HPLC-MS Use-Care and Maintenance, Troubleshooting

LIQUID CHROMAOGRAPHY
(Principal, operations and troubleshooting)
Presented by
Faisal Ghazanfar
Senior Scientific officer,
APCIC, PCSIR Labs. Complex, Karachi
Faisal Ghazanfar, PCSIR 2

Chromatography
Chromatography is a method by which a
sample mixture of solids, liquids or gases is
resolved into its components which are
detected on the basis of their physical
properties. There are various types of
chromatographic techniques e.g.
Gas chromatography, Liquid chromatography
(LC) etc.

Thermostatic
Column
Compartment

Applications of HPLC
 Find out up to ppm (part per millions) levels compounds in samples such
as caffeine, aspirin, steroid etc
 Quantitative and qualitative analysis

Liquid chromatography (LC)
 Any method of chromatography in which the
mobile phase is a Liquid. The liquid used as
the mobile phase is called the “eluent”.
 The stationary phase is usually a solid or a
liquid.
 In general, it is possible to analyze any
substance that can be stably dissolved in the
mobile phase
 Categorized by nature of the stationary
phase and separation process such as Normal
separation, Reverse separation.

Block Diagram for HPLC
(Isocratic system )
9
Pump
Sample injection unit
(injector)
Column
Column oven
(thermostatic
column chamber)
Detector
Eluent
(mobile phase)
Drain
Data processor
Degasser
Stationary Phase

Animation of HPLC
 Simple separation
 Isocratic system of HPLC
 Chromatogram
 Single pump

Major parts of HPLC
 Eluent (Mobile phase)
 Solvent Delivery Pump
 Sample Injection Unit
 Column
 Detectors (optical & mass)
 Auto sampler (New addition)
 MS (New detector)
 Data processor (computer)

Block Diagram for HPLC (Gradient system)
Pump
Degassing
Assy.
Solvent
Proportioning
Assy.
(Gradient)
Pressure
Sensor
Pump
Pulse
Damper
Vacuum
Pump
Computer
Data
Station
&
Printer
Detector
Assembly
Column
A B c D
Pre-
Filter
(Mobile phase)
Knobs
Waste
Drain
Valve
waste
waste
Column Oven
Injection
Head
(Sample in)
OR
Sample in
from
Autosampler
Loop

Eluent (Mobile phase)

Comparing Chromatography to the Flow of
a River...
14
Base
Water flow
Light leaf
Heavy stone
www.mtsu32.mtsu.edu

Mobile phase
 The liquid used as the mobile phase is
called the “eluent”.
 May be a mixture of A,B and A,B,C,D
 Sample flow through mobile phase.
 The ratios are form gradient that useful
and beneficial in detection of compound.
 Isocratic system (constant eluent composition)
 Gradient system (variable eluent composition)
 It form base line.
 Mixing mainly depend on mixer/pump.

Separations in HPLC
 Normal Phase:
Polar stationary phase and a non-polar, non-aqueous mobile
phase, and works effectively for separating analytes readily soluble
in non-polar solvents. If polarity of mobile phase increases,
adsorption (stickness on surface) increases and cause increase in
retention time, so it is not in common using as compare to reverse
phase. (NP-HPLC)
 Reversed Phase:
A non-polar stationary phase and an aqueous, moderately
polar mobile phase. (RP-HPLC or RPC). No adsorption with polar
solvents because stationary phase is non-polar.
 Advantage:
 it allows us to use relatively cheap and non-hazardous solvents like
methanol, ethanol, acetonitrile and even water. Not suitable for Strong
Acid and Strong Bases.
www.en.wikipedia.org

“Normal Phase”
Stationary Phase - POLAR
Mobile Phase -NON POLAR
+ - + - + - + - + - + - + - + - + - + - + - +
+ - + - + - + - + - + - + - + - + - + - + - +
Stationary Phase

“Reverse Phase”
Stationary Phase - NON POLAR
Mobile Phase - POLAR
-
+
-
-
+
+
Stationary Phase

Isocratic system of LC
• The Eluent (Mobile phase)
composition is constant in LC
– problems:
– Low analysis time (quick)
– Poor separation

Gradient system of LC
Gradient system
 Varying eluent composition e.g.
gradient starting at 10% methanol and
ending at 90% methanol after 20
minutes

LC Pump
(Finnegan LCQ surveyor LC Pump)

LC pump with connections ABCD

specification
 Flow rate
 Pressure
 Mixer
 Programming
 10uL/min – 200uL/min
 0.1 -- 6 bar depend on pump head
 Software based

LC Pumps
(Reciprocating type pumps; displacement pumps)
1. High Pressure Pump (Single Piston)
2. High Pressure Pump (Double Piston)
3. Low Pressure Pump (Diaphragm type)

1:Mobile Phase Delivery Pump:
Schematic Diagram of Plunger Pump
25
Motor and cam
Plunger
Plunger seal
Check
valves
Pump head
10 -100µL

2:Reciprocating piston pumps

2:Reciprocating Dual
piston pumps

Pump piston replacement
animations
 Replacement of
 Seal of head
 Check Valve at inlet and outlet with seal
 Piston replacement of high Pressure pump
 Change of spring
 Change of piston
 How open pump and close

Vacuum Degasser operation
The Vacuum Degasser consists of a vacuum
chamber, degassing tube, variable speed
vacuum pump, microprocessor controller,
sensor, and check valves. The mobile phase
flows into a degassing tube, which is inside a
vacuum chamber. Decreased pressure in the
chamber causes the outward movement of gas
dissolved in the mobile phase across the tube
wall, in accordance to Henry’s Law (cold drink)
thus degassing the mobile phase

Vacuum Degassing Assembly

Degasser

Mixer

Pulse damper maintain
constant flow
Pumps have intervals in their pumping
cycle when flow and pressure
momentarily decrease. This "off time" is
the interval when the piston has finished
its solvent delivery stroke and is starting
to refill. To maintain constant flow, such
pumps require a pulse compensator or
damper that stores energy during the
pumps' delivery stroke and returns an
appropriate amount of work to the fluid
during the pump off time. This help to
reduce base line noise.

Pulse damper

Pump Care
• Flush with water after running a buffer,
• Replace seals in a timely manner.
• Maintain check valves.
• Do not allow solids (ppt.) in the mobile
phase.

Injection unit

Rotary Sample Loop Injector
 Injector needles are
used ranging from 10
µL to 500 µL to inject
a sample onto the
sample loop
 Upon a 60° rotation
the pump introduces
the sample onto the
column in a reverse
direction that it was
loaded.
Reference 2

Manual Injector 4 port
Reference 1

Routine Care of Injectors
 Never use a pointed or
bevel tip needle.
 Rinse after the use of
buffer solutions.
 Avoid abrasive particles
by filtering samples
before injection.
 Use burr-free tubing to
avoid metals shavings
from getting into the
injector.

Injector animation
 How to pass sample into injector
 Load sample

HPLC-Columns
Column specification

Internal Diameter vs. flow
rate of column

Parts of column
 Entrance
 Guard column
 Frits
 Outer jacket (AL, SS)
 Main column
 Exit

Column Heaters

Column Heaters
•Some separations of complex mixtures must be temperature
optimized to achieve separations of overlapping peaks.
•Increased column temperature will also shorten retention times
for a given column dimension.
•Eliminates retention time variation due to room temperature
fluctuations.

How life of column will be
longer
 Filter your sample and mobile phase. Make sure the pH
of the mobile phase is within the working range of the
column.
 Flush the column with methanol or acetonitrile if it is
not going to be used for sometime.

Removing Buffers from a Reverse
Phase Column
• DO NOT FLUSH WITH 100% WATER AS YOUR FIRST
STEP -
• Substitute water for the buffer but leave the
remaining proportions the same. Run through about
5 column volumes.
• Wash through 10 column volumes of a strong organic
solvent, example - Methanol.
• If you plan to store the column, read the directions
in manual.
• If the phase collapses, a 50-50 water, organic
solvent wash for 30 minutes can restore it.

Fitting of column/GC

Bits & Bobs

Bits and Bobs
pipe
thread

Nuts and ferrule
 Check the condition of the nut and ferrule
 After repeated use, nuts (and especially
ferrules) will gradually become deformed
to the point of being incapable of
creating the seal they were designed to
make. Always keep an extra supply of all
the nuts and ferrules you are using so that
you can replace them quickly and avoid
unnecessary down time.

Fittings of pipes of HPLC
 SS fittings
 Polymer based fittings
 Column
 Ferrule connections with column
 Incompatible fittings may cause leakage

Common HPLC Detectors
 Refractive Index (RI) - universal
 Evaporative Light Scattering Detector (ELSD) –
universal
 UV/VIS light – selective
 Fluorescence – selective
 Electrochemical (ECD) selective
 Mass Spec (MS) - universal
Reference 3

Optical detectors in HPLC
 UV/ visible detector
 Photo-diode array detector
 Refractive index detector

Differential Refractive Index Detector
(Deflection-Type)
55
Light
Sample cell
Reference cell
Light-receiving
unit

Optical System of Differential
Refractive Index Detector (Deflection-
Type)
56
W lamp
Slit
Sample cell
Reference cell
Photodiode
The slit image moves if the
refractive index inside the
flow cell changes.

UV Detector
Lamps
optics
Sample in/out

Diode array Detectors
HPLC Detector UV Lamps (Deuterium) 190 nm to 400nm

MS/MS Detector (LCQ Advantage)

MS detector
 Ionization for GC/MS
 Electron Ionization/Impact (EI)
 Chemical Ionization (CI)
 Ionization for LC/MS
 Electro-spray (ESI)
 Atmospheric Pressure Chemical Ionization (APCI)
 All are fitted in a stack (ion source housing)
 MS
 Quadruple
 Dynode (Detection of ions)

Simple APCI
Faisal Ghazanfar, PCSIR
http://www.rzuser.uni-heidelberg.de/~bl5/ency/ency.html

Corona Discharge Needle

API - Stack

STACK
Ion source
placement
Ion source housing

Sample Ion Formation
Primary Ion Formation
e- + N2  N2
+ + 2e-
Secondary Ion Formation
N2
++ H2O  N2 + H2O+ H2O+ + H2O  H3O+ + HO
Proton Transfer
H3O+ + M  (M + H)+ + H2O
(hydronium add with molecule Proton)

Quadruple Mass Filter and ion Trap
http://www.asms.org

Quadropole
Quadropole

Dynode
Dynode/Detector
Vacuum section-Inside view of MS

Electronics of MS

Sheath(nitrogen)
nebulized/spray
Auxilaryoutside ESI to
guide spray gas
Sweep gas prevent in
stack to enter other gas

Ethene spectrum
(nis
tdemo) E
thene
10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40
0
50
100
14 24
25
26
27
28
29
H
H
H
H
Name: Ethene
Formula: C2
H
4
MW: 28
28 999 | 27 545 | 26 501 | 25 73 | 29 22 |
largest peaks:

Acetone
(nis
tdemo) Acetone
10 15 20 25 30 35 40 45 50 55 60 65 70
0
50
100
14
15
27
29 39
42
43
44
58
59
O
Formula: C3
H
6
O
Molecular weight: 58

Troubleshooting HPLC
 Preliminary checks
 How removes Leaks
 Retention Time
 Base line
 Pressure
 Peaks

No peaks or very small peaks
Possible cause Solution
Detector off Check detector
Broken connections to
recorder/computer
Check connections
No sample/
Wrong sample
Check sample. Be sure
it is not deteriorated.
Check for bubbles in the
vials
Wrong settings on
recorder or detector or
software
Check attenuation.
Check gain

No Flow
Pump off Start Pump
Flow interrupted
Check reservoirs. Check position of
the inlet tubing. Check loop for
obstruction or air. Check degassing
of mobile phase. Check
compatibility of the mobile phase
components.
Leak
Check fittings. Check pump for leaks
and precipitates. Check pump seals.
Air trapped in the system
Disconnect column and prime pump.
Flush system with 100% methanol
or iso-propanol.

Column and fitting leaks
Problem Possible cause Solution
Column end leaks
Loose fitting
Tighten or replace fitting
Cut tubing and replace
ferrule; disassemble
fitting, rinse and
reassemble.
Leak at detector Detector-seal failure
Replace detector seal or
gaskets.
Leak at injection
valve
Worn or scratched
valve rotor
Replace valve rotor
Leak at pump Pump seal failure
Replace pump seal; check
piston for scratches and, if
necessary, replace

Check Retention time
(sample time to travel from column)
Contamination buildup
Flush column occasionally with strong
solvent such as methanol
Equilibration time insufficient for
gradient run or changes in isocratic
mobile phase
Pass at least 10 column volumes through the
column for gradient regeneration or after
solvent changes
First few injections - active sites
Condition column by injecting concentrated
sample
Inconsistent on-line mobile-phase
mixing
Ensure gradient system is delivering a
constant composition; compare with
manually prepared mobile phase; partially
premix mobile phase (1ml check by
software)
Selective evaporation of mobile-phase
component
Cover solvent reservoirs; prepare fresh
mobile phase
Varying column temperature
Thermostat or insulate column; ensure
laboratory temperature is constant.

Checking retention time….
Decrease Retention
Times
Column overloaded with
sample
Decrease sample amount or use
larger-diameter column.
Increasing flow rate Check and reset pump flow rate.
Varying column temperature
Thermostat or insulate column;
ensure laboratory temperature is
constant
Increasing Retention
Times
Decreasing flow rate
Check and reset pump flow rate;
check for pump cavitations;
check for leaking pump seals
and other leaks in system
Changing mobile-phase
composition
Cover solvent reservoirs; ensure
that gradient system is
delivering correct composition.

Base line
Noise
Air bubbles in mobile phase Degas or use back pressure restrictor on detector
Positive-negative - difference in
refractive index of injection
solvent and mobile phase
Normal with many samples; use mobile phase as
sample solvent
Drifting
baseline
Negative direction (gradient
elution) - absorbance of mobile-
phase A
Use non-UV absorbing mobile phase solvents; use
HPLC grade mobile phase solvents; add UV
absorbing compound to mobile phase B.
Positive direction (gradient
elution) - absorbance of mobile
phase B
Use higher UV absorbance detector wavelength; use
non-UV absorbing mobile phase solvents; use HPLC
grade mobile phase solvents; add UV absorbing
compound to modile phase A.
Positive direction - contamination
buildup and elution
Flush column with strong solvent; clean up sample;
use HPLC grade solvents
Wavy or undulating - temperature
changes in room
Monitor and control changes in room temperature;
insulate column or use column oven; cover refractive
index detector and keep it out of air currents.

Base line….
Baseline noise
Continuous - detector lamp problem
or dirty cell
Replace UV lamp( each should last 2000 h; clean and
flush flow cell.
Gradient or isocratic proportioning -
lack of solvent mixing
Use proper mixing device; check proportioning
precision by spiking one solvent with UV absorbing
compound and monitor UV absorbance detector output.
Gradient or isocratic proportioning -
malfunctioning proportioning
valvesl
Clean or replace proportioning precision valves;
partially remix solvents.
Occasional sharp spikes - external
electrical interference
Use voltage stabilizer for LC system; use independent
electrical circuit.
Periodic - pump pulses
Service or replace pulse damper; purge air from pump;
clean or replace check valves.
Random - contamination buildup
Flush column with strong solvent; clean up sample; use
HPLC grade solvent
Spikes - bubble in detector
Degas mobile phase; use back pressure restrictor at
detector outlet.
Spikes - column temperature higher
than boiling point of solvent
Use lower column temperature.

Pressure
Decreasing Pressure
Insufficient flow
from pump
Loosen cap on mobile
phase reservoir
Leak in hydraulic
lines from pump to
column
Tighten or replace fittings;
tighten rotor in injection
valve
Leaking pump
check valve or seals
Replace or clean check
valves; replace pump
seals.
Pump cavitations
Degas solvent; check for
obstruction in line from
solvent reservoir to pump;
replace inlet-line frit

Pressure…..
Fluctuating
pressure
Bubble in pump Degas solvent;
Leaking pump check
valve or seals
Replace or clean check valves; replace
pump seals
High Back
Pressure
Column blocked with
irreversibly absorbed
sample
reverse-flush column with strong solvent
to dissolve blockage
Column particle size too
small (for example 3
micrometers)
Use larger particle size (for example 5
micrometer)
Mobile phase viscosity
too high
Use lower viscosity solvents or higher
temperature
Plugged frit in in-line
filter or guard column
Replace frit or guard column
Plugged (block)inlet frit Replace end fitting or frit assembly

Parts of column
 Entrance
 Guard column
 Frits
 Outer jacket (AL, SS)
 Main column
 Exit

Ghost peaks
Contamination
Flush column to remove
contamination; use HPLC-grade solvent
Elution of analytes retained
from previous injection
Flush column with strong solvent at end of
run; end gradient at higher solvent
concentration
Reversed-phase
chromatography –
contaminated water
Check suitability of water by running different
amounts through column and measure peak
height of interferences as function of
enrichment time; clean water by running it
through old reversed-phase column; use
HPLC-grade water.

Peaks…..
Negative
peaks
Refractive index detection –
refractive index of solute less
than that of mobile phase
Reverse polarity to make peak positive
UV-absorbance detection –
absorbance of solute less than
that of mobile phase
Use mobile phase with lower UV absorbance; if
recycling solvent, stop recycling when recycled
solvent affects detection
Peak
Doubling
Blocked Frit
Replace or clean frit; install 0.5-um porosity in-
line filter between pump and injector to
eliminate mobile-phase contaminants or
between injector and column to eliminate
sample contaminants
Coelution of interfering
compound from previous
injection
Flush column with strong solvent at end of ran;
end gradient at higher solvent concentration
Column overloaded
Use higher-capacity stationary phase; increase
column diameter; decrease sample amount

Peak doubling
To resolved doubling problem
of peak:
A new batch of mobile phase
was made and new auto
sampler wash solvent was used
with no improvement. The
entire system was flushed
thoroughly with acetonitrile in
an effort to clean the column
and wash the pump, auto
sampler and detector; this did
not appear to help……………firit?
Reverse column run?

Peak doubling

Peak doubling (channeling in column)

Peak fronting

Peaks…..
Peak Doubling
Column void or channeling
Replace column, or, if
possible, open top end fitting
and clean and fill void with
glass beads or same column
packing; repack column
Injection solvent too strong
Use weaker injection solvent
or stronger mobile phase
Sample volume too large
Use injection volume equal to
one-sixth of column volume
when sample prepared in
mobile phase for injection
Un-swept injector flow path Replace injector rotor
Peak Fronting
Channeling in column Replace or repack column
Column overloaded
Use higher-capacity stationary
phase; increase column
diameter; decrease sample
amount

Peak tailing
 Shopping in a corridor example.
 Column normally filled with silica.
 Cause due to secondary interaction of analytes
 (silanol interaction) with some thing to the
 stationary phase

Peaks…..
Tailing Peaks
Basic solutes - silanol interactions
use a stronger mobile phase; use base-
deactivated silica-based reversed-phase
column;
Beginning of peak doubling is also a tailing
peaks
See peak doubling
Chelating solutes - trace metals in base silica
Use high purity silica-based column with low
trace-metal content;
Silica-based column - degradation at high
temperature
Reduce temperature to less than 50 C
Spikes
Bubbles in mobile phase
Degas mobile phase;
ensure that all fittings are tight
Column stored without caps
Store column tightly capped; flush reversed-
phase columns with degassed methanol

Tailing Peaks
Silica-based column –
degradation at high
temperature
Reduce temperature to less than 50 C
Silica-based column – silanol
interactions
Decrease mobile-phase pH to suppress
silanol ionization; increase buffer
concentration; derivatize solute to
change polar interactions
Void formation at head of
column
Replace column, or, if possible, open
top end fitting and clean and fill in void
with glass beads or same column
packing; rotate injection valve quickly;
use injection valve with pressure
bypass; avoid pressure shock
Peaks…..

Symptoms of Dirty columns
 HIGH BACK PRESSURE. (15-20% to do reverse flush)
 CHANGING RETENTION TIMES.
 BROAD PEAKS AND TAILING.
 LOSS OF COLUMN RESOLUTION
Solution:
Regeneration of column /flushing of column
(purging column with pure acetonitrile)
(5% methanol + 95% water, 01hr)

Column fritt
 Filter like material, ring
shape of mcro-m
(size<0.5um), placed on
both sides of column.
 System back pressure
increases and, in some
instances, peaks become
distorted or split.
 the sample to be
distributed evenly across
the top of the column

Column frit
 When plugging of the inlet frit occurs there are two
ways to restore column performance. The easiest and
fastest way is to back flush particulates off the inlet
frit. This may not always work, but since it is so easy to
do, it is worth a try.

How do back flushing of inlet
frit
1. Connect the column to the chromatograph so
that the now is in the reverse direction. Do not
connect the column to the detector because
dislodged particulates from the inlet frit may
flow into the detector flow cell.
2. Back-flush the column with approximately 10
column volumes (V-pi*r^2*h) of mobile
phase.(~1ml/min upto 25ml)
3. Connect the column to the chromatograph so
that the flow is in the proper direction.
4. Check to see if chromatographic performance is
acceptable.
5. If problem still their, replace frit or guard
column

References
1. www.montclair.edu
2. http://www.restek.com/info_sixport.as
p
3. Robinson, J. W.; Skelly Frame, E.M.;
Frame II, G.M. Undergraduate
Instrumental Analysis, 6th ed.; Marcel
Dekker Inc.: NY, 2005; pp 797-835.
4. http://delloyd.50megs.com/moreinfo/
HPLC.htm
5. MAC-MOD Analytical Inc. HPLC Column
Companion
6. http://www.promochrom.com

Thank you
Q & A

HPLC-MS Use-Care and Maintenance, Troubleshooting

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