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HPLC
A Practical User’s Guide
SECOND EDITION
Marvin C. McMaster
WILEY-INTERSCIENCE
A John Wiley & Sons, Inc., Publication

Copyright © 2007 by John Wiley & Sons, Inc. All right reserved.
Published by John Wiley & Sons, Inc., Hoboken, New Jersey.
Published simultaneously in Canada.
No part of this publication may be reproduced, stored in a retrieval system, or transmitted in
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Library of Congress Cataloging-in-Publication Data:
McMaster, Marvin C.
HPLC, a practical user’s guide / Marvin C. McMaster. – 2nd ed.
p. cm.
Includes bibliographical references and index.
ISBN-13: 978-0-471-75401-5 (cloth)
ISBN-10: 0-471-75401-3 (cloth)
1. High performance liquid chromatography. I. Title.
QD79.C454M36 2007
543′.84–dc22
2006040640
Printed in the United States of America.
10 9 8 7 6 5 4 3 2 1

CONTENTS
PREFACE xi
I HPLC PRIMER 1
1 Advantages and Disadvantages of HPLC 3
1.1 How It Works / 4
1.1.1 A Separation Model of the Column / 5
1.1.2 Basic Hardware: A Quick, First Look / 7
1.1.3 Use of Solvent Gradients / 8
1.1.4 Ranges of Compounds / 9
1.2 Other Ways to Make My Separation / 9
1.2.1 FPLC—Fast Protein Liquid Chromatography / 10
1.2.2 LC—Traditional Liquid Chromatography / 10
1.2.3 GLC—Gas Liquid Chromatography / 11
1.2.4 SFC—Supercritical Fluid Chromatography / 11
1.2.5 TLC—Thin Layer Chromatography / 12
1.2.6 EP—Electrophoresis / 12
1.2.7 CZE—Capillary Zone Electrophoresis / 13
2 Selecting an HPLC System 15
2.1 Characteristic Systems / 16
2.1.1 Finding a Fit: Detectors and Data Processing / 16
2.1.2 System Models: Gradient Versus Isocratic / 16
2.1.3 Vendor Selection / 17
2.1.4 Brand Names and Clones / 17
2.1.5 Hardware–Service–Support / 18
2.2 System Cost Estimates / 19
2.2.1 Type I System—QC Isocratic (Cost: $10–15,000) / 19
2.2.2 Type II System—Research Gradient
(Cost: $20–25,000) / 19
v

2.2.3 Type III System—Automated Clinical
(Cost: $25–35,000) / 20
2.2.4 Type IV System—Automated Methods
(Cost: $30–50,000) / 21
2.3 Columns / 21
2.3.1 Sizes: Analytical and Preparative / 21
2.3.2 Separating Modes: Selecting Only What You Need / 22
2.3.3 Tips on Column Use / 23
3 Running Your Chromatograph 25
3.1 Set-up and Start-up / 25
3.1.1 Hardware Plumbing 101: Tubing and Fittings / 26
3.1.2 Connecting Components / 28
3.1.3 Solvent Clean-up / 30
3.1.4 Water Purity Test / 33
3.1.5 Start-up System Flushing / 34
3.1.6 Column Preparation and Equilibration / 35
3.2 Sample Preparation and Column Calibration / 36
3.2.1 Sample Clean-up / 36
3.2.2 Plate Counts / 37
3.3 Your First Chromatogram / 37
3.3.1 Reproducible Injection Techniques / 38
3.3.2 Simple Scouting for a Mobile Phase / 39
3.3.3 Examining the Chromatogram / 40
3.3.4 Basic Calculations of Results / 41
II HPLC OPTIMIZATION 43
4 Separation Models 45
4.1 Partition / 45
4.1.1 Separation Parameters / 48
4.1.2 Efﬁciency Factor / 49
4.1.3 Separation (Chemistry) Factor / 53
4.2 Ion Exchange Chromatography / 56
4.3 Size Exclusion Chromatography / 57
4.4 Afﬁnity Chromatography / 59
5 Column Preparation 61
5.1 Column Variations / 61
5.2 Packing Materials and Hardware / 64
5.3 Column Selection / 66
vi CONTENTS

6 Column Aging, Diagnosis, and Healing 73
6.1 Packing Degrading—Bonded-Phase Loss / 74
6.2 Dissolved Packing Material—End Voids / 77
6.3 Bound Material / 78
6.4 Pressure Increases / 81
6.5 Column Channeling—Center-Voids / 83
6.6 Normal Phase, Ion Exchange, and Size Columns / 84
6.7 Zirconium and Polymer Columns / 86
7 Partition Chromatography Modifications 89
7.1 Reverse-Phase and Hybrid Silica / 89
7.1.1 Ionization Suppression / 90
7.1.2 Ion Pairing / 91
7.1.3 Organic Modifiers / 92
7.1.4 Chelation / 92
7.2 Acidic Phase Silica / 93
7.3 Reverse-Phase Zirconium / 93
7.4 Partition Mode Selection / 94
8 “Nonpartition” Chromatography 95
8.1 Ion Exchange / 96
8.1.1 Cationic: Weak and Strong / 96
8.1.2 Anionic: Weak and Strong / 97
8.2 Size Exclusion / 98
8.2.1 Organic Soluble Samples / 98
8.2.2 Hydrophilic Protein Separation / 99
8.3 Affinity Chromatography / 101
8.3.1 Column Packing Modification / 102
8.3.2 Chelation and Optically Active Columns / 103
9 Hardware Specifics 105
9.1 System Protection / 105
9.1.1 Filters, Guard Columns, and Saturation Columns / 106
9.1.2 Inert Surfaces and Connections / 107
9.2 Pumping / 108
9.2.1 High- and Low-Pressure Mixing Controllers / 109
9.2.2 Checking Gradient Performance / 112
9.3 Injectors and Autosamplers / 113
9.4 Detectors / 116
9.4.1 Mass Dependent Detectors / 116
9.4.2 Absorptive Detectors / 119
9.4.3 Specific Detectors / 122
CONTENTS vii

9.5 Fraction Collectors / 123
9.6 Data Collection and Processing / 123
10 Troubleshooting and Optimization 125
10.1 Hardware and Tools—System Paciﬁcation / 125
10.2 Reverse Order Diagnosis / 129
10.3 Introduction to Data Acquisition / 132
10.4 Solvent Conservation / 133
III HPLC UTILIZATION 135
11 Preparative Chromatography 137
11.1 Analytical Preparative / 138
11.2 Semipreparative / 139
11.3 “True” Preparative / 139
12 Sample Preparation and Methods Development 143
12.1 Sample Preparation / 143
12.1.1 Deproteination / 144
12.1.2 Extraction and Concentration / 145
12.1.3 SFE (Cartridge Column) Preparations / 145
12.1.4 Extracting Encapsulated Compounds / 147
12.1.5 SFE Trace Enrichment and Windowing / 148
12.1.6 Derivatives / 151
12.2 Methods Development / 151
12.2.1 Standards Development / 152
12.2.2 Samples Development / 154
12.3 Gradient Development / 156
13 Application Logics: Separations Overview 159
13.1 Fat-Soluble Vitamins, Steroid, and Lipids / 159
13.2 Water-Soluble Vitamins, Carbohydrates, and Acids / 160
13.3 Nucleomics / 161
13.4 Proteomics / 162
13.5 Clinical and Forensic Drug Monitoring / 163
13.6 Pharmaceutical Drug Development / 164
13.7 Environmental and Reaction Monitoring / 164
13.8 Application Trends / 165
viii CONTENTS

14 Automation 167
14.1 Analog-to-Digital Interfacing / 167
14.2 Digital Information Exchange / 169
14.3 HPLC System Control and Automation / 169
14.4 Data Collection and Interpretation / 170
14.4.1 Preinjection Baseline Setting / 171
14.4.2 Peak Detection and Integration / 171
14.4.3 Quantitation: Internal/External Standards / 172
14.5 Automated Methods Development / 172
14.5.1 Automated Isocratic Development / 173
14.5.2 Hinge Point Gradient Development / 176
14.6 Data Exportation to the Real World / 177
14.6.1 Word Processors: .ASC, .DOC, .RTF, .WS, .WP
Formats / 177
14.6.2 Spread Sheets: .DIF, .WK, .XLS Formats / 178
14.6.3 Databases: .DB2 Format / 178
14.6.4 Graphics: .PCX, .TIFF, .JPG Formats / 178
14.6.5 Chromatographic Files: Metaﬁles and NetCDF / 178
15 Recent Advances in LC/MS Separations 181
15.1 A LC/MS Primer / 181
15.1.1 Quadrupole MS and Mass Selection / 183
15.1.2 Other Types of MS Analyzers for LC/MS / 185
15.1.3 LC/MS Interfaces / 187
15.1.4 LC/MS Computer Control and Data Processing / 189
15.2 Microﬂow Chromatography / 191
15.3 Ultrafast HPLC Systems / 192
15.4 Chip HPLC Systems / 192
15.5 Standardized LC/MS in Drug Design / 193
16 New Directions in HPLC 195
16.1 Temperature-Controlled Chromatography / 195
16.2 Ultrafast Chromatography / 196
16.3 Monolith Capillary Columns / 196
16.4 Micro-Parallel HPLC Systems / 197
16.5 Two-Dimensional HPLC Systems / 197
16.6 The Portable LC/MS / 198
CONTENTS ix

APPENDICES 201
APPENDIX A Personal Separations Guide 203
APPENDIX B FAQs for HPLC Systems and Columns 205
APPENDIX C Tables of Solvents and Volatile Buffers 211
APPENDIX D Glossary of HPLC Terms 213
APPENDIX E HPLC Troubleshooting Quick Reference 221
APPENDIX F HPLC Laboratory Experiments 227
Laboratory 1—System Start-up and Column Quality Control / 227
Laboratory 2—Sample Preparation and Methods Development / 229
Laboratory 3—Column and Solvent Switching and Paciﬁcation / 231
Appendix G Selected Reference List 233
INDEX 235
x CONTENTS

PREFACE
High-pressure liquid-solid chromatography (HPLC) is rapidly becoming the
method of choice for separations and analysis in many fields.Almost anything
that can be dissolved can be separated on some type of HPLC column.
However, with this versatility comes the necessity to think about the separa-
tion desired and the best way to achieve it. HPLC is not now and probably
never will be a turn-key, push-button type of operation. Many dedicated
system-in-a-box packages are sold for specific separations, but all of these still
offer wide possibilities for separation. Changing the column and the flow rate
lets you change the separation and the amount of sample you can inject. This
is not the worst thing in the world, for it does create great opportunity for the
chromatographer and a great deal of job security for the instrument operator.
Fortunately, controlling separations is not nearly as complicated as much of
the literature may make it seem. My aim is to cut through much of the detail
and theory to make this a usable technique for you. The separation models I
present are those that have proven useful to me in predicting separations. I
make no claim for their accuracy, except that they work.There are many excel-
lent texts on the market, in the technical literature, and on the Internet, con-
tinuously updated and revised, that present the history and the current theory
of chromatography separations.
This book was written to fill a need, hopefully, your need. It was designed
to help the beginning as well as the experienced chromatographer in using an
HPLC system as a tool.Twenty-five years in HPLC, first as a user, then in field
sales and application support for HPLC manufacturers, and finally working as
a teacher and consultant has shown me that the average user wants an instru-
ment that will solve problems, not create new ones.
I will be sharing with you my experience gained through using my own
instrument, through troubleshooting customer’s separations, and from field
demos; the tricks of the trade. I hope they will help you do better, more rapid
separations and methods development. Many of the suggestions are based on
tips and ideas from friends and customers. I apologize for not giving them
credit, but the list is long and my memory is short. It has been said that pla-
giarism is stealing ideas from one person and research is borrowing from many.
This book has been heavily researched and I would like to thank the many
xi

who have helped with that research. I hope I have returned more than I
borrowed.
I have divided this guide into three parts. The first part should give you
enough information to get your system up and running. When you have fin-
ished reading it, put the book down and shoot some samples. You know
enough now to use the instruments without hurting them or yourself. When
you have your feet wet (not literally I hope), come back and we will take
another run at the material in the book.
Part II shows you how to make the best use of the common columns and
how to keep them up and running. (Chapter 6 on column healing should pay
for the book in itself.) It discusses the various pieces of HPLC equipment, how
they go together to form systems, and how to systematically troubleshoot
system problems. We will take a look at the newest innovations and improve-
ments in column technology and how to put these to work in your research.
New detectors are emerging to make possible analysis of compounds and
quantities that previously were not detectable.
Finally, in Part III, we will talk about putting the system to work on real-
world applications. We will look at systematic methods development, both
manual and automated, and the logic behind many of the separations that
others have made. We will discuss how to interface the HPLC system to com-
puters and robotic workstations. I will also give you my best guesses as to the
direction in which HPLC columns, systems, detectors, and liquid chromato-
graphy/mass spectrometer (LC/MS) systems will be going.
It is important to give credit where it is due. Christopher Alan McMaster
created many of the illustrations in this text before he died of the ravages of
muscular dystrophy six years ago. I supplied hand-drawn sketches of the illus-
trations I used on boards in my classes. Chris turned them into art on his
Macintosh. His collaborative efforts are greatly missed.
A brief note is required about the way I teach. First, I have learned that
repetition is a powerful tool, not a sign of incipient senility as many people
have hinted. Second, I have found in lecturing that few people can stand more
than 45 minutes of technical material at one sitting. However, I have also
learned that carefully applied humor can sometimes act as a mental change of
pace. Properly applied, it allows us to continue with the work at hand. So, occa-
sionally, I will tiptoe around the lab bench. I do not apologize for it, but I
thought you ought to know.
The instrument itself is the most effective teacher.Think logically about the
system and the chemistry and physics occurring inside the column. You will
be surprised how well you will be able to predict and control your separation.
Remember! HPLC is a versatile, powerful, but basically simple separation
tool. It is a time machine that can speed your research and, thereby, allow you
to do many things not possible with slower techniques. It is both an analytical
and a preparative machine.When I finish, I hope you will have the confidence
to run your instrument, make your own mistakes, and be able to find your own
solutions.
xii PREFACE

Your HPLC success depends on three things:
1. The suitability of the equipment you buy,
2. Your ability to keep it up and running (or ﬁnd someone to service it),
and
3. The support you receive,starting out in new directions or in solving prob-
lems that come up.
Marvin C. McMaster
Florissant, MO
PREFACE xiii

1
ADVANTAGES AND
DISADVANTAGES OF HPLC
3
The first things we need to understand are how an HPLC system works, its
best applications and advantages over other ways of separating compounds,
and other techniques that might compliment or even replace it. Is there a
faster, easier, cheaper, or more sensitive method of achieving your results? The
answer is yes, no, maybe. It really depends on what you are trying to achieve.
HPLC’s virtue lies in its versatility! I have used it to separate compounds
of molecular weights from 54 to 450,000 Daltons. Amounts of material to be
detected can vary from picograms and nanograms (analytical scale) to micro-
grams and milligrams (semi-preparative scale) to multigrams (preparative
scale). There are no requirements for volatile compounds or derivatives.
Aqueous samples can be run directly after a simple filtration. Compounds with
a wide polarity range can be analyzed in a single run. Thermally labile com-
pounds can be run. I had one customer whose company made explosives for
primers. Her first job of the day was to explode samples of the previous day
run with a rifle. Her second job was to carry out an HPLC analysis of that
day’s run.
An HPLC offers a combination of speed, reproducibility, and sensitivity.
Typical runs take from 10 to 30min, but long gradients might consume 1 to
2hrs. I have seen 15- to 30-sec stat runs on 3-mm columns in hospital labora-
tories. Retention times on the same column, run to run, should reproduce by
1%. Two columns of the same type from the same manufacturer should give
5% or better retention time reproduction on the same standard set.
While the HPLC can be used in a variety of research and production
operations, there are a few places where it really shines. Because it can run
HPLC: A Practical User’s Guide, Second Edition, by Marvin C. McMaster
Copyright © 2007 by John Wiley & Sons, Inc.

underivatized mixtures, it is a great tool for separating and analyzing crude
mixtures with minimum sample preparation. I began my HPLC career analyz-
ing herbicide production runs as a method of trouble-shooting product yield
problems. HPLC was routinely used in the quality control lab to fingerprint
batches of final product using a similar analysis.I have helped my customers run
tissue extracts, agricultural run-off waters, urine, and blood samples with
minimum clean up. These samples obviously are not very good for columns
whose performance degrades rapidly under these conditions. Columns can
usually be restored with vigorous washing,but an ounce of prevention is gener-
ally more effective than a pound of cure and also much more time effective.
Standards purification is another role in which the HPLC excels. It is fairly
easy to purify microgram to milligram quantities of standard compounds using
the typical laboratory system.
Finally, used correctly, HPLC is a great tool for rapid reaction monitoring
either in glassware or in large production kettles. I started my analytical career
with a HPLC system cast-off by the Analytical Department and a 15-min train-
ing course by another plant monitoring chemist. He gave me an existing HPLC
procedure for my compound and turned me loose. The next day I was getting
research information. I could see starting material disappear, intermediates
form, and both final product and by-products appear. It was like having a
window on my reaction flask through which I could observe the chemistry of
the ongoing synthesis. Later, I used the same technique to monitor a produc-
tion run in a 6000-gallon reactor. The sampling technique was different, but
the HPLC analysis was identical.
Versatility, however, brings with it challenge. An HPLC is easily assembled
and easily run, but to achieve optimum separation, the operator needs to
understand the system, its columns, and the chemistry of the compounds being
separated. This will require a little work and a little thought, but the skills
required do offer a certain job security.
I don’t want to leave you with the impression that I feel that HPLC is the
perfect analytical system. The basic system is rather expensive compared with
some analytical tools; columns are expensive with a relatively short operating
life, solvents are expensive and disposal of used solvent is becoming a real
headache. Other techniques offer more sensitivity of detection or improved
separation for certain types of compounds (i.e., volatiles by GLC, large
charged molecules by electrophoresis). Nothing else that I know of, however,
offers the laboratory the wide range of separating modes, the combination of
qualitative and quantitative separation, and the basic versatility of the HPLC
system.
1.1 HOW IT WORKS
The HPLC separation is achieved by injecting the sample dissolved in solvent
into a stream of solvent being pumped into a column packed with a solid sep-
4 ADVANTAGES AND DISADVANTAGES OF HPLC

arating material. The interaction is a liquid-solid separation. It occurs when a
mixture of compounds dissolved in a solvent can either stay in the solvent or
adhere to the packing material in the column. The choice is not a simple one
since compounds have an affinity for both the solvent and the packing.
On a reverse-phase column, separation occurs because each compound has
different partition rates between the solvent and the packing material. Left
alone, each compound would reach its own equilibrium concentration in the
solvent and on the solid support. However, we upset conditions by pumping
fresh solvent down the column.The result is that components with the highest
affinity for the column packing stick the longest and wash out last. This dif-
ferential washout or elution of compounds is the basis for the HPLC separa-
tion. The separated, or partially separated, discs of each component dissolved
in solvent move down the column, slowly moving farther apart, and elute in
turn from the column into the detector flow cell. These separated compounds
appear in the detector as peaks that rise and fall when the detector signal is
sent to a recorder or computer. This peak data can be used either to quanti-
tate, with standard calibration, the amounts of each material present or to
control the collection of purified material in a fraction collector.
1.1.1 A Separation Model of the Column
Since the real work in an HPLC system occurs in the column, it has been called
the heart of the system. The typical column is a heavy-walled stainless steel
tube (25-cm long with a 3–5mm i.d.) equipped with large column compression
fittings at either end (Fig. 1.1).
Immediately adjacent to the end of the column, held in place by the column
fittings, is a porous, stainless steel disc filter called a frit. The frit serves two
purposes. It keeps injection sample particulate matter above a certain size
from entering the packed column bed. At the outlet end of the column it also
serves as a bed support to keep the column material from being pumped into
the tubing connecting out to the detector flow cell. Each column end fitting is
drilled out to accept a zero dead volume compression fitting, which allows the
column to be connected to tubing coming from the injector and going out to
the detector.
HOW IT WORKS 5
Figure 1.1 HPLC column design.

The most common HPLC separation mode is based on separating by dif-
ferences in compound polarity. A good model for this partition, familiar to
most first-year chemistry students, is the separation that takes place in a sep-
aratory funnel using immiscible liquids such as water and hexane. The water
(very polar) has an affinity for polar compounds.The lighter hexane (very non-
polar) separates from the water and rises to the top in the separating funnel
as a distinct upper layer. If you now add a purple dye made up of two com-
ponents, a polar red compound and a nonpolar blue compound, and stopper
and shake up the contents of the funnel, a separation will be achieved
(Fig. 1.2).
The polar solvent attracts the more polar red compound, forming a red
lower layer. The blue nonpolar dye is excluded from the polar phase and dis-
solves in the relatively nonpolar upper hexane layer. To finish the separation,
we simply remove the stopper, open the separatory funnel’s stopcock, and
draw off the aqueous layer containing the red dye, and evaporate the solvent.
The blue dye can be recovered in turn by drawing off the hexane layer.
The problem with working with separatory funnels is that the separation is
generally not complete. Each component has an equilibration concentration
in each layer. If we were to draw off the bottom layer and dry it to recover
the red dye, we would find it still contaminated with the other component, the
blue dye. Repeated washings with fresh lower layer would eventually leave
only insignificant amounts of contaminating red dye in the top layer, but would
also remove part of the desired blue compound. Obviously, we need a better
technique to achieve a complete separation.
The HPLC column operates in a similar fashion. The principle of “like
attracting like” still holds. In this case, our nonpolar layer happens to be a
moist, very fine, bonded-phase solid packing material tightly packed in the
column. Polar solvent pumped through the column, our “mobile phase,” serves
as the second immiscible phase. If we dissolve our purple dye in the mobile
phase, then inject the solution into the flow from the pump to the column, our
two compounds will again partition between the two phases. The more non-
Figure 1.2 Separation model 1 (separatory funnel).

polar blue dye will have a stronger partition afﬁnity for the stationary phase.
The more polar red dye favors the mobile phase, moves more rapidly down
the column than the blue dye, and emerges ﬁrst from the column into the
detector. If we could see into the column we would see a purple disc move
down the column, gradually separating into a fast moving red disc followed by
a slower moving blue disc (Fig. 1.3).
1.1.2 Basic Hardware: A Quick, First Look
The simplest HPLC system is made up of a high-pressure solvent pump, an
injector, a column, a detector, and a data recorder (Fig. 1.4).
Note: The high pressures referred to are of the order of 2000–6000psi. Since
we are working with liquids instead of gases, high pressures do not pose an
explosion hazard. Leaks occur on overpressurizing; the worse problems to be
expected are drips, streams, and puddles.
Solvent (mobile phase) from a solvent reservoir is pulled up the solvent
inlet line into the pump head through a one-way check valve. Pressurized in
HOW IT WORKS 7
Figure 1.3 Separation model 2 (HPLC column).
Figure 1.4 An isocratic HPLC system.

the pump head, the mobile phase is driven by the pump against the column
back-pressure through a second check valve into the line leading to the sample
injector. The pressurized mobile phase passes through the injector and into
the column, where it equilibrates with the stationary phase and then exits to
the detector flow cell and out to the waste collector.
The sample, dissolved in mobile phase or a similar solvent, is first loaded
into the sample loop and then injected by turning a handle swinging the
sample loop into the pressurized mobile phase stream. Fresh solvent pumped
through the injector sample loop washes the sample onto the column head
and down the column.
The separated bands in the effluent from the column pass through the
column exit line into the detector flow cell. The detector reads concentration
changes as changes in signal voltage. This change in voltage with time passed
out to the recorder or computer over the signal cable and is traced on paper
as a chromatogram, allowing fractions to be detected as rising and falling
peaks.
There are always two outputs from a detector, one electrical and one liquid.
The electrical signal is sent to the recorder for display and quantitation (ana-
lytical mode). The liquid flow from the detector flow cell consists of concen-
tration bands in the mobile phase. The liquid output from nondestructive
detectors can be collected and concentrated to recover the separated materi-
als (preparative mode).
It is very important to remember that HPLC is both an analytical and a
preparative tool. Often the preparative capabilities of the HPLC are over-
looked. While normal analytical injections contain picogram to nanogram
quantities, HPLCs have been used to separate as much as 1lb in a single injec-
tion (obviously by a candidate for the Guinness Book of World Records).
Typical preparative runs inject 1–3g to purify standard samples.
To be effective, the detector must be capable of responding to concentra-
tion changes in all of the compounds of interest, with sensitivity sufficient to
measure the component present in the smallest concentration. There are a
variety of HPLC detectors. Not all detectors will see every component sepa-
rated by the column. The most commonly used detector is the variable ultra-
violet (UV) absorption detector, which seems to have the best combination of
compound detectability and sensitivity. Generally, the more sensitive the
detector, the more specific it is and the more compounds it will miss. Detec-
tors can be used in series to gain more information while maintaining sensi-
tivity for detection of minor components.
1.1.3 Use of Solvent Gradients
Solvent gradients are used to modify the separations achieved in the column.
We could change the separation by changing the polarity of either the column
or the mobile phase. Generally, it is easier, faster, and cheaper to change the
character of the solvent.

The key to changing the separation is to change the difference in polarity
between the column packing and the mobile phase. Making the solvent polar-
ity more like the column polarity lets compounds elute more rapidly. Increas-
ing the difference in polarities between column and mobile phase makes
compounds stick tighter and come off later.The effects are more dramatic with
compounds that have polarities similar to the column.
On a nonpolar column running in acetonitrile, we could switch to a more
polar mobile phase, such as methanol, to make compounds retain longer and
have more time to separate. We can achieve much the same effect by adding
a known percentage of water, which is very polar, to our starting acetonitrile
mobile phase (step gradient). We could also start with a mobile phase con-
taining a large percentage of water to make nonpolar compounds stick tightly
to the top of the column and then gradually increase the amount of acetoni-
trile to wash them off (solvent gradient). By changing either the initial amount
of acetonitrile, the final amount of acetonitrile, or the rate of change of ace-
tonitrile addition, we can modify the separation achieved. Separation of very
complex mixtures can be carried out using solvent gradients. There are,
however, penalties to be paid in using gradients. More costly equipment is
required, solvent changes need to be done slowly enough to be reproducible,
and the column must be re-equilibrated before making the next injection. Iso-
cratic separations made with constant solvent compositions can generally be
run in 5–15min.True analytical gradients require run times of around 1hr with
about a 15-min re-equilibration. But some separations can only be made with
a gradient. We will discuss gradient development in a later section.
1.1.4 Ranges of Compounds
Almost any compound that can be retained by a column can be separated by
a column. HPLC separations have been achieved based on differences in
polarity, size, shape, charge, specific affinity for a site, stereo, and optical iso-
merism. Columns exist to separate mixtures of small organic acid present in
the Krebs cycle to mixtures of macromolecules such as antibody proteins and
DNA restriction fragments. Fatty acids can be separated based on the number
of carbons atoms in the chains or a combination of carbon number and degree
of unsaturation. Electrochemical detectors exist that detect separations at the
picogram range for rat brain catecholamines. Liquid crystal compounds are
routinely purified commercially at 50g per injection. The typical injection,
however, is of 20mL of solvent containing 10–50ng of sample.Typical runs are
made at 1–2mL/min and take 5–15min (isocratic) or 1hr (gradient).
1.2 OTHER WAYS TO MAKE MY SEPARATION
Obvious there are many other analytical tools in the laboratory that could
be used to make a specific separation. Other techniques may offer higher
OTHER WAYS TO MAKE MY SEPARATION 9

sensitivity, less expensive equipment, different modes of separation, or faster
and dirty tools for cleaning a sample before injection into the HPLC. Often,
a difficult separation can only be achieved by combining these tools in a
sequential analysis or purification. I’ll try to summarize what I know about
these tools, their strengths and drawbacks.
1.2.1 FPLC—Fast Protein Liquid Chromatography
FPLC is a close cousin of the HPLC optimized to run biological macromole-
cules on pressure-fragile agarose or polymeric monobead-based columns. It
uses the same basic system components, but with inert fluid surfaces (i.e.,
Teflon, titanium, and glass), and is designed to operate at no more than
700psi. Inert surfaces are necessary since many of the resolving buffers contain
high concentrations of halide salts that attack and corrode stainless steel sur-
faces. Glass columns are available packed with a variety of microporous, high-
resolution packings: size, partition, ion exchange, and affinity modes. A
two-pump solvent gradient controller, injector valve, filter variable detector,
and a fraction collector complete the usual system. The primary separation
modes are strong anion exchange or size separation rather than reverse-phase
partition as in HPLC.
FPLC advantages include excellent performance and lifetimes for the
monobead columns, inert construction against the very high salt concentra-
tions often used in protein chromatography, capability to run all columns types
traditionally selected by protein chemist, availability of smart automated injec-
tion and solvent selection valves, and very simple system programming. Dis-
advantages include lack of capability to run high-pressure reverse phase
columns, lack of a variable detector designed for the system, and lack of a true
autosampler. HPLC components have been adapted to solve the first two
problems, but have proved to be poor compromises.The automated valves can
partially compensate for the lack of an autosampler.
1.2.2 LC—Traditional Liquid Chromatography
LC is the predecessor of HPLC. It uses slurry packed glass column filled with
large diameter (35–60mm) porous solid material. Materials to be separated are
dissolved in solvent and applied directly to the column head.The mobile phase
is placed in a reservoir above the column and gravity fed to the column to
elute the sample bands. Occasionally, a stirred double-chamber reservoir is
used to generate linear solvent gradients and a peristaltic pump is used to feed
solvent to the column head. Packing materials generally made of silica gel,
alumina, and agarose are available to allow separation by partition, adsorp-
tion, ion exchange, size, and affinity modes.
A useful LC modification is the quick clean-up column.The simplest of this
is a capillary pipette plugged with glass wool and partially filled with packing
material.The dry packed column is wetted with solvent, sample is applied, and

the barrel is filled with eluting solvent. Sample fractions are collected by hand
in test tubes. A further modification of this is the sample filtration and extrac-
tion columns (SFE). These consist of large pore packing (30–40mm) trapped
between filters in a tube or a syringe barrel.They are used with either a syringe
to push sample and solvent through the cartridge or a vacuum apparatus to
pull solvent and sample through the packed bed into a test tube for collection.
Once the sample is on the bed, it can be washed and then eluted in a step-by-
step manner with increasingly stronger solvent. These are surprising powerful
tools for quick evaluation of the effectiveness of a packing material, sample
clean-ups, and broad separations of classes of materials. They are available in
almost any type of packing available for HPLC separations: partition, ion
exchange, adsorption, and size.
The basic advantages of LC technique are low equipment cost and the
variety of separation techniques available. Very large and very small columns
can be used,they can be run in a cold room,and cartridge columns are reusable
with careful handling and periodic washing. Disadvantages included relatively
low resolving power, overnight runs, and walking pneumonia from going in
and out of cold rooms.
1.2.3 GLC—Gas Liquid Chromatography
GLC uses a column packed with a solid support coated with a viscous liquid.
The volatile sample is injected through a septum into an inert gas stream that
evaporated the sample and carries it onto the column. Separation is achieved
by differential partition of the sample components between the liquid coating
and the continuously replaced gas stream. Eventually, each compound flushes
off the column and into the detector in reverse order to their affinity for the
column. The column is placed in a programmable oven and separation can be
modified using temperature gradients.
Advantages of the technique include moderate equipment prices, capillary
columns for high-resolution, rapid separations, and high-sensitivity detectors
and the possibility of direct injection into a mass spectrometer because of the
absence of solvents. Disadvantages include the need for volatile samples or
derivatives, limited range of column separating modes and eluting variables,
the requirement for pressurized carrier gases of high purity, and the inability
to run macromolecules.
1.2.4 SFC—Supercritical Fluid Chromatography
SFC is a relatively new technique using a silica-packed column in which the
mobile phase is a gas, typically carbon dioxide, which has been converted to a
“supercritical” fluid under controlled pressure and temperature. Sample is
injected as in a GLC system, carried by the working fluid onto the packed
column where separation occurs by either adsorption or partition. The sepa-
rated components then wash into a high-pressure UV detector flow cell. At

the outlet of the detector, pressure is released and the fluid returns to the
gaseous state leaving purified sample as a solid. Doping of carrier gas with
small amounts of volatile polar solvents such as methanol can be used to
change the polarity of the supercritical fluid and modify the separation.
Advantages of SFC include many of the characteristics of an HPLC sepa-
ration: high resolving power and fast run times, but with much easier sample
recovery. The technique is primarily used as a very gentle method for purify-
ing fragile or heat-labile substances such as flavors, oils and perfume fra-
grances. Disadvantages include high equipment cost, the necessity of working
with pressurized gases, poor current range of column operating modes and
available working fluids, and the difficulty of producing supercritical fluid
polarity gradients.
1.2.5 TLC—Thin Layer Chromatography
TLC separations are carried out on glass, plastic, or aluminum plates coated
with thin layers of solid adsorbant held to the plate with an inert binder. Plates
are coated with a thick slurry of the solid and binder in a volatile solvent, then
allowed to dry before using.Multiple samples and standards are each dissolved
in volatile solvent and applied as spots across the solid surface and allowed to
evaporate. Separation is achieved by standing the plate in a shallow trough of
developing solvent and allowing solvent to be pulled up the plate surface by
capillary action. Once solvent has risen a specific distance, the plates are dried
and individual compounds are detected by UV visualization or by spraying
with a variety of reactive chemicals. Identification is made by calculating rel-
ative migration distances and/or by specific reaction with visualizing reagents.
TLC can be used in a preparative mode by streaking the sample across the
plate at the application height, nondestructive visualization, and scraping the
target band(s) from the plate and extracting them with solvent. Short (3–4in)
TLC strips are an excellent quick and dirty tool for checking reaction mix-
tures, chromatography fractions, and surveying LC and HPLC solvent/packing
material combinations.Two-dimensionalTLC,in which each direction is devel-
oped with a different solvent, has proven useful for separating complex mix-
tures of compounds.
Advantages ofTLC include very inexpensive equipment and reagents,fairly
rapid separations, a wide variety of separating media and visualizing chemi-
cals, and use of solvents and mobile phase modifiers, such as ammonia, not
applicable to column separations. Disadvantages include poor resolving power
and difficulty in quantitative recovery of separated compounds from the media
and binder.
1.2.6 EP—Electrophoresis
EP takes advantage of the migration of charged molecules in solution toward
electrodes of the opposite polarity. Electrophoresis separating gels are cast in

tube or slab form by either polymerizing polyacrylamide support material or
casting agarose of controlled pore size in the presence of a buffer to carry an
electrical current. Sample is applied to the gel surface, buffer reservoirs and
positive and negative electrodes are connected to opposite end of the gel, and
electrical current is applied across the gel surface. Because electrical resistance
in the media generates heat, the gel surface is usually refrigerated to prevent
damage to thermally labile compounds. Compounds migrate within the gel in
relation to the relative charge on the molecule and, in size-controlled support
matrices, according to their size, charge, and shape. Two-dimensional GEP, in
which separation is made in one direction with buffer and in the second direc-
tion with denaturing buffers, has proved a powerful tool for protein and
polypeptide separations in proteomics laboratories.
Advantages of electrophoresis include relatively low-priced equipment, sol-
vents, and media, and very high resolving power for charged molecules, espe-
cially biological macromolecules. Disadvantages of EP include working with
high-voltage power supplies and electrodes in recovering separated compo-
nents from a polymeric matrix contaminated with buffer, relatively long sep-
aration times in many cases, and the effect of heat on labile compounds.
1.2.7 CZE—Capillary Zone Electrophoresis
CZE is a relatively new technique involving separations in a coated capillary
column filled with buffer under the influence of an electrical field. Samples are
drawn into and down the column using electrical charge potential. Migration
is controlled by the molecule’s charge and interaction with the wall coating.
Separated components are detected through a fine, drawn-out, transparent
area of the column using a variable UV detector or a fluorometer. Still under
development, CZE offers great potential as improvements are made in injec-
tion techniques and in column coatings to add modified partition, size, ion
exchange, and affinity capability. Mass spectrometer interfaces are used to
provide a definitive compound identification.
Advantages of CZE include very high resolving power, fairly short run
times, and lack of large quantities of solvent to be disposed. Disadvantages
include the fact that this is primarily an analytical tool with little capacity for
preparative sample recovery and that, again, there is the necessity of working
with relatively high-voltage transformers and electrodes. Resolving variables
are limited to column coating, applied voltage, buffer character, strength, and
pH.

2
SELECTING AN
HPLC SYSTEM
15
Over the years, I have encountered a common customer problem when it came
to buying HPLC systems. My customers wanted to buy exactly what they
needed to get the job done at the very best price.They wanted to be prepared
for future needs and problems, but they did not want to buy equipment they
did not need or that would not work.
Trustworthy advise on buying a system is often difﬁcult to obtain.The com-
missioned salesman for the HPLC company obviously could not be consid-
ered completely objective. The customer referral from the salesman might be
a little better, but companies seldom hand out a list of customers who have
encountered problems. Your local in-house HPLC guru would certainly be
more objective, but his information might not be current and his application
might be completely different from what you are trying to do. A consultant
would be more expensive, probably suffer from the same problems as the guru,
and is hard to ﬁnd without connections to one company or another.
This section, I hope, is the answer! I currently have no connection to an
HPLC company, although I have worked for four of the major players in the
past. I have taught HPLC extension courses for 16 years and have consulted
on a variety of other manufacturers’ systems for at least that long. I will try to
give you an objective look at the various types of problems that HPLC can
solve and my best recommendation for the equipment you’ll need to solve
each one and, at least, a ballpark price (2006 vintage) for each system.

2.1 CHARACTERISTIC SYSTEMS
Like buying computer software, the first step is to decide exactly what you will
be using the HPLC for today and possibly in the future. I’m not talking about
specific separations at this point; those decisions will be used to control column
selection, which we will discuss in a moment.What I’m really looking for is an
overall philosophy of use.
2.1.1 Finding a Fit: Detectors and Data Processing
Before we start, let me offer some general comments. In the past, fixed or filter
variable wavelength UV detectors have been sold with inexpensive systems.
Variable detectors were expensive and replacement lamps were expensive and
very short lived. This is no longer true and I would not consider buying an
HPLC system without a good single-channel variable UV detector. By the
same token, photo diode array UV detectors have been oversold. They may
have specific applications in method development laboratories, but in their
current form they provide useful array information only in a post-run batch
mode, not real time. Real time they are only used as very expensive variable
detectors. The computer necessary to extract useful information from the
three-dimensional output simply increases their cost. An inexpensive diode
array detector that could display a real-time summation chromatogram,
similar to a MS total ion chromatogram, with peaks annotated with retention
times and maximum absorption wavelength, would probably be worth pur-
chasing, but probably exists only in chemical science fiction.
The other piece of mandatory equipment that has changed recently is the
data acquisition computer. Previously, every inexpensive HPLC had to have a
strip chart recorder. The price differential between a computer-generated
annotated chromatogram and a strip chart has dropped to the point that it
doesn’t make sense not to have that capability in the lab. You may only inte-
grate 1 run out of 10, but when you need it, the capability will be there. Try
and avoid a computer system using a thermal or inkjet printer.The paper does
not store well for a permanent record. Often, it will be necessary to photocopy
the “keeper” chromatograms for further reference and archival storage.
2.1.2 System Models: Gradient Versus Isocratic
There are four basic system types. Type I are basic isocratic systems used for
simple, routine analysis in a QA/QC environment; often for fingerprinting
mixtures or final product for impurity/yield checking. Type II systems are flex-
ible research gradient systems used for methods development, complex gra-
dients, and dial-mix isocratics for routine analysis and standards preparation.
They fit the most common need for an HPLC system. Type III systems are
fully automated, dedicated systems used for cost-per-test, round-the-clock
analysis of a variety of gradient and isocratic samples typical of clinical and
environmental analysis laboratories. Type IV systems are fully automated gra-
16 SELECTING AN HPLC SYSTEM

dients with state-of-the-art detectors used for methods development and
research gradients.
2.1.3 Vendor Selection
If you’re looking for the name of “the” company to buy an HPLC from, I’m
afraid I’m going to have to disappoint you.First,that answer is a moving target.
Today one company might be the right choice; tomorrow they might have
manufacturing and design problems. For one type of system, such as a micro-
bore gradient HPLC or an ultra-fast system to interface to a mass spectrom-
eter, one company may be superior to the competition. For one application,
such as a biological purification, another company may stand out. Second,
HPLC equipment has improved so much that you are fairly safe no matter
which hardware you select. Control and data processing software design has
become critically important in the last few years in getting the most out of
your HPLC. Service and support have always been the differentiating factors
that really separate and define the best companies.
2.1.4 Brand Names and Clones
A single supplier working on an O.E.M. basis has always produced single com-
ponents that are used in different private-label systems sold by a variety of
manufacturers. It is still important to buy all of your components from the
same supplier to prevent a major outbreak of finger pointing in case of prob-
lems. Buying bits and pieces from many companies in a search for the “best
price” can produce many headaches when the pieces do not play well together.
If everything comes from one company, they are the ones who are responsi-
ble to help solve the problem. Just make sure they have a current reputation
of being in the business of providing for customer needs. Buying expensive
systems does not guarantee good customer support. Buying from the lowest
bidder or buying the cheapest system possible almost always ensures that you
are the customer support system. Low margin companies do not have large
budgets to plow into support facilities. By the same token, large companies
often have so much overhead that little is left for support.
A company’s support reputation may change with time and owners.
Support is expensive and only the best companies believe in it over the long
haul. Find out what a company’s reputation for customer support is today from
current users.
Your best support will probably come from your local sales and service rep-
resentatives. If they are good they can help you interface with the company
and make sure problems get solved. Remember that service representatives
solve electrical and mechanical, not chemical and column problems. If your
only tool is a hammer, every problem looks like a nail.
You must be able to distinguish between these two types of problems.With
luck, the sales representative will have the proper background and training to
be of some assistance in separating these problems. If that training consists of
selling used cars, it may not be of much assistance when your column pressure
CHARACTERISTIC SYSTEMS 17

reaches 4,000psi and your peaks have merged into a single mass. Find out how
much help your sales representative has been to you colleague in the lab across
the hall.
2.1.5 Hardware–Service–Support
With many laboratory instruments, equipment specifications alone control the
decision of which instrument you should buy. However, HPLC systems are so
flexible, can run so many types of columns, and have enough control variables,
that hardware decisions alone are insufficient in helping you decide which
system you need to solve your application problems. I finally designed a
diagram to aid in explaining how to buy an HPLC system (Fig. 2.1).
If you are buying a water bath for the laboratory, you need only consider
the temperature range and whether it is UL rated.All you do is turn it on and
set the temperature. Price and hardware considerations are enough to make
your decision. If it is critical to your work that the water bath always work,
you either buy a backup unit or you buy from a company that will provide
excellent and prompt on-site service. At this point, the second leg of the
success triangle comes into play. In an HPLC system, hardware, service, and
support are all critical to guarantee your HPLC success. If you buy from a
company that provides only hardware, you must provide the service and
support. If the company has good hardware and a responsive serviceperson,
but no support, then you must provide the support. This might mean reading
a book and attending courses to become “the HPLC expert.” It might mean
hiring an HPLC consultant. It might mean getting only a portion of the capa-
bility of your system.
The HPLC should be a tool to help you solve your research problems, not
a new research problem of its own. Think how much your time is worth. (If
you do not know, ask you boss, who knows well!) Selecting a company that
can provide excellent hardware, responsive and knowledgeable service, and
Figure 2.1 Hardware–service–support.

application support after the sale can be one of the most economical decisions
you will ever make, no matter what the initial cost of the system turns out
to be.
2.2 SYSTEM COST ESTIMATES
HPLC companies tend to sell Type II systems when a Type I will do, a Type
III system when a Type II would be sufficient for the job. I’ve tried to estimate
a range of prices for which I last sold these systems (1993). Precise system
prices are difficult to obtain from the manufacturers unless you are on GSA
pricing or a bid system. Inflation will drive these prices up; the very real com-
petition in this field tends to hold prices down. Let’s look at each type of
system in turn.
2.2.1 Type I System—QC Isocratic (Cost: $10–15,000)
This system is made up of a reservoir, pump, injector, detector, and an inte-
grator. The Rheodyne manual injector has pretty much become the standard
in the industry. It gives good, reproducible injections, but the fittings used on
it are specific for this injector and are different from any other fitting in the
system and very difficult to connect or disconnect because of tight quarters in
the back of the injector. I recommend a variable UV detector as your work-
horse monitor, then add other monitors as the need arises (i.e., electrochem-
ical detector for catacholamines, fluorometer for PNAs). The integrator lets
you record or integrate. If you dislike working with thermal paper, you can
photocopy for long-term storage or look around for a plain-paper integrator.
Stay with modular systems. Systems in a box are cheaper because of a common
power supply, but not nearly as flexible in case of problems with a single com-
ponent, with upgrading as required by a new application, or as available equip-
ment changes.
2.2.2 Type II System—Research Gradient (Cost: $20–25,000)
The Type II system comes in two flavors. They vary by the type of gradient
pumping system they contain: low-pressure mixing or high-pressure mixing.
The rest of the system is the same: injector, variable detector, and computer-
based data acquisition and control. Autosamplers would allow 24-hr opera-
tion, but most university research laboratories find graduate students to be less
expensive.
A few years ago I would have always recommended the high-pressure
mixing system, even though it was more expensive; performance merited the
difference in price. Today, it depends on the applications you anticipate
running. If you plan on running 45-min gradients to separate 23 different com-
ponents, some of them as minor amounts such as with PTH amino acids, then
SYSTEM COST ESTIMATES 19

I recommend a dynamically stirred, two-pump, high-pressure mixing system.
If, on the other hand, you’ll mainly be doing scouting gradients, dial-a-mix iso-
cratics, and the occasional uncomplicated gradient, the low-pressure mixing
system would be excellent and save you about $4,000. This system has the
advantage of giving you three- or four-solvent capability, which would be of
advantage in scouting and automated wash-out, but it requires continuous,
inert gas solvent degassing. I generally find low-pressure mixing gradient
reproducibility performance to be about 95% that of the high-pressure mixing
system. Gradients from 0 to 5% and 95 to 100% B may be worse than 95%
and should be checked before buying (see Chapter 9).
You can replace an integrator-based data acquisition system with a com-
puter-based system, but let the buyer beware. I am not impressed with most
of the control/data acquisition add-on systems I’ve seen. The system made by
Axxion runs on most systems, is competitively priced, and is reasonably
friendly. For maximum control and processing benefit, the computer and soft-
ware have to be carefully matched to the HPLC hardware. If I was going to
buy anything, I’d get data acquisition/processing only. My operating rule is to
“try it before you buy it” and think again. I’ve been using personal computers
for 25 years; I’m a fan, but I’m still not convinced that most people can upgrade
to a useful component system. Manufacturers carefully match computer and
HPLC hardware with optimized software and, even then, many control/pro-
cessing systems leave much to be desired. If you do buy a computer to acquire
data, keep your integrator or strip chart recorder. You will thank me.
2.2.3 Type III System—Automated Clinical (Cost: $25–35,000)
The most common job for these systems is the fast-running isocratic separa-
tion. They could be built up from the QC isocratic, but dial-a-mix isocratic is
faster and more convenient since they switch easily from job to job. These
systems come in the same two flavors as the research gradient, low- and
high-pressure mixing, but replace the manual injector with an autosampler,
allowing 24-hr operation. For thermally labile samples that need to be held
for a period of time before being injected, there are autosampler chillers
available.
The components in these systems tie together, start with a single start
command, and may be capable of checking on other components to make sure
of their status.The controllers usually will allow different method selection for
different injection samples. The more expensive autosamplers allow variable
injection volumes and bar code vial identification for each vial. Since these
laboratories must retain chromatograms and reports for regulatory compli-
ance and good laboratory practice, they are moving more toward computer
control/data acquisition. At the moment, this will add an additional $5,000 to
the cost above for software and hardware. This assumes that the computer
system replaces the controller and integrator at purchase.

2.2.4 Type IV System—Automated Methods (Cost: $30–50,000)
Another fully automated gradient system, this system is most commonly found
in industrial methods development laboratories. They usually have an
autosampler, a multi-solvent gradient, at least a dual-channel, variable UV
detector and computer-based control, and data processing system for reports.
They may add a fraction collector to be used in standards preparation.
Some laboratories will replace the variable detector with a diode array detec-
tor/computer combination that can run the cost of this system to $60,000. Of
course, you could have two Type II systems for the same price. Other detec-
tors, such as a caronal charged aerosol detector or a mass spectrometer and
interface module, will dramatically increase the system price. In 2004, I talked
to a laboratory director who had just purchased an automated gradient HPLC
system with a linear ion trap mass spectrometer that cost $220,000! It depends
on what you are trying to achieve and how heavily budgeted your department
is at the moment.
2.3 COLUMNS
The decision about which HPLC column to choose is really controlled by the
separation you are trying to make and how much material you are trying to
separate and/or recover. I did a rather informal survey of the literature and
my customers 15 years ago to see which columns they used. I found 80% of
all separations were done on some type of reverse-phase column (80% of
those were done on C18), 10% were size separation runs (most of these on
polymers and proteins), 8% were ion-exchange separations, and 2% were
normal-phase separation on silica and other unmodified media, such as zirco-
nium and alumina. The percentage of size- and ion-exchange separations has
increased recently because of the importance of protein purification in pro-
teomics laboratories and the growing use in industry of ion exchange on pres-
sure-resistant polymeric and zirconium supports.
2.3.1 Sizes: Analytical and Preparative
Columns vary in physical size depending on the job to be accomplished and
the packing material used. There are four basic column sizes: microbore
(1–2mm i.d.), analytical (4–4.5mm i.d.), semipreparative (10–25mm i.d.), and
preparative (1–5 in i.d.). Column lengths will range from a 3-cm ultrahigh
resolution, 1–3-mm packed microbore column to a 160-cm semipreparative
column with 5mm packing. The typical analytical column is a 4.2-mm i.d.
× 25-cm C18 column packed with 5mm media.
Size separation columns need to be long and thin to provide a sufficiently
long separating path. Preparative ion exchange and affinity columns should be
short and broad to provide a large separating surface.
COLUMNS 21

2.3.2 Separating Modes: Selecting Only What You Need
Column decisions should be made in a specific order based on what you are
trying to achieve. First, decide whether you are trying to recover purified mate-
rial or simply analyzing for compounds and amounts of each present (see
Fig. 5.4).
If you are going to make a preparative run, how much material will you
inject? Deciding this allows you to decide on an analytical (microgram
amounts) column, a semipreparative (milligram) column, or a preparative
(grams) column depending on the amounts to be separated (see Table 11.1).
Once the column size is decided, the next column decision is based on the
types of differences that will be needed to separate the molecules. The sepa-
rating factors might be size, the charge on the molecules, their polarities, or a
specific affinity for a functional group on the column.
For size differences, select a size-exclusion or gel-permeation column. A
further decision needs to be made based on the solubilities of the compounds.
Size separation columns are supposed to make a pure mechanical separation
dependent only on the diameters of the molecules in the mixture. Compounds
come off the column in order of size, large molecules first. Solvent serves only
to dissolve the molecules to they can enter the column pores and be separated
based on their resident times. Size columns come packed with either silica-
based, polymer-based, or gel-based packing in solvents specific for samples dis-
solved in either aqueous or organic solvents. Do not switch solvents or solvent
types on gel-packed columns; differential swelling can change the separating
range of the column, cause column voiding, or even crush the packing.
For charge differences, select either an anion-exchange or cation-exchange
column, either gel-based or bonded-phase silica or chelated zirconium.Anion-
exchange columns retain and separate anions or negatively charged ions.
Cation-exchange columns retain and separate positively charged cations.
Silica-based ion exchange columns are pressure resistant, but are limited to
pH 2.5–7.5 and degrade in the presence of high salt concentrations, which
limits cleaning charged contaminants off the column or separation of strongly
bound compounds. Zirconium-based ion exchange columns are resistant to
pressure, high temperature, and pH from 1-11, but they have Lewis acid func-
tionality that must be blocked to prevent non-ion exchange interacts that will
interfere with the separation. Column packing with bonded chelators has been
produced to overcome this problem.The functional group on either positively
or negatively charged columns can have permanent charges (strong ion
exchangers, either quaternary amine or sulfonic acid) or inducible charges
(weak ion exchangers, with carboxylic acid or secondary/tertiary amine). The
latter types can be cleaned by column charge neutralization through mobile-
phase pH modification. Ion exchangers do not retain or separate neutral
compounds or molecules with the same charge as the column packing.
For polarity differences, select a partition column. Look at solubilities in
aqueous and organic solvents again. Compounds soluble only in organic sol-

vents should be run on normal-phase (polar) columns. Compounds with struc-
tural or stereo isomeric differences should be separated on normal-phase
columns. Most compounds soluble in aqueous organic solvents should be run
on reverse-phase columns. Although C18 columns are commonly used, inter-
mediate phase columns, such as the phenyl, C8, cyano, and diol columns, offer
specificity for double bonds and functional groups. Additives to the mobile
phase can modify polarity-based separations, such a strong solvent changes,
pH modification, and ion pairing agents.
This selection of separating modes is an oversimplification, but it serves as
a good first approximation and will be expanded on in later sections of this
book. There is rarely such a thing as a pure size column or column packing
that separates solely by partition. Many size columns control pore size by
adding bonded phases that can exhibit a partition effect. The underlying silica
support can have a cation-exchange effect on a partition separation.A bonded
phase column’s pore size can introduce size exclusion effects. Most separations
are a combination of partition, size, and ion-exchange effects, generally with
one separating mode dominating and others modifying the interactions. This
can be a problem when trying to introduce simple, clean changes in a separa-
tion, but it can be used to advantage if you are aware that it might be present.
2.3.3 Tips on Column Use
Here are a few tips on column usage that will make your life easier:
1. Keep the pH of bonded-phase silica column between 2.0 and 8.0 (better
is pH 2.5–7.5). Solvents with a pH below 2.0 remove bonded phases; all
silica columns dissolve rapidly above pH 8.0 unless protected with a sat-
uration column.
2. Always wash a column with at least six column volumes (approximately
20mL for a 4mm × 25cm analytical column) of a new solvent or a bridg-
ing solvent between two immiscible solvents.
3. Do not switch from organic solvents to buffer solution or vice versa.
Always do an intermediate wash with water. Buffer precipitation is a
major cause of system pressure problems. You may be able to go from
less than 25% buffer to organic and get away with it, but you are forming
a very bad habit and that will get you into trouble later on. I usually keep
a bottle of my mobile phase minus buffer on the shelf for column
washout at the end of the day. This also can be used for buffer washout,
but a water bridge is still the best.
4. Do not shock the column bed by rapid pressure changes, by changes to
immiscible solvents, by column reversing, or by dropping or striking the
column or the floor or the desktop.
5. Pressure increases are caused by compound accumulation, by column
plugging with insoluble materials, or by solvent viscosity changes. It is
COLUMNS 23

poor practice to run silica-based columns above 4,000psi (see Chapter
10 on troubleshooting for cleaning). Keep organic polymer columns and
large-pore silica size columns below 1,000psi or lower if indicated in the
instructions supplied with the column. Set your pump overpressure
setting, if it has one, to protect your column. Solvents mixtures such as
water/methanol, water/isopropanol, and DMSO/water undergo large vis-
cosity changes during gradient runs and washouts.Adjust your ﬂow rates
and overpressure setting to accommodate these increases so the systems
does not shut down or overpressure columns.
6. Use deoxygenated solvents for running or storing amine or weak anion-
exchange columns (see “Packing Degradation,” in Chapter 6, for a
deoxygenating apparatus).
7. Wash out buffer, ion pairing reagents, and any mixture that forms solids
on evaporation before shutting down or storing columns. Store capped
columns in at least 25% organic solvent (preferably 100% MeOH or ace-
tonitrile) to prevent bacterial growth.

3
RUNNING YOUR
CHROMATOGRAPH
25
This chapter is designed to help you get your HPLC up and running. We will
walk through making tubing fittings, putting the hardware together, preparing
solvents and samples, initialization of the column, making an injection, and
getting information from the chromatogram produced. Let us begin with the
hardware and work our way toward acquiring information.
3.1 SET-UP AND START-UP
When your chromatograph arrives, someone will have to put it together. If you
bought it as a system, a service representative from the company may do this
for you. No matter who will put it together, you should immediately unpack
it and check for missing components and for shipping damage.
If you only bought components or if you are inheriting a system from
someone else, you will have to put it together yourself. More than likely, you
will need, at a minimum, the system manual, a 10-foot coil each of 0.010-in (10
thousandths) and 0.020-in (20 thousandths) tubing, compression fittings
appropriate to your system, cables to connect detectors to recorder/integra-
tors and pumps to the controller, and tools. Our model will be a simple, iso-
cratic system: a single pump, a flush valve, an injector, a C18 analytical column,
a fixed-wavelength UV detector, and a recorder (see Fig. 1.4). The first thing
we need to do is to get the system plumbed up or connected with small inter-
nal diameter tubing. For now, check the columns to make sure they were
shipped or were left with the ends capped. We will put them aside until later.

3.1.1 Hardware Plumbing 101: Tubing and Fittings
We will need 1/8-in stainless steel HPLC tubing with 0.020-in i.d. going from
the outlet check valve of the pump to the flush valve and on to the injector
inlet. Three types of tubing are used in making HPLC fittings, 0.04-in, 0.02-in,
and 0.01-in i.d.; the latter two types are easily confused. If you look at the ends
of all three types, 0.04-in looks like a sewer pipe, more hole than tube. Look
at the tubing end on; if you can see a very small hole and think that it is 0.01-
in it probably is 0.02-in. If you look at the end of the tubing and at first think
its a solid rod and then look again and can just barely see the hole, that’s 0.01-
in. From the injector to the column and from the column on to the detector
we will use 4-in pieces of this 0.010-in tubing.
It is critically important to understand this last point. There are two tubing
volumes that can dramatically affect the appearance of your separation; the
one coming from the injector to the column and from the column to the detec-
tor flow cell. It is important to keep this volume as small as possible. The
smaller the column diameter and the smaller the packing material diameter,
the more effect these tubing volumes will have on the separation’s appearance
(peak sharpness).
A case in point is a trouble-shooting experience that I had. We were visit-
ing a customer who had just replaced a column in the system. The brand new
column was giving short, broad, overlapping peaks. It looked much worse than
the discarded column, but retention times looked approximately correct. Since
the customer was replacing a competitive column with one that we sold, I was
very concerned. I asked her if she had connected it to the old tubing coming
from the injector and she replied that the old one did not fit. She had used a
piece of tubing out of the drawer that already had a fitting on it that would
fit. This is always dangerous since fittings need to be prepared where they will
be used or they may not fit properly. They can open dead volumes that serve
as mixing spaces. I had her remove the column and looked at the tubing. Not
only was tubing protruding from the fitting very short, the tubing was 0.04-in
i.d. This is like trying to do separations in a sewer pipe. We replaced it with
0.01-in tubing, made new fittings, and reconnected the column. The next run
gave needle-sharp, baseline-resolved peaks!
To make fittings, you need to be able to cleanly cut stainless steel tubing.
Do not cut tubing with wire cutters; that is an act of vandalism. Tubing is cut
like glass. It is scored around its circumference with a file or a micro-tubing
cutter. The best apparatus for this is called a Terry Tool and is available from
many chromatography suppliers. If adjusted for the internal diameter of the
tubing, it almost always gives cuts without burrs. If you do not have such a
tool, score around the diameter with a file. Grasp the tube on both sides of the
score with blunt-nosed pliers and gently flexed the piece to be discarded until
the tubing separates. Scoring usually causes the tubing to flare at the cut. A
flat file is used to smooth around the circumference. Then, the face of the cut
is filed at alternating 90° angles until the hole appears as a dot directly in the
26 RUNNING YOUR CHROMATOGRAPH

center of a perfect circle. The ferrule should then slide easily onto the tubing.
Make sure not to leave filings in the hole. Connect the other end to the
pumping system and use solvent pressure from the pump to wash them out.
The tubing is connected to the pump’s outlet check valve by a compression
fitting.The fitting is made up of two parts:a screw with a hex head and a conical
shaped ferrule (Fig. 3.1a).The top of the outlet valve housing has been drilled
and threaded to accept the fitting.
First, the compression screw then the ferrule are pushed on to the tubing;
the narrow end of the ferrule and the threads of the screw point toward the
tubing’s end.The end of the tubing is pushed snugly into the threaded hole on
the check valve. The ferrule is slid down the tube into the hole, followed by
the compression screw. Using your fingers, tighten the screw as snug as possi-
ble; then use a wrench to tighten it another quarter turn. As the screw goes
forward, it forces the ferrule against the sides of the hole and squeezes it down
onto the tubing, forming a permanent male compression fitting.The fitting can
be removed from the hole, but the ferrule will stay on the tubing. The tubing
must be cut to remove the ferrule.
It’s important not to overtighten the fitting. It should be just tight enough
to prevent leakage under pressure. Try it out. If it leaks, tighten it enough to
stop the leak. By leaving compliance in the fitting, you will considerably
increase its working lifetime. Many people overtighten fittings. If you work at
it, it is even possible to shear the head off the fitting. But please, do not.
There is a second basic type of compression fitting (Fig. 3.1b), the female
fitting, which you will see on occasion. Some column ends have a protruding,
threaded connector and will require this type of fitting. This fitting is made
SET-UP AND START-UP 27
Figure 3.1 Compression fittings. (a) Male fitting; (b) female fitting; (c) zero dead volume union.

from a threaded cap with a hole in the center. It slides over the tubing with
its threads pointed toward the tubing end. A ferrule is added exactly as above
and the tubing and the ferrule are inserted into the end of a protruding tube
with external threads. Tightening the compression cap again squeezes the
ferrule into the tapered end of the tube and down onto the tubing forming a
permanent fitting. The third type of device for use with compression fittings is
the zero dead volume union (Fig. 3.1c). A union allows you to connect two
male connection fittings. If these fittings are made in the union, it allows tubing
to be connected with negligible loss of sample volume.
You will find that stainless steel fittings will cause you a number of
headaches over your working career. An easier solution in many cases is the
polymeric “finger-tight” fittings sold by many supplier such as Upchurch and
SSI. These fittings slide over the tubing and are tightened like stainless steel
fittings, but are not permanently “swagged” onto the tubing and can be reused.
They are designed to give a better zero-dead-volume fitting, but they have
pressure and solvent limits.They are also more expensive, but only in the short
run.
3.1.2 Connecting Components
New pumps are generally shipped with isopropanol or a similar solvent in the
pump head, and this will need to be washed out. Always try and determine
the history of a pump before starting it up. Systems that have not been run for
a while may have dried out. If buffer was left in the pump, it may have dried
and crystallized. In any event, running a dry pump can damage seals, plungers,
and check-valves.
First we will need to hook up the pump inlet line. This usually consists of a
length of large-diameter Teflon tubing with a combination sinker/filter pushed
into one end and a compression fitting that will screw into the inlet fitting at
the bottom of the pump head on the other end. Drop the sinker into the
solvent reservoir and screw the other end into the inlet check valve housing.
The next step is to use compression fittings to hook the pump outlet to the
flush valve with a length of 0.02-in i.d. tubing.The flush valve is a small needle
valve used to prime the pump that allows us to divert solvent away from the
column when rapidly flushing the pump to atmospheric pressure. Open the
valve and the line is vented to the atmosphere. This removes the back-pres-
sure from the column, a major obstacle when trying to push solvent into a
plumbed system.
From the flush valve we can connect with fittings and 0.02-in tubing onto
the injector inlet port. The back of the injector usually has ports for an inlet,
an outlet, two ports for the injection loop, and a couple of wash ports. If a
sample loop is not in place, connect it, then make a short piece of 0.01-in i.d.
tubing with fittings to be used in connecting the column. Use the column end
to prepare the compression fitting that will fit into it (Fig. 3.2). At the outlet
end of the column, hook up with compression fittings a piece of 0.01-in tubing

that connects to the detector flow cell inlet line. When this is done, remove
and recap the column and set it aside.
Next, we are going to create a very useful tool for working with the HPLC
system. I call it a “column blank” or column bridge (Fig. 3.3). It bridges over
the place in the system where we would normally connect the column. It is
very valuable for running, problem diagnosis, and for cleaning a “column less
system.” It is made up of a 5-ft piece of 0.01-in tubing with a male compres-
sion fitting on each end screwed into a zero-dead-volume union
(female/female). Our column blank now has two ends simulating the end fit-
tings on the column.
Figure 3.2 Column inlet compression fitting.
Figure 3.3 Column blank.

Connect one end of your column blank to the tubing from the injector
outlet; the other end is connected to the line leading to the detector flow cell.
We have one more fluid line to connect to complete our fluidics. A piece of
0.02-in tubing can be fitted to the detector flow cell outlet port to carry waste
to a container. In some systems, this line will be replaced with small-diameter
Teflon tubing.
In either case, the line should end in a back-pressure regulator, an
adjustable flow resistance device designed to keep about 40–70psi back-pres-
sure on the flow cell to prevent bubble formation that will interfere with the
detector signal. Air present in the solvent is forced into solution during the
pressurization in the pump. The column acts as a depressurizer. By the time
our flow stream reaches the detector cell, the only pressure in the system is
provided by the outlet line. If this is too low, bubbles can form in the flow cell
and break loose, resulting in sharp spikes in the baseline. The back-pressure
regulator prevents this from happening.
The final connections are electrical. A power cable needs to be connected
to each pump. Check the manuals to see whether fuses need to be installed
and do so if required. Finally, connect the 0–10mV analog signal connectors
on the back of the detector to the strip chart recorder. Connect red to red,
black to black. If a third ground wire is present in the cable, connect it only at
one end, either the detector or the recorder end. (Note: The ground wire con-
nects to the cable shield, which is wrapped around the other two wires in the
cable. If no ground is connected, no shielding of the signal occurs. If both ends
of a ground are connected, the shield becomes an antenna; worse than no
shield at all.)
Now our system is ready to run. We will need to prepare solvent, flush out
each component, then connect, flush out, and equilibrate the column before
we are ready to make our first injection of standard.
3.1.3 Solvent Clean-up
Before we tackle the column, let us look at how to prepare solvents for our
system. I have found that 90% of all system problems turn out to be column
problems. Many of these can be traced to the solvents used, especially water.
Organic solvents for HPLC are generally very good. There are three rules
of thumb to remember: always use HPLC grade solvents, buy from a reliable
supplier, and filter your solvents and check them periodically with your HPLC.
Most manufacturers do both GLC and HPLC quality control on their solvents;
some do a better job than others. The best way to find good solvents is to talk
to other chromatographers.
Even the best solvents need to be filtered. I have received HPLC-grade ace-
tonitrile, from what I considered to be the best manufacturer of that time, that
left black residue on a 0.54-mm filter. There is a second reason to filter sol-
vents. Vacuum filtration through a 0.54-mm filter on a sintered glass support is
an excellent way to do a rough degassing of your solvents. Because of filter

and check valve arrangements, some pumps cavitate and have problems
running solvents containing dissolved gases.
There are numerous filter types available for solvent filtration. The cellu-
lose acetate filters should be used with aqueous samples containing less than
10% organic solvents. With much more organic in the solvent, the filter will
begin to dissolve and contaminate your sample. Teflon filters are used for
organic solvent with less than 75% water. The two types are easily told apart;
the Teflon tends to wrinkle very easily, while the cellulose is more rigid. If you
are using the Teflon filter with high percentages of water in the solvent, wet
the filter first with the pure organic solvent, then with the aqueous solvent
before beginning filtration. If you fail to do this it will take hours to filter a
liter of 25% acetonitrile in water. Nylon filters for solvent filtration can be
used with either aqueous or organic solvents. They work very well as a uni-
versal filter, but use with very acidic or basic solutions should be avoided as
they break down the filter.
If you’re still having pumping problems after vacuum filtration, try placing
the filtrate in an ultrasonication bath for 15min (organic solvents) or 35min
(aqueous solvents). Ultrasonic baths large enough to accept a 1-L flask are in
common use in biochemistry labs and are very suitable for HPLC solvent
degassing. Stay away from the insertion probe type of sonicator; they throw
solvent and simply make a mess. Ultrasonication is much better than heating
for degassing mixed solvents. There is much less chance of fractional distilla-
tion with solvent compositional change when placing mixtures in an ultrasonic
bath. One manufacturer actually made a system that was designed to remove
dissolved gas by heating mobile phase under a partial vacuum. Obviously
they never used rotary vacuum flash evaporators in their labs, at least not
intentionally!
Other techniques recommended for solvent degassing involve bubbling
gases (nitrogen or helium) through the solvent. Helium sparging is partially
effective, but expensive when used continuously. It is required in some low-
pressure mixing gradient systems, as will be described later. The only other
time I use any of these techniques is in deoxygenating solvent for use with
amine or anionic exchange columns, which tend to oxidize (see Fig. 6.4).
Water is the major offender for column contamination problems. I have
diagnosed many problems, which customers have initially blamed on detector,
pumps, and injectors, that turned out to be due to water impurities. Complex
gradient separations are especially susceptible to water contamination effects.
In one case, the customer was running PTH amino acid separation, a
complex gradient run on a reverse-phase column. He would wash his column
with acetonitrile, then water, and run standards. Everything looked fine. Five
or six injections later his unknown results began to look weird. He ran his stan-
dards again only to find the last two compounds were gone. He blamed the
problem on the detector. I said it looked like bad water. He exploded, told me
that his water was triple distilled and good enough for enzyme reactions. It
was good enough for HPLC, he said. Over the following 6mo we replaced

every component in that system as each in turn was blamed for the chro-
matography problem. Eventually, the customer borrowed HPLC-grade water
from another institution, washed his column with acetonitrile, then with water.
The problem disappeared and never came back—until he went back to his
own water. Nonpolar impurities co-distilling with the water were accumulat-
ing at the head of the column and retaining the late runners in the column.
While HPLC grade water is commercially available, I have found it to be
expensive and to have limited shelf life. The best technique for purifying
water seems to be to pass it through a bed of either reverse-phase packing
material or of activated charcoal, as in a Milli-Q system. Even triple distilla-
tion tends to co-distill volatile impurities unless done using a fractionation
apparatus.
I have used an HPLC and an analytical C18 column at 1.0mL/min overnight
to purify a liter of solvent for the next day’s demonstration run. The next
morning, I simply washed the column with acetonitrile, then with water, equi-
librated the column with mobile phase, and ran my separation. It might be
better to reserve a column strictly for water purification if you are going to
use this technique regularly.
An even better solution is to use vacuum filtration through a bed of reverse-
phase packing. Numerous small C18 SFE cartridges are available that are used
for sample clean-up and for trace enrichment.They are a tremendous boon to
the chromatographer for sample preparation, but also can be of help in water
clean-up. These SFE cartridges are a dry pack of large pore size C18 packing
and must be wetted before use with organic solvent, then with water or an
organic solution.You wash first with 2mL of methanol or acetonitrile and then
with 2mL of water before applying dissolved sample. If you forget and try to
pass water or aqueous solutions through them, you well get high resistance
and nonpolars will not stick.SFE cartridges contain from 0.5 to 1.0g of packing
and will hold approximately 25–50mg of nonpolar impurities. If care is taken
not to break their bed, they can be washed with acetonitrile and water for
reuse. Eventually, long eluting impurities will build up and the SFE must be
discarded. I have used them about six times, cleaning about a liter of single
distilled water on each pass. If larger quantities of water are required, com-
mercially available reverse phase, vacuum cartridge systems using large-pore,
reverse-phase packing designed to purify gallons of water at a time are
available.
The most common choice for large laboratories are mixed bed, activated
charcoal, and ion exchange systems that produce water on demand. These
systems usually have a couple of ion-exchange cartridges and one activated
charcoal filter in series. They work very well, but I prefer to have the charcoal
as the last filter in the purification bank. After all, we are trying to remove
organics. I find that the ion-exchange resins break down after about 6mo and
begin to appear in the water.The system uses an ion conductivity sensor as an
indicator of water purity, but water that passes this test still may be unsuitable
for HPLC use.

3.1.4 Water Purity Test
The final step is to check the purity of the solvents. Again, I have found the
C18 column to be an excellent tool for this purpose. Select either 254nm or the
UV wavelength you will be using for the chromatogram.Wash the column with
acetonitrile until a flat UV baseline is established and then pump water though
the column at 1.0mL/min for 30min. This allows nonpolar impurities to accu-
mulate on the column. The final step is to switch back to acetonitrile. I prefer
to do this by running a gradient to 100% acetonitrile over 20min. If no peaks
appear after 5min at final conditions, the water is good. The chromatogram
(Fig. 3.4) gives you an idea of the expected baseline appearance.
Peaks that appear during the first acetonitrile washout are ignored as impu-
rities already on the column.Watch the baseline on switching to water.At 254
nm, the baseline should gradually elevate. If instead it drops, you may have
impurities in your acetonitrile. If the baseline makes a very sharp step up
before leveling off, you may have a large amount of polar impurities in the
water. Polar impurities probably will not bother you on reverse-phase columns
but might have some long-term accumulation effects. Peaks appearing during
the acetonitrile gradient come from nonpolar impurities in the water that accu-
mulated on the column and are now eluting.
I have done this with water from a Milli-Q system in need of regeneration.
Even though their indicator glow light shows no evidence of charged mater-
ial being released from the ion exchanger, peaks that will effect reverse-phase
chromatography show up at around the 70% acetonitrile portion of the gra-
dient run.
Figure 3.4 Water purity test.

If your water passes this test at the wavelength you will be using for your
chromatography, you are ready to use it to equilibrate the column. The next
step is to flush out the dry system and prepare to add the column.
3.1.5 Start-up System Flushing
Fill the solvent reservoir with degassed, filtered solvent by pouring it down the
wall of the flask to avoid remixing air into it. I usually start pumps up with
40–50% methanol in water. Even if the pump was shut down and allowed to
stand in buffer, there is a good chance this will clear it. It is also a good idea
to loosen the compression fitting holding the tubing in the outlet check valve
at the top of the pump head to relieve any system back-pressure. This is an
especially important step to use if the column is still connected.When running
with a column blank, as we are, it is less important.
The first step is to insure that the pump is primed. This may mean pushing
solvent from an inlet manifold valve through the inlet check valve and into
the pumping chamber.A few pumps on the market, like the old Waters M6000,
use spring-loaded check valves, so you may have to really work to get solvent
into the chamber. With other pumps, you open a flush valve and use a large
priming syringe to pull solvent through the pumphead. The next step is either
to turn the pump flow to maximum speed or uses the priming function of the
pump, which does the same thing.
As soon as the pump begins to pump solvent by itself, tighten down the
outlet compression fitting and drop the flow rate to about 1mL/min.The pump
is ready to run and should be allowed to pump into a beaker for a few minutes
to wash out any machining oils, if new, or soluble residues or dissolved buffer
if old.
Before we move on, let us talk about shutting down a pump.The pump seal
around the plunger is lubricated by the contents of the pumping chamber.
There is always a microevaporation through this seal/plunger combination,
whether the pump is running or not. Buffers and other mobile phases con-
taining dissolved solids should not be left in a pump when it is to be turned
off overnight. This evaporation causes crystallization on the sapphire plunger
and can result in either breakage or seal damage on starting up the pump. Sol-
vents containing dissolved solids should always be washed out before shut
down. I prefer to wash out and leave a pump in 25–50% methanol/water to
prevent bacteria growth in the fluidics system.
Occasionally, I have had to leave buffer in a pump overnight. In such a case,
I leave the pump running slowly (0.1mL/min.) and leave enough solvent in
the reservoir so that it can run all night. This has the additional value of
washing the column overnight. If the column is clean and doesn’t require
further washing, you can throw the detector outlet into your inlet reservoir
and recycle the solvent, ensuring you will not run out.
Now we can move past the flush valve to the next major system compo-
nent, the injector. Whichever position you find the injector handle in, leave it

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