Biotage Selekt User manual

Biotage®Selekt
User Manual

Biotage®Selekt User Manual | © Biotage 2020
Contents
Biotage®Selekt
User Manual
CONTENTS
System Overview
1 Columns
1 Racks and Vessels
2 Solvent Supply
2 Internal UV Detector
2 External Detector
2 Collection and Fractionation Methods
3 E-mail Functionality
3 Audible Alarm
3 Lighting
3 Biotage®Safety Valve
3 Spektra Software License (Optional)
Prepare the System
4 Mount Column Holders
4 Install Biotage®Safety Valve (Optional)
5 Mount a Biotage®SNAP XL Column (Optional)
6 Inspect the Tubing
6 Start Up the System
7 Setup of Automatic Conversion
Between Normal and Reversed Phase
7 Assign Solvents and Set Reservoir Volumes
7 Prime the Solvent Inlets
7 Flush the System
Set Up a Purification
8 Specify the Gradient
10 Specify the Information Parameters
10 Specify the Column Parameters
11 Specify the Collection Parameters
11 Specify the Rack Parameters
 Start, Monitor, and Control a Purification
13 Start a Purification
13 Monitor the Purification in Progress
14 Manual UV Zero
14 Start and End an Isocratic Segment
15 Add, Empty, and Replace Racks During the Run
16 Manually Fractionate
16 Line Flush, Decompression, and Detector Flush
16 Auto Extend
16 Pause, End, or Abort a Purification
16 Edit a Purification
17 Confirm Cleanup
 Unload a Purification
18 Flush the Column with Air
18 Purge the Column
18 Unload the Run
18 Flush the System
18 Shut Down the System
 Results
19 Search the Results
20 Analysis of the Result
21 Customize the Report
21 Add a Report Note
21 Export the Report
22 Base a New Run on a Previous Run
 Flushes and Purge
23 Flush
23 Flow Paths
24 Air Flush
24 Purge
 Data Administration
25 Administrate Column Types
25 Administrate Solvents
26 Administrate Racks
26 Administrate Results
26 Administrate User Accounts
 System Settings
27 System
27 Purification
28 Optional Detectors
28 Network
29 Licenses
 Maintenance
30 Back Up and Restore the System’s Database
30 Export System Logs
30 Calibrate the Internal UV Detector
31 Clean the Exterior of the System
31 Clean the Flow Cell of the Internal UV Detector
32 Clean or Release Check Valves
32 Leaks
34 Replace the Fuses
34 Replace the Needle
34 Sonicate Solvent Inlet Filters
 Troubleshooting
35 Fraction Collector-Related Problems
35 Gradient Problems
35 Internal UV Detector-Related Problems
36 Leak Detected
36 Overpressure Detected
36 Pump-Related Problems
37 QR Reader Problems
37 Contact Biotage®1-Point Support™
 Solvent Specifications
 General Information
39 Consumables and Accessories
39 Manufacturer
39 Contact Us
 Notes


System Overview
System Overview
Biotage®Selekt is an automated flash purification system with
a built-in QR reader for Biotage®Sfär columns, RFID reader for
Selekt collection racks, UV detector, pump, fraction collector,
and touch screen.
Optional accessories from Biotage that can be used with the
system are Biotage®Solvent Detector, an instrument tray,
a secondary solvent containment, and a safety valve. It is also
possible to connect an external detector with analog output
signal, and connect the system to a network to enable e-mail
functionality such as notifications and auto send of reports.
Columns
The system has two column channels. Columns can be placed
both on the right side of the system and on the front (up to 50g);
see Figure 1.
Figure 1.Biotage®Selekt with two columns.
QR Reader
All Biotage®Sfär columns have a QR code that can be read
by the QR reader underneath the touch screen; see Figure 2.
When scanning a column using the QR reader, the system will
be able to trace all runs performed on the system using that
specific column based on its ID.
Figure 2.Scanning a Biotage®Sfär column.
Racks and Vessels
The system collects fractions into a variety of collection racks
and vessels. The following Selekt racks are available:
» 48 positions for 13 x 100 mm tubes
with a vessel volume of 9 mL.
» 35 positions for 16 x 100 mm tubes
with a vessel volume of 14 mL.
» 35 positions for 16 x 150 mm tubes
with a vessel volume of 22 mL.
» 28 positions for 18 x 150 mm tubes
with a vessel volume of 27 mL.
» 15 positions for 25 x 150 mm tubes
with a vessel volume of 45 mL.
» 6 positions for 120 mL flasks.
» 10 positions for 240 mL flasks.
» 8 positions for 480 mL flasks.
The predefined vessel volumes can be lowered if desired.
The collection bed can either hold a collection tray with up to
three of the racks with vessel volumes up to 120 mL (Figure 3),
or one of the 240 or 480 mL flask racks.
One collection tray is standard, but by extending the fraction
collector, it is possible to use two collection trays at the same
time. The maximum collection volume with no rack change is
3840 mL for standard bed and 7680 mL for extended bed.
RFID Tags
All Selekt collection racks have an RFID (radio-frequency
identification) tag that is automatically identified by the system
when placed on the collection bed. The tag contains information
on the rack type and the run(s) that is/are currently in the rack,
if performed on the same system, or which system it was last
used on.
Figure 3.Collection tray with three racks.

Biotage®Selekt User Manual | © Biotage 2020
System Overview
Solvent Supply
The system is equipped with four solvent inlets found on the
right side of the system (S1-S4).
Secondary Solvent Containment with
Biotage®Solvent Detector*
A maximum of four 5-L reservoirs can be placed on the optional
secondary solvent containment; see Figure 4. Larger reservoirs
than 5 L must be placed elsewhere.
Note: To be compliant with the US secondary containment
regulations, do not use reservoirs larger than 4 L.
Figure 4.The optional secondary solvent containment.
Solvent and Waste Monitoring
The system can maintain a running calculation of the fluid levels
in the reservoirs based on information entered by the user.
With solvent and waste monitoring enabled, the system will:
» Inform the user when there is not enough
solvent or waste capacity for a run.
» Issue an on-screen notification when a solvent
level is below 20% of the set capacity.
» Issue an on-screen notification when the waste
level is above 85% of the set capacity.
» Pause the system when it is time to refill a
solvent reservoir (when 10% is left) or empty
the waste reservoir (when 95% full).
Instrument Tray with Biotage®Solvent Detector*
An optional instrument tray with a solvent detector is available
for safe unattended operation. When solvent is detected, the
system is paused and all pump functionality disabled until the
solvent detector is dry again.
Figure 5.The optional instrument tray with a solvent detector.
Internal UV Detector
The system includes either a 200 to 400 nm UV detector or
a 198 to 810 nm UV-VIS detector.
External Detector
It is possible to connect an external detector with analog
output signal. For more information, see the Biotage®Selekt
Installation and Safety document (P/N 416182).
Collection and Fractionation Methods
Available detection signals are:
» λ-All: The system uses average absorbance
within a user-defined wavelength range for
collection and fractionation. Only available on
systems with a Spektra software license.
» UV1 and UV2: The system uses one or two wavelength
signal(s) for collection and fractionation.
» EXT: The system uses the signal from an external
detector for collection and fractionation. Optional.
Possible collection and fractionation parameters are
Collect All, Threshold, and Valley Fractionation. The system
always fractionates on volume, which is when a test tube or
bottle reaches the specified vessel volume or a user-defined
maximum fraction volume for the run. At any time, you can
manually switch to a new collection vessel by pressing in
the chromatogram.
Any signal combination can be used for collection and
fractionation. Signals that are not used for collection can be
used for monitoring.
Figure 6.The Collection panel expanded on a system with a Spektra
software license and an external detector connected.
*It is only possible to connect one Biotage Solvent Detector to the system.


System Overview
E-mail Functionality
With the system connected to an e-mail server, it is possible for
the users to:
» Receive e-mail notifications when user interaction
is required for their runs, e.g. when a rack has to
be replaced, a solvent needs to be replenished,
a waste reservoir needs to be emptied, and a leak
is detected by Biotage®Solvent Detector.
» Automatically receive the report by e-mail when
their purification run has been completed.
» Send reports and logs from the system by e-mail.
Figure 7.E-mail notifications and auto send of reports are enabled and
disabled individually in each user account.
Audible Alarm
When the audible alarm is enabled in the system settings,
a warning will sound if an error has occurred.
Lighting
To provide better visibility and status information for the user,
there is a light strip underneath the touch screen and a mirror
behind the collection racks.
When the light strip is enabled in the system settings, the color
indicates the status of the system:
» White: System idle or processing.
» Orange: User interaction required for the run on channel 1.
» Blue: User interaction required for the run on channel 2.
» Green: Run completed.
» Red: System error. The system needs to be restarted.
Biotage®Safety Valve
The optional safety valve (P/N 417115SP) enables you to use
columns or combinations (e.g. column and dry load vessel)
with a combined column volume larger than 0.8 L and up to
a maximum of 3.1 L.
The safety valve is designed to open at 8 bar and discharge
fluid until the pressure drops below 8 bar.
Figure 8.The safety valve connected to a SNAP XL column mounted on
the system.
Spektra Software License (Optional)
The following features are included in the Spektra software
license that is sold separately:
» λ-All detection. The system uses average
absorbance within a user-defined wavelength
range for collection and fractionation.
» UV Baseline Correction. When the UV baseline
correction option is turned on, the gradient run is
preceded by a light absorbance detection phase.
During this phase, the light absorbance of the used
solvents (A, B, and modifier) is measured for the whole
detector range using either the initial gradient mix to the
end mix A/B or the initial gradient mix to 100% solvent B.
The measurement results in a baseline that is subtracted
from the detector signal during the gradient run.
» Absorbance spectrum. The absorbance spectrum for
the whole detector range is displayed during the run.
» Tool for spectrum analysis. The analysis view shows the
chromatogram and the absorbance spectrum for the whole
detector range for a selected point in the chromatogram.

Biotage®Selekt User Manual | © Biotage 2020
Prepare the System
Mount Column Holders
The system is shipped with column holders for Sfär columns
of different sizes. Ensure that they are mounted in the desired
positions on the system.
Figure 9 shows how to mount a column holder on the right side
of the system. There are also two positions for column holders
on the front of the system that can be used for Biotage columns
up to 50g; see Figure 10.
Figure 9.Slide the column holder screw into the desired position on
the right side of the system and then place the holder over the screw
and fasten.
Figure 10.Biotage columns up to 50g can be placed on the front of
the system.
Install Biotage®Safety Valve (Optional)
Warning
» Always use Biotage Safety Valve (P/N 417115SP) when
processing columns or combinations (e.g. column and dry
load vessel) with a total CV larger than 0.8 L.
» Never use columns or combinations with a total CV larger
than 3.1 L.
» Do not over-tighten the fittings or the tubing may become
damaged.
The optional safety valve (P/N 417115SP) enables you to use
columns or combinations (e.g. column and dry load vessel)
with a combined column volume larger than 0.8 L and up to
a maximum of 3.1 L.
The safety valve is designed to open at 8 bar and discharge
fluid until the pressure drops below 8 bar.
Prepare the System
Required tools:
» Torx T6 screwdriver.
» Open-end wrench, 14 mm.
» Open-end wrench, 17 mm.
To install the safety valve:
1. Fit the supplied drain tube to the outlet of the safety valve
(see A in Figure 11) using the two open-end wrenches.
2. Mount the safety valve to the right side of the system:
a. Slide the valve into one of the rails on the right side of
the system; see Figure 11.
b. When the safety valve is in the desired position,
tighten the fastening screw (see B in Figure 11) using
the Torx T6 screwdriver.
3. Connect the tubing leading from the C1 or C2 port on the right
side of the system (see Figure 15 on page 6), depending
on which channel you want to use, to the connection at the
bottom of the safety valve (see C in
Figure 11 ).
4. Connect the extra tube supplied with the safety valve to the
connection at the top of the valve (see D in Figure 11).
Note: This tube is to be connected to the Luer fitting at
the top of the column. For instructions on how to mount
a SNAP XL column onto the system, see “Mount a Biotage®
SNAP XL Column (Optional)” on page 5.
5. Insert the drain tube into the system’s waste reservoir.
Figure 11
DD
AA
CC
BB
.The safety valve. A: Drain tube. B: Screw for fastening the
valve to the system. C: Tube from the C1 or C2 port on the right side of
the system. D: Tube going to the top of the column.


Prepare the System
Mount a Biotage®SNAP XL
Column (Optional)
Warning
» Always use Biotage Safety Valve (P/N 417115SP) when
processing columns or combinations (e.g. column and dry
load vessel) with a total CV larger than 0.8 L.
» Never use columns or combinations with a total CV larger
than 3.1 L.
» Do not over-tighten the fittings or the tubing may become
damaged.
Note: When using SNAP XL columns, it is not possible to have
the optional secondary solvent containment placed on top of
the system.
Mount the Biotage®SNAP XL Column Holder
The Biotage®SNAP XL column holder must be ordered
separately (P/N 412422).
1. Slide one screw (see A in Figure 12) into one of the two
lower rails on the right side of the system.
2. Slide the column holder into position with the fastening
bracket (see B in Figure 12) in the same rail as the screw.
3. Slide the other screw into the same rail.
4. Lock the column holder in the desired position using the
two screws; see the column holder to the right in Figure 12.
Note: The top screw is used for adjusting the column holder to
the length of the used column.
Figure 12
CC
AA
BB
DD
.SNAP XL column holder. A: Holder screws. B: Fastening
bracket. C: Bottom column loop. D: Top column loop.
Mount the Biotage®SNAP XL Column
Two SNAP XL fittings with Luer connections are required and
must be ordered separately; see Figure 14 on page 6.
1. Remove the stoppers from the top and bottom of the column.
2. Place the column in the bottom loop on the column holder
(see C in Figure 12) and then unfasten and lower the top loop
(see D in Figure 12) until it is in contact with the column (see
Figure 13). Tighten the screw.
Figure 13.The top screw is used for adjusting the column holder to the
length of the used column.
3. Fasten the SNAP XL fittings to the top and bottom of the
column; see Figure 14 on page 6.
4. Connect the tubing leading from the C1 or C2 port on the right
side of the system (see Figure 15 on page 6), depending
on which channel you want to use, to the connection at the
bottom of the safety valve (see C in Figure 11).
5. Connect the tube leading from the connection at the top of
the safety valve (see D in Figure 11) to the Luer fitting at the
top of the column.
6. Connect the tubing leading to the R1 or R2 port on the right
side of the system (see Figure 15 on page 6), depending
on which channel you want to use, to the Luer fitting at the
bottom of the column.
7. Insert the drain tube (see A in Figure 11) into the waste
reservoir.

Biotage®Selekt User Manual | © Biotage 2020
Prepare the System
Figure 14
P/N 412358
P/N 412537
.SNAP XL column with SNAP XL fittings with Luer connections.
Figure 15.The C1, C2, R1, and R2 ports on the right side of the system.
Inspect the Tubing
Warning
» Shut down the system before replacing any tubing. Use only
tubing designed for the Selekt system and supplied by Biotage.
Inspect all tubes before each run to ensure that they do not
show signs of wear or damage and that they are properly
connected and tightened. Use caution when finger tightening
fittings to prevent stripped threads or crushed ferrules.
All external tubing on the system except for the tubing on the
collection arm can be replaced by the user.
Note: All tube types, dimensions, and lengths are essential
for the performance of the system. Only replace tubes with the
equivalent tubes designed for the Selekt system and supplied
by Biotage.
Start Up the System
Turn on the system using the power switch located on the left
side of the system; see Figure 16.
Figure 16.The power switch is located on the left side of the system.


Prepare the System
Setup of Automatic Conversion Between
Normal and Reversed Phase
Selekt automatically converts system solvents from normal to
reversed phase when the following criteria are met:
» Previous run was performed on the other channel.
» Previous run was performed using a column intended
for the other chemistry type (reversed/normal
phase) than the one used for the current run.
» None of the runs use more than two solvents,
i.e. no modifier, solvent C, or solvent D.
» The strong solvent of the previous run
is still connected to the system.
Automatic conversion is performed between the runs as
follows:
1. The system pumps 100% of the strong solvent of
the previous run via bypass.
2. The system pumps 100% of the strong solvent of
the current run via bypass.
Assign Solvents and Set Reservoir Volumes
When a purification is run, the software determines which
solvent inlets are connected to the solvents used in the run.
Note: For reversed-phase purification with methanol and
water, it is strongly recommended to premix the water with
5% of methanol and degass either through vacuum or
sonication. Degassing of protic solvent blends decreases
out-gassing of entrapped air during gradient elution, which
will impact gradient performance and flow rates.
Note: With solvent and waste monitoring enabled (see
page 27), the capacity and current fluid level must be entered
each time you empty a waste reservoir or refill a solvent.
Note: All four solvent inlets must be primed with solvent to
achieve the specified pump performance.
1. In the software, press Menu and then Solvent Setup.
2. Assign a solvent to each solvent inlet using the solvent
drop-down lists (see Figure 17).
To add solvents to the list, press Solvent Administration.
For more information, see page 25.
3. If solvent monitoring is enabled, enter the capacity and
the current solvent level of each solvent reservoir.
4. If waste monitoring is enabled, enter the capacity and
the current waste level of the waste reservoir.
5. Prime the solvent inlets that have been assigned a new
solvent; see below.
Figure 17.The Solvent Setup window with solvent and waste monitoring
enabled.
Prime the Solvent Inlets
Before you start a purification on your system, you might need
to prime the solvent inlets to:
» Remove any air bubbles from the pump and the
solvent inlets by flushing them with solvents.
» Empty the solvent inlets of solvents used in the previous
purification and fill them with new solvents.
Note: All four solvent inlets must be primed with solvent to
achieve the specified pump performance.
Note: We recommend to have all solvent reservoirs on the same
physical height to improve accuracy in the solvent mixing.
1. In the software, press Menu and then Solvent Setup.
2. Prime the solvent inlets by pressing the corresponding
Prime buttons (see Figure 17). Note that 27 mL of the
assigned solvent is used for each prime.
Flush the System
If the automatic line flush is disabled on your system (see
page 27), ensure to flush the column flow path before each
run (see page 18).

Biotage®Selekt User Manual | © Biotage 2020
Set Up a Purification
Warning
» Never exceed the maximum pressure or flow rate for the
used column.
» Always use Biotage Safety Valve (P/N 417115SP) when
processing columns or combinations (e.g. column and dry
load vessel) with a total CV larger than 0.8 L.
» Never use columns or combinations with a total CV larger
than 3.1 L.
» Never use the system without a column mounted or the column
inlet and outlet tubing coupled together, on both channels.
Note: For instructions on how to mount a SNAP XL column onto
the system, see page 5.
1. In the software, select the column channel to be used by
pressing Channel 1 or Channel 2 in the lower right corner,
or by swiping left or right on the channel tab along the edge.
2. To base the purification on a previous run, press Runs and
then see “Base a New Run on a Previous Run” on page 22.
3. Either scan your column using the QR reader underneath
the touch screen (see Figure 18) or select the column type
from the Type drop-down list in the Column panel (see
Figure 19).
Note: If using a column or a combination of a column and
e.g. dry load vessel with a total CV larger than 0.8 L, a safety
valve supplied by Biotage (P/N 417115SP) must be used.
For more information, see page 4.
Figure 18.The QR reader is located underneath the touch screen.
4. Place the column in a column holder on the right side of the
system or on the front (up to 50g).
5. Connect the correct inlet and outlet tubing to the column.
The tubes for channel 1 are labeled C1 with orange tags and
the tubes for channel 2 are labeled C2 with blue tags.
6. Ensure that the inlet and outlet tubing on the other (unused)
channel are coupled together.
7. Place the collection rack(s) that you want to use on the
collection bed. Racks with vessel volumes up to 120 mL
require the collection tray. Selekt racks are automatically
identified by the system when placed on the collection bed.
If automatic rack detection has been disabled (see page 27),
select the collection rack manually (see “Specify the Rack
Parameters” on page 11).
8. Set up the run parameters as described in the following
sections.
Note: If the button is available in the bottom right corner, one
or more run parameters are either missing or incorrect. Press
for more information.
Figure 19.The run setup view.
Specify the Gradient
The gradient can be set up using the gradient graph or the
gradient table. It is also possible to calculate a gradient from
Rfvalues obtained from TLC analysis (see page 9).
Gradient Graph and Table
Expand the gradient graph by pressing and the gradient table
by pressing .
Change the length unit by selecting CV, mm:ss, or mL from the
unit drop-down menu in the gradient table or the expanded
gradient graph.
Set Up a Purification


Set Up a Purification
To add a gradient segment, press the +button in the gradient
table or the expanded gradient graph. The new segment will be
added after the selected segment or node or at the end of the
gradient if nothing is selected.
To delete a node or segment, select it and press the –button in
the gradient table or the expanded gradient graph.
To increase or decrease the length of a gradient segment or
change the solvent mix, either 1) drag the segment or node to
the desired position in the gradient graph, or 2) change the
value in the gradient table.
Note that it is possible to zoom in and out of the gradient using
the pinch-to-zoom feature. To reset the zoom, press .
Gradient Parameters
» Unit or CV/mL/mm:ss: The gradient length unit. CV (column
volumes), milliliters, or minutes and seconds; see Figure 20.
» Start: The percentage of the strong solvent at
the beginning of the gradient segment.
» End: The percentage of the strong solvent
at the end of the gradient segment.
» A-D: The solvents to be used.
» M/Modifier: If you want to use a fixed percentage of
modifier during the purification, select the solvent
to be used and its percentage in the solvent mix.
» Equil./Equilibration: The column is equilibrated before the
run, unless this options is turned off. The equilibration
volume and flow rate are set automatically based on the
selected column type. To see the settings, expand the
Column panel (see Figure 24 on page 10). We strongly
recommend that the equilibration is not turned off.
Figure 20.The gradient length unit can be selected in the gradient table
(as shown above) and in the expanded gradient graph (see Figure 21).
Figure 21.The expanded gradient graph. Gradient markers along the top
and right show the length and solvent percentage for the segments.
Calculate a Gradient from TLC Data
Note the following when using the TLC to Gradient editor:
» Accuracy of prediction can be reduced if using
alcohols, such as methanol and ethanol, very volatile
modifiers such as diethyl ether, or modifiers that
permanently alter the properties of the silica.
» Reversed-phase TLC is not supported.
» Slight variations in migration rates may occur if samples are
applied too close to the edge of the TLC plate. Apply samples
at least 10 mm from the edge to avoid the edge effect.
To calculate a purification gradient from the Rfvalues obtained
from TLC analysis:
1. Open the TLC to Gradient editor (see Figure 22 on
page 10) by pressing TLC.
2. Select the Strong Solvent text box and enter the percentage
of the strongest (most polar) solvent in the TLC analysis.
3. Mark the solvent front of the TLC plate by sliding the Front
line to the correct position.
4. Enter the Rfvalue of the product of interest in the RfProduct
text box or by sliding the Product line to the correct position
on the TLC plate.
5. Enter the Rfvalue of the impurity closest below and above
the product in the RfImpurity 1 and RfImpurity 2 text boxes
or by sliding the corresponding lines to the correct positions
on the TLC plate. A value for RfImpurity 1 is required.

 Biotage®Selekt User Manual | © Biotage 2020
Set Up a Purification
6. If you have two plates, press Add Plate and repeat steps
2 through 5 for the second plate. One plate gives a linear
gradient and two plates give a step gradient.
7. To calculate a purification gradient, press Create.
Figure 22.The TLC to Gradient editor.
Specify the Information Parameters
» User: The name of the user. If you have not been assigned
a user name, please contact your system supervisor.
» Run Name: The name of the run. If left blank, the
name will be auto-generated based on date and
time when the purification is performed.
» Comments: Comments on the purification run. (Optional.)
Figure 23.The Information panel expanded.
Specify the Column Parameters
» Sample Mass: The crude sample mass.
» Type: The column type. Either scan the column using
the QR reader underneath the touch screen or select
a column type from the drop-down list. If a column is
scanned, the icon is shown in the Column panel.
If the column name is orange or red, its load capacity
is smaller than the entered sample mass.
Note: If using a column or a combination of a column and
e.g. dry load vessel with a total CV larger than 0.8 L, a safety
valve supplied by Biotage (P/N 417115SP) must be used.
For more information, see page 4.
» Flow Rate: The default (recommended) flow rate
for the selected column type is preselected.
If you want to change it, consider that the maximum
flow rate applied depends on the following:
» The maximum pressure or flow rate setting for the
column and any other accessories used in the setup.
» The maximum aspiration rate(s)
defined for the used solvent(s).
Note: If you expand the Column panel, all of the settings
for the selected column type are displayed (see Figure 24).
If the column has been scanned, the column’s ID and the
number of times it has been used is also displayed. For more
information, see “Administrate Column Types” on page 25.
Figure 24.The Column panel expanded.


Set Up a Purification
Specify the Collection Parameters
» λ-All*:Select whether the average absorbance within
a user-defined wavelength range should be used for
collection and fractionation (Collect), used for monitoring
(Show), or not be shown during the run (Hide).
» UV1 and UV2: Select whether the wavelength signals should
be used for collection and fractionation (Collect), used for
monitoring (Show), or not be shown during the run (Hide).
» EXT: Select whether a signal from an external
detector (optional) should be used for collection
and fractionation (Collect), used for monitoring
(Show), or not be shown during the run (Hide).
» Wavelengths*:The shortest and longest wavelength to be
included in the λ-All signal. The range is 200 to 400 nm
(UV detector) or 198 to 810 nm (UV-VIS detector).
» Wavelength: The wavelength to be used for UV1
and UV2. The range is 200 to 400 nm (UV detector)
or 198 to 810 nm (UV-VIS detector).
» Threshold: Used to collect samples when the
signal level exceeds the set threshold.
» Collect All: Used to collect the entire run.
» UV Baseline Correction*: When this option is turned on,
the gradient run is preceded by a light absorbance
detection phase. During this phase, the light absorbance
of the used solvents (A, B, and modifier) is measured for
the whole detector range using either the initial gradient
mix to the end mix A/B or the initial gradient mix to
100% solvent B (see “System Settings” on page 27).
The measurement results in a baseline containing the
maximum absorbance of the solvents. During the gradient
run, the baseline is subtracted from the detector signal
affecting UV1, UV2, λ-All, and the absorbance spectrum.
*Only available on systems with a Spektra software license.
Figure 25.The Collection panel expanded on a system with a Spektra
software license and an external detector connected.
Specify the Rack Parameters
Load Racks
The Selekt racks have RFID tags that are automatically identified
by the system when placed on the collection bed. RFID racks
have the icon in the expanded Rack panel (see Figure 26).
If the RFID reader is disabled in the system settings (see
page 27), it is possible to select the collection rack type
manually by expanding the Rack panel (see Figure 26).
Figure 26.The Rack panel expanded on a system with extended
collection bed and rack sharing enabled in the system settings (Start
Collection is set to First Empty Vessel). Rack A was used in the previous
run but still has empty vessels that can be used by the next run. Rack C
is disabled and will not be used for collection. Note that it is also possible
to select the rack type from the drop-down list, if e.g. the RFID reader is
disabled in the system settings.
Assign Racks to the Run
To assign or remove a rack from the run, expand the Rack panel
(see Figure 26) and set/clear the check box in front of the rack.
The following racks will automatically be assigned to your run:
» A rack that you place on the collection bed.
» A rack that was assigned to but not used by the previous run.
» The last rack used in the previous run, if it still has
one or more empty vessels or rows that are allowed
to be used in the next run according to the system
settings (see “Rack Sharing” on page 12 ).
Note: If you do not want to share the last rack used in the
previous run, either remove it from the system or clear the check
box in front of the rack.

 Biotage®Selekt User Manual | © Biotage 2020
Set Up a Purification
Rack Sharing
The system offers the possibility to have the first fraction(s) of
a run collected in the last rack used by the previous run if the
following applies:
» The Start Collection parameter in the system settings
is set to First Empty Row or First Empty Vessel.
» The last rack used in the previous run:
» Contains at least one row of empty vessels
or one empty vessel, depending on the Start
Collection setting (see previous bullet).
» Has not already been shared by five runs.
» Is enabled in the Rack panel when the run is started.
Figure 27.There are two Start Collection options in the system settings
that allow two consecutive runs to share a rack, First Empty Row and First
Empty Vessel. The first collection vessel to be used is highlighted with
a thicker border.
Collection Order
The system uses the assigned racks in alphabetical order in
regard to their positions on the tray. The dispensing order is
left to right starting with the front vessel row. The first vessel
that will be used for the run is highlighted with a thicker border;
see Figure 27.
Note: If the run is sharing a rack with the previous run,
collection will start in the shared rack independent of the
positions of other racks assigned to the run. For more
information see “Rack Sharing” above.
Max Fraction Volume
If you want to use a lower fraction volume than the one defined
for the selected rack(s), expand the Rack panel, enable the
Max Fraction Volume option (see Figure 26 on page 11), and
enter the desired volume. Note that this setting will only be
applied on racks with a higher vessel volume.


Start, Monitor, and Control a Purification
Start, Monitor, and Control a Purification
Warning
» Read and follow the safety precautions against static electricity
in the Biotage®Selekt Installation and Safety document
(P/N 416182) that is supplied with the system.
» Always ensure that the settings for the column selected in the
software are correct for the column to be used before starting
a run. Never exceed the maximum pressure or flow rate for the
used column.
» Never use the system without a column mounted or the column
inlet and outlet tubing coupled together, on both channels.
» Keep hands away from the collection arm area until the arm has
returned to its home position (in the inner right corner) and the
system is paused or in standby.
» The system may be pressurized when paused.
» Monitor the waste reservoir to prevent overflow during operation.
Start a Purification
1. Ensure that a sufficient quantity of the correct solvent
is present in each solvent reservoir and that the waste
reservoir has sufficient capacity for the run. To view the
estimated solvent consumption for the run, press Solvents
and Waste.
2. Start the purification by pressing . If the button is
disabled, press in the bottom right corner for more
information.
If solvent and waste monitoring is enabled, you will be
notified if there is not enough solvent or waste capacity
for the run when you press .
3. When the Sample Load dialog opens, load your sample.
4. Start the gradient run by pressing the appropriate button in
the Sample Load dialog. We recommend that a gradient run
is not started until the UV lamp is sufficiently warmed up.
Figure 28.The default run view with the Spektra software license
installed.
Monitor the Purification in Progress
While a purification is running, a dynamic chromatogram and
the programmed gradient are displayed in the run view (see
Figure 28). The gradient mix in the graph and the table are
presented without any modifier. If a Spektra software license
has been installed on your system, an absorbance spectrum for
the whole detector range is also displayed.
You can expand the chromatogram by pressing (full width) or
(full size), the spectrum (if available) by pressing and the
gradient table by pressing . Change the length unit by selecting
CV, mm:ss, or mL from the drop-down menu in the gradient
table (see Figure 28) or in the fully expanded chromatogram
(see Figure 29).
Figure 29.The chromatogram can be expanded to full width or full size.
Fractions
Fractions that are already collected can be located by matching
their colors and numbers in the chromatogram with the vessel
colors and numbers in the Rack panel (see Figure 28). Fractions
from the same peak have the same color. Fractions only
collected due to the Collect All option are colored gray.

 Biotage®Selekt User Manual | © Biotage 2020
Start, Monitor, and Control a Purification
Chromatogram
The signals and the thresholds are displayed in the
chromatogram using the following colors:
= Light absorption measured by the internal detector for
the whole λ-All range and the threshold in mAU. (Requires a
Spektra software license.)
= Light absorption measured by the internal detector
at wavelength UV1 and the threshold in mAU.
= Light absorption measured by the internal detector
at wavelength UV2 and the threshold in mAU.
= Signal from the external detector (when connected)
and the threshold in mV.
The defined wavelengths and real-time measurements of the
absorption are displayed in the Collection panel.
Zoom in on the Chromatogram
It is always possible to zoom in and out of the gradient and
chromatogram using the pinch-to-zoom feature (see Figure 30).
It is possible to zoom in one direction (X or Y) or both directions
(X and Y). To reset the zoom, press .
Figure 30.Zoomed-in chromatogram.
Current Solvent Mix
The percentage of pumped solvents (excluding the modifier,
if used) are displayed underneath the chromatogram during
the whole run (see Figure 28 and Figure 29 on page 13).
Status in the Top Pane
» Conversion: When reversed phase is run on one
channel and normal phase on the other, a solvent
flush is performed between runs that are using
different channels. Note that conversions are not
performed when one of the runs uses more than two
solvents. For more information; see page 7.
» Equilibration Flush: The system empties the
solvent inlets of solvents used in the previous
purification and fills them with new solvents.
» Equilibration: The system is running a column equilibration.
» Purge: The system releases the column pressure.
» Sample Load: Sample can be loaded onto the column.
» UV Warm-Up: The UV lamp is being warmed up.
» UV Zero: The system is setting the UV zero level using
the solvent mix used at the start of the gradient.
» Baseline Detection: The system is measuring the light
absorbance of the used solvents (A, B, and modifier)
for the whole detector range. During the gradient
run, the baseline is subtracted from the signal.
» Baseline Flush: After baseline detection,
the system is flushed with the solvent mix
used at the start of the gradient.
» Gradient: The system is running a purification.
» Line Flush, Purge, and Detector Flush: At the end
of a run, i.e. after the gradient purification stage is
completed or ended by the user, the system performs
the flushes that are enabled in the system settings
(see page 27) and a system decompression (purge).
» Finished: The purification run was completed
or ended/aborted by the user.
» Failed: The purification run failed.
Manual UV Zero
During the gradient run, it is possible to manually set the
current UV absorbance level to zero AU by pressing in the
chromatogram (see Figure 30). This feature can be enabled/
disabled in the system settings; see page 27.
Note: The button is only enabled when UV Baseline
Correction is turned off in the run setup.
Start and End an Isocratic Segment
At any time during the gradient run, you can start an isocratic
segment by enabling the Hold option in the chromatogram
(see Figure 30). End the segment by disabling the option.


Start, Monitor, and Control a Purification
Add, Empty, and Replace
Racks During the Run
Note: To add/remove racks during a run, the run must
be paused.
If more fractions are to be collected than can fit in the available
rack(s), the system automatically pauses, the collection arm
returns to the home position (the inner right corner), and you
are prompted to load and/or assign more racks to the run.
To assign a rack to the run, expand the Rack panel and set the
check box in front of the rack.
Note: Rack sharing with another run is only possible at the
start of a run; see “Rack Sharing” on page 12.
Empty a Rack
When a Selekt rack that has been used in previous run(s)
is removed from the system and then reinserted, it is
automatically cleared and enabled for the run in progress.
When a Selekt rack that has been used for the run in progress is
removed from the system and then reinserted, it is not cleared
automatically. To clear the rack, press Empty in the Rack panel.
Note: If the RFID reader is disabled in the system settings, all
racks have to be manually cleared in the Rack panel.
Rack has been used by the run
in progress.
Rack has been removed.
Rack has been reinserted. If all vessels
are empty, press Empty.
Rack was used in a previous run or runs.
When removed and then reinserted, it is
automatically emptied in the software.
Table 1.Unload and empty a rack when the RFID reader is enabled,
system paused.
Rack B has been used by the run in
progress and Rack A was used in a
previous run or runs.
When replacing all vessels with empty
ones, press Empty.
When replacing the rack with another
type of rack, select the correct type from
the Select Rack drop-down list.
When removing the rack and leaving the
rack position empty, select None from
the Select Rack drop-down list.
Table 2.Unload and empty a rack when the RFID reader is disabled,
system paused.
Rack has been removed.
Rack reinserted before the run is
resumed. Collection will be resumed
in the vessel with thicker border. If all
vessels are empty, press Empty.
Rack reinserted after the run was
resumed. Empty vessels cannot be used.
If all vessels are empty, press Empty.
The rack can then be reused.
Table 3.Unload the rack in use when the RFID reader is enabled, system
paused.
Resume the Run
Before you resume the run, ensure that the setup in the Rack
panel corresponds to what is loaded onto the collection bed.
The system uses the assigned racks in alphabetical order in
regard to their positions on the tray. Collection will be resumed
in the vessel that is highlighted with a thicker border in the Rack
panel; see Figure 31.
Figure 31.The Rack panel. Rack A is used in the current run but has been
removed, and rack B is assigned to the run but has not yet been used.
If the run is resumed without rack A being in position, the collection will be
resumed in rack B.

 Biotage®Selekt User Manual | © Biotage 2020
Start, Monitor, and Control a Purification
Manually Fractionate
At any time during the gradient run, you can switch to a new
collection vessel by pressing in the chromatogram.
Line Flush, Decompression,
and Detector Flush
At the end of a run, i.e. after the gradient purification stage
is completed, the system performs a line flush (if enabled),
system decompression (purge), and a detector flush (if
enabled). To enable or disable flushes and specify whether
enabled flushes are collected or not, see page 27.
Auto Extend
If the collection criteria are still met (any signal is above
threshold level) when the system reaches the end of a
purification, the system extends the gradient purification
stage of the run with 25% of the total gradient length using
the final conditions of the run.
Pause, End, or Abort a Purification
Note: Pausing a purification may cause gradient inconsistency
due to heat, solvent and sample diffusion, etc.
Pause and Resume a Purification Run
1. To pause the purification in progress, press .
The collection arm returns to its home position (in the
inner right corner) and the system is paused.
2. To resume the run from the point at which it was paused,
press .
End the Equilibration Step or
End or Abort the Purification Run
1. Press . The collection arm returns to its home position
(in the inner right corner) and the system is paused.
2. Press .
3. When the System Paused dialog opens, select one of the
available options:
» Skip Equilibration: End the equilibration
step and move on to the gradient.
» Abort: End the purification run without
performing any flushes.
» Cleanup: End the purification run and perform the
flushes that are enabled in the system settings
and a system decompression (purge).
Edit a Purification
Edit on the Fly
The following run parameters can be changed without pausing
the purification run:
» The run comment in the Information panel.
» The flow rate in the Column panel.
» All collection parameters in the Collection panel
except for the UV baseline correction; see “Specify
the Collection Parameters” on page 11.
» The gradient except for adding new solvent combinations.
» The modifier percentage.
All changes except for changes to the gradient are instant.
When editing the gradient, the modified gradient is purple and
the ongoing gradient is black (see Figure 32). The modified/
purple gradient is applied when you press .
Figure 32.When editing the gradient while the system is processing,
the modified gradient is purple and the ongoing gradient is black.
The modified/purple gradient is applied when you press .
Pause to Edit a Purification in Progress
With the system paused, it is not only possible to change all the
run parameters that can be changed without pausing (see “Edit
on the Fly” above), but it is also possible to add new solvent
combinations to the gradient and change the Max Fraction
Volume setting in the Rack panel.
1. Press . The collection arm returns to its home position
(in the inner right corner) and the system is paused.
2. Edit the run settings; see “Set Up a Purification” on
page 8. To undo all changes, press .
Note: To add a solvent combination to the gradient,
expand the chromatogram to full size by pressing .
3. To apply the changes and resume the run, press .


Start, Monitor, and Control a Purification
Confirm Cleanup
If the Confirm Cleanup option is enabled on the system, the
Gradient Run Completed dialog appears before cleanup is
performed, giving the user the option to manually extend the
run (see Figure 33). To extend, press Extend Run, edit the run
settings, and then resume the run. By default the gradient is
extended with 25% of the total gradient length using the final
conditions of the run.
Figure 33.If the Confirm Cleanup option is enabled on the system,
the Gradient Run Completed dialog appears before cleanup is performed,
giving the user the possibility to extend the run.

 Biotage®Selekt User Manual | © Biotage 2020
Unload a Purification
Warning
» Never flush or purge the system without a column mounted
or the column inlet and outlet tubing coupled together, on
both channels.
Flush the Column with Air
Empty the column of remaining solvents using the air flush
feature; see page 24.
Purge the Column
Any remaining pressure after a purification can be released
using the purge feature; see page 24.
Unload the Run
When the purification is finished, unload the column and
rack(s). To avoid leakage, plug the column inlet and outlet
fittings and couple the column inlet and outlet tubes together
(see Figure 34).
Remove Racks in the Software
When the RFID reader is not enabled in the system settings
(see page 27), racks that are unloaded have to be removed
manually in the software by selecting None in the
corresponding Select Rack drop-down list.
Figure 34.When a run is finished, couple the column inlet and outlet
tubes together.
Unload a Purification
Flush the System
If the last purification of the day is performed with a halogenated
solvent (e.g. DCM), we recommend that you assign methanol or a
similar solvent to the inlet line used with the halogenated solvent
(see page 7) and flush with at least 30 mL (see page 23).
Shut Down the System
Warning
» Failure to perform an orderly system shutdown may result in
user data corruption and/or remaining pressure.
An orderly system shutdown helps prevent data corruption.
For critical applications, the use of a suitable Uninterruptable
Power Supply (UPS) may help avoid data loss during a power
outage.
1. When the system is not processing, press Menu, Shut Down,
and then Yes to confirm.
2. When the message saying it is safe to turn off the system
appears on the touch screen, turn off the system. The power
switch is located on the left side of the system; see Figure 35.
3. If desired, unplug the power cord from the power outlet.
Figure 35.The power switch is located on the left side of the system.