Phenomenex GC User manual

GC Column Care Guide
GC Column Installation............................................................................................. 1-2
GC Column Conditioning and Testing ........................................................................... 3
GC Hints and Tips
Protecting the GC Column and Extending Life Time.................................................. 4
Carrier Gas Selection and Flow Optimization............................................................ 5
Column Storage .................................................................................................... 5
Chemical Compatibility / Solvent Rinsing of Zebron™Capillary Columns..................... 6

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1
© 2009 Phenomenex, Inc. All rights reserved.
A. Capillary GC Installation with a Traditional GC Nut
Note: GC columns do not have a specific directional flow when received from the manufacturer. Upon initial use of your new Zebron™column, Phenomenex recommends
the practice of dedicating one specific end of the column for injector installation only. This is particularly important when dealing with active/caustic or contaminating
compounds. If these compounds are routinely injected onto the column, degradation of the phase will occur - leading to higher bleed. A typical first step to remedying
(removing) this bleed would be to trim 10 cm from the front (injector) end of the column and keep trimming this inlet end of the column as necessary. Trying to remedy any
bleed issues by trimming the column may not work if both ends have been interchangeably installed into the inlet.
Injector Installation
Place a capillary nut and ferrule on the injector end of the GC column,1.
allowing a section of column to protrude. Trim one to two centimeters
(cm) from the protruding end to remove ferrule contamination that may
have entered the column (Figure 1). Inspect the cut with a magnifier to
ensure that a smooth, clean, square-cut edge has been made – cut again
if necessary (Figure 2).
Carefully hang the column in the GC oven, being cautious not to scratch or2.
damage the polyimide coating on the capillary tubing. Rotate the column
to avoid sharp bends of the capillary column and any contact of the
column with oven surfaces.
Insert the column into the injector exactly the correct distance specified3.
in the instrument manual. Tighten the ferrule nut finger-tight then ½ turn
with a wrench. If the column can still be moved, tighten another ¼ turn
until the column is secure.
Adjust the carrier gas.4.
Detector Installation
Note: For users with sensitive detectors such as MS and ECD, column
conditioning steps should be performed before installing the column to prevent
contamination and frequent maintenance of the detector.
Place the column nut and ferrule past the end of the column and cut a1.
centimeter or two off the end of the column (Figure 1). Be sure that the
ferrule is the right size and pointing in the correct direction. Inspect the
cut with a magnifier and ensure that the cut is square and smooth (Figure
2). Cut again if needed.
Insert the outlet end of the column into the detector exactly the distance2.
prescribed in the instrument manual. Distances will vary between
detectors. Tighten the ferrule nut finger-tight then ½ turn with a wrench.
If the column can still be moved, tighten another ¼ turn until the column
is secure.
Inspect the column connections for leaks using an electronic leak3.
detector. Leaks at the inlet end may introduce oxygen to the column that
will result in increased column bleed and damage to the column phase.
Figure 1: Cutting Fused Silica Tubing Figure 2: Proper and Improper Cut Capillary End
score capillary with
smooth edge of
wafer at a 45° angle
apply force in a
downward direction
tubing should break
cleanly
inspect cut with a
magnifying glass
b
a
Examples of: (a) A Properly Cut Fused Silica Column End
(b) An Improperly Cut End
Correct Incorrect
4X
GC Column Installation

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B. Capillary GC Installation with the Cool-Lock™Nut
Avoid burning your fingers again – cools with the oven•
No Wite-Out•®needed
Achieve the proper installation depth each and every time•
No need for wrench with hand-tightened connections•
~exclusive~
patent pending
1. Insert column through column nut and
ferrule. Cleanly cut ≥ 1 cm of the column
that is protruding from the nut and ferrule.
Insert the end of the column and column
nut into the bottom of the Cool-Lock Nut
Installation Gauge.
1
2. Hand-tighten the column nut into the gauge
until the ferrule starts to compress. Adjust the
length of the column to the desired length.
Further tighten the nut into the gauge until the
column cannot slide. If using the Cool-Lock
Nut, tighten its bottom ferrule. Make sure lower
body/ferrule is in the full extension position.
Otherwise, mark the column at the base of the
column nut to ensure the correct installation
depth after installation.
2
3. Unscrew the installation gauge and install
the nut and column into the instrument.
4. Make sure Cool-Lock Nut is in the full
extension position to achieve the correct
premeasured position, and allow for proper
leak checking.
3
Cool-Lock GC Capillary Nut*
Part No. Description Unit
AG0-8319 Cool-Lock GC Capillary Nut For Use with
Short-Style Ferrules
ea
AG0-8320 Cool-Lock GC Capillary Nut For Use with
Long-Style Ferrules
ea
AG0-8349 Cool-Lock Nut Installation Gauge ea
Replacement Ferrules
AG0-4701 GC Capillary Ferrules Graphite 1⁄16 in. to 0.5 mm ID 10/pk
AG0-4704 GC Capillary Ferrules Graphite 1⁄16 in. to 0.8 mm ID 10/pk
*Guaranteed t for Agilent 5850, 5890, 6890, 6850 GC systems
Agilent GC Systems Shimadzu GC Systems
Cool-Lock GC Capillary Nut**
Part No. Description Unit
AG0-8419 Cool-Lock GC Capillary Nut For Use with
Short-Style Ferrules
ea
AG0-8420 Cool-Lock Nut Installation Gauge ea
**Guaranteed t for Shimadzu QP-2010 and QP 2014 GC systems
GC Column Installation

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3
A. Column Conditioning
Allow sufficient time for the carrier gas to flow through the column to1.
purge any oxygen that may be in the system.
Raise the temperature of the column to the maximum isothermal2.
operating temperature that is listed on the individual Zebron™GC
Column Test Report. Maintain this temperature until a constant baseline
is achieved. Conditioning times will depend on the phase identity and
thickness, with thicker films taking longer to stabilize. If necessary
in order to minimize the downtime of the instrument, columns can be
conditioned overnight at the maximum isothermal temperature.
B. Installation Testing
Inject a detectable unretained sample, such as methane for an FID, to determine
dead volume time and linear gas velocity at the desired column temperature.
Adjust gas pressure for optimal flow depending on carrier gas selection.
The non-retained peak must have ideal peak shape or installation is faulty1.
and needs to be redone.
C. Checking for Leaks
Use a thermoconductivity detector to check for leaks. It is highly sensitive to
H2, He, and N2and will not contaminate the instrument or column. Liquid leak
indicators are not recommended for capillary columns. There is the risk of
drawing the liquid into the column or fittings and contaminating the system.
NOTE: If Vespel®ferrules are being used, leakage can occur after the initial
heating phase due to ferrule deformation. Be sure that the fitting is re-tightened
after this initial heating phase, and then carefully check all corrections for leaks.
D. Test Column with Zebron’s Text Mix
Good chromatographic practices include the use of Performance Check
Standards to establish the baseline performance characteristics of your column
and to monitor any changes over time. Test solutions should evaluate column
inertness, efficiency and resolution in an easy-to-use format. Most Phenomenex
test mixes are supplied ready to use at a concentration of 250 μg/mL in glass
ampules.
Match your column phase to the correct standard to set up initial running
conditions. Should you have any questions on the proper use of these Check
Standards, contact your local Phenomenex GC Specialists.
Zebron’s Text Mix
Suitable for Phenomenex Zebron•™and equivalent brands
Convenient way to check column performance•
Affordable and easy-to-use•
Zebron Phase Test Mix
Part Number
ZB-1 AG0-5155
ZB-1ms AG0-7805
ZB-1HT AG0-5155
ZB-5 AG0-5155
ZB-5ms AG0-7578
ZB-5MSi AG0-8362
ZB-5HT AG0-5155
ZB-35 AG0-5156
ZB-1701 AG0-5156
ZB-1710P AG0-5156
ZB-50 AG0-5157
ZB-624 AG0-5159
ZB-WAX AG0-5158
ZB-WAXPLUS™AG0-7869
ZB-FFAP AG0-5158
ZB-XLB AG0-7578
ZB-Drug-1 AG0-8431
Grob Test AG0-5154
GC Column Conditioning and Testing

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A. Four Key Steps to Protecting the GC Column and
Extending Lifetime
It is important to protect the column and instrument components from exposure
to dirty samples. Non-volatile or high molecular weight components can
contaminate the stationary phase, causing peak resolution, lower accuracy, and
poor column lifetime. Cutting off the damaged portion will usually restore the
column performance, but over time performance will degrade to a point where
the column can no longer be used. If you are experiencing rapid degradation of
column performance, there are several simple ways to help protect your column
and increase lifetime:
1. Ensure Proper Sample Preparation
a.Filter your samples prior to injection with Phenex™syringe filters (see
Appendix A for details).
b.Use Strata®or Strata
™-X* SPE Cartridges to eliminate contaminants (see
Appendix D for details).
2. Use a Guardian™or Z-Guard
a.Guard Columns – Standard Guards. Z-Guard columns are 5 or 10 meter
pieces of deactivated tubing that are connected to an analytical column
using a glass press-fit connector. The tubing acts like a trap for non-
volatile residues that would otherwise damage the stationary phase of your
analytical column.
b.Guardian Integrated Guard Columns. Unlike traditional guard columns,
there is no mechanical connection between the guard and the analytical
column. The result: all the benefits of a guard column without the possibility
of leaks or activity resulting from a faulty connection. Please contact a
Phenomenex GC Specialist for information on the Guardian.
3. Use a Wool Liner
The liner is the first line of defense for the column and the style chosen can make
a big difference in how much contamination gets onto the column. The easiest
thing to do is to add a small amount of silanized glass wool to a liner, which
traps the non-volatile compounds and prevents them from entering the column
(Figure 3). See Appendix B for other recommended GC accessories.
Caution: glass wool can also add activity for acids, bases, and pesticides.
Crushing the glass wool can lead to increased activity, so it is recommended to
purchase pre-packed liners, rather than try to pack your own.
Figure 3. Some liners that are available pre-packed with glass wool or provide
additional column protection:
4. “Baking Out” the Column
The easiest way to reduce column contamination is to add a short, high
temperature bake out at the end of the standard GC method. This bake out helps
remove high boiling contaminants that would otherwise remain in the column
and cause damage. To bake out, the final oven temperature needs to be set
high enough to ensure elution of these compounds, but not so high as to cause
thermal damage. This can be done either isothermally, or more commonly, via a
gradient or ballistic increase until the last components elute from the column.
Caution: NEVER exceed the upper temperature limits of the column. DO NOT
exceed more than 15 minutes at the upper isothermal temperature limit specified
for the column.
Description
GC Model No.
Dimensions
ID x L x OD
(mm)
Material*
(deactivated)
Quartz Wool
(Y / N) Mfr. No. Part No. Unit
Split/Splitless
5880/5890/6890 4 x 78.5 x 6.3 B (y) Y 210-4004 AG0-7515 5/pk
AG0-7582 25/pk
Split/Splitless, Recessed Gooseneck Liner
5880/5890/6890 4 x 78.5 x 6.45 B (y) Y 5183-4691
5183-4692
AG0-4661
AG0-4662
5/pk
25/pk
Cup Splitter/Split Liner
5880/5890/6890 4 x 78.5 x 6.3 B (n) N 5183-4699 AG0-4647 5/pk
5183-4700 AG0-4648 25/pk
Cup Splitter/Split Liner
AutoSystem™3.5 x 100 x 5 B (n) N 0330-5181 AG0-4663 5/pk
Splitless Single Taper/Liner
5880/5890/6890 4 x 78.5 x 6.45 B (y) Y 5183-4693
5183-4694
AG0-4657
AG0-4658
5/pk
25/pk
* B = Borosilicate; Deactivated = Yes (y) or No (n)
GC Hints and Tips
*Strata-X is patented by Phenomenex, Inc.

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5
B. Carrier Gas Selection and Flow Optimization
It is advisable to use the highest purity gas possible. Ultra high purity (99.99 %),
ultra pure carrier (99.995 %), or even research grade (99.9999 %) is preferred
to minimize critical impurities, instrument downtime and troubleshooting. Three
types of gas are commonly used as a carrier gas:
Hydrogen (H1. 2): Hydrogen will yield maximal number of theoretical
plates for thin film columns and the high efficiency is largely retained at
velocities higher than uopt. Hydrogen is not generally recommended due to
its hazardous nature.
Helium (He): When hydrogen is not used, helium is the best alternative for2.
speed and sensitivity.
Nitrogen (N3. 2): Nitrogen is the last choice for thin film columns. For thick
film columns, nitrogen yields the highest number of theoretical plates.
However, the optimal velocity is fairly low (long analysis times), and the
loss in efficiency at higher velocities is high. If resolution is sufficient,
hydrogen or helium are good alternatives.
Figure 4: Carrier Gas Selection and Velocity Optimization Plots
C. Column Storage
Important! The column may be left in the instrument for short-term storage.
Ensure a flow of carrier gas through the column at 100-200 °C. For long-term
storage, disconnect from the GC and cap or seal the capillary ends. Oxygen
and moisture can degrade or irreversibly damage the column, especially
cyanopropyl-based phases. Wax (polyethylene glycol) and cyanopropyl-based
phases are also susceptible to UV-induced degradation and should be shielded
from light (fluorescent or sunlight). Store the column in the original box. Upon
reinstallation, cut column ends to ensure that septum fragments or other debris
have not been left in the column.
Carrier Gas Length
H(u) curves for different gases H(u) curves for different
column lengths
Film Thickness Retention Factor
H(u) curves for different film
thicknesses
H(u) curves for different k values
Optimal velocities
for low dfvalues:
uopt
(cm/sec)
H240
He 25
N210
Optimal velocities
for high dfvalues:
uopt
(cm/sec)
H225
He 15
N27
GC Hints and Tips
Request your free technical note on:
Considerations when Switching from
Hydrogen to Helium
TN-2037

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D. Chemical Compatibility / Solvent Rinsing of Zebron™Capillary Columns
Important! Water and organic solvents such as those listed in Table 1 will not damage Zebron column stationary phases. However, inorganic acids and bases should
be completely avoided or rapid degradation and permanent damage to the stationary phase will result. In the event chemical damage is incurred, the removal of 0.5-2
meter of capillary off the front end will often restore column performance. Select the rinse solvent from the Table below.
Table 1. Phase Compatibility with Rinsing Solvents
Table 2. Rinsing Conditions
Column ID (mm) Rinse Solvent Volume (mL) Pressure (psig)
0.25 540
0.32 540
0.53 10 20
Important: Rinse from the back to the front of the column to avoid pushing inlet contaminants further into the column.
Phase Water Methanol CH2Cl2CHCl3Acetone Hexane
ZB-1
ZB-1ms
ZB-1HT Inferno™
ZB-5
ZB-5ms
ZB-5MSi
ZB-5HT Inferno™
ZB-XLB
ZB-624
ZB-35
ZB-1701
ZB-1701P
ZB-50
ZB-WAXPLUS™AVOID
ZB-WAX AVOID
ZB-FFAP AVOID
MR-1
MR-2
ZB-Drug-1
ZB-BAC1
ZB-BAC2
ZB-Bioethanol
OK
GC Hints and Tips

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7
Phenex™Syringe Filters
4 mm Diameter
for ≤ 2 mL sample volumes
15 mm Diameter
for 2 - 10 mL sample volumes
25-28 mm Diameter
for 10 - 100 mL sample volumes
Membrane Type/Size Part No. Unit Part No. Unit Part No. Unit
0.45 µm
Phenex-RC
(Regenerated Cellulose)
AF0-3103-12 100/Pk AF0-2103-12 100/Pk AF0-8103-121100/Pk
AF0-3103-52 500/Pk AF0-2103-52 500/Pk AF0-8103-521500/Pk
Phenex-PTFE 2
(Polytetrafluoroethylene)
AF0-3102-12 100/Pk AF0-2102-12 100/Pk AF0-1102-12 100/Pk
AF0-3102-52 500/Pk AF0-2102-52 500/Pk AF0-1102-52 500/Pk
0.20 µm
Phenex-RC
(Regenerated Cellulose)
AF0-3203-12 100/Pk AF0-2203-12 100/Pk AF0-8203-121100/Pk
AF0-3203-52 500/Pk AF0-2203-52 500/Pk AF0-8203-521500/Pk
Phenex-PTFE 2
(Polytetrafluoroethylene)
AF0-3202-12 100/Pk AF0-2202-12 100/Pk AF0-1202-12 100/Pk
AF0-3202-52 500/Pk AF0-2202-52 500/Pk AF0-1202-52 500/Pk
Please inquire with Phenomenex about other Phenex Syringe filters offerings.
Above syringe filters are non-sterile. Housing is made of medical-grade polypropylene (PP) and offer luer lock inlet/slip outlet connections, unless otherwise indicated.
1. 26 mm diameter.
2. Hydrophobic membrane. Can be made hydrophilic by pre-wetting with IPA.
Syringe Filter Applications and Recommended Membranes
Application / Sample Recommended
Fitler
First Alternative Second Alternative
HPLC and GC Sample Prep RC PTFE PES
Aggressive or Pure Organic Solvents PTFE RC NY
Protein Analysis / Biological Samples PES RC GF/CA
High Particulate Loads RC NY PTFE
Environmental Methods RC PTFE NY
Food and Beverage RC PTFE NY
Clinical / Toxicology RC PES NY
For Sample Filtration Prior to GC Analysis
Less system downtime•
More consistent, reproducible results•
Increased column lifetime•
If Phenex™Syringe Filters do not perform
as well or better than your current syringe
filter product of similar membrane,
diameter and pore size, return the product
with comparative data within 45 days for
a FULL REFUND.
Appendix A
Try a Sample Pack!
visit: www.phenomenex.com/sample

www.phenomenex.com 8
GuideRight™Injection Hole Septa
The GuideRight™through-hole guides the needle during injection. Septum
performance and lifetime increase while downtime due to bent needles or dirty
injection ports decreases. Choose from either high temperature PhenoGreen™or
PhenoRed™, both rated to 400 °C.
Other Recommended GC Accessories
Gold Inlet Base Seals
Prevents analyte adsorption•
Improves detection sensitivity•
Improves method reproducibility•
Fits all Agilent 5890/6890 split/splitless injection ports•
Part No. Description Similar to Mfr. No.* Unit
Standard, single groove for splitless applications, 0.8 mm dia. inlet hole
AG0-7518 Gold Inlet Base Seal, splitless (single groove), 0.8 mm 18740-20885 2/pk
AG0-7519 Gold Inlet Base Seal, splitless (single groove), 0.8 mm 18740-20885 10/pk
High Split Flow, cross groove for split applications, 0.8 mm dia. inlet hole
AG0-7520 Gold Inlet Base Seal, split (double groove/cross), 0.8 mm 5182-9652 2/pk
AG0-7521 Gold Inlet Base Seal, split (double groove/cross), 0.8 mm 5182-9652 10/pk
Replacement Inlet Seal Washers
AG0-8397 Inlet Seal Washers, Gold Plated, for Agilent GC injection port — 12/pk
Long Graphite Ferrules
• High-purity graphite signicantly reduces ferrule bleed
• Special construction minimizes “aking”
• Stable to 450 °C - excellent for high temperature use
Part No. Description Unit
0.4 mm Ferrule ID
AG0-4698 Graphite Ferrule in. to 0.4 mm 10/pk
AG0-4699 Graphite Ferrule in. to 0.4 mm 50/pk
0.5 mm Ferrule ID
AG0-4701 Graphite Ferrule in. to 0.5 mm 10/pk
AG0-4702 Graphite Ferrule in. to 0.5 mm 50/pk
0.8 mm Ferrule ID
AG0-4704 Graphite Ferrule in. to 0.8 mm 10/pk
AG0-4705 Graphite Ferrule in. to 0.8 mm 50/pk
Part No. Description Unit
PhenoGreen in. (9.5 mm) Diameter
AG0-7874 PhenoGreen 400 Injector Septa 50/pk
PhenoGreen 7⁄16 in. (11 mm) Diameter
AG0-7875 PhenoGreen 400 Injector Septa 50/pk
PhenoRed in. (9.5 mm) Diameter
AG0-7916 PhenoRed 400 Injector Septa 50/pk
PhenoRed 7⁄16 in. (11 mm) Diameter
AG0-7917 PhenoRed 400 Injector Septa 50/pk
Appendix B

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9
Flat Bottom
20 mL
Round Bottom
20 mL
Headspace Vials
Compatible With The Following Autosamplers
Brand Model Round
Bottom
Flat
Bottom
Agilent HS 7694 •
Carlo-Erba HS 850 •
Dani HS 39.50 / 86.50 •
Fisons HS 850 •
PerkinElmer HS 100 / 101 / 40 •
Tekmar-Dohrmann 7000HT •
ThermoQuest HS 850, Trace GC
2000 + HS 2000
•
Varian Genesis • •
Headspace Autosampler Vials
Part No. Description 100/pk
AH0-7546 Headspace Vial 20 mL clear, round bottom,
23 x 75 mm
AH0-7547 Headspace Vial 20 mL clear, at bottom,
23 x 75 mm
AH0-7548 Aluminum Seal, with PTFE/Silicone septum,
0.130” thickness
AH0-7550 Aluminum Seal, with Pharma-Fix molded
pressure-release septum
AG0-8350 Aluminum Seal, Magnetic Crimp Cap, 20 mm
TEF/SIL, blue
Vials
Appendix C
Limited Volume Vials
Part No. Description 100/pk
AH0-7508 QsertVial Kit, Silicone/PTFE septa
AH0-7505 QsertVial Kit, Silicone/PTFE septa with pre-slit
QsertVial™
QsertVial kits, Clear wide-mouth vial, 12 x 32 mm, 300 µL volume, with write-on
patch.
CD™Vial
CD Vial kits, Clear wide-mouth vial, 12 x 32 mm, 1.5 mL volume
Part No. Description 100/pk
AH0-7509 CD Vial Kit, Silicone/PTFE septa
AH0-7506 CD Vial Kit, Silicone/PTFE septa with pre-slit
Kit packs include caps.

www.phenomenex.com 10
Trademarks
Zebron, Inferno, Cool-Lock, Phenex, Strata-X, Guardian, GuideRight, PhenoRed, PhenoGreen, and WAXPLUS are trademarks of Phe-
nomenex, Inc. Strata is a registered trademark of Phenomenex, Inc. Wite-Out is a registered trademark of BIC Corporation. Vespel
and Teon are registered trademarks of E.I. du Pont de Nemours and Co. CD Vial and Qsert Vial are trademarks of AR Corporation.
© 2009 Phenomenex, Inc. All rights reserved.
Disclaimer
Subject to Phenomenex terms and conditions, which may be viewed at
www.phenomenex.com/TermsAndConditions.
Strata®and Strata™-X SPE Products
SPE products can help to eliminate contaminants and matrix effects for increase
signal-to-noise ratios and longer column lifetimes. Phenomenex has two types
of SPE sorbents:
Product Offerings:
Strata - Silica Solid Phase Extraction (SPE) Products1.
Used for cleaning samples, concentrating analytes, and solvent-•
switching quickly and easily
Removes contaminants and eliminate matrix effects for improved•
separation and column lifetime
Selecting a SPE Sorbent: Please call your Phenomenex Sample Preparation Specialist for help in selecting the right SPE sorbent
for your analysis.
Standard Tubes for
Traditional SPE
Formats: Strata and Strata-X SPE products are available in multiple formats:
Teflon®-Coated Tubes for
Extra Inert Analysis
Large Volume/Flash
Analysis Cleanup
96-Well Plates for High-Throughput
Tab-less Tubes
20 x 2.0 mm
On-line Extraction Cartridges Large Volume
Strata-X-Polymeric Solid Phase Extraction (SPE) Sorbents.2.
(Same functions as Strata but with the additional benefits):
De-conditioning resistant surface resists dry out and de-activation and•
provides worry-free manual and automated processing
pH stability from 1-14 for flexible method development•
Ability to load up to 66 % more in comparison to silica-based sorbents•
per gram
Appendix D
If Strata and Strata-X SPE products do
not perform as well or better than your
current SPE product of similar phase,
mass and size, return the product with
comparative data within 45 days for a
FULL REFUND.

GU6177040 9_ L
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