Graphic of varying sizes of red spherical beads

What are compensation beads?

Compensation beads capture species-specific antibodies conjugated to fluorophores and other types of reagents. The purpose of these beads is to set voltages and gating parameters for obtaining accurate fluorescence signal.

Overview of flow cytometry compensation beads

Flow cytometry multicolor experiments may need compensation when there is fluorescence spillover (Figure 1). Pairing fluorochromes based on antigen density, fluorochrome brightness, and separating by channels helps minimize the effects from spillover and may remove the need for compensation from smaller experiments. However, as the number of parameters and colors increase, so does the complexity of removing overlapping signal. Calculating compensation requires controls including unstained, fluorescence minus one (FMOs), and single-color samples. Learn more about basics of panel design and flow cytometry controls.

Beads are recommended when:

  • Multiple fluorophore emissions overlap in the same detector (Figure 1)
  • Poorly expressed markers do not express a large distinction between positive and negative populations
  • Limited amount of sample is available to setup/run controls and collect enough events for meaningful data
  • Creating large multicolor immunophenotyping panels to set accurate single-color compensation
  • When performing multiple plates or large experiments, bead controls will help with standardization and save sample

Figure 1. An example of overlapping emissions from three fluorophores on the Invitrogen Flow Cytometry Panel BuilderFluorescence signal may overlap if emission spectrums are broad and captured in a different detector specific for another fluorochrome. The overlap or spillover of this emission signal can provide false results. To remove fluorescence spillover, the mathematical process of compensation provides the signal of interest by subtracting the overlap between the two fluorochrome in the same channel.



Compensation bead selection guide

Consideration needs to be taken when picking a compensation bead to set positive and negative signals for antibodies in a flow cytometry experiment. We offer several compensation beads specifically designed for flow cytometry antibodies, fluorescent proteins, and reagents.

 UltraComp eBeads Plus compensation beads*UltraComp eBeads compensation beadsAbC Total Antibody Compensation Bead kit*OneComp eBeads compensation beads
ApplicationImmunophenotyping 
ReactivityHuman, rabbit, hamster, mouse, and rat antibodiesHamster, mouse, and rat antibodies with recognition of the kappa and lambda chainsHamster, mouse, rabbit, and rat antibodiesHamster, mouse, and rat antibodies with recognition of the kappa and lambda chains
FormatOne vial, dispense as a single dropOne vial, dispense as a single dropOne vial positive beads, one vial negative beadsOne vial, dispense as a single drop
Laser compatibilityCompatible with most standard lasers, UV to 633 nm. Improved for polymer dye use from violet laser.Compatible with most standard lasers, UV to 633 nmCompatible with most standard lasers, UV to 633 nm.Compatible with most standard lasers, but not with UV or violet lasers
Size25 tests | 100 tests
Cat. No.01-3333-41 | 01-3333-4201-2222-41 | 01-222-42A10513 | A1049701-1111-41 | 01-1111-42
 * More antibody binding compensation beads available. Goat and sheep host species should use single color cell and FMO controls, not beads. 
 ArC Amine Reactive Compensation Bead kit (LIVE/DEAD)
ApplicationCell viability assay
ReactivityLIVE/DEAD fixable dead cell stains*
FormatOne vial positive beads, one vial negative beads
Laser compatibilityCompatible with most standard lasers, UV to 633 nm
Size25 tests | 100 tests
Cat. No.A10628 | A10346
* Also applicable to similar amine reactive dyes
 GFPmCherryRFPCFPYFP
ApplicationGFP (Green Fluorescent Protein); labeled beads are present at 3 levels of GFP-like intensitymCherry (monomeric red fluorescent protein); labeled beads are present at 3 levels of mCherry-like intensityRFP (Red Fluorescent Protein); labeled beads are present at 3 levels of RFP-like intensityCFP (Cyan Fluorescent Protein); labeled beads are present at 3 levels of CFP-like intensityYFP (Yellow Fluorescent Protein); labeled beads are present at 3 levels of YFP-like intensity
ReactivityGFP isoformsmCherry isoformsRFP isoformsCFP isoformsYFP isoforms
FormatOne vial, dispense as a single dropOne vial, dispense as a single dropOne vial, dispense as a single dropOne vial, dispense as a single dropOne vial, dispense as a single drop
Laser compatibility488 nm561 nm561 nm405 nm488 nm
Size1 mL (25 tests)1 mL (25 tests)1 mL (25 tests)1 mL (25 tests)1 mL (25 tests)
Cat. No.A10514A54743A54740A54742A54741
 UltraComp eBeads Plus compensation beads*UltraComp eBeads compensation beadsAbC Total Antibody Compensation Bead kit*OneComp eBeads compensation beads
ApplicationImmunophenotyping 
ReactivityHuman, rabbit, hamster, mouse, and rat antibodiesHamster, mouse, and rat antibodies with recognition of the kappa and lambda chainsHamster, mouse, rabbit, and rat antibodiesHamster, mouse, and rat antibodies with recognition of the kappa and lambda chains
FormatOne vial, dispense as a single dropOne vial, dispense as a single dropOne vial positive beads, one vial negative beadsOne vial, dispense as a single drop
Laser compatibilityCompatible with most standard lasers, UV to 633 nm. Improved for polymer dye use from violet laser.Compatible with most standard lasers, UV to 633 nmCompatible with most standard lasers, UV to 633 nm.Compatible with most standard lasers, but not with UV or violet lasers
Size25 tests | 100 tests
Cat. No.01-3333-41 | 01-3333-4201-2222-41 | 01-222-42A10513 | A1049701-1111-41 | 01-1111-42
 * More antibody binding compensation beads available. Goat and sheep host species should use single color cell and FMO controls, not beads. 
 ArC Amine Reactive Compensation Bead kit (LIVE/DEAD)
ApplicationCell viability assay
ReactivityLIVE/DEAD fixable dead cell stains*
FormatOne vial positive beads, one vial negative beads
Laser compatibilityCompatible with most standard lasers, UV to 633 nm
Size25 tests | 100 tests
Cat. No.A10628 | A10346
* Also applicable to similar amine reactive dyes
 GFPmCherryRFPCFPYFP
ApplicationGFP (Green Fluorescent Protein); labeled beads are present at 3 levels of GFP-like intensitymCherry (monomeric red fluorescent protein); labeled beads are present at 3 levels of mCherry-like intensityRFP (Red Fluorescent Protein); labeled beads are present at 3 levels of RFP-like intensityCFP (Cyan Fluorescent Protein); labeled beads are present at 3 levels of CFP-like intensityYFP (Yellow Fluorescent Protein); labeled beads are present at 3 levels of YFP-like intensity
ReactivityGFP isoformsmCherry isoformsRFP isoformsCFP isoformsYFP isoforms
FormatOne vial, dispense as a single dropOne vial, dispense as a single dropOne vial, dispense as a single dropOne vial, dispense as a single dropOne vial, dispense as a single drop
Laser compatibility488 nm561 nm561 nm405 nm488 nm
Size1 mL (25 tests)1 mL (25 tests)1 mL (25 tests)1 mL (25 tests)1 mL (25 tests)
Cat. No.A10514A54743A54740A54742A54741


Antibody compensation beads

UltraComp, UltraComp Plus, and OneComp eBeads for compensation

eBeads are microspheres that contain a mixture of antibody-coated positive compensation beads and uncoated negative compensation beads, combined in one vial. This set of compensation beads are useful when using many lasers and multiple antibodies from different species.

The advantages of these types of  beads include:

  • Easily expand your panels and retain the cells you need since eBeads have low autofluorescence and provide signal sensitivity
  • Designed for ease of use with combined positive and negative beads in one vial and dispense as a single drop
  • Binds a wide range of species and is excited by most lasers

Figure 2. Staining of UltraComp eBeads Plus compensation beads with 14 different Invitrogen eFluor 450 dye-conjugated monoclonal antibodies, including one of each subclass commonly used in flow cytometry. Beads were stained with 0.25 µg of each antibody and analyzed by flow cytometry. Each histogram represents one staining antibody.

AbC Total Antibody Compensation kit

AbC compensation bead kits contain two types of specially modified polystyrene microspheres: 1) AbC capture beads (also called positive beads), which bind all isotypes of the specific immunoglobulin, and 2) negative beads, which have no antibody binding capacity. These compensation beads produce extremely bright signals.

Each kit offers:

  • Distinct positive and negative populations of beads that can be used to set compensation: negative beads are added after labeling of the positive bead in order to avoid any transfer of fluorescence over time to the negative bead
  • Very bright positive signal, which is helpful when using antibodies conjugated to very bright fluorophores like PE
  • Reagents that can be combined with other compensation beads including ArC Amine Reactive Compensation Beads

AbC compensation kits are available to recognize either mouse or rat and hamster.



LIVE/DEAD compensation beads

ArC Amine Reactive compensation beads

Viability dyes are useful to gate live vs dead cells in flow cytometry experiments. ArC Amine Reactive Compensation Beads were developed to bind Invitrogen LIVE/DEAD Fixable Dead Cell Stains and other similar amine reactive dyes. LIVE/DEAD dyes added to these beads will produce a more similar spectrum as compared to compensating based on the sole fluorophore.

Properties of these beads include:

  • 2 drop kit for accurate and bright positive signal
  • The ability to combine the AbC Total Antibody Compensation Bead kit and ArC Amine Reactive Compensation Bead kit together to determine compensation in multicolor immunophenotyping experiments

When using compensation beads for amine reactive dyes, a control with purely dead cells both unstained and stained with LIVE/DEAD can be added to adjust gating.

Add ArC Amine Reactive Compensation Beads today

Figure 4. Staining profile of the ArC Amine Reactive Compensation Bead Kit components with 3 LIVE/DEAD Fixable Dead Cell Stain kits. (A)LIVE/DEAD Fixable Violet dye stained beads were analyzed with 405 nm excitation, emission was collected with a 450/50 nm bandpass filter. (B)LIVE/DEAD Fixable Green dye stained beads were analyzed with 488 nm excitation, emission was collected with a 525/50 nm bandpass filter. (C)LIVE/DEAD Fixable Far Red dye stained beads were analyzed using 633 nm excitation, emission was collected with a 660/20 nm bandpass filter.



Fluorescent protein compensation beads

BrightComp eBeads Compensation Beads

BrightComp eBeads compensation beads are modified microspheres stained with a dye that has a near-identical spectral match to GFP, mCherry, RFP, CFP, and YFP at 3 levels of intensity. BrightComp eBeads allow for easy compensation of samples with different levels of GFP, mCherry, RFP, CFP, and YFP expression (Figure 5).

These beads offer:

  • Consistent, accurate, and simple-to-use reagents for setting flow cytometry compensation when using GFP, mCherry, RFP, CFP, or YFP
  • Ease-of-use with a single drop containing both negative and positive beads

Try these beads with your experiment, and save more of your sample

Figure 5. Multiple intensities of BrightComp eBeads Compensation Beads. Fluorescent proteins can be expressed at varying levels, resulting in the detection of a range of fluorescent intensities. When setting compensation, selecting the bead peak with a higher intensity than the experiment sample is recommended. Data were acquired on a flow cytometer using a 488 nm laser and emission was collected using 525/50 nm filter for GFP, a 561 nm laser and emission using 620/15 nm filter for mCherry, a 561 nm laser and emission using 585/16 nm filter for RFP, a 488 nm laser and emission using 530/30 nm filter for YFP, a 405 nm laser and emission using 440/50 nm filter for CFP.


How to use compensation beads?


Learn how to pick and prepare the correct single color control. Understand the difference between cells and beads.

Below is a general outline of how to use the compensation beads. Use the technical data sheet from the product for detailed protocols.

Step 1: It is necessary for compensation beads to bind the antibody or reagent used in the specific experiment. Use the selection guide to pick the correct compensation bead that binds the species or reagent and can be excited by the appropriate laser.

Step 2: Add the same antibody or reagent used in samples.

Step 3: Vortex or flick to mix. Incubate for 15-30 min in the dark.

Step 4: Wash with the same Flow Cytometry Staining Buffer used in sample staining, then centrifuge, and decant. Resuspend in Flow Cytometry Staining Buffer. Beads are ready to set compensation settings.

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Not for resale. Super Bright Polymer Dyes are sold under license from Becton, Dickinson and Company.