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Which beads should I use for my immunoprecipitation?

Which beads should I use for my immunoprecipitation?

In detail, all beads have very low background binding due to the highly specific binding of the Nano-Traps.

ChromoTek's Nano-Traps are optimized for the immunoprecipitation (IP) of proteins and their interacting factors. Nano-Traps comprise of a Nanobody/ V_HH conjugated to beads. For 5 Nano-Traps, e.g. GFP-Trap^®, Halo-Trap, RFP-Trap^®, Spot-Trap^®, and V5-Trap^® we offer different types of beads:

Agarose beads
Magnetic Agarose beads
Magnetic Particles M-270

Based on the properties of the different beads (see table), we recommend:

Agarose beads for very low background and high binding capacity IP
Magnetic Agarose beads for magnetic separation and high binding capacity IP
Magnetic Particles M-270 for IP of very large proteins/complexes

ChromoTek_GFP-Trap_Agarose

Immunoprecipitation with GFP-Trap.
I: Input, FT: Flow-Through, B: Bound

	Agarose	Magnetic Agarose	Magnetic Particles M-270
Low background*	+++	++	++
Binding capacity	+++	+++	+
Size of tagged protein*	Small to large	Small to large	Small to very large
Bead separation	centrifugation	magnetic	magnetic

*Please note that these are general guidelines. For a specific protein or complex, the optimal experimental conditions have to be tested.

In detail, all beads have very low background binding due to the highly specific binding of the Nano-Traps. In comparison, Agarose beads have the lowest background. The background of Magnetic Agarose beads and Magnetic Particles M-270 is at slightly higher. Hence, Agarose is recommended if a very low background is needed.

For automated immunoprecipitation or when magnetic handling is preferred in general, Magnetic Agarose or Magnetic Particles M-270 shall be used. However, Magnetic Agarose is recommended if a higher binding capacity is required.

The size and shape of your protein of interest (POI) may require the use of the non-porous Magnetic Particles M-270, because larger proteins or protein complexes can’t access the Nanobodies/ V_HHs inside the pores of agarose and magnetic agarose beads. Note that smaller proteins may form multimers or may be part of larger complexes and hence have larger sizes than expected.

	Beads
	Agarose	Magnetic Agarose	Magnetic Particles M-270
Matrix	Agarose (4% cross-linked)	Magnetic agarose (6% cross linked)	Magnetic Particles M-270
Bead form	Porous	Porous; sold iron core	Solid
Ligand	Nanobody/ V_HH	Nanobody/ V_HH	Nanobody/ V_HH
Protein size*	Small to large size	Small to large size	Small to very large size; all sizes
Color	White	Black	Brown
Medium particle size	~90 µm	~40 µm	2.8 µm
Binding capacity	Very high	Very high	Medium
Background	Very low	Low	Low
Magnetic separation & automation	no	Yes	Yes
May be centrifuged up to	2,500 x g	800 x g	8,000 x g