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Bulletin 826E
HPLC Troubleshooting Guide
How to identify, isolate, and correct the most common HPLC problems
Although HPLC method development has been improved by advances in column technology and instrumentation, problems still arise. In this guide we offer
you a systematic means of isolating, identifying, and
correcting many typical problems.
The important segments of an HPLC system are the
same, whether you use a modular system or a more
sophisticated unit. Problems affecting overall system
performance can arise in each component. Some common problems are discussed here. Solutions to these
problems are presented in easy-to-use tables.
E000648
CONTENTS:
Isolating HPLC Problems ................................................... 2
How to Prevent Mobile Phase Problems ............................ 2
Isolating Pump Problems .................................................. 3
Injector and Injection Solvents .......................................... 3
Column Protection ........................................................... 3
Getting the Most from Your Analytical Column ................ 3
Solving Detector Problems ................................................ 4
Column Heater, Recorder ................................................. 4
Keeping Accurate Records ................................................ 4
Problem Index .................................................................. 4
HPLC Problems, Causes and Remedies ........................ 5-13
Restoring Your Column's Performance ...................... 14-15
Preventing and Solving Common Fitting Problems .......... 16
A Selection of Column Protection Products ............... 17-20
sigma-aldrich.com
Figure A.
To prevent bubbles in the system, degas the mobile phase. Generally an in-line degasser is a first choice, but sparging with helium can
be an alternative if the mobile phase does not contain any volatile
components.
Use ion pair reagents carefully. The optimum chain length and
concentration of the reagent must be determined for each analysis.
Concentrations can be as low as 0.2 mM, or as high as 150 mM, or
more. In general, increasing the concentration or chain length
increases retention times. High concentrations (>50%) of acetonitrile or some other organic solvents can precipitate ion pair reagents. Also, some salts of ion pair reagents are insoluble in water
and will precipitate. Avoid this by using sodium-containing buffers
in the presence of long chain sulfonic acids (e.g., sodium dodecyl
sulfate), instead of potassium-containing buffers.
Volatile basic and acidic modifiers, such as triethylamine (TEA) and
trifluoracetic acid (TFA), are useful when you wish to recover a
compound for further analysis. These modifiers also let you avoid
problems associated with ion pair reagents. They can be added to
the buffer at concentrations of 0.1 to 1.0% TEA or 0.01 to 0.15%
TFA. Increasing the concentration may improve peak shape for
certain compounds, but can alter retention times.
Recycling the mobile phase used for isocratic separations has
become more popular in recent years as a means of reducing the
cost of solvents, their disposal, and mobile phase preparation time.
An apparatus such as the Supelco SRS-3000 or SRS-1000 Solvent
Recovery System uses a microprocessor controlled switching valve
to direct the solvent stream to waste when a peak is detected. When
the baseline falls under the selected threshold, uncontaminated
solvent is directed back to the solvent reservoir.
Injector
Column
Oven
Debubbler
Pre-injector
Filter
Helium
Supply
Precolumn
Filter
Pump
Solvent
Return
Line
Back-Pressure
Regulator
Detector
Waste
Solvent Recovery
System
Column and
Integrated Guard
Column
Solvent Reservoir
and Inlet Filters
Data System
Pulse Damper
794-0746
3.
4.
5.
6.
7.
8.
The injector rapidly introduces the sample into the system with
minimal disruption of the solvent flow. HPLC systems currently use
variable loop, fixed loop, and syringe-type injectors. These are
activated manually, pneumatically, or electrically.
Mechanical problems involving the injector (e.g., leaks, plugged
capillary tubing, worn seals) are easy to spot and correct. Use a precolumn filter to prevent plugging of the column frit due to physical
degradation of the injector seal. Other problems, such as
irreproducible injections, are more difficult to solve.
Variable peak heights, split peaks, and broad peaks can be caused
by incompletely filled sample loops, incompatibility of the injection
solvent with the mobile phase, or poor sample solubility. Whenever
possible, dissolve and inject samples in mobile phase. Otherwise, be
sure the injection solvent is of lower eluting strength than the
mobile phase (Table 3). Be aware that some autosamplers use
separate syringe washing solutions. Make sure that the wash
solution is compatible with and weaker than the mobile phase. This
is especially important when switching between reversed and
normal phase analyses.
Column Protection
Although not an integral part of most equipment, mobile phase
inlet filters, pre-injector and pre-column filters, and guard columns
greatly reduce problems associated with complex separations. We
recommend that all samples be filtered through 0.45 m or 0.2 m
syringe filters. We strongly recommend the use of guard columns.
Filters and guard columns prevent particles and strongly retained
compounds from accumulating on the analytical column. The
useful life of these disposable products depends on mobile phase
composition, sample purity, pH, etc. As these devices become
contaminated or plugged with particles, pressure increases and
peaks broaden or split. As an example, Figure B presents a clear case
for the use of guard columns. For more about column protection,
see the product pages of this guide and request Bulletin 781.
Same analytical
column after
replacing
Supelguard column
3
1
5 6
Amitriptyline
Imipramine
Desmethyldoxepin
Nortriptyline
Desipramine
Protriptyline (int. std.)
8
56
4
Min
4
Min
794-0809, 794-0810
<500 g
<100 mg
<500 mg
Problem Index
Problem
Problem No.
Baseline
drift
noise, irregular
noise, regular
12
14
13
4
3
Ghost peaks
19
15
10
11
7
8, 9
Peaks
height change
missing
negative
no peaks
unresolved
16
2
18
1
6
Selectivity change
17
Trademarks
FPLC Amersham Pharmacia Biotech
Iso-Disc, Pelliguard, Sigma-Aldrich, Supelco,
SUPELCOSIL, Supelguard, Trizma Sigma-Aldrich Co.
LO-Pulse Scientific Systems, Inc.
Rheodyne Rheodyne, Inc.
Swagelok Crawford Fitting Co.
Teflon E.I. du Pont de Nemours & Co., Inc.
Table 1.
Problem
Probable Cause
Remedy/Comments
794-0747
Problem
794-0748
Problem
794-0749
Normal
1. Pump off.
2. Flow interrupted/obstructed.
3. Leak.
794-0747
794-0748
1. Start pump.
2. Check mobile phase level in
reservoir(s). Check flow throughout
system. Examine sample loop for
obstruction or air lock. Make sure
mobile phase components are
miscible and mobile phase is
properly degassed.
3. Check system for loose fittings.
Check pump for leaks, salt buildup,
unusual noises. Change pump seals
if necessary.
4. Disconnect tubing at guard column
(if present) or analytical column inlet.
Check for flow. Purge pump at high
flow rate (e.g., 5-10 mL/min.), prime
system if necessary. (Prime each
pump head separately.) If system has
check valve, loosen valve to allow air
to escape. If problem persists, flush
system with 100% methanol or
isopropanol. If problem still persists,
contact system manufacturer.
Problem
Probable Cause
Remedy/Comments
Normal
Problem
4. Leak at column inlet end fitting.
794-0751
Normal
794-0750
Problem
794-0752
Problem
Probable Cause
Remedy/Comments
1. Leak.
Problem
794-0747
Problem
794-0754
Normal
794-0755
Problem
794-0756
Problem
Probable Cause
Remedy/Comments
794-0757
Problem
Problem
Normal
794-0747
Problem
794-0759
Problem
Probable Cause
Remedy/Comments
1. Column overloaded.
2. Sample solvent incompatible with
mobile phase.
794-0760
Problem
794-0761
794-0762
Problem
794-0763
Problem
Probable Cause
Remedy/Comments
794-0748
Problem
794-0764
Normal
2. Pump pulsations.
794-0748
Problem
794-0765
10
6. Leak.
Problem
Probable Cause
Remedy/Comments
Normal
794-0748
Problem
794-0766
Normal
794-0767
Problem
794-0768
11
Problem
Probable Cause
Remedy/Comments
794-0769
Problem
794-0770
794-0771
Problem
794-0772
12
Problem
Probable Cause
Remedy/Comments
794-0747
1. Check polarity.
2. Use mobile phase with lower
refractive index, or reverse recorder
leads.
3. Adjust or change sample solvent.
Dilute sample in mobile phase
whenever possible.
4. a. Change polarity when using
indirect UV detection, or
b. Change UV wavelength or use
mobile phase that does not
adsorb chosen wavelength.
Problem
794-0773
794-0760
Normal
Problem
Further Recommendations
We also suggest referring to the maintenance and troubleshooting
sections of your instrument manual. Modern HPLC systems often
have self-diagnostic capabilities that help isolate the problem area
within the instrument. For persistent problems relating to the
column or your particular analysis, please contact Supelcos Technical
Service Department.
The remaining pages in this guide include procedures for restoring
column performance following loss in resolution, retention, or
Table 2.
Silica Column
Flush with the following:
1. 50 mL hexane
2. 50 mL methylene chloride
3. 50 mL 2-propanol
4. 50 mL methanol
5. 25 mL methylene chloride
6. 25 mL mobile phase
Evaluate column performance according to
conditions specified by the manufacturer.
Note:
See also the Silica Column Regeneration Solution listed on page 15 for
rejuvenating a deactivated silica column.
14
Table 3.
Solvent
Polarity
Hexane
Isooctane
Carbon tetrachloride
Chloroform
Methylene chloride
Tetrahydrofuran
Diethyl ether
Acetone
Ethyl acetate
Dioxane
Acetonitrile
2-Propanol
Methanol
Water
nonpolar
UV
Cutoff
Refractive Index
at 20 C
Solvent Strength,
o (silica)
Viscosity
at 20 C, cP
no
no
no
no
no
yes
no
yes
poorly
yes
yes
yes
yes
yes
200
200
263
245
235
215
215
330
260
215
190
210
205
1.3750
1.3910
1.4595
1.4460
1.4240
1.4070
1.3530
1.3590
1.3720
1.4220
1.3440
1.3770
1.3290
1.3328
0.00
0.01
0.14
0.31
0.32
0.35
0.29
0.43
0.45
0.49
0.50
0.63
0.73
>0.73
0.33
0.50
0.97
0.57
0.44
0.55
0.23
0.32
0.45
1.54
0.37
2.30
0.60
1.00
polar
Typical values
flow rate:
temp.:
det.:
injection:
1. Benzene
2. Benzanilide
3. Acetanilide
33175
12
Well defined test mixes enable you to troubleshoot chromatographic problems, optimize system efficiency, and evaluate columns under conditions where their performance is understood. We
ship our test mixes in amber ampuls to prevent photodegradation,
and we include instructions for proper use and interpretation of
results.
Choose from column-specific or application-specific mixes. Refer to
our catalog for our extensive selection of test mixes, or call our
Technical Service Department.
3
0
4
Min
2
Min
0
2
4
Min
15
Figure D.
1/16" Nut
Porous
Frit
Packing
794-0785
Endfitting
16
794-0786
Filtration Apparatus 2
250 mL Reservoir
Clamp
Description
Funnel Base
1000 mL Flask
Cap
910-0113
Cat. No.
58061
58062-U
58063
58074
58064
58068
58070-U
58075
58071
58065
58066
58067
58060-U
58053
4 Channel
The Supelco Mobile Phase Degassing system with its smart sensor
not only detects and alerts you to leaks, it also communicates with
the vacuum pump. If a change in vacuum is detected due to mobile
phase flow rate changes, the pump can compensate by changing its
speed. The validation output records vacuum level to satisfy system
compliance and validation requirements. The degassing system has
a Teflon AF membrane, with NO-OX fittings and tubing.
Description
E000923
Cat. No.
55018-U
Filters
A precolumn filter is essential for protecting HPLC columns against particulate matter which can accumulate on the column frit, leading
to split peaks and high back pressure. Sources of particles include mobile phases (especially when buffers are mixed with organic solvents),
pump and injector seals, and samples. Use a 2.0 m frit to protect columns containing 5 m or larger particles, or a 0.5 m frit for columns
with particles smaller than 5 m.
Supelco Filter
Direct-connect; protects analytical and
guard columns. Our precolumn filter can be
connected directly, hand-tight, into any HPLC
column or guard column listed in our current
catalog, or with any other column that has
Valco-compatible endfittings. PEEK cap and
body, 2 m stainless steel frit. For a metal-free
system, order PEEK/Teflon replacement frits
(Cat. No. 57430-U).
Description
P000551
Cat. No.
Z22732-3
Z29087-4
Z22733-1
57430-U
Biocompatible, metal-free.
P000548
Cat. No.
59269
59271
59273
59272
Most HPLC fittings, except SSI and some Waters fittings, have 10-32 threads.
Cat. No.
59262-U
59264
59265
Most HPLC fittings, except SSI and some Waters fittings, have 10-32 threads.
18
Cat. No.
58420-U
58279-U
59037
59129
58284
Isolation
Technologies
Precolumn Filter
In-line installation.
P000549
High capacity inlet filter minimizes dead volume and band broadening, to prevent loss of
column efficiency while protecting your column. Frit porosity: 0.5
m. Complete as shown.
Description
Cat. No.
57675-U
57676-U
57677
57678
P000555
Cat. No.
55079
55078
55080-U
55081
Patented continuous flow design (see figure) flow is uninterrupted when you switch from LOAD to INJECT
Injector includes a 20 L sample loop and is supplied with a VESPEL rotor seal that can be replaced with a Tefzel rotor seal for operation
at pH 0-14. Factory set at 5000 psi (345 bar), adjustable to 7000 psi (483 bar). Model 7725i has an internal position sensing switch.
From Pump
MBB Passage
MBB Port
To Column
6
To
Loop
Description
3
5
4
From
Loop
796-0423
Cat. No.
57620-U
57621
58830-U
57633
57634
57635
57636
55049
57622
57623
57624
57625
57626
57627
57628-U
57629-U
57630
57631
57632
Optimize
Technologies Pump
Replacement Parts
A preventative maintenance program that includes routine replacement
of pump parts that are subP000583
ject to wear will help you
avoid costly downtime. Our extensive selection of Optimize Technologies check valves, seals, and pistons meet or exceed pump
manufacturers' specifications. For the most up-to-date selection of
pump parts, refer to the current Supelco catalog, or call our
Technical Service Department.
Pulse Damper
Pulse Damper without Cabinet
Cat. No.
58455
58442
19
Installation Is Simple
SRS-1000
Autoclean Valve
(option with SRS-3000)
Injector
Flush Mobile
Solvent Phase
Reservoir
Recycle
Waste
Reservoir
Waste
Data System
Solvent Recycled
Solvent to Waste
1.
2.
3.
4.
5.
6.
Uracil
Phenol
Benzaldehyde
N,N-Diethyl-m-toluamide
Toluene
Ethylbenzene
5
6
Threshold
0
3
Min
Description
6
713-0516
Cat. No.
57431
57432
57435
506125
506133
CE approved.
World Headquarters
(800) 244-1173
T100826E
AIV
Valve in
SRS-3000/
SRS-1000
Column
Pump
995-0148, 897-0035
Detector
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