintenance Guide
71500045204/Revision B
Copyright © Waters Corporation 2010
All rights reserved

ii
Copyright notice
© 2010 WATERS CORPORATION. PRINTED IN THE UNITED STATES OF
AMERICA AND IN IRELAND. ALL RIGHTS RESERVED. THIS
DOCUMENT OR PARTS THEREOF MAY NOT BE REPRODUCED IN ANY
FORM WITHOUT THE WRITTEN PERMISSION OF THE PUBLISHER.
The information in this document is subject to change without notice and
should not be construed as a commitment by Waters Corporation. Waters
Corporation assumes no responsibility for any errors that may appear in this
document. This document is believed to be complete and accurate at the time
of publication. In no event shall Waters Corporation be liable for incidental or
consequential damages in connection with, or arising from, its use.
Trademarks
Millennium, PrepPak, and Waters are registered trademarks of Waters
Corporation, and AutoBlend, Delta-Prep, Empower, LAC/E, PowerLine,
PrepLC, Radial-Pak, and “THE SCIENCE OF WHAT’S POSSIBLE.” are
trademarks of Waters Corporation.
Milli-Q is a registered trademark of Millipore Corporation.
Other registered trademarks or trademarks are the sole property of their
owners.

iii
Customer comments
Waters’ Technical Communications department invites you to tell us of any
errors you encounter in this document or to suggest ideas for otherwise
improving it. Please help us better understand what you expect from our
documentation so that we can continuously improve its accuracy and
usability.
We seriously consider every customer comment we receive. You can reach us
at [email protected].
Contacting Waters
Contact Waters®with enhancement requests or technical questions regarding
the use, transportation, removal, or disposal of any Waters product. You can
reach us via the Internet, telephone, or conventional mail.
Safety considerations
Some reagents and samples used with Waters instruments and devices can
pose chemical, biological, and radiological hazards. You must know the
potentially hazardous effects of all substances you work with. Always follow
Waters contact information
Contacting medium Information
Internet The Waters Web site includes contact
information for Waters locations worldwide.
Visit www.waters.com.
Telephone and fax From the USA or Canada, phone 800
252-HPLC, or fax [phone].
For other locations worldwide, phone and fax
numbers appear in the Waters Web site.
Conventional mail Waters Corporation
34 Maple Street
Milford, MA 01757
USA

iv
Good Laboratory Practice, and consult your organization’s safety
representative for guidance.
Safety advisories
Consult Appendix A for a comprehensive list of warning and caution
advisories.
Operating this instrument
When operating this instrument, follow standard quality-control (QC)
procedures and the guidelines presented in this section.
Applicable symbols
Audience and purpose
This guide is intended for personnel who install and maintain the Waters®
Prep Series HPLC system.
Symbol Definition
Manufacturer location
Authorized representative of the European
Community
Confirms that a manufactured product complies
with all applicable European Community
directives
Australia C-Tick EMC Compliant
Confirms that a manufactured product complies
with all applicable United States and Canadian
safety requirements
Consult instructions for use

v
Intended use of the Waters Prep Series HPLC system
Use the Waters Prep Series HPLC system to isolate and purify a wide variety
of samples. The Waters Prep Series HPLC system is for research use only.
Calibrating
To calibrate LC systems, follow acceptable calibration methods using at least
five standards to generate a standard curve. The concentration range for
standards should include the entire range of QC samples, typical specimens,
and atypical specimens.
When calibrating mass spectrometers, consult the calibration section of the
operator’s guide for the instrument you are calibrating. In cases where an
overview and maintenance guide, not operator’s guide, accompanies the
instrument, consult the instrument’s online Help system for calibration
instructions.
Quality-control
Routinely run three QC samples that represent subnormal, normal, and
above-normal levels of a compound. Ensure that QC sample results fall within
an acceptable range, and evaluate precision from day to day and run to run.
Data collected when QC samples are out of range might not be valid. Do not
report these data until you are certain that the instrument performs
satisfactorily.
ISM classification
ISM Classification: ISM Group 1 Class B
This classification has been assigned in accordance with CISPR 11 Industrial
Scientific and Medical (ISM) instruments requirements. Group 1 products
apply to intentionally generated and/or used conductively coupled
radio-frequency energy that is necessary for the internal functioning of the
equipment. Class B products are suitable for use in both commercial and
residential locations and can be directly connected to a low voltage,
power-supply network.

vi
EC authorized representative
Waters Corporation (Micromass UK Ltd.)
Floats Road
Wythenshawe
Manchester M23 9LZ
United Kingdom
Telephone: [phone]
Fax: [phone]
Contact: Quality manager

Table of Contents vii
Copyright notice ................................................................................................... ii
Trademarks ............................................................................................................ ii
Customer comments ............................................................................................ iii
Contacting Waters ............................................................................................... iii
Safety considerations .......................................................................................... iii
Safety advisories................................................................................................. iv
Operating this instrument ................................................................................. iv
Applicable symbols ............................................................................................. iv
Audience and purpose......................................................................................... iv
Intended use of the Waters Prep Series HPLC system ..................................... v
Calibrating ........................................................................................................... v
Quality-control ..................................................................................................... v
ISM classification .................................................................................................. v
ISM Classification: ISM Group 1 Class B .......................................................... v
EC authorized representative ........................................................................... vi
1 Overview .................................................................................................. 1-1
Waters Prep series ............................................................................................ 1-2
PrepLC system................................................................................................. 1-2
Delta-Prep system............................................................................................ 1-3
Waters Prep series modules ............................................................................ 1-5
Accessories ..................................................................................................... 1-13
Getting started ................................................................................................. 1-14
Starting the system ....................................................................................... 1-14
Using the front panel..................................................................................... 1-16
Displaying help .............................................................................................. 1-19
Shutting down the system............................................................................. 1-19
Configuring the controller............................................................................. 1-19
Table of Contents

viii Table of Contents
2 Installing the System ............................................................................ 2-1
Setting up and inspecting ............................................................................... 2-2
Unpacking and installing the system............................................................. 2-2
Selecting the site.............................................................................................. 2-3
Electrical requirements .................................................................................. 2-5
Electrical conditions ........................................................................................ 2-5
Voltage selections............................................................................................. 2-5
Assembling the system ..................................................................................... 2-7
Connecting Rheodyne injectors....................................................................... 2-7
Connecting the M-1000 PrepPak module (optional) ...................................... 2-9
Connecting additional devices......................................................................... 2-9
Attaching the interface cable and power cord.............................................. 2-13
Connecting IEEE-488 interfaces................................................................... 2-15
Connecting to the Waters 746 data module ................................................. 2-20
Liquid line connections.................................................................................. 2-21
Connecting a helium tank to the fluid handling unit ............................ 2-30
Helium specifications..................................................................................... 2-30
Sparging ......................................................................................................... 2-31
Connecting compression fittings ................................................................... 2-31
Setting up the plunger wash ........................................................................ 2-33
Considerations ............................................................................................... 2-34
Connecting the plunger wash tube ............................................................... 2-34
Connecting to the injection panel (PrepLC system)..................................... 2-35
Connecting to the column rack (Delta-Prep system) ................................... 2-37
Installing sample injection options ............................................................ 2-40
Installing the small-scale sample injection valve option (PrepLC system) 2-40
Using an autoinjector .................................................................................... 2-41
Making electrical connections ....................................................................... 2-41
Connecting liquid lines when using a Waters autoinjector......................... 2-41
Connecting a fraction collector ................................................................... 2-42
Making the remote start connection............................................................. 2-42
Making chart mark connections ................................................................... 2-42

Table of Contents ix
Installing analytical and preparative columns ....................................... 2-43
PrepLC system............................................................................................... 2-43
Delta-Prep system.......................................................................................... 2-45
Making detector connections ....................................................................... 2-48
PrepLC or Delta-Prep system ....................................................................... 2-48
Connecting detector semi-prep cells ............................................................. 2-48
Using the RI detector with the flow splitter option ..................................... 2-49
3 Troubleshooting, Testing, and Maintenance ................................... 3-1
Troubleshooting ................................................................................................ 3-2
Troubleshooting steps...................................................................................... 3-2
Troubleshooting flowcharts............................................................................. 3-5
Chromatography troubleshooting ................................................................. 3-16
Hardware troubleshooting ............................................................................ 3-23
Software troubleshooting .............................................................................. 3-31
Performance tests ........................................................................................... 3-36
Self-diagnostics .............................................................................................. 3-36
Extended tests................................................................................................ 3-37
Maintenance procedures ............................................................................... 3-47
Column rack tubing configuration................................................................ 3-47
Fluid handling unit maintenance ................................................................. 3-48
Replacing fuses .............................................................................................. 3-67
Maintaining rheodyne manual injectors ...................................................... 3-71
A Safety Advisories .................................................................................. A-1
Warning symbols ............................................................................................... A-2
Task-specific hazard warnings........................................................................ A-2
Specific warnings ............................................................................................. A-3
Caution symbol .................................................................................................. A-5
Warnings that apply to all Waters instruments ......................................... A-6
Electrical and handling symbols ................................................................. A-12
Electrical symbols .......................................................................................... A-12
Handling symbols .......................................................................................... A-13

x Table of Contents
B Specifications ........................................................................................ B-1
C Spare Parts ............................................................................................ C-1
D Solvent Considerations ....................................................................... D-1
Clean solvent ..................................................................................................... D-2
Solvent miscibility ........................................................................................... D-3
How to use miscibility numbers (M-numbers) .......................................... D-5
Buffered solvents ............................................................................................. D-6
Solvent head height ......................................................................................... D-6
Solvent viscosity ............................................................................................... D-6
Solvent degassing ............................................................................................ D-7
Solvent degassing methods ............................................................................ D-8
Index ..................................................................................................... Index-1

1-1
1Overview
Waters produces its Prep Series high performance liquid
chromatography (HPLC) systems in two configurations:
• Waters PrepLC™ System
• Waters Delta-Prep™ System
Tip: Although the two systems share many features, certain aspects
nevertheless differ. This guide addresses both differences and
similarities.
Contents
Topic Page
Waters Prep series 1-2
Getting started 1-14

1-2 Overview
Waters Prep series
The Waters Prep Series offers these features:
• Two pump configurations:
–150-mL
flow rate with 500-µL pump heads at 4000 psi
–300-mLflow rate with 1000-µL pump heads at 2000 psi
Tip: Fitted with 1000- μ L pump heads, the PrepLC or Delta-Prep system
can operate at twice the flow rate of a 500-
μ L pump head system,
permitting separation of larger sample loads.
• Four-solvent gradient capability (Auto•Blend™ method)
• Pump purge valve to facilitate priming and purging of solvent lines
• Plunger wash with integral pumping system
• Single keypad control of PowerLine™ system and/or gradient conditions
• Ability to configure the system to recall certain default conditions
• Methods storage that lets you access previously created gradient, event,
and detector tables
• Preprogrammed gradient profiles
• System control of external PowerLine detectors and autoinjectors is
through an IEEE-488 interface
• RS-232 serial communications interface for connecting to an optional
data workstation or integrator
• Shelf unit to house system modules in an integrated assembly that
optimizes the volume of interconnecting tubing
PrepLC system
The PrepLC system performs both analytical and preparative scale
chromatography. Use its pump with either 500- or 1000-µL volume heads. The
500-µL pump heads allow flow rates of 1 to 150 mL/min and the 1000-µL
heads a rate of 4 to 300 mL/min.
The PrepLC system uses 0.040-inch ID tubing, which accommodates large-
and small-scale operation. To optimize system performance, you can change
critical tubing in the flow path to 0.009-inch ID or 0.040-inch ID, depending on
flow rate and backpressure.

Waters Prep series 1-3
Waters PrepLC system
Delta-Prep system
The Waters Delta-Prep system is an HPLC system capable of analytical and
preparative scale chromatography.
Use the system’s pump with either 500- or 1000-µL volume heads. The 500-µL
pump heads permit flow rates of 1 to 150 mL/min, and the 1000-µL heads
permit flow rates of 4 to 300 mL/min.
The system allows easy scale up, so you need not replumb to change between
small- and large-scale operations. Instead, select either operating mode with a
column-switching valve.
Waters PrepLC System
SAMPLE INJECTOR
SYSTEM PUMP
PURGE
Injector panel
Controller
Fluid handling unit

1-4 Overview
Waters Delta-Prep system
Delta-Prep system components
PrepLC System controller – Houses system electronics and controls the
solvent gradient, flow rate, sparging, and external events. It also provides
connection terminals and communication ports for operating with external
devices.
Fluid handling unit – Contains components for delivering solvents from
their reservoirs to the injector or column. It consists of the pump and plunger
wash pump, solvent sparge valve assembly, and solvent proportioning valve
assembly.
Column rack –Holds these items:
• Rheodyne injectors
• Gradient mixers
• Pump purge valve
• Scale switching valve
• 0.009-inch ID and 0.040-inch ID stainless steel tubing arrangements
Controller
2487 detector
Fluid handling unit
Drip tray
Drip tray
Column rack

Waters Prep series 1-5
• Space for three analytical or semi-prep columns
• One 2-inch preparative column, and/or an M-1000 compression chamber
for PrepPak®cartridges.
Rheodyne 7725i injector – For small scale injections, incorporates a 100-µL
fixed sample loop, though you can install loops whose injection volumes vary.
Optional loops, available from Waters, handle fixed volumes from 5 to 200-µL.
Rheodyne 3725i injector – For large-scale injections, incorporates a 20-mL
fixed sample loop, though you can install loops of varying injection volumes.
Optional loops, available from Waters, handle fixed volumes from 2 to 20 mL.
Purge valve – Lets you divert pump output to waste (e.g., when purging the
system) or through the injector, columns, etc.
Scale switching valve – Lets you choose large- or small-scale tubing
systems. In the small-scale system, the injector is in a flow path plumbed with
0.009-inch ID tubing. In the large-scale system, solvent flows from the pump
to the large-scale injector through 0.040-inch ID tubing.
Inlet and outlet ports – Accepts pump outflow. The inlet port receives
solvent for both small- and large-scale flow paths, which flow to separate
outlet ports. The flow from these outlets goes to the detector flow cell.
Purge outlet port – Flow goes from the inlet port to this outlet port when
you set the purge valve to Purge.
Waters Prep series modules
This section addresses these Prep Series major modules:
• Fluid handling unit
• PrepLC controller
• Rheodyne 3725i injector (PrepLC and Delta-Prep systems)
• Rheodyne 7725i injector (Delta-Prep system only; optional for PrepLC
system)
• Column rack (Delta-Prep system only)
• Injector panel (PrepLC system only)
Fluid handling unit
The figure below shows the internal workings of the fluid handling unit, which
delivers solvents from their reservoirs to the injector.

1-6 Overview
Waters Prep series fluid handling unit
Fluid metering
Solvent selection and proportioning take place on the low pressure (intake)
side of the solvent delivery system.
The fluid handling unit can proportion up to four solvents at a time with a
high degree of reproducibility, even when those solvents compose extremely
disproportionate mixtures. The solvent proportioning valve produces
predictable gradient segments, regardless of solvent compressibility and
system backpressure.
Flow path
Solvents are helium-sparged in their reservoirs and proportioned at the
solvent proportioning valve. They then flow to the pump inlet manifold, where
the flow path branches at two inlet check valves. The pump heads draw
solvent through the valves, moving 500 and 1000 μL with each stroke, with a
maximum flow rate of 150 and 300 mL/min.
From the pump heads, solvents converge at a tee fitting (150 mL) or common
outlet check valve (300 mL) before flowing to a pressure transducer. Flow
continues from the pressure transducer outlet to the system purge valve.
Plunger wash
The fluid handling unit contains an active plunger wash system. This helps
lubricate the plunger, reducing wear, and flushes away any mobile phase or
Solvent
reservoir
lines (4)
Plunger wash
inlet line
Connectors
and fittings
drawer
Drip tray
Pump head
Outlet check
valves (2)
Inlet check
valves (2)
Manual sample
inlet valve

Waters Prep series 1-7
sample forced past the pump seal from the discharge side of the pump. Wash
solvent flows from a reservoir to the wash pump and then to a cavity behind
the main pump seal of one pump head. From there, it flows to the cavity
behind the second head’s seal. It then returns to the reservoir or proceeds to
waste, depending on your choice.
The wash pump runs whenever the controller is on, circulating solvent by
pushing a small volume along the flow path, one pulse per minute.
PrepLC controller
The figure below shows the Waters PrepLC controller, which controls solvent
composition, flow rate, sparging, and external events, during a run.
PrepLC controller front panel
The controller’s rear panel, shown below, provides connection terminals and
communication ports for operating with external devices.
Liquid crystal
display
Screen keys (4)
Function
keys (4)
HOME key Cursor movement keys
Number keys (11) CLEAR key
Contrast
keys (2)
ENTER key
On/off
switch

1-8 Overview
PrepLC controller rear panel
Rear panel
This section describes the electrical connections to the controller’s rear panel.
Event Switches (Connect to terminals S1, S2, S3, S4 and Ground) –
Four switches on the rear panel control column-switching valves, fraction
collectors, or similar external devices that require a contact closure at their
input. These switches, whose maximum current capacity is 1 A each, are
actuated directly or programatically, according to the mode you specify in the
operating software. The controller’s OPERATE METHOD screen allows direct
control of the switches. Program control is through the time-based PROGRAM
EVENT screen, where you must specify each switch as ON, OFF, or PULSE.
Tip: These terminals are always positive with respect to ground: +5 VAC = Off
(open switch); 0 VAC = On (closed switch).
The figure below depicts devices that require a TTL-compatible output
connection.
Caution: Do not use cables longer than 9.8 feet (3 meters) when you
connect to the screw-type barrier terminal strips. Also, attach the cable
shield to the chassis ground of one instrument only
RS-232
connector
IEEE-488
connector
Pump interfac
e
connector
Auxiliary fuse
Pump fuse
AC power inlet
Plug-in
terminal
receptacles

Waters Prep series 1-9
Tip: If the device you are connecting to has a Gnd (ground) terminal, you must
connect it to the controller’s ground terminal.
Connection for devices to TTL-compatible outputs
The figure below depicts devices that require 12 Vac auxiliary power.
Tip: The Gnd terminals are not used.
Connection for devices requiring 12-volt auxiliary power
Inject Switch (Connect to terminals Inject and Gnd) – For a system that
includes a non-TTL injector, a run begins with the injector’s signal to the
inject start terminal. When the controller acts as a PowerLine system device
(see “Configuring the controller” on page 1-19), an autoinjector begins the run
and sends its signal through the inject start terminal or the IEEE-488
communications interface.
The inject start terminal becomes an output when you forgo using an injector
in favor of starting the run with screen keys. Thus the inject start terminal
synchronizes controller operation with that of fraction collectors, integrators,
and other devices that require a start signal.
Stop Flow (Connect Stop Flow and Gnd) – Accepts a contact closure
signal to stop the pump when radial compression falls below 650 psi. The
signal can originate with a programmable detector for Stop Flow scanning or
with the pressure monitor on the M-1000 PrepPak module.
Hold (Connect Hold and Gnd) – Produces an output signal that prevents
further injections in cases of catastrophic events: power failure, pressure
shutdown, or when abort conditions arise. Connect it with any compatible
device that must be stopped when any of these events happen.
S1 to S4
Gnd
Contact closure or
TTL-to-gnd device
+
_
Device requiring +
12V power
S1 to S4
Gnd
_

1-10 Overview
Chart (+, –) 10-mV full scale output – Plots output, which represents pump
percentage composition (%A through %D) or flow rate, to a recording device
you specify as a Chart OUT parameter on the SETUP screen.
Tip: Because of the delay associated with system volume,“Pump percentage
composition” refers to solvent composition at the proportioning valve and not
the column or detector.
Pressure (+, –) 10-mV full scale output – Directs pressure trace output
from the pump transducer (0 to 4000 psi).
Connector types
The rear panel terminal strip contains these signal connections:
Open Collector (S1, S2, S3, S4) – Output signals that control inputs
requiring contact closures, TTL-level signals, or open collector outputs. They
also trigger solenoid valves and other power devices that require current up to
1-A current. You can program the controller to turn these signals on and off or
produce a 0.2-second pulse.
Digital Output (Hold) – Useful for signaling the logic inputs of other
devices. It is compatible with TTL inputs or inputs expecting contact closures.
If the controlled input is polarized, connect the grounds together and the input
terminal to the Hold output.
Analog Output (Press +/–, Chart +/–) – Special output produces a DC
voltage whose magnitude is proportional to the physical parameter monitored.
The outputs’ full scale voltage range 10 mV. The Press terminals present only
a voltage representation of the current system backpressure. The Chart
terminals are configured through the controller to produce a voltage
proportional to the composition of solvent reservoir A, B, C, or D, or to the
current flow rate.
Digital Input (INJ, Stop Flow) – Driven by several outputs, including TTL
signals, open collector outputs, or contact closures. If the outputs driving these
inputs are polarized, connect the ground terminals together and the signal
terminals together.
Tip: Stack multiple instruments (see the figure “Stacked IEEE-488 connections
in a Waters workstation” on page 2-16) or connect them in series. Thus you
might connect the 7725i injector, a Waters non-PowerLine autoinjector, and a
Waters 746 integrator.
Tip: An autoinjector connected to this terminal starts the run. (Waters
autoinjectors start the run through PowerLine control.) The time required to