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Automated labeling and multisample processing
MACSQuant® Analyzer quick guide
Configuring a rack
Multisample processing on the MACSQuant® Analyzer is
accomplished with the MACS® MiniSampler combined
with the MACS Reagent Rack 4 and MACS Cooling Tube
Racks. The most common racks used for multisampling
are Chill 5 and Chill 96 allowing for processing of up to
96 samples in a single batch. Several different types of
cell samples or analysis panels can be configured on the
same rack. Samples can also be automatically labeled
with fluorochrome-conjugated antibodies, cocktails, or
fluorescent dyes prior to measurement.
This quick guide walks you through the steps to select
positions in a Chill Rack and upload reagents in the reagent
To select a sample rack
1.Click on the ‘Experiment‘ tab.
Overview of the Cooling Tube Racks
Chill 5
Chill 96 rack/
96 rack
24×5 mL
96-well microtiter
Option on
Rack drop-down
rack graphic
Table 1: Common Cooling Tube Racks used for multisample processing
on the MACSQuant Analyzer
2.Select the required rack type from the ‘Rack‘ dropdown
3.The corresponding rack is now displayed in bottom left
corner. A layer version of rack will also be displayed in
middle of screen. If not, one can be opened by clicking
the icon.
To select rack positions
1.Use the left mouse button to activate the desired well
(alternatively, use the touchscreen).
2.Wells can be selected (
reclicking the well.
) and deselected (
3.Only wells in selected state (
using the ‘Experiment‘ tab.
) by
) can be programmed
4.Multiple wells (column, row, rack) can be selected by
using the right mouse button while clicking on:
a. Upper left circle for entire rack.
b. Column number for entire column.
c. Row letter for entire row.
5.Refer to table 2 for overview of rack configuration and
to section 6.7.2 in the user manual for more information.
6.Use the ‘Experiment‘ tab to change parameters of the
experiment (flow rate, uptake volumes, etc.) and
‘Custom‘ (instrument settings, analysis templates) or
‘Express‘ (MC cocktail analysis templates) settings.
7.Refer to the MACSQuant Analyzer quick guide:
Setting up an experiment for data acquisition in
custom mode or the user manual for more details.
User action with
left mouse button
or fingertip action
on touch-screen
Configuring autolabeling parameters for rack positions
1.With the designated rack open (refer above to: To select
a sample rack), select wells for autolabeling.
Default open circle indicates no
operation: Clear.
Single click on
Closed green circle with orange
rim: Sample selected for
measurement. Orange circle
indicates that the sample is
activated and any alterations
made to the measurement
strategy (e.g. labeling) will only
apply to sample positions with
this designation.
2.With the well(s) in ‘selected‘ mode ( ), click the
reagent(s) required for autolabeling that sample
(refer to figure 1) from the ‘Autolabel‘ tab.
3.Repeat for other samples if samples require different
reagents for autolabeling.
4.If using MC Cocktails for autolabeling, a predefined
analysis template can also be assigned to the wells
using ‘Express‘ mode under the ‘Settings‘ tab.
Double click on
Closed green circle:
Sample selected for
Closed blue circle:
Measurement in progress.
Before starting the run, check that:
1.The experiment definitions are correctly assigned to
each well and samples are placed accordingly.
Closed gray circle:
Measurement finished.
2.Sufficient quantities of reagents and buffers are
provided, and that the waste bottle is empty.
Closed yellow circle:
Processing of sample has
commenced, e.g., sample has
been labeled and incubation is
Table 2: Summary of rack configurations
Defining automated labeling
3.The reagents have been assigned in the reagent
manager and placed without cap on reagent rack.
4.The instrument is correctly calibrated and compensated
for the samples.
Note: Use the ‘Experiment Table‘ under the ‘View‘
menu to quickly confirm the experimental set up.
Setting up the reagent manager
1.Open the reagent manager by selecting ‘Reagents‘
under the ‘Edit‘ menu or by clicking ‘add‘ in the ‘Autolabel‘ tab.
2. Select reagent rack position (R1, R2, etc.).
3.Select the reagent from the category and reagent
dropdown lists.
Alternatively, scan the reagent using the barcode reader.
Note: Propidum iodide (PI) is listed under ‘Universal‘.
4.Samples can be automatically diluted prior to
measurement by selecting a buffer dilution from S1 or S2.
5.Define time, titer, and order for incubation.
Note: MACS MC Cocktails and fluorochromeconjugated antibodies have predefined time and titer.
6.Order is used if more than one reagent might be added
to the same sample, but requires different incubation
times (e.g. antibody and PI).
7.Once all reagents are uploaded (a total of four reagents
+ buffer A or B), click ‘Apply‘.
Figure 1: MC CD14 Cocktail is selected for autolabeling.
The corresponding annotations have been uploaded.
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8.In the ‘Autolabel‘ tab, see the uploaded reagents
available to apply to the rack positions (figure 1).
Note: The annotations are automatically adjusted
according to the MACS Reagents that have been
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