Spot-Trap Agarose

Spot-Trap® Agarose is an affinity bead for immunoprecipitation (IP) of Spot-tagged proteins
It comprises an anti-Spot-Tag® VHH/ Nanobody coupled to agarose beads.

More information about the Spot capture and detection tag can be found here.

Spot-Tag sequence PDRVRAVSHWSS

Immunoprecipitation/ Co-IP
Mass spectrometry
ChIP/ RIP analysis
On-bead enzyme assays
For protein purification use Spot-Cap

When use Spot-Trap? When use Spot-Cap? Click here.

Product Size Code Price Buy
Product Spot-Trap Agarose Size 250 µL (10 reactions) Code eta-10 Price $ 275
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Product Spot-Trap Agarose Size 500 µL (20 reactions) Code eta-20 Price $ 475
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Product Spot-Trap Agarose Size 2.5 mL (100 reactions) Code eta-100 Price $ 2050
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Product Spot-Trap Agarose Size 5 mL (200 reactions) Code eta-200 Price Please inquire
Product Spot-Trap Agarose Size 10 mL (400 reactions) Code eta-400 Price Please inquire
Product Spot-Trap Agarose Kit Size 500 µL (20 reactions) Code etak-20 Price $ 595
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Product Spot Peptide Size 1 mg Code ep-1 Price $ 85
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Product Binding Control Agarose Beads Size 500 µL (20 reactions) Code bab-20 Price $ 75
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Product Spin Columns Size 10 units Code sct-10 Price $ 35
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Product Spin Columns Size 20 units Code sct-20 Price $ 60
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Product Spin Columns Size 50 units Code sct-50 Price $ 130
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Product Spot VHH, recombinant binding protein Size 250 µL Code etb-250 Price $ 455
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Dissociation constant KD of 6 nM

Wash buffer compatibility
2 M urea, 2 M NaCl, 10 mM DTT, 2 % Nonidet P40 Substitute, 1 % Triton X-100, 0.1 % SDS

Spot-Tag sequence motif PDRVRAVSHWSS

Binding capacity
10 µL slurry bind about 7 µg of recombinant Spot-Tag fusion protein (30 kDa)

Coupled Nanobody/ VHH
Recombinant, monoclonal anti-Spot-Tag single domain antibody (sdAb) fragment

Bead properties
Bead size: ~ 90 µm (cross-linked 4 % agarose beads)
Storage buffer: 20 % EtOH

- SDS sample buffer
- 10 mM NaOH pH 12
Please consider whether elution is really needed. We recommend on-bead assays like on-bead digestion for MS analysis.
For protein purification and efficient elution with Spot peptide at +4°C we recommend Spot-Cap™ affinity resin.

Compatibility with mass spectrometry
The Spot-Trap is optimized for on-bead digestion. Complete tryptic digest results in 4-5 peptides.

How to cite this product
RRID: AB_2827590

Storage instructions
Shipped at ambient temperature. Upon receipt store at 4°C. Stable for one year.

Should I use an N-terminal or C-terminal Spot-fusions? Can I also insert the Spot-Tag in the middle of my protein?

Both, an N- or C-terminal fusion work well.
The use of the Spot-Tag for internal protein tagging has to be tested case by case. The Spot-Tag peptide has to exist in a linear form and be accessible without steric hindrance from other parts of the protein of interest. An internal Spot-Tag is only likely to be recognized by the Spot-Tag nanobody if inserted into a sufficiently large and unstructured loop, an inherently unstructured domain or a lengthy domain linker.

How can I detect my Spot-fusion in Western blot application?

You can use ChromoTek's Spot-Label to detect your Spot-tagged fusion protein. Alternatively, you can use ChromoTek's Spot-Binding protein (Spot VHH, product code: etx-250) followed by incubation with a conventional anti-Llama or anti-His6 secondary antibody.

How long should I incubate my Spot-fusion sample with Spot-Label for Western blot and IF applications?

Optimal results are achieved through overnight incubation.

Should I use an N-terminal or C-terminal fusion tag?

Both the N-terminal or C-terminal fusion tag work well with the traps.

How can I avoid unspecific protein interactions binding to the trap?

For preclearing of your sample we recommend to use our binding controls (bab-20 or bmab-20).

Please find more information in our Troubleshooting guide

How many mammalian cells are required for an immunoprecipitation reaction?

For one immunoprecipitation reaction, we recommend using ~10^6 - 10^7 mammalian cells. The yield is also dependent on the expression level of your protein of interest and the interaction partners.

How much cell extract should I use for an immunoprecipitation reaction?

For other type of cells than mammalian cells, we recommend using 0.5 - 1.0 mg of cell extract.

Do I need to elute bound proteins from the beads for mass spectrometry analysis?

No, you can directly conduct an on-bead digestion after immunoprecipitation. This procedure allows faster and more efficient sample preparation and a potential higher yield.
Please find more information here:

Preomics kit

Protocol on-bead digestion

Do I need to elute my protein of interest from the beads for enzymatic assays?

No, you can directly perform your enzymatic assay on the beads if the active center is not blocked.

Please find more information in our application note "enzymatic activity assay"

What is the amount of trap slurry I need for one immunoprecipitation reaction?

25 µL slurry are sufficient for one pull-down reaction as the affinity of the traps is very high.

How can I elute bound Spot-tagged protein from the Spot-Trap?

You can elute your Spot-fusion with 2xSDS-sample buffer or you can use 10 mM NaOH pH 12 (adjust pH immediately after elution). For protein purification and efficient elution with Spot peptide at +4°C we recommend Spot-Cap™ affinity resin.

Specifications of Spot-Trap Agarose, Magnetic Agarose, and Magnetic Beads





Magnetic Agarose

Magnetic Beads


Agarose (4% cross-linked)

Magnetic agarose (6% cross linked)

Magnetic Beads M-270

Bead form


Porous; sold iron core



Spot VHH

Spot VHH

Spot VHH

Spot-tagged protein size*

Small to large size

Small to large size

Small to very large size; no size limitation





Medium particle size

90 µm

40 µm

2.8 µm

Binding capacity**

7 µg/ 10 µL

7 µg/ 10 µL

0.9 μg/ 10 μL


Very low



Magnetic separation & automation




May be centrifuged up to

2,500 x g

800 x g

8,000 x g

* Does depend on protein size and shape, protein multimers, complexes and interaction partners

** Determiend with a recombinant Spot-Tag fusion protein (30 kDa)


  • NO contaminating heavy and light antibody chains
  • Just 4-5 peptides in mass spec.
  • Recombinantly expressed without batch-to-batch variation
  • Well-characterized and validated
  • Ready to use
  • Short incubation time of 30-60 minutes

Spot-Trap Agarose Kit

The Spot-Trap Agarose is also available in a kit, including:

  • Spot-Trap Agarose
  • Lysis* and wash buffers

*The lysis buffer provided is suitable for mammalian cells. For other cell types use another suitable lysis buffer.

Spin columns

Binding Control for Agarose Beads


“Therefore, we considered that small Spot-Tag is better than large GFP-tag in terms of affecting functions of fused protein(s). The obtained IP/MS data showed many interesting candidates that may function with “protein X” in cells. We are now validating these interactions. In conclusion, Spot-Tag and Spot-Trap system works very well in IP/MS experiments.”
Associate Professor, University of Tokushima, Japan

“Mass spec results look great.  High specificity, low background, and I am seeing more interacting partners of my protein of interest than with the HA epitope tag that I have historically used.  I am very pleased with the results.”
Graduate Student, Cornell University, NY, USA

“I just finished testing the Spot-Tag. I obtained interesting results by performing a small scale purification of my fusion protein, the protein is very pure and there are no non-specific bands on the beads.”
Assistant Engineer, CNRS, Lyon, France

“The Spot-Trap test worked really well (equivalent efficiency to Twin-Strep tag)….in detergent.”
Postdoctoral researcher, University of Oxford, UK

“The Spot-Tag works well for pulldowns; much better than the Strep-tag, at least for my constructs.”
Contractor, NIH, Bethesda, MD, USA

“GFP-Trap and Spot-Trap both specifically bind Spot-GFP, and Spot-Trap appears at least as efficient as GFP-Trap.”
Senior Research Associate, University of Bristol, UK

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Only for research applications, not for diagnostic or therapeutic use!